Online Posters

Click on a title on the left panel to see the abstract.

P-1

Effect of the group size on the evolution of cooperation in the presence of an exit option

Shun Kurokawa¹

¹Japan Advanced Institute of Science and Technology

The existence of cooperation is a mysterious phenomenon from the perspective of natural selection. How cooperation could have evolved is one of the central topics in evolutionary biology. If cooperators maintain interaction with cooperators and halt interaction with defectors, then cooperation can pay and can be favored by natural selection. This is called an exit option. Here, not only cooperation in dyadic interactions but also cooperation in sizable groups can be observed. Rivalry is about whether usage of the benefit by one individual reduces its availability to others or not. A common good is a rivalrous good, whereas a public good is a non-rivalrous good. In this poster, by analyzing n-player prisoner’s dilemma games, I examine whether the effect of the group size on cooperation is positive or negative in the context of exit option. The findings are as follows. When goods are common goods, the condition under which cooperators are not dominated by defectors becomes more strict as the group size increases. Thus, the effect of the group size on the evolution of cooperation is negative. In contrast, surprisingly, when goods are public goods, the condition under which cooperators are not dominated by defectors becomes looser as the group size increases. Thus, the effect of the group size on the evolution of cooperation is positive. In previous work, it has been considered that explaining the existence of cooperation in sizable groups is more difficult than explaining the existence of cooperation in dyadic interactions even when goods are public goods. Taking it into consideration, I believe that my finding in the case of public goods is significant.

P-2

Genetic Diversity analysis in the Dwarf Snakehead (Channa gachua) from Brantas River

Kiki Nur Azam Kholil¹, Fachreza Gusti Hamurdana¹, Monica Anindita Lutfitasari¹, Wahyu Endra Kusuma¹

¹Department of Aquaculture, Faculty of Fisheries and Marine Science, University of Brawijaya, Malang 65145, Indonesia

Dwarf snakehead (Channa gachua) is a freshwater fish from genus Channa. This fish has been known for its high economic value and is generally largely used as a healthy diet and medicine. This species has also been used as an ornamental fish commodity because of its beautiful coloration in their body. It has been reported that this species is currently difficult to catch in some tributary areas of Brantas River, the second longest river in Java Island. Conservation or domestication efforts are urge to be done to protect the sustainability of this fish in the wild. We collected individuals of C. gachua from three localities of upstream, middle stream and downstream of Brantas River. By using mitochondrial DNA cytochrome c oxidase subunit I, we analyzed phylogenetic position of individuals from Brantas Rivera between other species from the genus Channa. We also evaluate the genetic diversity by calculation genetic diversity indices e.g., number of haplotypes (h), haplotypes diversity (hd), and nucleotide diversity (π). Based on these analysis, genetic diversity of dwarf snakehead population in Brantas River population is high. The result show h=6, hd=0.817, and π=0.0043 from 18 individual. The result of population structure analysis by using pairwise fixation index (F_st) indicates a significant difference in genes between populations compares to another population using data from GenBank and other publication, and the process of gene flow is very unlikely to occur within population. The result of phylogenetic tree using maximum likelihood method showed that there are 2 clade population groups of dwarf snakehead fish occur in Brantas river.

P-3

Genetic Diversity Analysis of the Yellow Rasbora (Rasbora lateristriata) in Tegal, Central Java, Indonesia

Muhammad Nurfaiq Hibatullah¹, Wahyu Widia Ningrum¹, Wahyu Endra Kusuma¹

¹Department of Aquaculture, Faculty of Fisheries and Marine Science, Universitas Brawijaya, Malang 65145, Indonesia

Rasbora (Cypriniformes: Cyprinidae) is one of the most affected organism groups under the degradation of Sundaland biodiversity due to several anthropogenic pressures. Lack of basic scientific knowledge (e.g., genetic diversity) hindered the conservation efforts that were essential to be implemented to protect the species in their natural habitat. In recent years, some molecular studies have attempted to discover more information on its species members, notably in the Yellow Rasbora (Rasbora lateristriata), which is categorized as a vulnerable species by IUCN. Previous study with strong evidence suggested that R. lateristriata form a species complex, consisting of possibly four different species. One of the species identified from Tegal, Central Java, however based on a limited number of samples. The present study was conducted to gain more comprehensive phylogenetic and genetic information on the Tegal individuals by collecting nucleotide sequences of the mitochondrial COI gene region from more individuals and localities. Fish samples were collected from several sampling sites in Tegal, Central Java. The obtained sequences were compared with R. lateristriata species complex data from the GenBank. The haplotype diversity (h) and nucleotide diversity (π) were calculated to infer the genetic diversity of Tegal individuals. Pairwise fixation index (Φ_ST) was estimated to detect the possibility of gene flow across the species complex. Maximum likelihood tree was also reconstructed to see the evolutionary relationship among other Rasbora species. Our results indicated only minor genetic differentiations among the Tegal sampling sites, in contrast to the large differentiations found for many other sampling sites in Java Island. A recent population expansion was detected in the Tegal individuals while population bottleneck was suggested for a few groups in other regions. All Tegal individuals acquired were nested in Clade 3 group according to the phylogenetic tree.

P-4

Comparative transcriptome analysis for cold acclimation in Drosophila albomicans at different climatic regions

Shikha Singh¹, Tomohiko Kimura¹, Koichiro Tamura^1,2

¹Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
²Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan

Cold tolerance is a key determinant of temperature adaptation in small ectotherms like insects. The geographic distribution of these species strongly depends on their ability to survive with local environmental conditions following climate change or habitat expansion. A fruit fly species, Drosophila albomicans, distributed in tropical regions of Southeast Asia until the mid-1980scurrently has a wider geographic distribution to the Asian temperate regions. The strains from various temperate regions of this species have a higher cold tolerance in terms of survival time at 1℃ with significant improvement by cold acclimation at 20℃ for several days. It is plausible that the efficiency of cold acclimation was improved during the distribution expansion in the temperate strains. To clarify the effect of cold acclimation, we used high-throughput mRNA sequencing (RNA-seq) to examine the changes in the transcriptome of D.albomicans adults during cold acclimation. In this study, we use five strains from China, Taiwan, and Japan with five biological replicates to find differentially expressed genes (DEGs) between cold acclimation and non-acclimation conditions. Comparing the DEGs between the strains, however, we did not find DEGs shared by all strains. This might be due to the genes with changed expression across genotypes tend to have interactions with other genes, i.e., genotype-specific responses to the same environmental change by cold acclimation. Therefore, we also compared differences in the amino acid sequences and those in the expression level for each gene between the strains to examine how sequence and expression divergences are related. However, we did not find a significant correlation between them in any pairwise comparison. From our analysis, we speculate that the prediction of differences in gene expression from the sequence is complicated due to complex interactions between genes.

P-5

Changes in gene expression and morphology of amphibious fish in terrestrial environments

Yuki Kimura¹, Nobuaki Nakamuta², Shinji Kanda³, Susumu Hyodo³, Masato Nikaido¹

¹School of Life Science and Technology, Tokyo Institute of Technology
²Faculty of Agriculture, Iwate University
³Atmosphere and Ocean Research Institute, The University of Tokyo

　About 350 million years ago, some lineages of fish began to adapt to terrestrial environment. Even before that event, bony fishes had already acquired adaptive traits for terrestrial environment as represented by lung. It is believed that Polypterus is the only extant species that retains such traits as ancestral characters. In this study, we kept Polypterus on forced land environment for a month and explored the differentially expressed genes of gills and kidneys between two experimental conditions, in water and on land. In addition, we conducted morphological observations and measurement of osmotic pressure on polypterus of these two conditions. Consequently, we revealed that the number of cilia in the gills were significantly reduced and osmotic regulation in the kidney was up-regulated. This forced rearing experiment of Polypterus may provide important insights into our understanding of the process of water to land transition in vertebrates.

P-6

Molecular mechanisms underlying metamorphosis in the insect order Odonata.

Genta Okude^1,2,4, Minoru Moriyama², Takema Fukatsu^1,2,3, Ryo Futahashi²

¹The University of Tokyo
²National Institute of Advanced Industrial Science and Technology (AIST)
³University of Tsukuba
⁴National Institute of Genetics

Odonata insects (dragonflies and damselflies) represent one of the most ancestral insects with metamorphosis, in which their morphology and behavior change drastically from aquatic larvae to terrestrial adults. Little is known about the molecular mechanisms underlying the metamorphosis of Odonata mainly due to the following obstacles: (1) Lack of model Odonata species that are experimentally tractable and maintainable in the laboratory; (2) Lack of basic information on the metamorphosis and life cycle traits of Odonata such as the number of ecdysis and larval morphological changes; and (3) Lack of molecular genetic tools applicable to Odonata. To overcome these difficulties, we focused on the blue-tailed damselfly Ischnura senegalensis as a promising model species (Okude et al., 2017, Zool. Sci.) and established RNAi method combined with electroporation (Okude et al., 2017, Appl. Entomol. Zool.; Okude et al., 2021, J. Vis. Exp.). To screen for genes involved in metamorphosis of Odonata, we performed comprehensive RNA-sequencing of I. senegalensis using 82 samples from various developmental stages, body regions and sexes. Comparative RNA-sequencing analyses between the penultimate instar larvae and adults identified eight larva-specific and seven adult-specific candidate genes, including three transcription factors, Krüppel homolog 1 (Kr-h1), E93 and broad. RNAi experiments showed that E93 is essential for adult morphogenesis and Kr-h1 represses E93 expression as reported in other insects. On the other hand, broad RNAi in the abdominal epidermis produced grayish pigmentation different from either larva or adult. Subsequent screening of candidate downstream genes for Kr-h1, broad, and E93 revealed that, unlike other insects, broad regulates a subset of larva-specific and adult-specific genes without being mediated by Kr-h1 and E93. These results provide basic information on molecular mechanisms underlying the metamorphosis of dragonflies, which shed light on the evolution of insect metamorphosis.

