Biology subjects

Zapata, F.

Publications and source records attributed to Zapata, F..

4 recordsLinked to original sources

bioRxiv2018

Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups, however there was little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 30 siphonophore species analyzed in combination with 13 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose twice.

evolutionary biology↗

bioRxiv2017

Revising transcriptome assemblies with phylogenetic information in Agalma1.0

MotivationOne of the most common transcriptome assembly errors is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. It is difficult to identify these errors during assembly, but in a phylogenetic analysis these errors can be diagnosed from gene trees containing clades of tips from the same species with improbably short branch lengths.\n\nResultstreeinform is a module implemented in Agalma1.0 that uses phylogenetic analyses across species to refine transcriptome assemblies. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene.\n\nAvailability and Implementationtreeinform is implemented in Agalma1.0, available at https://bitbucket.org/caseywdunn/agalma.\n\nContactaugust_guang@brown.edu\n\nSupplementary informationSupplementary information is available at bioRxiv.

bioinformatics↗

bioRxiv2017

Atlantean Evolution in Darwin’s Finches—Issues and Perspectives in Species Delimitation using Phenotypic Data

Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: (1) reliance on graphical analyses of phenotypic space that do not consider the frequency of phenotypes; (2)exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and (3) use of measures of central tendencies to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwins ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of \"Sisyphean\" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. Approaches allowing one to fit normal mixture models without a priori information about species limits offer new perspectives in the kind of inferences available to systematists, with significant repercusions on ideas about the structure of biological biodiversity. [morphology; normal mixture model; phenotype; principal components analysis; species limits; variable selection.]

evolutionary biology↗

bioRxiv2017

Pairwise comparisons are problematic when analyzing functional genomic data across species

AbstractThere is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions, and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to be more similar than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead we find they reflect species relationships. These reanalyses concretely demonstrate the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.\n\nSignificanceComparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here we demonstrate that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We re-examined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study had found support for the ortholog conjecture and the other had concluded that the evolution of gene expression was different between animal phyla than within them. Our results demonstrate that to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.

genomics↗