Symposium proposal | |
Organizer: | The 2nd AsiaEvo Conference Organizing Committee |
The topic of this symposium is omnibus. |
OS1-1
Wolbachia in scale insects: A unique pattern of infection prevalence, high genetic diversity, and host shifts
Ehsan Sanaei1
1School of Biological Science, The University of Queensland, Australia
Wolbachia is one of the most successful endosymbiotic bacteria of arthropods. It is a master manipulator, modifying its hosts’ biology in many ways to increase its vertical (maternal) transmission. Wolbachia can also undergo host shifts that can be mediated by ecological vectors such as shared host plants or parasitoids. Here, I screened 687 specimens from 151 scale insect species that were mostly collected in Asia and Australia for Wolbachia infection. I fitted the distribution of within-species prevalence of Wolbachia to our data and compared it to distributions fitted to an up-to-date dataset compiled from surveys across all arthropods. In contrast to other hemipteran groups, the prevalence of Wolbachia in scale insects follows a distribution similar to exponential decline (most species are predicted to have low prevalence infections). By conducting Illumina pooled amplicon sequencing of 59 infected scale insect samples and 16 direct associates of scale insects (including wasps and ants), I determined 63 Wolbachia strains in these species belonging to supergroup A, B, and F. I observed a lack of congruency between Wolbachia and scale insect phylogeny and identified several putative host-shifts events. Finally, I fitted a Generalised Additive Mixed Model (GAMM) to assess factors influencing Wolbachia sharing among scale insect species. I found strong effects of host phylogeny without any significant contribution of host geography. There were high rates of Wolbachia sharing among closely related species (i.e., host-shifting mostly happens between species of the same genus) with a sudden drop off in sharing with increasing phylogenetic distance. This finding can explain a large number of reported Wolbachia host-shifting among congeneric species.
OS1-2
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies
Qiqing Tao1,2, Jose Barba-Montoya1,2, Sudhir Kumar1,2,3
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
2Department of Biology, Temple University, Philadelphia, PA 19122, USA
3Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
2Department of Biology, Temple University, Philadelphia, PA 19122, USA
3Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
Precise time calibrations needed to estimate ages of species divergence are not always available due to fossil records' incompleteness. Consequently, clock calibrations available for Bayesian dating analyses can be few and diffused, i.e., phylogenies are calibration-poor, impeding reliable inference of the timetree of life. We examine the role of speciation birth-death tree prior on Bayesian node age estimates in calibration-poor phylogenies and test the usefulness of an informative, data-driven tree prior to enhancing the accuracy and precision of estimated times. We present a simple method to estimate parameters of the birth-death tree prior from the molecular phylogeny for use in Bayesian dating analyses. The use of a data-driven birth-death (ddBD) tree prior leads to improvement in Bayesian node age estimates for calibration-poor phylogenies. We show that the ddBD tree prior, along with only a few well-constrained calibrations, can produce excellent node ages and credibility intervals, whereas the use of an uninformative, uniform (flat) tree prior may require more calibrations. Relaxed clock dating with ddBD tree prior also produced better results than a flat tree prior when using diffused node calibrations. Our results have practical applications because the ddBD tree prior reduces the number of well-constrained calibrations necessary to obtain reliable node age estimates. This would help address key impediments in building the grand timetree of life, revealing the process of speciation, and elucidating the dynamics of biological diversification.
OS1-3
Quantitative analysis on the adaptiveness of conspicuous consumption using a gene-culture coevolution model
Hidenori Komatsu1, Nobuyuki Tanaka2, Aoshi Suzuki3, Yasuhiro Hashimoto3, Liu Guanghao4, Yu Chen4
1Energy Innovation Center, Central Research Institute of Electric Power Industry
2Environmental Science Research Laboratory Central Research Institute of Electric Power Industry
3Division of Computer Science, University of Aizu
4Graduate School of Frontier Sciences, The University of Tokyo
2Environmental Science Research Laboratory Central Research Institute of Electric Power Industry
3Division of Computer Science, University of Aizu
4Graduate School of Frontier Sciences, The University of Tokyo
Previous qualitative surveys have suggested that the conspicuous consumption of expensive products with low practical value serves as a signal to show one’s personality traits. To analyze the adaptive significance of this signaling quantitatively, we developed a gene-culture coevolution model based on multi-agent simulations. While each agent behaves according to its true personality traits, it purchases products that modify the survivability and appearance of the personality traits, and produces offspring through mating based on the apparent modified personality traits. The products also evolve via the interactions of the agents. Through this model analysis, we show that conspicuously consumed products can evolve and contribute to the reproductive success of the consumers. The model could also evolve preferences for others’ personality traits as observed in the real world. The apparent modified personality traits tended to be localized into multiple clusters, even when there was low variance of true personality traits, suggesting that conspicuous consumption might be a source of diversification in mating strategies.