P-7

Evolutionary history of egg hunting cichlids in Lake Victoria　

Minami Imamoto¹, Haruna Nakamura¹, Mitsuto Aibara¹, Takehiko Ito¹, Masato Nikaido¹

¹School of Life Science and Technology

In Lake Victoria East Africa, ecologically and morphologically diverse 500 cichlid species have been evolved in last 15,000 years, through explosive adaptive radiation. Among variety of eating habits in Lake Victoria cichlids, paedophage, literally “hunts” other cichlid’s eggs and fries, is one of the most unique feeding behaviors. In this study, I particularly focus on one peadophagus species Haplochromis sp. “matumbi hunter”. To answer the question, what caused explosive adaptive radiation, recent study proposed the hypothesis: hybridization between two ancestral lineages facilitated adaptive radiation in Lake Victoria. However, genome wide analysis of Lake Victoria species and their ancestral lineages suggested that matumbi hunter is distantly related to other species. Thus, it could be said that matumbi hunter went through unique evolutional pathway unlike hybridization of ancestral lineages. This study aims to discuss the mechanism fueled acquisition of various ecologies and morphologies, inferred by evolutionary history of matumbi hunter.

P-8

Whole-genome comparative analyses among subpopulations in Lake Victoria cichlid, Haplochromis chilotes

Haruna Nakamura¹, Mitsuto Aibara¹, Masato Nikaido¹

¹School of Life Science and Technology, Tokyo Institute of Technology

Lake Victoria cichlids with highly diverse in their morphology and ecology have been generated in just 15,000 years, which are a textbook example of adaptive radiation. The low degree of genomic differentiation among Lake Victoria cichlids gives us a great opportunity to find the genomic signatures which indicate the local adaptation. Haplochromis chilotes, the Lake Victoria cichlid represented by its thick lip, has been reported to be differentiated depends on geographic locations in body length and color, so it is suitable to elucidate the evolutionary process in both genomic and phenotypic characteristics. In this study, we performed whole-genome comparative analyses among subpopulations in H. chilotes including a closely related species, H. sp. ‘short head chilotes’. We found that H. chilotes had several subpopulations corresponding with the morphological descriptions. Molecular phylogenetic analysis and the estimation of divergence time implied that H. sp. ‘short head chilotes’ diverged earlier than other subpopulations of H. chilotes. Finally, we detected candidate genes for adaptation that were highly differentiated among subpopulations. We will discuss about our results with their phenotypic diversity.

P-9

A new method for estimating nucleotide substitution rates

Misawa, K^1,2,3

¹Kansai Medical University
²Yokohama City University
³Riken

SARS-CoV-2 is the cause of the worldwide epidemic of severe acute respiratory syndrome. Evolutionary studies of the virus genome will provide a predictor of the fate of COVID-19 in the near future. Recent studies of the virus genomes have shown that C to U transitions are overrepresented in the genome sequences of SARS-CoV-2. A new model incorporating unidirectional C to U substitutions was developed. I applied the new model to SARS-CoV-2 sequences from 74 infected persons on the Diamond Princess (Sekizuka et al. 2020. PNAS 117: 20198-20201, Hoshino et al. 2021, Gene 779: 145496). The results suggest that the time reversible models underestimate the substitution rate, because time-reversible models assume the number of substitutions from C to U is the same as that of U to C. The new model provides better estimates. I gratefully acknowledge Pathogen Genomics Center, National Institute of Infectious Diseases where genetic sequence data were generated and shared via the GISAID Initiative, on which this research is based.

P-10

The Evolution of Molybdenum Dependent Nitrogenase in Cyanobacteria

Tokumasa Horiike¹, Tomoaki Watanabe²

¹Department of Bioresource Sciences, Shizuoka University
²United Graduate School of Agricultural Science, Gifu University

Nitrogen fixation is the chemical process by which nitrogen in the atmosphere is converted into ammonia and other nitrogen-containing organic compounds. It is performed by a variety of bacteria, including Cyanobacteria. Previous studies have shown that several groups of Cyanobacteria have the ability to fix nitrogen; however, because these groups are scattered throughout the Cyanobacterial lineage, the evolutionary history of nitrogen fixation in these bacteria has not been clarified. In this study, we attempted to identify the origin of nitrogen fixation development in Cyanobacterium by focusing on molybdenum dependent nitrogenase, a major nitrogen fixing enzyme. We compared a phylogenetic tree from 179 species of Cyanobacteria to one generated from nitrogen fixation-related genes. We also compared the genomic locations of those genes. As a result, we found that nitrogen fixing genes were acquired in the Cyanobacterium common ancestor and subsequently lost in some lineages. The results demonstrate that inconsistencies between species phylogeny and organism characteristics can occur and be caused not only by horizontal gene transfer, but also by gene loss.

P-11

Development of a program for constructing ortholog data set using taxonomic information.

Tomoaki Watanabe¹, Tokumasa Horiike²

¹United Graduate School of Agricultural Science, Gifu University.
²Department of Bioresource Sciences, Shizuoka University.

For phylogenetic inference of species, it is necessary to construct a data set that contains only orthologs which are homologs generated by species divergence and does not contain out-paralogs which interfere with correct inference. In our previous research, "Ortholog Finder" which is the first program that detect and remove hidden out-paralogs (remained out-paralogs after differentially gene loss) was developed. However, some limitations exist in the algorithm of Ortholog Finder. For this reason, we improved Ortholog Finder and succeeded in removing more hidden out-paralogs by using more taxonomic information. We also generated sequence data containing hidden out-paralogs using a sequence simulation program and evaluated the performance of the improved Ortholog Finder using the simulated sequence data. The results showed that the improved Ortholog Finder can estimate orthologs more accurately than the existing programs which construct a data set of orthologs and leads to more accurate phylogenetic inference of species.

P-12

Genetic variation of multigene olfactory receptor family in humans

Muhammad Shoaib Akhtar¹, Ryuichi Ashino¹, Yoshihito Niimura², Kazushige Touhara³, Amanda D. Melin⁴, Shoji Kawamura¹

¹Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
²Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Japan
³Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
⁴Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Canada

The human genome contains roughly 400 intact and 440 pseudogenized olfactory receptor (OR) genes. However, the intact/pseudogene composition of the entire OR gene family among human populations remains unclear. This is largely due to reliance on whole genome sequence data, which are often incomplete, especially for multigene families. We employed a target capture approach, probing OR genes followed by massive-parallel sequencing. Study populations included 17 ethnic groups from African-, European- and Asian-origins with diverse historical subsistence. We designed probes for 554 OR genes based on the human reference genome hg38 and the chimpanzee genome Pantro3.0. Targeted genes are 398 annotated intact OR genes in hg38, 4 “alt” intact OR sequences in hg38, 99 OR “fresh” pseudogenes in hg38, 53 chimpanzee intact OR genes of which orthologs are absent in hg38. A variant effect prediction algorithm is utilized to identify intact and disrupted OR genes. To validate algorithm, each identified disrupted gene was examined if it has an open reading with at least 250 amino acids and can make a 7-transmembrane structure. Principal component analysis indicated a larger differentiation among populations in olfactory receptors than in neutral references. Target capture improved intact/pseudogene distinction and revealed population specific intact/pseudogene polymorphism in 134 OR genes. Out of these 134genes, 5 genes are annotated as pseudogenes in human reference genome hg38 and 1 OR gene is absent in hg38 but intact in chimpanzee. In addition to the intact/pseudogene polymorphism, many genes showed copy number variation across populations. Many of the nucleotide and copy number variations were found to be associated with either a single population or within one geographic region.

P-13

A phylogeny-free evolutionary probability method for testing neutrality at amino acid and nucleotide sites

Yujia Cai¹, Koichiro Tamura^1,2

¹Department of Biological Sciences, Tokyo Metropolitan University
²Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University

A fundamental issue in evolutionary biology is to know how changes in genotypes cause changes in phenotypes. In recent years the genome-wide association studies (GWAS) have been developed to solve this issue. However, as a nucleotide or amino acid is fixed in population quickly by natural selection, the applicability of the variation-dependent GWAS is limited. In this context, the variant-independent evolutionary probability (EP) method was developed. However, the EP method requires a guide phylogenetic tree, which is not always reliably estimable. This study proposes a new evolutionary probability method, named EPuCov (evolutionary probability using the covariance), that does not require a guide tree. Using computer simulations and empirical data analyses, we found that the EPuCov method shows a better performance to identify non-neutral amino acid substitutions with ten times faster computation time than the original EP method. Our computer program implements the EPuCov method for both amino acid and nucleotide sequence data, providing a user-friendly graphical user interface.

P-14

Identification and potential involvement of LTR retrotransposons in cold tolerance of Kandelia obovata

Chuangchao Zou¹, Yushuai Wang¹, Renchao Zhou¹, Tian Tang¹

¹State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China

Transposable elements (TEs) play an important role in the capacity of their host to respond to environmental challenges. Mangrove forests are restricted to tropical and subtropical intertidal regions, and winter temperature is known to constrain mangrove distributions. Here we examine latitudinal variation of TE insertions in association with range-limiting climate factors in Kandelia obovata, one of the most cold-tolerant mangroves, using population genomic analyses. We find Gypsy long terminal repeat (LTR) retrotransposons are more abundant and much younger than Copia LTR retrotransposons in the genome of K. obovata. Allele frequencies of 23 TE insertions, mainly from the Gypsy superfamily, are significantly correlated with local temperatures across populations from different latitudes, of which the vast majority show negative correlation. We also find differential expression of clinically varying TEs or their flanking genes between cold-tolerant and non-cold-tolerant plants of K. obovata, which involves genes with known function in DNA repair and stress response. Our results indicate that TEs are important source of clinical variation within species and also shed light on the potential role of TEs in plant local adaptation.

