Discovering research articles containing evolutionary timetrees by machine learning.

MOTIVATION: Timetrees depict evolutionary relationships between species and the geological times of their divergence. Hundreds of research articles containing timetrees are published in scientific journals every year. The TimeTree (TT) project has been manually locating, curating and synthesizing timetrees from these articles for almost two decades into a TimeTree of Life, delivered through a unique, user-friendly web interface (timetree.org). The manual process of finding articles containing timetrees is becoming increasingly expensive and time-consuming. So, we have explored the effectiveness of text-mining approaches and developed optimizations to find research articles containing timetrees automatically. RESULTS: We have developed an optimized machine learning system to determine if a research article contains an evolutionary timetree appropriate for inclusion in the TT resource. We found that BERT classification fine-tuned on whole-text articles achieved an F1 score of 0.67, which we increased to 0.88 by text-mining article excerpts surrounding the mentioning of figures. The new method is implemented in the TimeTreeFinder (TTF) tool, which automatically processes millions of articles to discover timetree-containing articles. We estimate that the TTF tool would produce twice as many timetree-containing articles as those discovered manually, whose inclusion in the TT database would potentially double the knowledge accessible to a wider community. Manual inspection showed that the precision on out-of-distribution recently published articles is 87%. This automation will speed up the collection and curation of timetrees with much lower human and time costs. AVAILABILITY AND IMPLEMENTATION: https://github.com/marija-stanojevic/time-tree-classification. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

TimeTree 5: An Expanded Resource for Species Divergence Times.

We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species' evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now ADA-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org.

Phylogenomic data resolve the historical biogeography and ecomorphs of Neotropical forest lizards (Squamata, Diploglossidae).

Few studies have been conducted on the biogeography and phylogenetic relationships of Neotropical forest lizards (Diploglossidae) because of incomplete taxon sampling, conflicting datasets, and low statistical support at phylogenetic nodes. Here, we enhance a recent nine-gene dataset with a genomic dataset of 3,232 loci and 642,775 aligned base pairs. The resulting phylogeny includes 30 diploglossid species, 10 of the 11 genera, and the three subfamilies. It shows significant support for all supra-specific taxa in either maximum likelihood or Bayesian analyses or both. With this well-supported phylogeny, we further investigate the historical biogeography of the group and how diploglossids reached the Caribbean islands. Our analyses indicate that Antillean diploglossid lizards originated from at least two overwater dispersals from South America. Our tests for the strength of convergent evolution between morphologically similar taxa support the recognition of a soil and a tree ecomorph. In addition, we propose grass, ground, rock, and swamp ecomorphs for species in this family based on ecological and morphological data and analyses.

Using Ancestry-Informative SNPs to Quantify Introgression of European Alleles into North American Red Foxes.

A recent study demonstrated that British red foxes introduced to the mid-Atlantic coastal plain (ACP) of the eastern United States during the late 18th century successfully interbred with indigenous American red foxes despite half a million year's divergence. However, a large disparity in frequency of European mitochondria (27%) versus Y chromosomes (1%) left unclear the magnitude of genetic exchange. We sought to quantify genomic introgression using 35 autosomal and 5 X-chromosome ancestry-informative markers (AIMs) in conjunction with diagnostic Y chromosome single nucleotide polymorphism (Y-SNP) markers to characterize the modern state of red foxes in the eastern United States and to gain insight into the potential role of reproductive barriers. European admixture was highest in the ACP and apparently restricted to the central eastern United States. We estimated only slightly (and nonsignificantly) European ancestry in autosomal than X-chromosome markers. European ancestry from autosomal and X-chromosome markers (36.4%) was higher than the corresponding mitochondrial (mt) DNA estimate (26.4%) in the ACP. Only 1 of 124 males (<1%) in the ACP had European Y chromosomes, which was similar to the neighboring regions, in which 2 of 99 (2%) males carried a European Y chromosome (the same haplotype). Although we could not rule out drift as the cause of low European Y-chromosome frequency, results were also consistent with F1 male infertility. In the future, more extensive genomic sequencing will enable a more thorough investigation of possible barrier genes on the X chromosome as well as throughout the genome.