OS1-4
Does vertebrate embryogenesis recapitulate its evolutionary history?
Masahiro Uesaka1, Shigeru Kuratani1,2, Naoki Irie3,4
1RIKEN Center for Biosystems Dynamics Research
2RIKEN Cluster for Pioneering Research
3Department of Biological Sciences, The University of Tokyo
4Universal Biology Institute, The University of Tokyo
2RIKEN Cluster for Pioneering Research
3Department of Biological Sciences, The University of Tokyo
4Universal Biology Institute, The University of Tokyo
Recapitulation is a hypothetical concept assuming that animal embryogenesis parallels its evolutionary history, sequentially developing from more ancestral features to more derived ones. Previous comparative transcriptome studies have shown the conserved gene expression profiles at the mid-embryonic period of vertebrate embryogenesis rather than at the earliest stage. These results refute the recapitulation throughout embryogenesis but not during the embryogenesis after the conserved mid-embryonic period. In fact, a reasonable number of morphological traits regarded to be consistent with the recapitulation are enriched at later developmental stages. However, few quantitative studies have been done to test the recapitulation.
This talk will show molecular-based supports for the recapitulative pattern of gene regulatory activities in the mid-to-late embryogenesis. We collected the ATAC-seq data set from early-to-late embryos of four vertebrates (mouse, chicken, quail, and medaka) and estimated gene regulatory regions and their evolutionary ages. In all the examined species, we found that, from the conserved mid-embryonic period onward, genomic regions tend to become sequentially accessible in a similar order of their evolutionary ages, suggesting that evolutionarily newer gene regulations tend to be activated sequentially at later stages.
In this talk, as well as present the supportive evidence for the recapitulation, we will discuss the potential evolutionary bias of developmental changes being added toward later stages in embryogenesis and an attempt to integrate the recapitulation and the hourglass model.
OS1-5
Machine learning enables predicting future gene-content evolution of diverse bacteria
Naoki Konno1, Wataru Iwasaki1,2
1Department of Biological Sciences, Graduate School of Science, the University of Tokyo
2Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo
2Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo
Diverse organisms evolve through changing their genomes, and prediction (i.e., forecast) of those changes is a long-standing and challenging problem. While recent studies revealed the predictability of short-term, DNA sequence-level evolution (e.g., laboratory evolution and cancer evolution), few studies have tried to predict long-term, gene content-level evolution. Here we show that gene-content evolution of metabolic systems is predictable across diverse bacterial phyla. We first reconstructed the gene content of ancestors based on that of 2,894 current bacterial species. Then, gene gain/loss probabilities were predicted for each branch in the phylogenetic tree by random forest and logistic regression, where the input feature was the gene content of the parental ancestor. Surprisingly, cross-validation showed that both gains and losses were overall predictable, suggesting evolutionary constraints or selection pressures are widely shared among taxa. Among various metabolic functions, xenobiotics degradation showed especially high predictability of gene gain. Therefore, we interpreted the input features crucial for the prediction and suggested that the gene gain order of xenobiotics degradation was constrained by functional dependencies among metabolic reactions. We further mapped metagenome-based habitat information of individual species onto phylogeny, then revealed that some of the shared evolutionary patterns of gene gain were observed when different taxa underwent similar habitat changes. Finally, we predicted the future gene gain/loss from the gene content of the extant species. Pangenome analyses of 114 species revealed that the species predicted to gain/lose a gene often included strains that have already gained/lost the gene, which strongly supports the validity of the future forecasting. This study will give us insights into general rules underlying biological system evolution in nature and clues for rational engineering of metabolic pathways.
OS1-6
The dinosaurian femoral head experienced a cryptic evolutionary shift in morphogenetic process.