P-15

The function and the localization of dual-obligate endosymbionts in the aphid, Ceratovacuna japonica

Shunta Yorimoto^1,2, Mitsuru Hattori³, Shuji Shigenobu^1,2

¹Development of Basic Biology, School of Life Science, Graduate University for Advanced Studies
²Laboratory of Evolutionary Genomics, National Institute of Basic Biology
³Faculty of Environmental Science, Nagasaki University

Many animals and plants are associated with microbial symbionts in their body. Aphids and the bacterial endosymbiont Buchnera are obligate and mutualistic association, which neither can reproduce independently. Aphids harbor Buchnera in their specialized large cells called bacteriocytes that form a symbiotic organ (bacteriome). Buchnera provides the host with essential amino acids and vitamins, that aphids cannot synthesize and that are deficient in plant phloem sap, aphids’ sole dietary component. In addition to Buchnera, aphids are often associated with additional bacteria, called facultative symbionts. Facultative symbionts are erratically distributed and not essential for survival of the hosts, but they contribute to the aphid fitness and phenotype in some cases. However, little is known about the molecular mechanism and the evolution of multi-partner symbiotic system. Here we focus on the symbiosis of the aphid species, Ceratovacuna japonica (Hemiptera: Sternorrhyncha: Hormaphidinae). To investigate bacterial symbionts of C. japonica comprehensively, we performed 16S rDNA amplicon sequencing analysis to the samples collected from natural populations in Japan. In addition to Buchnera, two other bacterial symbionts (hereafter, symbiont X, Y) were detected from C. japonica and symbiont X were found from all populations we assayed. To reveal the function of these bacterial symbionts, we determined their complete genomes. The genome size of Buchnera in C. japonica is about 200 kbp smaller than 600 kbp, the typical size of Buchnera genomes. Buchnera genome of C. japonica is missing several genes to synthesize essential nutrients for the host. However, these missing genes in Buchnera were found from the genome of symbiont X. These results suggest that symbiont X has established the mutualistic association with the host through collaboration with Buchnera. To reveal the localization and the transmission process of the bacterial symbionts, we performed fluorescence in situ hybridization using probes specific to each symbiont. Buchnera and symbiont X were harbored inside distinct bacteriocytes, whereas both symbionts are localized within the same bacteriomes. Both symbionts are vertically transmitted to the offspring and then separated to each bacteriocyte during their embryogenesis. These results suggest that symbiont X are also obligate association with the host. This dual-obligate endosymbiotic system of C. japonica will shed light on the molecular mechanism and evolution of multi-partner symbiotic system.

P-16

Human L and M opsin gene loci originated from juxtaposition of spectrally distinct alleles in the catarrhine common ancestor

Yuka Matsushita¹, Naoko Takezaki², Amanda D. Melin³, Shoji Kawamura¹

¹Dept. Integrated Biosci., Grad. Sch. Frontier Sci., Univ. Tokyo
²Faculty of Med., Kagawa Univ.
³Dept. Anthropol. Archaeol. and Dept. Med. Genet., Univ. Calgary

Catarrhine primates (including humans) have routine trichromatic color vision. This is enabled by L and M opsin genes arrayed on the X chromosome. On the other hand, most of platyrrhines and some species of lemuriforms have polymorphic color vision achieved by spectrally distinct L/M opsin alleles of a single locus gene. It is generally assumed that the L and M opsin gene loci in catarrhines and the L/M opsin alleles of platyrrhines (and lemuriforms) originated independently. However, the L and M opsin genes of catarrhines are susceptible to gene conversion and homogenization between them, which obscures their evolutionary history. To obtain entire coding sequences of the L/M opsin genes from catarrhines, platyrrhines, tarsiers and strepsirrhines, we applied the target capture and massive parallel sequencing methods to their genomic DNA samples. To lessen the homogenizing effect on reconstruction of the phylogenetic relationships of L and M opsins, we used only gene regions (282 bp in total) which are highly divergent between the L and M opsin genes in catarrhines. Using the maximum likelihood method, we showed that the L and M sequences of catarrhines split before catarrhines and platyrrhines split. Hence, the L and M opsin genes of catarrhines originated from juxtaposition of already differentiated L and M alleles and not from duplication of identical sequences and subsequent divergence.

P-17

Genetic barriers to gene flow maintain the segregation of evolutionary speed during hybridization

Tianzhu Xiong¹

¹Department of Organismic and Evolutionary Biology, Harvard University

The evolutionary speed hypothesis predicts that the rates of molecular evolution are positively correlated with temperature as a result of shorter generation time and faster mutation. It has been partially supported by comparing homologous genes from different species inhabiting different habitats. In the present study, we show on a genomic scale that evolution is significantly faster in warmer regions even between incipient species of butterflies with a continuous hybrid zone. The segregation of evolutionary speed is achieved through gene flow reduction at various genetic barriers within the hybrid zone. The increment of substitution rate in the warm region can be largely explained by an extra generation with no detectable difference in the mutation spectrum.

P-18

A key factor for parallel evolution of hypertrophied lips in East African cichlid fishes

Ryo Hatashima¹, Atsushi Toyoda², Rei Kajitani¹, Takehiko Itoh¹, Masato Nikaido¹

¹School of Life Science and Technology, Tokyo Institute of Technology
²Comparative Genomics Laboratory, National Institute of Genetics

The cichlid fishes of East African Great Lakes are textbook example of adaptive radiation. In particular, hypertrophied lips, which have evolved independently in cichlids of each Great Lake, are textbook example of parallel evolution. Using QTL mapping and expression analyses (RNA-seq, qPCR and in-situ hybridization), we found two candidate genes (A and B) that may relate to hypertrophied lips in cichlids. We found the loss of gene expressions of A and B was common in cichlids with hypertrophied lip of each Lakes, suggesting that this may be the key factor for parallel evolution. Given that the patterns of mutation in gene B were distinct among cichlids of each Lake, loss of expression of gene B occurred independently. In addition, no missense or nonsense mutations were observed in gene A of cichlids with hypertrophied lip, suggesting that the loss of gene expression was caused by cis regulatory mutations. Moreover, genome wide comparative analyses identified many structural variations in the genomic regions of A and B, implying that the mutations were related to genomic fragility. This study may illustrate how parallel evolution occurred in rapid adaptations of cichlids.

P-19

Elucidating genetic mechanism of cichlid hypertrophic lips, using differentially expressed gene analysis

Nagatoshi Machii¹, Ryo Hatashima¹, Haruna Nakamura¹, Tatsuki Nagasawa¹, Masato Nikaido¹

¹Tokyo Institute of Technology

As a result of adaptive radiation of cichlid fish inhabiting East African Great Lakes Victoria, Malawi and Tanganyika, they acquired the huge diversity. In the process of diversification, researchers found many examples of parallel evolution and pay attention to the genetic mechanism of how to get similar traits. Hypertrophic lips are one of the best examples of parallel evolution. Although species with a hypertrophic lip has been found in the different lineages and its research has been carried out in the ecological and morphological context, the genetic basis of hypertrophic lips remains unclear. Therefore, I conducted differentially expressed gene analysis using RNA-seq data from 23 individuals of 9 species (3 with hypertrophic lips and 6 with normal lips) in each lake to search for genetic factors of lip hypertrophy. As a result, genes that forms extracellular matrix such as collagen and versican, one of proteoglycans, were detected. I will discuss the possibility that these genes are related to lip hypertrophy.

P-20

Comparative transcriptome analysis of mushroom bodies in a sawfly and honey bee suggests functional differentiation of Kenyon cells during the evolutionary history of hymenopteran insects

Takayoshi Kuwabara¹, Hiroki Kohno¹, Masatsugu Hatakeyama², Takeo Kubo¹

¹The Univ. of Tokyo, Biol. Sci.
²NARO, Div. Insect Adv. Tech., Inst. Agrobiol. Sci.

In the honey bee, the mushroom bodies (MBs), a higher-order center of the insect brain, comprise several subtypes of intrinsic neurons, termed Kenyon cells (KCs). The number of KC subtypes in the hymenopteran insects is suggested to have increased in association with the behavioral evolution. However, how the number of KC subtypes has increased remains unknown. In the present study, we focused on a turnip sawfly Athalia rosae, a primitive hymenopteran insect that has only one KC subtype. Aiming at investigating the similarity of transcriptomes between the sawfly KCs and each honey bee KC subtype, we used RNA-seq analysis to identify sawfly genes that are up-regulated in the MBs than other brain regions and analyzed orthologues of genes that correspond to newly identified genes as expressed in a KC subtype-preferential manner in the honey bee brain using the previously reported honey bee MB single-cell RNA-seq data. As results, some population of sawfly genes that correspond to marker genes for each honey bee KC subtype were expressed in the sawfly KCs. These results imply that novel KC subtypes have been acquired in the honey bee through functional differentiation and specialization from a primitive, possibly multifunctional KCs during the evolutionary history of hymenopteran insects.

P-21

Propagation and maintenance of hybridization-derived adaptive radiation potential: insights from evolutionary computer simulations.

Kotaro Kagawa^1,2, Ole Seehausen²

¹Tohoku University
²Swiss Federal Institute of Aquatic Science and Technology (EAWAG)

Adaptive radiations often show remarkable repeatability where single lineages undergo multiple episodes of adaptive radiations in distant places and separate timepoints. Increasing evidence suggests that hybridization can fuel adaptive radiation by creating adaptive genetic variation through recombining genes from genetically differentiated lineages. However, this mechanism requires rare coincidence in space and time between a hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only locally and it will persist only for a short period. By the same reason, hybridization-derived genetic variation seems unlikely to promote repeated occurrence of adaptive radiations within single lineages. Here, we propose a new hypothesis that posits that fission and fusion of lineages within a lineage of hybrid origin enables long-term maintenance and spatial spread of adaptive genetic variation, thereby promoting repeated occurrence of adaptive radiation. We confirm the theoretical validity of this hypothesis with evolutionary computer simulations considering two scenarios of recurrent adaptive radiations: recurrent adaptive radiations (1) in distant places and (2) in separate timepoints divided by a temporal period during which the environmental condition is unsuitable for adaptive radiation. Our results suggest that genetic variation generated by single episodes of hybridization, spatially narrowly confined, can affect macroevolutionary processes at large spatial and temporal scales, such as phylogenetically nested recurrent adaptive radiations.

