scholarly journals Genomic data do not support comb jellies as the sister group to all other animals

2015 ◽  
Vol 112 (50) ◽  
pp. 15402-15407 ◽  
Author(s):  
Davide Pisani ◽  
Walker Pett ◽  
Martin Dohrmann ◽  
Roberto Feuda ◽  
Omar Rota-Stabelli ◽  
...  
Keyword(s):  
Complex Traits ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Nervous Systems ◽  
Conventional View ◽  
Evolution Of Complexity ◽  
Genomic Gene ◽  
Choice Of Species ◽  
Genome Scale ◽  
Inappropriate Choice

Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the “Ctenophora-sister” hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide
Keyword(s):  
Common Ancestor ◽  
Sister Group ◽  
The Other ◽  
Gene Content ◽  
Statistical Hypothesis ◽  
Phylogenetic Position ◽  
Last Common Ancestor ◽  
Statistical Hypothesis Testing ◽  
Animal Phylogeny ◽  
Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

Gyrothyris williamsi sp. nov. and inter-relationships of some taxa from waters around New Zealand and the southern oceans (Rhynchonelliformea: Terebratelloidea)

2007 ◽  
Vol 98 (3-4) ◽  
pp. 425-435 ◽  
Author(s):  
Maria Aleksandra Bitner ◽  
Bernard L. Cohen ◽  
Sarah. L. Long ◽  
Bertrand Richer de Forges ◽  
Michiko Saito
Keyword(s):  
New Zealand ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Sister Group ◽  
Last Common Ancestor ◽  
Rdna Sequences ◽  
Sw Pacific ◽  
Rates Of Evolution ◽  
The Antarctic

ABSTRACTThis paper describes a terebratelloid articulate brachiopod, Gyrothyris williamsi sp. nov., based on 95 specimens from seamounts on the Lord Howe Rise, Coral Sea, SW Pacific Ocean. The new species is attributed to Gyrothyris on the basis of (a) morphological and growth trajectory similarities; (b) phylogenetic analyses of an alignment of DNA sequence (∼2900-sites) obtained from nuclear-encoded small- and large-subunit ribosomal RNA genes (SSU and LSU); and (c) the presence of a distinctive, two-part deletion in the LSU gene. It is distinguished morphologically from Gyrothyris mawsoni and its subspecies by both internal and external morphology and by its isolated geographical distribution, which extends the patchy, known range of this genus to an area some 2000 km north of its previous northern limit around New Zealand. Phylogenetic analyses of the rDNAs and of mitochondrial cox1 gene sequences (663 sites) confirm previous indications that the New Zealand endemic terebratelloid genera form a clade (Neothyris (Calloria, Gyrothyris, Terebratella), but the position of Terebratella with respect to Calloria and Gyrothyris remains weakly established. These sequences disagree inexplicably about the closeness of the relationship between Neothyris parva and N. lenticularis. Analyses of the first sequences from Calloria variegata, a species restricted to the Hauraki Gulf, New Zealand, are consistent with the possibility that it originated locally, and recently, from C. inconspicua. Magellania venosa from S. America/Falklands joins with Antarctic Magellania fragilis and M. joubini to form an rDNA clade that excludes Terebratalia as the putative sister-group of the New Zealand terebratelloid clade. The cox1 (but not the rDNA) sequences of the New Zealand clade pass a test for clock-like rates of evolution, and maximum likelihood pairwise distances suggest that if genetic isolation between the ancestor of Antarctic Magellania and the last common ancestor of the New Zealand terebratelloid clade was initiated by separation of the Antarctic and New Zealand plates ∼90 Mya, isolation from M. venosa was initiated earlier, perhaps ∼145 Mya. However, in the simple phylogenetic reconstruction presented here from cox1 sequences, S. American and Antarctic Magellania spp. do not yield a well-supported clade, perhaps because of differences in base composition.

scholarly journals WheatNet: A genome-scale functional network for hexaploid bread wheat, Triticum aestivum