Shiro Egawa1,2, Peter J. Bishop3,4,5, Romain Pintore3, Henry P. Tsai6, Christopher T. Griffin2, Joao F. Botelho7, Daniel Smith-Paredes2, Sterling J. Nesbitt8, John R. Hutchinson3, Bhart-Anjan S. Bhullar2
1RIKEN BDR, Japan
2Yale Univ. YPM, USA
3The Royal Veterinary College, UK
4Harvard Univ. MCZ, USA
5Queensland Museum, Australia
6Missouri State Univ., USA
7Pontificia Universidad Católica de Chile, Chile
8Virginia Tech, USA
2Yale Univ. YPM, USA
3The Royal Veterinary College, UK
4Harvard Univ. MCZ, USA
5Queensland Museum, Australia
6Missouri State Univ., USA
7Pontificia Universidad Católica de Chile, Chile
8Virginia Tech, USA
Significant evolutionary shifts in vertebrate locomotive behavior often involve minute anatomical transitions. In particular, the erect and parasagittal locomotion of dinosaurs is linked with considerable medial extension or overhang of the proximal end of the femur. This morphology has been central to discussions of the form and function of their locomotor apparatus. Here, we reconstructed the morphogenetic (developmental) evolution of the proximal end of the femur from early dinosaurs to modern birds. Embryology of living archosaurs (close relatives; neontology) suggests the acquisition of the greater overhang of the femoral head by gradual mediad growth of the proximal end. On the other hand, the fossil record (paleontology) suggests it was acquired by retroverting torsion of the proximal end about the long axis. We reconcile this apparent conflict by inferring that the medial overhang of the dinosaur femoral head was initially acquired by torsion, which was then superseded by mediad growth. Subtle anatomical evolution and its timing support this hypothesis.
OS1-7
Exploring the origin of wing color pattern diversification in the ladybugs by focusing on the key regulatory locus pannier
Toshiya Ando1, Taro Nakamura1, Teruyuki Niimi1
1Division of Evolutionary Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences
2Department of Basic Biology, School of Life Science, the Graduate University for Advanced Sciences (SOKENDAI)
3PRESTO, Japan Science and Technology Agency
2Department of Basic Biology, School of Life Science, the Graduate University for Advanced Sciences (SOKENDAI)
3PRESTO, Japan Science and Technology Agency
What kind of modifications in the developmental genetic background of organisms have led to the diversification of their morphology? To address this issue, we investigated the genetic background of diversification of the color patterns in ladybugs. We focused on a key genetic locus h, associated with >200 color patterns of the Asian multicolored ladybird beetle, Harmonia axyridis. Our genome sequencing and genetic linkage analysis revealed that h encodes a GATA transcription factor gene pannier. During the development of pupal forewing, pannier was highly expressed in the presumptive region of the black coloration. Our RNAi experiments revealed that pannier promotes black pigmentation and inhibits red pigmentation. To explore the origin of the wing coloration function of pannier, we performed RNAi experiments targeting pannier in additional seven ladybug species. We found that the regulatory origin mediated by the pannier locus is estimated to be before the divergence of the subfamily Coccinellinae. We also found several pannier-independent color pattern formation mechanisms in several derived lineages. These data suggested that regulatory modifications at the pannier locus are crucial for color pattern diversification in ladybugs. These results led us to focus on the regulatory modifications at the pannier locus and to analyze the gene structure and transcriptional regulatory sequences of pannier in H. axyriidis and another ladybug, the seven-spotted ladybird beetle Coccinella septempunctata. Interestingly, repeated chromosomal rearrangements in the 100-kb-scale first intron of pannier were highly associated with the emergence of novel color patterns in H. axyridis. We will discuss how chromosomal rearrangements would drive phenotypic shifts in organisms by modulating the developmental systems. We will also report on the current technological progress in analyzing transcriptional regulatory sequences in the 100 kb-scale pannier introns.
OS1-8
Mycena genomes resolve the evolution of fungal bioluminescence
Huei-Mien Ke1, Hsin-Han Lee1, Yu-Ching Liu1, Min R. Lu1,2, Meiyeh Jade Lu1, Jo-Wei Allison Hsieh2,3, László G. Nagy4,5, Pao-Yang Chen2,3, Hsiao-Wei Kao6, Isheng Jason Tsai1
1Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
2Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
3Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
4Synthetic and Systems Biology Unit, Biological Research Centre, 6726 Szeged, Hungary
5Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117 Hungary
6Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
2Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
3Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
4Synthetic and Systems Biology Unit, Biological Research Centre, 6726 Szeged, Hungary
5Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, 1117 Hungary
6Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life; yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. Luciferase cluster members were coexpressed across developmental stages, with the highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.
*This article has been published. Proceedings of the National Academy of Sciences, 117(49):31267-31277. doi: 10.1073/pnas.2010761117.