P-22

Parallel evolution of trehalose biosynthesis machinery in metazoans

Yuichiro Hara¹, Reira Shibahara², Koyuki Kondo², Wataru Abe³, Takakazu Kunieda²

¹Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science
²Department of Biological Sciences, Graduate School of Science, The University of Tokyo
³Department of Biology, Dokkyo Medical University

Trehalose is utilized for diverse physiological functions including blood sugar, energy resource, and potent protectant in some animals. However, only limited number of metazoan taxa are known to produce trehalose endogenously, employing trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP), which hampers the elucidation of their evolutionary origins. To address this, we scrutinized the available genome resources and identified bifunctional TPS-TPP genes in various taxa. The scan extended our newly assembled genome of a desiccation-tolerant tardigrade Paramacrobiotus sp. TYO, revealing that this tardigrade activates endogenous TPS-TPP genes, resulting in production of trehalose, upon desiccation. TPS-TPP gene phylogeny indicated a monophyletic group of many of the metazoans including arthropods, namely ‘pan-metazoan’ genes, that were acquired in their common ancestors. Furthermore, the results illuminated that the two tardigrade lineages, nematodes, and bdelloid rotifers, all of which include desiccation-tolerant species, lost the ‘pan-metazoan’ genes but acquired the TPS-TPP homologs independently via horizontal transfer. Our results illustrate parallel evolution of trehalose synthesis via recurrent loss and horizontal transfer of the TPS-TPP genes in animals, which could facilitate the acquisition and/or augmentation of anhydrobiotic lives.

P-23

Possibility of assortative mating via putative pheromone receptor V1R2 in East African Cichlid

Riki Kawamura¹, Ken Murata², Shoko Shimizu¹, Yuziro Kawabe¹, Kazushige Touhara², Masato Nikaido¹

¹School of Life Science and Technology, Tokyo Institute of Technology
²Department of Applied Biological Chemistry, The University of Tokyo

Animals maintain their species by assortative mating based on visual and chemical information. East African cichlid is known as a model organism of assortative mating since they experienced astounding adaptive radiation in the African Great Lakes. So far, assortative mating in cichlid has been explained by the diversified nuptial colors and visual senses. However, it has been reported that not only visual information but also chemical information is required for assortative mating in cichlid. In addition, we can observe behavior to put their nose close to each other’s cloaca during mating suggesting that they are sniffing chemicals in the urine. Recently, we found a highly diverged polymorphism (clade I and clade II) in vomeronasal type-1 receptor V1R2, a putative pheromone receptor. Furthermore, the signature of positive selection was found in the putative ligand-binding pocket, suggesting the differentiation in the ligand selectivity. We hypothesized that this diversity of V1R2 receptors would induce assortative mating by accepting different chemicals. In this presentation, we will discuss this hypothesis based on the result of in situ hybridization analysis of c-fos in the olfactory epithelium, LC-MS/MS analysis of cichlid urine, and expression analysis of V1R2 receptor.

P-24

Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing

Shangzhe Zhang¹, Wenyu Liu¹, Xinfeng Liu¹, Jianquan Liu¹

¹State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University

Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72Mb and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 37,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.

P-25

Sika deer in Nara Park is a genetically unique population that has survived in a religious sanctuary.

Toshihito Takagi¹, Ryoko Murakami², Shingo Kaneko¹, Harumi Torii³, Hidetoshi B Tamate²

¹Fukushima University
²Yamagata University
³Nara University of Education

Deer have been a vital resource to humans since ancient times and, as a result, human activities including, hunting and land use, have influenced deer populations across the globe. Here, we investigated the historic anthropogenic influences on the genetic structure of Japanese sika deer inhabiting the Kii Peninsula using mitochondrial DNA (mtDNA) and short sequence repeats (SSR). The Kii Peninsula, located in the center of the Japanese archipelago, was the location of the first dynasty's capital in Japan and has maintained human activities since ancient times. In particular, the northern part of Nara Prefecture still retains temples and shrines built in the 7th century. These areas have been maintained as a city park called “Nara Park” and have been inhabited by wild Japanese sika deer for over 1000 years. These deer are religiously protected as messengers of the gods, and the whole area of Nara Park is considered a sanctuary for deer. However, there are no boundaries in the park, such as a fences, and deer move freely in and out of the sanctuary. Therefore, the genetic mixing between the deer in the sanctuary and those in other parts of the Kii peninsula remain unclear. The mtDNA analysis identified 18 haplotypes in the Kii Peninsula. Among the deer population in the Nara Park sanctuary, only one haplotype was identified and the haplotype was not shared with deer in surrounding areas. The SSR analysis revealed three distinct genetic groups in the Kii Peninsula: an eastern, a western, and a Nara Park group. Combined mtDNA and SSR analysis suggested that the eastern group has high genetic diversity, which is likely as a result of favorable habitat conditions and relatively low anthropogenic influence. Additionally, the religiously protected deer population around Nara park diverged from the ancestral population about 2,000 years ago, which coincided with the human population growth in this region. The increase in the human population demanded additional land for settlement or field use and required more hunting of deer for resources, which may have resulted in the decline and isolation of the deer population. Our results suggest that the deer inhabiting the Nara Park sanctuary is a rare fragmented population as a result of ancient human activities and has been maintained for more than a thousand years through subsequent religious protection.

P-26

Evolution of mammalian face as a deviation from the ancestral constraint

Hiroki Higashiyama¹, Hiroki Kurihara¹

¹The University of Tokyo

The anatomical framework of the jaw bones has traditionally been thought to be highly conserved among the jawed vertebrates, including mammals. However, here we provide the evidence that the rostralmost bone in mammals (so-called incisive bone) is not homologous with the rostralmost bone (premaxilla) in non-mammalian vertebrates. Through the comparative embryological study including monotreme and cell lineage tracing experiments by using the transgenic mice, we demonstrated that the mammalian upper jaw was established by a drastic rostral shift in the maxillary prominence from the pharyngeal arch, unlikely in the reptiles. The palaeontological study using the synapsid fossils also supported that the main body of the incisive bone is homologous with the reptilian septomaxilla rather than the premaxilla. The present finding provides a revision of the anatomical framework for the vertebrate cranium especially for the rostralmost jaw bone “premaxilla”, and helps explain some of the key morphological changes during the mammalian evolution, such as the semi-motile nose.

P-27

How fish got their complex color patterns

Seita Miyazawa¹

¹Graduate School of Frontier Biosciences, Osaka University

Fish exhibit a fascinating variety of color patterns, but mechanisms underlying the diversity remain largely unknown, particularly for complex and camouflaged colorations. A mathematical model predicts that intricate color patterns can be formed by "pattern blending" between simple motifs via hybridization. I analyzed the skin patterns of more than 18k fish species and found strong mechanistic associations between camouflaged labyrinthine patterns and simple spot motifs, showing remarkable consistency with the pattern blending hypothesis. Genomic analyses confirmed that the coloring on multiple labyrinthine fish species has originated from pattern blending by hybridization, and phylogenetic comparative analyses have further substantiated the pattern blending hypothesis in multiple major fish lineages. These findings provide a plausible mechanistic explanation for the characteristic diversity of fish colorations and suggest a novel evolutionary process of complex and camouflaged markings by means of pattern blending.

P-28

Adaptive introgression in Pomatorhinus musicus

Yuchen Fu¹, Jia-fen Yeh¹, Cheng-te Yao², Dong Fong³, Shou-Hsien Li¹

¹Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
²Taiwan Endemic Species Research Institute, Nantou, Taiwan
³Kunming Institute of Zoology, Kunming, China

Adaptive introgression, the introgressed genetic variants under positive selection and enjoying adaptive advantages, could serve as an important genetic source for organisms to cope with the ever-changing environment.Streak-breasted scimitar babbler (Pomatorhinus ruficollis, Timaliidae, Aves) is a common passerine widely resides in south, southeast and eastern China mainland while its sister species Taiwan scimitar babbler (Pomatorhinus musicus) is an endemic species of Taiwan Island. Previous studies suggested two species had a substantial level of gene flow from P. ruficollis to P. musicus. To address the question, we sequenced the whole genome of P. ruficollis and P. musicus at the first. Then, we would like to detect the introgressed genomic regions within P. musicus genome, and examine whether the introgressed genomic region is under positive selection.

P-29

Comparative genomics of high-quality genomes two Paradise Fishes, Macropodus hongkongensis and M. opercularis

Zhongxing Wang¹, Rongfeng Cui¹

¹School of Ecology, Sun Yat-sen University, Guangzhou, China

Relaxed selection resulted from environmental changes is an important but often neglected force in biological evolution, where an increase of genetic load often ensues. Previous studies have shown that gene flow has the potential to lower genetic load by introducing beneficial alleles across species. Macropodus hongkongensis and M. opercularis are two closely related Paradise fishes (Osphronemidae) native to south China, the latter being well known for their brilliant coloration and aggressive behavior. Despite having a similar morphology, the two species differ in coloration and segregate geographically, where M. hongkongensis resides in high elevation streams and M. opercularis on lowland. Our preliminary data show a smaller effective population size of the former. The two species can readily hybridize in the lab, making them an ideal system for speciation and adaptive introgression studies. To date, we have obtained high-quality, chromosome-level de novo assemblies from one male M. hongkongensis and one male M. opercularis from Shenzhen and Guangzhou respectively, combining Nanopore, HiC and stLFR technologies. We estimated the genome size of M. hongkongensis to be 446 Mb(n=23) and M. opercularis to be 438 Mb(n=23). Both reference genomes attained complete Busco genes of >98.7%, indicating a high continuity and completeness. We experimented with assembly polishing using only HiC data, and found it effective in fixing small-scale errors. We plan to perform gene annotation and identify structural variation regions, followed by subsequent analysis aiming for locating relaxed selection on genomic regions.

