Symposium proposal | |
Organizer: | The 2nd AsiaEvo Conference Organizing Committee |
The topic of this symposium is omnibus. |
OS2-1
Rooting the animal tree of life - more is less in phylogenetic accuracy?
Yuanning Li1,2, Xing-Xing Shen3, Casey W. Dunn1, Antonis Rokas2
1Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
2Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
3State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
2Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
3State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
Identifying our most distant animal relatives has emerged as one of the most challenging problems in phylogenetics. This debate has major implications for our understanding of the origin of multicellular animals and of the earliest events in animal evolution, including the origin of the nervous system. Some analyses identify sponges as our most distant animal relatives (Porifera-sister hypothesis), and others identify comb jellies (Ctenophora-sister hypothesis). These analyses vary in many respects, making it difficult to interpret previous tests of these hypotheses. To gain insight into why different studies yield different results, an important next step in the ongoing debate, we systematically test these hypotheses by synthesizing 15 previous phylogenomic studies and performing new standardized analyses under consistent conditions with additional models. We find that Ctenophora-sister is recovered across the full range of examined conditions, and Porifera-sister is recovered in some analyses under narrow conditions when most outgroups are excluded and site-heterogeneous CAT models are used. We additionally find that the number of categories in site-heterogenous models is sufficient to explain the Porifera-sister results. Furthermore, our cross-validation analyses show CAT models that recover Porifera-sister have hundreds of additional categories and fail to fit significantly better than site-heterogeneous models with far fewer categories. Systematic and standardized testing of diverse phylogenetic models suggests that we should be skeptical of Porifera-sister results both because they are recovered under such narrow conditions and because the models in these conditions fit the data no better than other models that recover Ctenophora-sister.
OS2-2
A new sex determination gene in insects
Yuan Zou1, Elzemiek Geuverink0, Eveline C. Verhulst0, Leo W. Beukeboom0, Louis van de Zande0
1State Key Laboratory of Biocontrol, Ecology and Evolution, School of Ecology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
2Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
2Groningen Institute for Evolutionary Life Sciences, University of Groningen, Post Office Box 11103, 9700 CC, Groningen, Netherlands
Insect sex determination depends on a primary instruction during early zygotic development. This primary instruction induces (female instruction) or represses (male instruction) the production of a functional transformer (TRA) protein. Hymenopteran insects have haplodiploid sex determination; males develop from unfertilized eggs and are haploid, whereas females develop from fertilized eggs and are diploid. The allelic state of the complementary sex determiner (csd) gene in the honeybee is the only identified instructive sex determination signal thus far in hymenopterans. To identify the instructor gene of the parasitoid wasp Nasonia vitripennis, that has no csd, we compared transcriptomes of early male and female embryos. We identified a new gene, wasp overruler of masculinization (wom), that is only expressed in early diploid embryos and only from the paternal, not the maternal allele. Wom is required for female development, as its knockdown led to male development of diploid embryos. Wom knockdown also significantly decreased tra transcripts, indicating that its mode of action is activation of zygotic tra expression. It encodes a P53-domain protein that may act as a transcription factor in Nasonia sex determination. This study is another demonstration of the diverse recruitment of primary instructions in insect sex determination.
OS2-3
Landscape and evolution of the Y chromosome in the Asian malaria mosquito
Arunachalam Ramaiah1,2, Mahul Chakraborty1, J.J. Emerson1,3
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
2Tata Institute for Genetics and Society, Center at inStem, Bangalore, KA 560065, India
3Center for Systems Biology, University of California, Irvine, CA 92697, USA
2Tata Institute for Genetics and Society, Center at inStem, Bangalore, KA 560065, India
3Center for Systems Biology, University of California, Irvine, CA 92697, USA
The mosquito Anopheles stephensi is a primary vector of human Malaria in urban Asia that has recently invaded Africa. Despite advances in genome sequencing and assembly, repeat-rich Y chromosomes remain underrepresented in nearly all recent assemblies. Given the important role of Y chromosomes in male biology, we implemented an enrichment approach employing long-read sequencing and Hi-C scaffolding to reassemble and identify segments of the An. stephensi Y chromosome neglected by traditional assembly methods. This approach improved upon the most extensive assembly of the Y-chromosome reported in any Anopheles species by 83%. The Y-linked sequence we recovered is mostly repeats, with long terminal repeat retrotransposons making up the bulk of the sequence content. In addition to the repeat content, we identified extensive homology between Y-linked sequence and genes on the other chromosomes. Among sequences, more than 15% are homologous to the X chromosome when only 10% of the genes in the genome are X-linked, an enrichment of more than 50%. The majority of duplicate sequences likely represent gene traffic originating outside the Y chromosome. However, the excess of X-derived sequences could stem from a number of processes, including mutation bias, resolution of sexual antagonism, or residual homology from ancestral autosomes that gave rise to the X and Y. While duplications to the Y are reported in Drosophila, this is, to our knowledge, the first time that an origination bias from the X has been observed in Diptera.
