scholarly journals Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits

2017 ◽  
Author(s):  
Ehsan Kayal ◽  
Bentlage Bastian ◽  
M Sabrina Pankey ◽  
Aki Ohdera ◽  
Monica Medina ◽  
...  
Keyword(s):  
Life Histories ◽  
Bayes Factor ◽  
Tree Of Life ◽  
Ancestral State ◽  
Functional Classes ◽  
Phylogenetic Resolution ◽  
Phylogenomic Analyses ◽  
Colonial Body ◽  
Genome Scale ◽  
Scale Data

The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including symbiosis, colonial body plans and elaborate life histories, however, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome scale data for each major cnidarian lineage. Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests of multiple origins strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago.

scholarly journals Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits

2017 ◽  
Author(s):  
Ehsan Kayal ◽  
Bentlage Bastian ◽  
M Sabrina Pankey ◽  
Aki Ohdera ◽  
Monica Medina ◽  
...  
Keyword(s):  
Life Histories ◽  
Bayes Factor ◽  
Tree Of Life ◽  
Ancestral State ◽  
Functional Classes ◽  
Phylogenetic Resolution ◽  
Phylogenomic Analyses ◽  
Colonial Body ◽  
Genome Scale ◽  
Scale Data

The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including symbiosis, colonial body plans and elaborate life histories, however, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome scale data for each major cnidarian lineage. Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests of multiple origins strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago.

scholarly journals Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers

2018 ◽  
Author(s):  
Akanksha Pandey ◽  
Edward L. Braun
Keyword(s):  
Solvent Accessibility ◽  
Phylogenetic Signal ◽  
Tree Of Life ◽  
Striking Difference ◽  
Relative Solvent Accessibility ◽  
Animal Evolution ◽  
Phylogenomic Analyses ◽  
Cat Model ◽  
Protein Datasets ◽  
Genome Scale

AbstractPhylogenomics has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life. This could reflect the poor-fit of the models used to analyze heterogeneous datasets; that heterogeneity is likely to have many explanations. However, it seems reasonable to hypothesize that the different patterns of selection on proteins based on their structures might represent a source of heterogeneity. To test that hypothesis, we developed an efficient pipeline to divide phylogenomic datasets that comprise proteins into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had different signals for the deepest branches in the metazoan tree of life. Sites located in different structural environments did support distinct tree topologies. The most striking difference in phylogenetic signal reflected relative solvent accessibility; analyses of sites on the surface of proteins yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge-ctenophore clade. These differences in phylogenetic signal were not ameliorated when we repeated our analyses using the site-heterogeneous CAT model, a mixture model that is often used for analyses of protein datasets. In fact, analyses using the CAT model actually resulted in rearrangements that are unlikely to represent evolutionary history. These results provide striking evidence that it will be necessary to achieve a better understanding the constraints due to protein structure to improve phylogenetic estimation.

scholarly journals Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

2020 ◽  
Author(s):  
Joseph F. Walker ◽  
Xing-Xing Shen ◽  
Antonis Rokas ◽  
Stephen A. Smith ◽  
Edwige Moyroud
Keyword(s):  
Large Scale ◽  
Simulated Data ◽  
Tree Of Life ◽  
Rate Of Molecular Evolution ◽  
History Of ◽  
Patterns And Processes ◽  
Genome Scale ◽  
The Impact ◽  
Alignment Length ◽  
Scale Data

AbstractThe genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit “outlier” behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.

scholarly journals Ensembl Genomes 2020—enabling non-vertebrate genomic research

2019 ◽  
Vol 48 (D1) ◽  
pp. D689-D695 ◽  
Author(s):  
Kevin L Howe ◽  
Bruno Contreras-Moreira ◽  
Nishadi De Silva ◽  
Gareth Maslen ◽  
Wasiu Akanni ◽  
...  
Keyword(s):  
Reference Genome ◽  
Analysis Data ◽  
Tree Of Life ◽  
Genomic Research ◽  
Vertebrate Species ◽  
Online Tools ◽  
Recent Developments ◽  
Future Strategy ◽  
Genome Scale ◽  
Scale Data

Abstract Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.

scholarly journals Species boundaries in the messy middle -- testing the hypothesis of micro-endemism in a recently diverged lineage of coastal fog desert lichen fungi

2021 ◽  
Author(s):  
Jesse Jorna ◽  
Jackson Linde ◽  
Peter Searle ◽  
Abigail Jackson ◽  
Mary-Elise Nielsen ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
High Throughput Sequencing ◽  
Incomplete Lineage Sorting ◽  
Cost Effective ◽  
Species Boundaries ◽  
Lineage Sorting ◽  
Coastal Fog ◽  
Genome Scale ◽  
Scale Data

Species delimitation among closely related species is challenging because traditional phenotype-based approaches, e.g., morphology, ecological, or chemical characteristics, often produce conflicting results. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, e.g., hybridization/introgression and incomplete lineage sorting, and computational limitations. Here we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler in the family Ramalinaceae. The species delimitation models tend to support more specious groupings, but were unable to infer robust, consistent species delimitations. The results of our study highlight the problem of delimiting species, particularly in groups such as Niebla, with complex, recent phylogeographic histories.

scholarly journals Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

2017 ◽  
Vol 8 ◽  
Author(s):  
Maria del Carmen Montero-Calasanz ◽  
Jan P. Meier-Kolthoff ◽  
Dao-Feng Zhang ◽  
Adnan Yaramis ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
Genome Scale ◽  
Data Call ◽  
Scale Data

scholarly journals CausalR: extracting mechanistic sense from genome scale data

2017 ◽  
Vol 33 (22) ◽  
pp. 3670-3672 ◽  
Author(s):  
Glyn Bradley ◽  
Steven J Barrett
Keyword(s):  
Genome Scale ◽  
Scale Data
Sign in / Sign up

Export Citation Format

Share Document