P-30

Degenerative molecular evolution of a neofunctionalized sex-determining gene dmy during species diversification in Oryzias fish

Yusaku Ogita¹, Kei Nakasako¹, Fuga Fujimura¹, Kei Tamura¹, Nobuhiko Takamatsu¹, Michihiko Ito¹

¹Department of Bioscience, School of Science, Kitasato University, 1-15-1 Kitasato, Minamiku Sagamihara, Kanagawa, 252-0373, Japan.

Animal sex-determining genes (SDGs), which direct female and male development, are diversified even among closely related species. These genes could emerge independently in their evolutionary contexts. We previously proposed that undifferentiated (homomorphic) sex chromosomes easily allow switching of an SDG with another new one. Xenopus frog and Oryzias fish, which both have homomorphic sex chromosomes, possess dm-W and dmy as SDGs, respectively. The two SDGs independently emerged from duplication of a masculinizing gene dmrt1 during Xenopus or Oryzias diversification. Our recent work revealed that both the genes could have acquired sex-determining function by a common molecular mechanism under positive selection. However, the molecular mechanisms on the switching of SDGs remains largely unknown. Here, we analyzed molecular evolution of dmy among three Oryzias species and performed functional analysis of DMY as DNA-binding protein. Interestingly, some ancestral or non-ancestral amino acid substitutions from DMRT1 to DMY might enhance or reduce the DNA-binding activity, respectively. Then we propose an evolutionary model that once established SDGs often have evolved degeneratively with weakly deleterious mutations.

P-31

Parapatric speciation with long-term gene flow of two sexual dichromatic pheasants

Zheng Li¹, Jie Zhou¹, Wei Liang², Lu Dong¹

¹MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
²College of Life Science, Hainan Normal University

Understanding speciation has long been a fundamental goal of evolutionary biology. It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species, in which sexual selection may play an important role by generating and maintaining sexual dimorphism. The mechanism of how sexual selection operated in speciation with gene flow remains an open question and the subject of many research. Two species in genus Chrysolophus, golden pheasant (C. pictus) and Lady Amherst's pheasant (C. amherstiae), which both exhibit significant plumage dichromatism, are currently parapatric in the southwest China with several hybrids recordings in field. In this research, we estimated the pattern of gene flow during the speciation of two pheasants using the Approximate Bayesian Computation (ABC) based on the multiple genes data. The results provide clear evidence that the gene flow between two pheasants were consistent with the prediction of isolation with migration model, indicating that there was long-term gene flow after the initially divergence ( ca. 2.2 million years ago), and the secondary contact around 30 ka induced ongoing gene flow to now. With a new assembled de novo genome of Lady Amherst’s pheasant, we reconstructed the demographic history of the two pheasants by pairwise sequentially Markovian coalescent (PSMC) which also supported the conclusion. KEY WORDS: Golden pheasant (Chrysolophus pictus), Lady Amherst’s pheasant (Chrysolophus amherstiae), speciation, gene flow, Approximate Bayesian Computation (ABC), pairwise sequentially Markovian coalescent (PSMC).

P-32

Genetic and cellular basis of orange spot formation in the guppy (Poecilia reticulata)

Mayuko Kawamoto¹, Yuu Ishii¹, Masakado Kawata¹

¹Graduate School of Life Sciences, Tohoku University

In the guppy (Poecilia reticulata), females tend to prefer males with larger and more highly saturated orange spots. To understand the regulatory mechanism of orange spot formation, we performed RNA-seq analysis and observation of xanthophores, which are pigment cells composing orange spots, in the male guppy skin. First, the expression patterns of genes specific to orange spots and certain color developmental stages were estimated using RNA-seq. The results showed that genes affecting secondary differentiation of xanthophores were upregulated in orange skin and changed expression levels according to color development, suggesting that such genes contribute to orange spot formation. Second, the color and distribution of xanthophores in the male guppy skin were observed to confirm secondary differentiation of xanthophores. We found that light yellow xanthophores were present in dull skin and immature males, while bright orange xanthophores, which appeared to be secondarily differentiated, were concentrated in orange spots. These findings imply that orange spots are formed by secondary differentiation of xanthophores.

P-33

Evolution of responsiveness between parents under conflict and non-conflict conditions

Fumiaki Y. Nomano¹

¹Sokendai, The Graduate University for Advanced Studies

Biparental care in which two parents cooperate to rear the offspring often involves the adjustment of investment level in response to the partner’s investment. The conflict of interest due to the cost not fully shared between the partners is invoked to explain such responsiveness. Using an individual-based model, I examined the evolution of mutual responses by parents to the partner’s care investment under two conditions: pair bond with and without a chance of re-mating after the partner’s death. The former condition favoured a lower investment level than the latter non-conflict condition as predicted previously. The evolution of responsiveness partially recovered the reduced investment under the conflict condition. A similar level of responsiveness evolved in both conflict and non-conflict conditions, which suggests that the conflict of interest arising from the prospect for re-mating is not solely responsible for the evolution of responsiveness in biparental care systems.

P-34

Larval competition molds male harm at the imaginal stage in evolutionary experiments

Wataru Mukaimine¹, Yukihiko Toquenaga²

¹Doctoral Program in Biology, University of Tsukuba
²Faculty of Life and Environmental Sciences, University of Tsukuba

Male harm is an essential component of sexual selection. The intensity of male harm varies even within species, but few studies have focused on larval resource competition as a cause of male harm. We examined the evolutionary relationship between male harm and larval competition using multi-generation experiments with bean weevils Callosobruchus maculatus. We established the four experimental evolution lines with the combination of two treatments: larval contest/scramble resource competition and adult polygamy/monogamy mating environment. After 40 generations, we recorded the mating duration, male ejaculate amount, number of eggs laid by females after a single mating, and weights of males and females. Additionally, we recorded the number of eggs laid by females when the male density was high or low. Both larval and adult selection affected the body weights of both sexes, with contest and polygamy being heavier than scramble and monogamy. There was no significant difference in mating duration or ejaculate amount among the four selection regimes. The number of eggs laid by females at different male densities suggests that tendency for male harm to be more significant in the polygamy line than in monogamy. In polygamous lines, the egg's decrease due to male density in the contest was fewer than in the scramble. These results imply that differences in body weight according to larval resource competition may alter either male or female resistance and affect male aggressiveness regardless of mating duration and ejaculate amount.

P-35

Visual adaptation of an Amazon fish species, the sailfin tetra Crenuchus spilurus, living in the black and clear water habitats

Elio de Almeida Borghezan^1,2, Tiago Henrique da Silva Pires², Jansen Zuanon², Yohey Terai³, Hideki Sugiura¹, Miho Inoue-Murayama¹, Shiro Kohshima¹, Takushi Kishida^1,4

¹Wildlife Research Center of Kyoto University, Japan
²National Institute of Amazonian Research, Amazonas, Brazil
³Graduate University for Advanced Studies, Sokendai, Japan
⁴Museum of Natural and Environmental History, Shizuoka, Japan

Natural selection shapes sensory systems to optimally tune to characteristics of the environment. Amazon aquatic environments are highly distinct in their underwater lighting condition, since light spectrum is affected by compounds in the water column and by the rainfall. The sailfin tetra (Crenuchus spilurus, Characiformes) is a sexual dimorphic fish species that lives in small streams of black and clear water types of the Amazon basin. This species is composed by two phylogenetically distinguished lineages, one inhabiting black stream waters in the Negro River basin and the second one inhabiting mostly clear stream waters throughout the remaining species distribution. Interestingly, one population (named Coari) which belongs to the clear water lineage currently lives in black water. Here, we studied the nucleotide sequences, the expected maximum absorbance wavelength (λmax), and the expression levels of the LWS (Long Wavelength Sensitivity) opsin genes of Black water and Clear water lineages including the Coari population. We found three copies of the LWS1 and two copies of the LWS2 genes with different λmax to each other in the sailfin tetra samples. There are little sequence variations among individuals. The amino acid positions expected to affect the λmax of the LWS pigments did not vary in all populations. However, relative expression level of each LWS gene differs greatly among populations. In highly variant environments and in systems that possess several copies of the same gene, adaptations may occur in the gene expression profile rather than in the fine tune between environmental light and protein light sensitivity.

P-36

Response profiles of bitter taste receptors in egg-laying mammals provide insight into foraging behavior and functional evolution of the receptors in mammals.

Akihiro Itoigawa¹, Takashi Hayakawa^2,3, Yang Zhou⁴, Adrian Manning⁵, Guojie Zhang⁴, Frank Grutzner⁶, Hiroo Imai¹

¹Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University
²Faculty of Environmental Earth Science, Hokkaido University
³Japan Monkey Centre
⁴Department of Biology, University of Copenhagen
⁵Fenner School of Environment and Society, The Australian National University
⁶The Environment Institute, University of Adelaide

Bitter taste, mediated by bitter taste receptors (TAS2Rs), is an important sense for mammals to detect potentially harmful substances in food. The TAS2R gene repertoire and each receptor function are believed to adapt to the food environment of each mammal. However, TAS2R functions are unknown in monotremes (egg-laying mammals: platypus and echidna). We comprehensively surveyed agonists of all TAS2Rs in platypus and short-beaked echidna and compared their functions with orthologous TAS2Rs of marsupial and placental mammals (i.e., therians). As result, the deorphanized monotreme receptors were functionally diversified. Although monotremes have a strikingly small TAS2R repertoire, some platypus TAS2Rs had broad receptive ranges of agonists but not in echidna, which mainly consumes ants and termites, indicating that receptive ranges of TAS2Rs were associated with feeding habits in monotremes. Furthermore, we found some monotreme and therian orthologous receptors responding to one of the major feeding deterrents from plants and insects, suggesting that detection of such substances may be a shared and ancestral function among mammals.