OS2-4
Sex chromosome evolution of the birds and monotremes
Jing Li1
1University of Konstanz
Pekin duck (Anas platyrhynchos) has a typical avian karyotype that consists of macro- and micro-chromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chicken. To elucidate the evolution of sex chromosome architectures between Pekin duck and chicken, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multi-platform scaffolding techniques. The major improvement of genome assembly and annotation quality resulted in successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. The Pekin duck W chromosome contains 2.5-fold more genes relative to chicken. Parallel to the independently evolved human Y chromosome, the Pekin duck W evolved massive dispersed palindromic structures, and a sequence divergence pattern with the Z chromosome that reflects stepwise suppression of homologous recombination. Egg-laying mammals were the first to diverge from the common ancestor of modern mammals and provide key insights into mammalian evolution and the innovations that have occurred in the three mammalian lineages present on earth today. Here we report the generation and analyses of high-quality reference genomes for two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus). The new platypus genome assembly anchors almost the entire genome onto chromosomes, dramatically improving the previous draft genome and gene annotation. We provide evidence that the extraordinary monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusual extensive interactions between the multi-X and -Y chromosomes that are shared by their human autosomal homologues. The monotremes are belonging to one important clade of mammals. However, their sex chromosomes are not homologous to human chrX, but homologous to chicken chrZ. The eutherian sex determining gene SRY is also missing in monotremes. In addition, like birds, the monotremes lack dosage compensation as well. Overall, the analyses of the Pekin duck and monotremes provide new insights into the transition of sex chromosome evolution between mammals and birds.
OS2-5
Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Luohao Xu1, Zhen Huang2, Lingzhan Xue3, Yu Gao4, Dapeng Li5
1University of Vienna
2Fuzhou Normal University
3Freshwater Fisheries Research Institute of Fujian
4Yunnan Agricultural University
5Huazhong Agricultural University
2Fuzhou Normal University
3Freshwater Fisheries Research Institute of Fujian
4Yunnan Agricultural University
5Huazhong Agricultural University
The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they recently diverge. Here we produced a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes we have resolved the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using re-sequencing data, we identified a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identified an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.
OS2-6
Molecular mechanism underlying venation pattern is reused to pattern eyespot rings in Bicyclus anynana butterflies.
Tirtha Das Banerjee1, Antonia Monteiro1,2
1Department of Biological Sciences, National University of Singapore-117557
2Science Division, Yale-NUS college, Singapore-138527
2Science Division, Yale-NUS college, Singapore-138527
Novel traits are hypothesized to emerge from the reuse of pre-existent gene regulatory networks to novel developmental contexts. Eyespot patterns on the wings of nymphalid butterflies are a relatively novel trait that emerged in the space between wing veins, another novel trait, but a much ancestral one. We studied the developmental mechanisms that differentiate the rings of color in an eyespot, as well as the mechanisms that pattern the wing veins in Bicyclus anynana butterflies. We showed that a system of positional information involving a common set of genes is governing the differentiation of both traits. We propose that the gene regulatory network involved in patterning wing veins was co-opted to differentiate the eyespot color rings in nymphalid butterflies.
OS2-7
Genetic origins and sex-biased admixture of the Huis
Xixian Ma1, Wenjun Yang2
1Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences
2Key Laboratory of Fertility Preservation and Maintenance, the General Hospital, Ningxia Medical University
2Key Laboratory of Fertility Preservation and Maintenance, the General Hospital, Ningxia Medical University
The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (FST = 0.0015) is only slightly larger than that between northern and southern HAN (FST = 0.0010), largely attributed to the western ancestry in NXH (~10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (FST = 0.0187), especially, NXH derived much less western ancestry (~10%) compared with the Uyghurs (~50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ~1,025 years ago, reflecting the intensive west-east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ~500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, i.e., excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.
OS2-8
Deep sampling of Saccharomyces cerevisiae in a continental island reveals ancestral genetic diversity in abundant wild lineages
Tracy Jiaye Lee1, Yu-Ching Liu1, Wei-An Liu1, Yu-Fei Lin1, Hsin-Han Lee1, Huei-Mien Ke1, Chia-Lun Hsieh1, Kuo-Fang Chung1, Isheng Jason Tsai1
1Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
Saccharomyces cerevisiae, a budding yeast, is one of the most important model organisms in genetics, cellular and molecular biology. While research interests have previously focused on the evolution of multiple domestication, recent phylogenomic studies have started to address questions regarding the origin of “wild” populations and their natural life histories. Wild S. cerevisiae populations can be found on a variety of habitats and exhibit high genetic diversity and clear population structure, providing an excellent model for studying its natural diversity and ecology. To fully capture the abundance, distribution and diversity of natural S. cerevisiae, we collected a total of 2,428 samples which resulted in 121 isolates that were subsequently sequenced. We constructed a global phylogeny comprised of 340 isolates including previously published genomes from both domestic and natural populations. In addition to the discovery of multiple natural populations in Taiwan, we also found cases where Taiwanese and Chinese isolates formed monophyletic groups, and among them the TW1+CHN-IX represents the most divergent lineage to date. Moreover, even though natural populations tend to show strong population structure and lack of genetic admixture, we identified mosaic isolates, which provided an opportunity to investigate genetic admixture on various substrates for a mostly asexual species. Surprisingly, diversity estimates in Taiwanese populations were found to be comparable to populations on a continent scale. These results will assist us in quantifying its natural diversities, and understanding the dispersal and demographic events of the wild populations.