表紙・目次 : 『千葉医学雑誌』 93巻3号 2017年6月

Exabayes phylogeny based on partitioned, concatenated analysis of 97 UCE loci (corresponding to our 100% complete matrix, with sequences of 55 of 55 taxa present for each locus)

Crowdsourced morphometrics data

This zip file contains geometric morphometric landmark data collected by Mechanical Turk workers, as well as BAMM input and output files

Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life

<div><p>Explaining the dramatic variation in species richness across the tree of life remains a key challenge in evolutionary biology. At the largest phylogenetic scales, the extreme heterogeneity in species richness observed among different groups of organisms is almost certainly a function of many complex and interdependent factors. However, the most fundamental expectation in macroevolutionary studies is simply that species richness in extant clades should be correlated with clade age: all things being equal, older clades will have had more time for diversity to accumulate than younger clades. Here, we test the relationship between stem clade age and species richness across 1,397 major clades of multicellular eukaryotes that collectively account for more than 1.2 million described species. We find no evidence that clade age predicts species richness at this scale. We demonstrate that this decoupling of age and richness is unlikely to result from variation in net diversification rates among clades. At the largest phylogenetic scales, contemporary patterns of species richness are inconsistent with unbounded diversity increase through time. These results imply that a fundamentally different interpretative paradigm may be needed in the study of phylogenetic diversity patterns in many groups of organisms.</p> </div

scripts

scripts and readme files used in processing of all data. Same directory structure kept

all_extractedseq_renamed

All transcripts categorized as venom from all species. The headers are sequence ID, species, gene superfamily, and coverage

fish-500-loci-enrichment-probes.fasta.gz

Fasta file of 120 BP probe sequences commercially synthesized to target UCE loci in ray-finned-fishes

Age-richness relationships within 12 higher taxonomic groups with dense subclade sampling, compared to expected relationships under a relaxed-rate model of among-clade variation in net diversification rates.

<p>“Clades” gives the number of subclades within each taxon, and <i>N</i> is the total species richness based on our compilation (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001381#pbio.1001381.s008" target="_blank">Table S2</a>). β gives observed PGLS slope for the relationship between log(richness) and clade age (in millions of years) for each group. Two-tailed <i>p</i> values for test of null hypothesis (β = 0) are given in parentheses after slope. SES gives the standardized effect sizes of the observed slope relative to model-predicted values under two relative extinction rates (ε); the corresponding cumulative tail probability is given in parentheses.</p

Phylogenetic distribution of species richness across the eukaryotic tree of life.

<p>(A) Time-calibrated tree of 1,397 clades of multicellular eukaryotes; length of gray bars indicates relative log-transformed species richness of each group. (B) Total species richness of major groups. Clade colors in (A) correspond to names in (B).</p

fish-probe-matches-to-genome-enabled.sqlite.gz

SQLITE database of LASTZ matches between data from genome-enabled taxa and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment

fish-genetree-results-from-cloudforest.tre.gz

Gene trees generated by CLOUDFOREST