P-37

Detection and comparison of codon bias in eight Anolis species

Fuku Sakamoto¹, Shunsuke Kanamori¹, Luis M. Díaz², Antonio Cádiz³, Yuu Ishii¹, Takuro Nakayama⁴, Katsushi Yamaguchi⁵, Shuji Shigenobu⁵, Masakado Kawata¹

¹Tohoku Univ.
²Mus. Nat. Hist. of Cuba
³Habana Univ.
⁴Tsukuba Univ.
⁵Natl. Inst. for Basic Biology

In protein-coding regions in genomes, the substitution rates for synonymous sites which do not change amino acid sequences with their nucleotide mutations have been assumed to be neutral, and thus, the synonymous sites have been used for the estimation of neutral models. However, synonymous sites may be subject to selection. Synonymous codons are disproportionately used in genomes of many species and some recent studies suggested that usage of synonymous codons could affect translation from mRNAs to proteins and mRNA stability. In this study, we used genomes of Anolis lizards, which had adapted to various habitats and are used as model organisms of adaptive radiation, and attempted to examine the tendency of synonymous codon usage in each species. Here we will show the results of codon usage bias in the whole genome of each species and its interspecies comparison.

P-38

The evolutionary tuning of thermal perception related to habitat selection in frogs

Shigeru Saito^1,2,3, Claire T. Saito^1,2, Takeshi Igawa⁴, Shohei Komaki⁵, Makoto Tominaga^1,2,3

¹Division of Cell Signaling, National Institute for Physiological Sciences
²Thermal Biology Group, Exploratory Research Center on Life and Living Systems (ExCELLS)
³Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies)
⁴Amphibian Research Center, Hiroshima University
⁵Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization

Frog species utilize different niches for breeding since the season and water environments for spawning vary among species. Accordingly, the tadpoles of each species can be exposed to different thermal conditions. In the present study, tadpoles of five frog species that are spatially and temporally inhabit different niches were investigated. We compared heat tolerance as well as avoidance temperatures by behavioral assay. These two parameters were positively correlated with each other, and the species differences were consistent with thermal niches of each species. Moreover, the species difference in avoidance temperatures was 2.3 times larger than that in heat tolerance, suggesting the importance of heat avoidance responses in habitat selection. In addition, functional characterizations of heat sensor TRPA1 revealed that its thermal property shifted with the avoidance temperature of the species. Combined, our findings suggest that functional shift in the heat sensor played a crucial role in thermal adaptation processes.

P-39

IN SEARCH OF GENOMICS SIGNS OF ADAPTATION TO COLDER CLIMATE: A LESSON FROM DROSOPHILA ALBOMICANS

Sultan Lulecioglu¹, Yoshitaka Ogawa¹, Koichiro Tamura^1,2

¹ Department of Biological Sciences, Tokyo Metropolitan University
² Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University

According to previous studies, Drosophila albomicans population in Japan is predicted to originate from Taiwan. Since Japan is northern to Taiwan and has a lower average temperature than Taiwan, we hypothesized that in the process of population expansion to the colder climate of Japan, the genomic structure of the population in Japan is expected to undergo some changes to adapt to the colder climate. Therefore, we conducted population genomic analyses of natural populations of both Japan and Taiwan to find out any genomic sign of adaptation to the colder climate. We used whole-genome sequence data of 50 flies from each population for statistical inference of genomic changes via site frequency spectrum and haplotype-based tools. The results suggest small differences rather than strong candidate regions of selection; in addition, different detection tools appear to suggest different regions of emerging changes.

P-40

Variation in ovarian diapause phenotype within a natural population of Drosophila suzukii

Takako Fujichika¹, Tsunaki Asano¹, Aya Takahashi^1,2

¹Department of Biological Sciences, Tokyo Metropolitan Univ.
²Research Center for Genomics and Bioinformatics, Tokyo Metropolitan Univ.

Many insects which inhabit the temperate zone shift to a physiological state called diapause in late autumn to survive the stressful environment of winter. Some wild fruitflies like Drosophila suzukii suppress the development of their reproductive organs when the arrival of winter is anticipated. Such ovarian diapause is induced under certain environmental conditions such as short daytime and low temperature. However, because of the unpredictable temperature fluctuation in the autumn, the timing of diapause induction may have different consequences on fitness every year. While inducing diapause too early might lower the fitness by losing some generations, an extended reproduction might risk the survival of the offspring. Therefore, due to such fluctuation in fitness, large variations in the sensitivity and strength of diapause induction are expected within natural populations. Consistent with this prediction, we found a considerably large variation in diapause induction under the same light cycle and temperature conditions among the three strains sampled from a single natural population. Next, since the reproductive diapause in Drosophila females has been almost exclusively investigated using virgin females, we conducted the experiments using mated females. The results showed that mating had a consistent effect inhibiting diapause induction across all strains, although female receptivity to mating attempts may vary. We also investigate whether or not the strong effect of mating is due to sex peptide transferred during copulation as part of the seminal fluid. The effect of sex peptide on diapause induction varied among strains. These results indicate a large genetic variation underlying the responses to various conditions, which influences the induction of ovarian diapause in a natural population of this species.

P-41

Functional divergence of the pigmentation gene melanocortin-1 receptor (MC1R) in six endemic Macaca species on Sulawesi island

Xiaochan Yan¹, Yohey Terai², Kanthi Arum Widayati³, Akihiro Itoigawa¹, Laurentia Henrieta Permita Sari Purba³, Fahri Fahri⁴, Bambang Suryobroto³, Hiroo Imai¹

¹Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Japan
²Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
³Department of Biology, Institut Pertanian Bogor University, Bogor, Indonesia
⁴ Department of Biology, Tadulako University, Palu, Indonesia

Coat color is often highly variable within and between animal taxa. Among hundreds of pigmentation-related genes, Melanocortin-1 receptor (MC1R) plays key roles in regulating the synthesis of the dark eumelanin and the red–yellow pheomelanin. Six macaque species, known as Sulawesi macaques, diverged rapidly from a common ancestor in allopatric on Sulawesi island. Unlike most macaques, Sulawesi macaques commonly have a dark coat color, with divergence in shade and color pattern. Notably, M. maura in the southwest has the most primitive phenotype (brownish), and M. nigra in the northernmost area is the most derived (dark). To clarify the genetic and evolutionary basis for coat color in Sulawesi macaques, we investigated the MC1R sequence and functional properties, including basal cAMP production and α-MSH-induced activity in vitro. We found fixed amino acid substitutions in each species, and the six species-specific variants corresponded with variation in activity. We further confirmed that five key substitutions significantly influenced basal activity of MC1R. In particular, the M. maura-specific variant exhibited comparable functional characteristics to M. nemestrina, consistent with its primitive phenotype. Overall, our results suggest that fixed differences in MC1R resulted in different functional characteristics and might contribute to divergence in color among the six Sulawesi macaque species.

P-42

Allele-specific gene expression analysis on rapidly evolving male genitalia between recently diverged Drosophila species

Kentaro M Tanaka¹

¹Department of Biological Sciences, Tokyo Metropolitan University

Male external genitalia evolves rapidly in animals with internal fertilization. It is generally thought that rapid genital evolution has been driven by sexual selection and contributed to establishment of reproductive barrier between species by male and female genital incompatibility. Identification of genes underlying the rapid morphological divergence would provide an opportunity to deepen our understanding on speciation process. A young species pair, Drosophila simulans and D. mauritiana exhibits striking differences in the external male genital structures, which are playing important role in opening, grasping and holding female genitalia during mating. From previous studies, more than 20 genomic regions was estimated to contribute these interspecific differences, yet only one gene was identified so far. To pinpoint causative genes rapidly, here I screened candidate genes that acquired genitalia-specific cis-regulatory changes by allele-specific expression analysis. Hybrid male genitalia at two developmental time points (30 and 45 hours after puparium formation) showed 629 allele-specific genes whose expression pattern is consistent with parental expression differences. By comparing to non-genital tissue at the same developmental time, 210 genes was retained as genitalia specific candidates. Some of these genes are involved in regulation of cell size, extracellular matrix assembly and cell death in D. melanogaster. Further functional analysis will not only provide a list of genes underlying rapid male genital divergence through cis-regulatory changes, but also demonstrate the utility of tissue-specific and allele-specific gene expression analysis for morphological evolution.

P-43

Ancestral reconstruction of mycophagy in the Drosophilidae

Yang Zhang¹, Takehiro K. Katoh², Cédric Finet³, Hiroyuki F. Izumitani¹, Masanori J. Toda⁴, Hide-aki Watabe⁴, Toru Katoh⁵

¹Department of Natural History Science, Graduate school of Science, Hokkaido University, Sapporo 060-0810, Japan
²Laboratory of Ecology & Evolutionary Biology, Yunnan University, Kunming 650091, China
³Division of Science, Yale-NUS College, 138527, Singapore
⁴Hokkaido University Museum, Hokkaido University, Sapporo 060-0810, Japan
⁵Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan

According to the previous phylogenetic hypothesis, it is suggested that mycophagy has independently evolved on several lineages in the Drosophilidae. However, the reconstruction depends significantly on the basal tree topology and taxon sampling used for ancestral reconstruction. So in this study, based on our well-resolved phylogenetic tree, we reconstruct the ancestral states of food habit to infer the evolution of mycophagy in the Drosophilidae. We found that fungus-feeding habit has been gained independently in two lineages. The most recent common ancestor (MRCA) of the subgenus Drosophila was estimated to have acquired mycophagy by expanding its ancestral feeding niche on fermenting fruits to decayed fungi, while the MCRA of the Zygothrica genus group shifted its niche from fruits to fungi as a specialist probably preferring fresh fruiting bodies.