OS1-9
The evolutionary steps to creating a perfect chemical weapon
Agneesh Barua1, Alexander Mikheyev2
1Okinawa Institute of Science and Technology Graduate University
2Australian National University
2Australian National University
How complex phenotypes originate is a central question in evolutionary biology. While some adaptations arise de novo, most arise through gradual changes in pre-existing traits. However, the complexity of most traits makes finding the mechanisms governing their change a challenge. Venoms consist of proteinaceous cocktails where each protein can be mapped to a specific gene. This high level of genetic tractability makes them ideal systems to uncover the mechanisms behind trait evolution. Using quantitative genetics, network biology, and phylogenetics, I have identified specific mechanisms that led to the origin of oral venoms in mammals and reptiles. Oral venoms originated from an ancient conserved gene regulatory network whose primary role was maintaining cellular homeostasis during increased protein production. This ancient system could tolerate high protein loads, facilitating the parallel recruitment of various protein families into the ancient venom. Following the recruitment of toxins, the complexity of the venom increased by sequence and copy number variation of toxins. High copy numbers enhanced the venom system’s phenotypic flexibility, allowing it to further diversify through changes in evolutionary rates and by altering the combinations of toxins used. These features enabled animals to refine their venom cocktails to form the most optimal formulations. Through my research, I solve a decades-long question regarding the early origins of venom by providing the first unified, deep evolutionary model for the evolution of venom in tetrapods.
OS1-10
Divergent neural circuits for skin pattern change in cephalopods
Xitong Liang1
1Max Planck Institute for Brain Research, Frankfurt, Germany
Coleoid cephalopods (octopus, squid, and cuttlefish) have the ability to change their skin patterns instantaneously for camouflage or communication. How such complex behaviors arise and evolve is a fascinating question. Their skin patterns are generated in great part by an extensive array of variable-sized pigment cells called chromatophores. This chromatophores system is unique to cephalopods, but also diverse among different species. Using this system, the cuttlefish Sepia officinalis generates 2d skin patterns that match certain statistics of its surrounding visual environment. Thousands to millions of chromatophores are controlled in parallel and coordinated in an extremely flexible way to generate countless patterns. A different cephalopod, the bobtail squid Euprymna berryi, camouflages by covering itself with sand. Its chromatophores change size mostly synchronously, switching entire animal between transparency and dark pigmentation. To study the neural basis underlying these divergent chromatophore dynamics, we compare the neuronal and network properties of chromatophore motor control between these two species. By tracing their axons in descending nerves, we identified chromatophore motoneurons in both species. Although those motoneurons show similar electrical properties, the ratio of motoneurons to chromatophores is ~9-fold higher in Sepia than in Euprymna. Electrical stimulation further suggested a somatotopic organization of motoneurons in Sepia, while such maps were absent in Euprymna. We developed the first preparation to carry out whole-cell recordings and calcium imaging on chromatophore motoneurons, in conjunction with observing the dynamic activity of the chromatophores, elicited by stimulating the upstream visual system. This approach begins to uncover the principles of organization of neural circuits generating high-dimensional motor output, and may reveal how such neural circuits have diverged adaptively during evolution.
OS1-11
Genetic differentiation and demographic trajectory of the insular Formosan and Orii's flying foxes
Kung-Ping Lin1, Shu-Miaw Chaw2, Yun-Hua Lo1, Masako Izawa3, Shiang-Fan Chen4, Wen-Ya Ko1
1Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
2Biodiversity Research Center, Academia Sinica , Taipei , Taiwan
3Kitakyushu Museum of Natural History and Human History , Fukuoka , Japan
4Center for General Education, National Taipei University , New Taipei City , Taiwan
2Biodiversity Research Center, Academia Sinica , Taipei , Taiwan
3Kitakyushu Museum of Natural History and Human History , Fukuoka , Japan
4Center for General Education, National Taipei University , New Taipei City , Taiwan
Insular flying foxes are keystone species in island ecosystems due to their critical roles in plant pollination and seed dispersal. These species are vulnerable to population decline because of their small populations and low reproductive rates. The Formosan flying fox (Pteropus dasymallus formosus) is one of the five subspecies of the Ryukyu flying fox. P. d. formosus has suffered from a severe decline and is currently recognized as a critically endangered population in Taiwan. On the contrary, the Orii’s flying fox (P. d. inopinatus) is a relatively stable population inhabiting Okinawa Island. Here, we applied double digest restriction-site associated DNA sequencing to study these two subspecies for a total of seven individuals. We detected significant genetic structure between the two populations. Despite their contrasting contemporary population sizes, both populations harbor very low degrees of genetic diversity. We further inferred their demographic history based on the joint folded site frequency spectrum and revealed that both P. d. formosus and P. d. inopinatus had maintained small population sizes for a long period of time after their divergence. Recently, these populations experienced distinct trajectories of demographic changes. While P. d. formosus suffered from a drastic ~10-fold population decline not long ago, P. d. inopinatus underwent a ~4.5-fold population expansion. Our results suggest separate conservation management for the two populations—population recovery is urgently needed for P. d. formosus while long-term monitoring for adverse genetic effects should be considered for P. d. inopinatus.