2017 ◽  
Author(s):  
Tak Lee ◽  
Sohyun Hwang ◽  
Chan Yeong Kim ◽  
Hongseok Shim ◽  
Hyojin Kim ◽  
...  
Keyword(s):  
Complex Traits ◽  
Gene Networks ◽  
Unique Feature ◽  
Single Gene ◽  
Functional Network ◽  
System Level ◽  
Edge Information ◽  
Integrated Network ◽  
A Genome ◽  
Genome Scale

Gene networks provide a system-level overview of genetic organizations and enable the dissection of functional modules underlying complex traits. Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. A unique feature of WheatNet is that each network node represents either a single gene or a group of genes. We computationally partitioned gene groups mimicking homeologous genes by clustering 99,386 wheat genes, resulting in 20,248 gene groups comprising 63,401 genes and 35,985 individual genes. Thus, WheatNet was constructed using 56,233 nodes, and the final integrated network has 20,230 nodes and 567,000 edges. The edge information of the integrated WheatNet and all 20 component networks are available for download.

scholarly journals Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

2020 ◽  
Vol 6 (45) ◽  
pp. eabd0079
Author(s):  
Xing-Xing Shen ◽  
Jacob L. Steenwyk ◽  
Abigail L. LaBella ◽  
Dana A. Opulente ◽  
Xiaofan Zhou ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Filamentous Fungi ◽  
Common Ancestor ◽  
Evolutionary Change ◽  
Sequence Evolution ◽  
Last Common Ancestor ◽  
Molecular Sequence ◽  
Genome Wide ◽  
Similarities And Differences ◽  
Genome Scale

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

scholarly journals Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Yongxin Li ◽  
Akihito Omori ◽  
Rachel L. Flores ◽  
Sheri Satterfield ◽  
Christine Nguyen ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Developmental Stages ◽  
Sister Group ◽  
Body Plan ◽  
The Body ◽  
Last Common Ancestor ◽  
Evolution And Development ◽  
Gene Sets ◽  
Green Sea Urchin ◽  
Feather Star

AbstractEchinoderms are an exceptional group of bilaterians that develop pentameral adult symmetry from a bilaterally symmetric larva. However, the genetic basis in evolution and development of this unique transformation remains to be clarified. Here we report newly sequenced genomes, developmental transcriptomes, and proteomes of diverse echinoderms including the green sea urchin (L. variegatus), a sea cucumber (A. japonicus), and with particular emphasis on a sister group of the earliest-diverged echinoderms, the feather star (A. japonica). We learned that the last common ancestor of echinoderms retained a well-organized Hox cluster reminiscent of the hemichordate, and had gene sets involved in endoskeleton development. Further, unlike in other animal groups, the most conserved developmental stages were not at the body plan establishing phase, and genes normally involved in bilaterality appear to function in pentameric axis development. These results enhance our understanding of the divergence of protostomes and deuterostomes almost 500 Mya.

scholarly journals Shedding light: A phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves

2020 ◽  
Author(s):  
Jingchun Li ◽  
Sarah Lemer ◽  
Lisa Kirkendale ◽  
Rüdiger Bieler ◽  
Colleen Cavanaugh ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Structural Integrity ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Last Common Ancestor ◽  
Ancestral State ◽  
Marine Animals ◽  
Giant Clams ◽  
Rapid Divergence ◽  
Anatomical Adaptations

Abstract Background Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. Results In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae, and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. Conclusions The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exadaptation existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

scholarly journals Evolution of mechanisms controlling epithelial morphogenesis across animals: new insights from dissociation-reaggregation experiments in the sponge Oscarella lobularis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Amélie Vernale ◽  
Maria Mandela Prünster ◽  
Fabio Marchianò ◽  
Henry Debost ◽  
Nicolas Brouilly ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Protein Composition ◽  
Sister Group ◽  
Epithelial Morphogenesis ◽  
Cell Junctions ◽  
Last Common Ancestor ◽  
Cell Matrix ◽  
Cell Matrix Adhesion ◽  
Cell Cell