P-44

Do echinoderms have more derived molecular developmental programs than chordates? - introducing

Jason Cheok Kuan Leong¹, Yongxin Li², Masahiro Uesaka³, Yui Uchida^1,4, Echinoderm Genomes Sequencing Consortium⁵, Wen Wang², Naoki Irie^1,4

¹Dept of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
²State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
³RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan.
⁴Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
⁵Niigata University, Japan; Chinese Academy of Sciences, China; Brown University; California Institute of Technology; California State University; Boston University, USA

Which species and embryos are more derived? Species retaining ancestral features, such as living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of individual traits, and no consensus has been made toward quantifying “degree of phenotypic evolution” of certain species or embryos as a whole. The vertebrate mid-embryonic, body plan-establishing phase has been suggested to be highly evolutionarily conserved than the earlier or later stages, but these previous studies have yet to reveal which specific species or clade retains more ancestral developmental systems than others. Similarly, echinoderms are often regarded as a group of “highly derived” species as they evolved the unique pentaradial body plan, but it still remains to be tested if they indeed experienced greater changes to their developmental systems than their sister groups. By utilizing gross embryonic transcriptomic profiles of echinoderms and chordates, we propose a new method, “derivedness index”, to quantify the degree of overall phenotypic derivedness of embryos. In contrast to “conservation” which mainly focuses on features or genes commonly shared among species being compared, the derivedness index we developed also considers those that were lost or newly obtained during evolution. In the long term, we anticipate that this index would serve as a quantitative guide to search for constrained developmental phases or processes as less evolvable embryos are expected to be less derived.

P-45

Ex-situ conservation genetics contributes to spider monkeys in Japan

Haruka Kitayama¹, Atsushi Shirai², Kei Nemoto³, Yuko Tawa⁴, Koshiro Watanuki^3,5, Takashi Hayakawa^3,6

¹Graduate School of Environmental Science, Hokkaido University
²Saitama children's Zoo Park
³Japan Monkey Centre
⁴Kyoto City Zoo
⁵Wildlife Research Center, Kyoto University
⁶Faculty of Environmental Earth Science, Hokkaido University

Spider monkeys (Ateles sp.) are one of the most endangered primates ranging from the Yucatan Peninsula throughout Amazonia. The current consensus of their classification is split into 7 species. However, species identification of Ateles individuals is quite difficult because their morphological traits are gradually changed and drastically diversified among species especially in pelage color and its patterning. This problem makes it difficult to perform conservation not only in wild but also in captive populations. At present, there are ~150 living spider monkeys captive in ~30 Japanese zoos as a result of >70-year generation changes. To understand the genetic structure of the Ateles population in Japan and promote its ex-situ conservation, we carried out population genetic analysis. We extracted genomic DNA of 127 individuals from their fresh hair follicles. We determined nucleotide sequences of 3 mitochondrial DNA regions and nucleotide lengths of 9 nuclear microsatellite loci in all individuals. We found ancestries of 4 species (A. chamek, A. fusciceps, A. geoffroyi and A. hybridus) from mitochondrial DNA analysis. Nuclear microsatellite analysis showed that there were at least 29 hybrid individuals, >20% of the current Japanese population. Hybrid individuals seem to show morphologically intermediate traits of the parent species. These findings can contribute to the more appropriate management of captive spider monkeys and provide new insights into Ateles geography and evolution.

P-46

Programmed genome rearrangement eliminates of germline developmental genes in sea lamprey which plays a key role in spermatogenesis

Tamanna Yasmin¹, Phil Grayson², Margaret F. Docker¹, Sara V. Good^1,3

¹Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
²Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA, 02115
³Department of Biology, University of Winnipeg, Winnipeg, Manitoba R3B 2E9, Canada

In some multicellular organisms, germline and somatic cells harbor different genomes due to the process of programmed genome rearrangement (PGR), which jettisons part of the germline genome from somatic cells early in embryonic development. Depending on the species, the genomic regions eliminated during PGR may be involved in germline-somatic differentiation and/or sex determination. In the basal vertebrate sea lamprey, PGR occurs in ~ the 7th embryonic cell division on the third day post-fertilization. Here, RNA-sequence analysis was performed on sea lamprey gonads from 10 definitive females, 11 definitive males, two undifferentiated larvae, and five prospective males prior to initiation of sexual differentiation (n=28) to assess the expression of germline-specific genes (GSG) during gonad differentiation. First, we employed a genome-guided de novo assembly pipeline to create a comprehensive gonadal superTranscriptome using RNA-seq data of all 28 samples and generated gene annotations and normalized gene counts for both known and novel genes using the Trinotate pipeline and DESEQ2, respectively. Next, we identified germline-specific regions (GSR) in the chromosome level sea lamprey reference genome by comparing coverage of testes vs. blood DNA using sea lamprey chromosome level reference genome, and we identified GSGs by using sea lamprey gonadal superTranscriptome. Lastly, to characterize the genes in the GSR, we identified putative orthologues of the sea lamprey genes with those in 10 other chordate taxa using the program Orthofinder. We find that chromosome 81, as well as 49 unassembled scaffolds, are part of the GSR and identify 638 germline-specific genes (489 novels) representing 163 unique gene names, approximately half (92) of which exist in two more duplicated copies in the GSR, and approximately half (89) of which have paralogues present in one or more copies in the somatic genome. Remarkably, we find that almost all GSGs are expressed in one or more stages of male gonad development but are not expressed in female gonads at any stage, despite evidence that females appear to share the GSR with males – a few highly-expressed ovarian genes fall within the GSR. Equally compelling, the somatic paralogues of the male-biased GSR genes exhibit expression in both male and female gonads at multiple time points while the germline-specific paralogs of these genes exhibited highly sex- and stage- biased expression. In particular, the GSR genes had a 36X greater odds of being expressed in prospective males or males undergoing spermatogonial differentiation in mid to late metamorphosis. Lastly, employing publicly available RNA-seq data of day 1 to day 5 old embryos, we find little evidence that the GSR genes are expressed in early embryogenesis. Overall, we conclude that the GSR of sea lamprey plays an important role in male gonad differentiation and potentially sex determination.

P-47

The evolution of body color pattern of Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae)

Wahyu Endra Kusuma¹, Yoshinori Kumazawa²

¹Department of Aquaculture, Faculty of Fisheries and Marine Science, University of Brawijaya, Malang 65145, Indonesia
²Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya, Japan

Rasbora lateristriata is a small freshwater fish that is believed to have wide distributional boundary in Indonesia, ranging from Java to Bali, Lombok and Sumbawa Islands. We collected specimens from various locations of these Islands and performed molecular phylogenetic analyses to evaluate intraspecific phylogenetic relationships, as well as interspecific phylogenetic relationships among other Rasbora species. Our phylogenetic analyses using two mitochondrial and two nuclear gene sequences suggested that the currently recognized R. lateristriata is a species complex with at least four major clades that possibly represent different species. We also examined thirty-eight morphological characters including body color patterns to find that the four major clades in this species complex are morphologically very similar to each other without clear morphological segregation. However, we noticed that combination of two morphological characters of body color pattern, i.e., supra anal pigmentation (SAP) and basicaudal blotch (BCB), can discriminate between the four major clades. Individuals from Clade 1 can be identified with the presence of SAP and the absence of BCB. The absence of both SAP and BCB was shared by Clade 2 individuals. Clade 3 individuals shared the absence of SAP and the presence of BCB. Clade 4 individuals shared the presence of both SAP and BCB. The presence of SAP and BCB in this species complex appeared to be a plesiomorphic character state since SAP and BCB appear to have been preserved during the diversification of R. sumatrana group, a sister group of the R. lateristriata species complex. However, they were lost independently among some major clades in these two species complexes.

P-48

Structural variation and gene tree discordance in great apes

Yafei mao¹

¹University of Washington

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation. We present a fully annotated, high-quality bonobo genome assembly, constructed without guidance from the human or chimpanzee reference genomes, by utilizing a multiplatform approach that includes long-read whole-genome sequence, fluorescence in situ hybridization, full-length cDNA sequencing, strand-sequencing, and optical mapping data. We generate a bonobo genome assembly where >98% genes are completely annotated and 99% of the gaps are closed, including resolution of about half of the segmental duplications and almost all full-length mobile elements. We compare the bonobo genome to other apes and identify >5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure, or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of gene tree discordance estimating that ~5.1% of the human genome is genetically closer to chimpanzee/bonobo and >36.5% of the genome shows gene tree discordance if we consider a deeper phylogeny including gorilla and orangutan. Notably, we show that 26% of human–chimpanzee/human–bonobo gene tree discordance segments are nonrandomly distributed and genes within these clustered segments show significantly accelerated amino acid evolution when compared to the rest of the genome.

P-49

Drift and selection signatures in cryptic speciation of White Cloud Mountain minnow (Tanichthys albonubes)

Chao Li¹, Jun Zhao¹

¹South China Normal University

Cryptic speciation describes the evolutionary processes that one single species diverged into two or more cryptic species. Revealing the mechanisms underlying cryptic speciation is key to understanding the formation of new species and estimation the real biodiversity of the world. For highly isolated species with small effective population size (Ne), both genetic drift and divergent selection are predicted to play important roles. Herein, The White Cloud Mountain minnow (Tanichthys albonubes) was used as a study system which has been shown to be a species complex comprising seven cryptic species in our previous work. We determined the roles of genetic drift and selection using a restriction site-associated DNA sequencing (RAD-seq) and full length transcriptome sequencing. By analyzing 7068 SNP loci, we found genetic drift dominates over selection in cryptic speciation of White Cloud Mountain minnow species complex. The genetic diversity of six cryptic species were negatively correlated to their pairwise Fst with non-cryptic species T. micagemmae. Besides, short-term Ne of these cryptic species showed positively relationships with their nucleotide diversity, suggestive of strong genetic drift effects. To determine the genetic basis of selection, we conducted model-based and nonmodel-based methods to detect outliers and annotated these loci to the newly generated transcriptome. Results showed that 17 candidate genes (15 known genes and two unknown genes) may have significant impacts on the evolutionary processes of T. albonubes complex. These known genes mainly involved in biological functions such as development of nervous system and regulation, immune response, transcriptional regulation, visual perception and protein catabolism. Overall, this study provides new insight into cryptic speciation and facilitates our understanding of cryptic species.

P-50

Genetic basis of wing dimorphism in planthoppers

Haijun Xu¹

¹Zhejiang University

Many insects are capable of developing into either long-winged (LW) or short-winged (SW)/wingless morphs, which contributes significantly to their ecological success in natural and agricultural habitats. However, the molecular mechanisms underlying wing polymorphism remains elusive. Recently, we found that an insulin receptor (InR2) and a transcription factor FoxO served as master genes that determine wing-morph switching in the wing-dimorphic planthopper (BPH) Nilaprvata lugens, a destructive rice pest in Asia. Silencing either InR2 or FoxO transformed wing development from SW to LW morphs. We generated a homozygous InR2 mutant by CRISPR/Cas9-meidated genome editing. InR2 had distinct and overlapping functions with InR1 on life-history traits of BPH. The gene expression dynamics of wingbuds showed that a wing-patterning gene Vestigal was spatio-temporally induced in InR2 mutants during the sensitive stage for wing-morph switching. Further analysis showed the InR2-FoxO signaling cascade regulates Vestigal expression through binding to a FoxO response element (GTAAACA) located in the first intron of Vestigial. Silencing of Vestigal could antagonize InR2 or FoxO effect, redirecting from LW to SW morphs. These findings reveal that the insulin signaling pathway regulate wing dimorphism in the BPH via cross-talking with the wing-patterning network. These findings significantly contribute to our understandings of genetic basis of wing polymorphism in insects.

P-51

Callitriche as a model for the evolution of stomatal patterning in angiosperms

Yuki Doll¹, Hiroyuki Koga¹, Hirokazu Tsukaya¹

¹The University of Tokyo

After being acquired in the land plant ancestor, stomata have helped plants’ adaptation to new environments. Today, we see diverse patterns of stomatal development in lineages of angiosperms. However, despite recent progress in genetics of stomatal development in the model plant Arabidopsis, the genetic and evolutionary mechanisms of how such diverse patterns originated are still largely unexplored. Here we propose the genus Callitriche (Plantaginaceae; Lamiales) as a novel experimental system to tackle this mystery. We found in Callitriche that stomatal development occurs via different processes in species of different lifestyles. This finding hints at the presence of adaptive significance behind different patterns of stomatal development. In addition, we revealed that the simple shift in the expression patterns of two key transcription factors might underlie the diversification of stomatal patterning in Callitriche. We will discuss how the accumulating knowledge in Callitriche can contribute to our understanding of the evolutionary history of stomatal patterning in angiosperms.

P-52

Author are not specified

Affiliations are not specified

P-53

Testing the flexibility of dosage compensation by utilizing the neo-sex chromosomes in Drosophila

Masafumi Ogawa¹, Masafumi Nozawa^1,2

¹Department of Biological Sciences, Tokyo Metropolitan University
²Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University

Dosage compensation (DC) is the mechanism to counteract dosage imbalance of X-linked genes between sexes. In Drosophila, the expression level of X-linked genes becomes double in males. However, when the X chromosome is returned to an autosome, which has occurred many times in evolutionary history, males will have two copies of this “old” X chromosome. In this case, DC on the old X chromosome causing the overexpression may be rather deleterious and need to be suppressed. To test the flexibility of DC after the sex-chromosome turnover, we have crossed females of a species with neo-sex chromosomes with males of its closely-related species without neo-sex chromosomes and made the hybrids that mimic the condition immediately after the sex-chromosome turnover. Comparing the gene expression in the hybrid males with their parental males, we are currently evaluating the flexibility of DC in Drosophila.

P-55

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

Jacob L. Steenwyk¹, Thomas J. Buida III², Yuanning Li¹, Xing-Xing Shen³, Antonis Rokas¹

¹Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
²Nashville, Tennessee, United States of America
³Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.

P-56

Identifiability for phylogenetic trees from the covariance structure

Jan van Waaij¹, Carsten Wiuf¹

¹University of Copenhagen

In this talk, I am interested in the identifiability of the evolutionary history from the covariance structure of SNP allele frequency data. Two well-known estimators for disentangling the evolutionary history are the estimator W from Pickrell & Pritchard (2012) and the matrix of all pairs of f₂ statistics as in Patterson e.a. (2012). I show that these estimators contain the same information in that there is a linear transformation of one into the other. However, these estimators do not allow for the placement of the root (if a tree). To remedy this, I suggest a new estimator that uses the SNP allele frequency data differently and uniquely determines the evolution tree. The work is an ongoing collaboration with Carsten Wiuf.

P-57

The origin and diversity of dominant groups in evergreen broad_leaved forests (EBLFs): Insights from the phylogeography of Phoebe zhennan complex

Jianhua Xiao¹, Lang Li¹, Jie Li¹

¹Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Chin

A combination of the phylogenetic analysis, population genetic analysis, population dynamic history inferring and ENM methods were carried out to explore the relationships and divergence pattern of Phoebe zhennan complex using RAD-seq data. The study results showed that: 1) P. hui and P. bournei are monophyletic, but P. zhennan is not monophyletic. High gene flow in P. bournei x P. zhenan and P. hui x P. bournei were observed. 2) The phylogeographic break of P. hui x P. bournei may be located at the western edge of the Sichuan Basin, and the phylogeographic break of P. bournei x P. zhenan was found across the boundary of the second and third landforms in China. 3) There may be many reasons for the geographic pattern of the Phoebe nanmu complex group: 1) Small interspecific genetic distance, extensive gene flow, and possible incomplete reproductive isolation; 2) Environmental heterogeneity and geographic isolation, such as West China The highly heterogeneous landscape of the rainy zone of west China, The mountain ranges at the boundary between the second and third steps in China; 3) Ancient tectonic events, such as the rapid uplift of the Qinghai-Tibet Plateau, the birth of modern Yangtze River, and the initiation and intensification of the East Asian monsoon system.

P-58

Comparison and evaulation of rapid methods for phylogenomic dating

Jose Barba¹

¹Temple University

Increasingly larger phylogenomic datasets encompassing a greater number of species and genes are available to generate molecular timetrees. Because of the practical limitations of current Bayesian methods for phylogenomic scale datasets, rapid relaxed-clock dating methods (e.g., RelTime and treePL) are increasingly used to analyze phylogenomic datasets with thousands of sequences. However, their performance is yet to be compared on the same datasets, so the powers and pitfalls of selecting between these approaches remain unclear. We compared the accuracy, bias, and coverage probabilities of RelTime and treePL time estimates by analyzing computer-simulated datasets in which evolutionary rates varied extensively among lineages. RelTime estimates were consistently more accurate than treePL, particularly when evolutionary rates were autocorrelated or shifted convergently among lineages. The 95% confidence intervals (CIs) around RelTime dates showed correct coverage probabilities for all relaxed clock models (95% on average). However, treePL produced rather low coverage probabilities due to overly narrow confidence intervals. RelTime is also computationally more efficient than treePL. Therefore, RelTime is a more accurate and efficient method for inferring timetrees using large-scale molecular datasets.

P-59

Mutations on homolog gene can be an adaptive evolution solution to gene loss

Liye Zhang¹, Guosheng Ma¹, Xiaojing Zhao¹

¹School of Life Science and Technology, ShanghaiTech University,China

Recent studies suggest gene loss may shape genome evolution. Gene loss commonly induces a transient aneuploidy as an adaptive mechanism. The aneuploidy is gradually replaced by more efficient point mutations. Using the acute eviction of Ulp2 SUMO-specific protease yeast model, researchers showed that mutations in the upstream SUMO-ligating enzymes were more efficient long-term adaptation mechanism. Using the same model, we intended to search for alternative/additional long-term adaptation mechanisms. Interestingly, by sequencing multiple independent evolved strains, we identified two independent mutations on the homolog gene ULP1. Introducing these two ULP1 point mutations rescued the ULP2 deletion phenotype (including the aneuploidy and slow doubling time upon gene loss). Our analysis of public genomics data in budding yeast also identified cases of such adaptive mutations on homolog genes upon gene loss. Taken together, our results suggested homolog gene adaptive evolution might be an alternative long-term solution to gene loss.

P-60

The evolution of body color pattern of Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae)

Wahyu Endra Kusuma¹, Yoshinori Kumazawa²

¹Department of Aquaculture, Faculty of Fisheries and Marine Science, University of Brawijaya, Malang 65145, Indonesia
²Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya, Japan

Rasbora lateristriata is a small freshwater fish that is believed to have wide distributional boundary in Indonesia, ranging from Java to Bali, Lombok and Sumbawa Islands. We collected specimens from various locations of these Islands and performed molecular phylogenetic analyses to evaluate intraspecific phylogenetic relationships, as well as interspecific phylogenetic relationships among other Rasbora species. Our phylogenetic analyses using two mitochondrial and two nuclear gene sequences suggested that the currently recognized R. lateristriata is a species complex with at least four major clades that possibly represent different species. We also examined thirty-eight morphological characters including body color patterns to find that the four major clades in this species complex are morphologically very similar to each other without clear morphological segregation. However, we noticed that combination of two morphological characters of body color pattern, i.e., supra anal pigmentation (SAP) and basicaudal blotch (BCB), can discriminate between the four major clades. Individuals from Clade 1 can be identified with the presence of SAP and the absence of BCB. The absence of both SAP and BCB was shared by Clade 2 individuals. Clade 3 individuals shared the absence of SAP and the presence of BCB. Clade 4 individuals shared the presence of both SAP and BCB. The presence of SAP and BCB in this species complex appeared to be a plesiomorphic character state since SAP and BCB appear to have been preserved during the diversification of R. sumatrana group, a sister group of the R. lateristriata species complex. However, they were lost independently among some major clades in these two species complexes.