Abstract Background The ancestral presence of epithelia in Metazoa is no longer debated. Porifera seem to be one of the best candidates to be the sister group to all other Metazoa. This makes them a key taxon to explore cell-adhesion evolution on animals. For this reason, several transcriptomic, genomic, histological, physiological and biochemical studies focused on sponge epithelia. Nevertheless, the complete and precise protein composition of cell–cell junctions and mechanisms that regulate epithelial morphogenetic processes still remain at the center of attention. Results To get insights into the early evolution of epithelial morphogenesis, we focused on morphogenic characteristics of the homoscleromorph sponge Oscarella lobularis. Homoscleromorpha are a sponge class with a typical basement membrane and adhaerens-like junctions unknown in other sponge classes. We took advantage of the dynamic context provided by cell dissociation-reaggregation experiments to explore morphogenetic processes in epithelial cells in a non-bilaterian lineage by combining fluorescent and electron microscopy observations and RNA sequencing approaches at key time-points of the dissociation and reaggregation processes. Conclusions Our results show that part of the molecular toolkit involved in the loss and restoration of epithelial features such as cell–cell and cell–matrix adhesion is conserved between Homoscleromorpha and Bilateria, suggesting their common role in the last common ancestor of animals. In addition, sponge-specific genes are differently expressed during the dissociation and reaggregation processes, calling for future functional characterization of these genes.

scholarly journals Narrow-sense heritability estimation of complex traits using identity-by-descent information

2017 ◽  
Author(s):  
Luke M. Evans ◽  
Rasool Tahmasbi ◽  
Matthew Jones ◽  
Scott I. Vrieze ◽  
Gonçalo R. Abecasis ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Fundamental Parameter ◽  
Last Common Ancestor ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Heritability Estimation ◽  
Causal Variants ◽  
Heritability Estimates

ABSTRACTHeritability is a fundamental parameter in genetics. Traditional estimates based on family or twin studies can be biased due to shared environmental or non-additive genetic variance. Alternatively, those based on genotyped or imputed variants typically underestimate narrow-sense heritability contributed by rare or otherwise poorly-tagged causal variants. Identical-by-descent (IBD) segments of the genome share all variants between pairs of chromosomes except new mutations that have arisen since the last common ancestor. Therefore, relating phenotypic similarity to degree of IBD sharing among classically unrelated individuals is an appealing approach to estimating the near full additive genetic variance while avoiding biases that can occur when modeling close relatives. We applied an IBD-based approach (GREML-IBD) to estimate heritability in unrelated individuals using phenotypic simulation with thousands of whole genome sequences across a range of stratification, polygenicity levels, and the minor allele frequencies of causal variants (CVs). IBD-based heritability estimates were unbiased when using unrelated individuals, even for traits with extremely rare CVs, but stratification led to strong biases in IBD-based heritability estimates with poor precision. We used data on two traits in ~120,000 people from the UK Biobank to demonstrate that, depending on the trait and possible confounding environmental effects, GREML-IBD can be applied successfully to very large genetic datasets to infer the contribution of very rare variants lost using other methods. However, we observed apparent biases in this real data that were not predicted from our simulation, suggesting that more work may be required to understand factors that influence IBD-based estimates.

scholarly journals The last common ancestor of most bilaterian animals possessed at least 9 opsins

2016 ◽  
Author(s):  
MD Ramirez ◽  
AN Pairett ◽  
MS Pankey ◽  
JM Serb ◽  
DI Speiser ◽  
...  
Keyword(s):  
Gene Family ◽  
Complex Traits ◽  
Common Ancestor ◽  
Opsin Gene ◽  
Last Common Ancestor ◽  
Phylogenetic Information ◽  
Animal Evolution ◽  
Animal Phyla ◽  
Evolution Understanding

AbstractThe opsin gene family encodes key proteins animals use to sense light and has expanded dramatically since it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors.

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