Biology subjects

Burleigh, G.

Publications and source records attributed to Burleigh, G..

3 recordsLinked to original sources

bioRxiv2022

Reconciling GenBank names with standardized avian taxonomies to improve linkage between phylogeny and phenotype

Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequence data from around the globe, facilitating biodiversity research. However, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have led to widespread scientific name changes. Taxonomic instability, or "splits, lumps, and shuffles", present logistical challenges to large-scale biodiversity research because species or populations may be listed under different names in different data sources, or because different species or populations may be listed under previous names. Consequently, distributional and trait data are often difficult to link directly to DNA sequence data without extensive and time consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize all avian names in use in NCBI GenBank, a primary source of genetic data, to a widely-used and regularly-updated avian taxonomy: eBird/Clements. Of 14,341 avian species or subspecies names used by GenBank, 11,031 names directly matched an eBird/Clements name, which were linked to over 6 million nucleotide sequences. For the remaining unique avian names in GenBank, we used Avibases taxonomic concepts, taxonomic descriptions in Cornells Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names were linked to over 600,000 nucleotide sequences, approximately 9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under two or more GenBank names. Our avian GenBank naming reconciliation is open source and available at GitHub, where it can be updated to correspond with future annual eBird/Clements taxonomic updates. LAY SUMMARY- 23% of avian names on GenBank do not match eBird/Clements, a widely-used standardized avian taxonomy - 600,000 nucleotide sequences on GenBank are associated with names that do not match eBird/Clements - 10% of eBird/Clements names have nucleotide sequences listed under multiple GenBank names - We provide an open source taxonomic reconciliation to mitigate difficulties associated with non-standardized name use for GenBank data

zoology↗

bioRxiv2020

Chromosome fusions shape an ancient UV sex chromosome system

Non-recombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration1,2. The correlation between suppressed recombination and degeneration is clear in animal XY systems1,2, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions3,4. Here we test for degeneration in the bryophyte UV sex chromosome system through genomic comparisons with new female and male chromosome-scale reference genomes of the moss Ceratodon purpureus. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes show signs of weaker purifying selection than autosomes, we find suppressed recombination alone is insufficient to drive gene loss on sex-specific chromosomes. Instead, the U and V sex chromosomes harbor thousands of broadly-expressed genes, including numerous key regulators of sexual development across land plants.

evolutionary biology↗

bioRxiv2019

INTERACTION BETWEEN PLOIDY, BREEDING SYSTEM, AND LINEAGE DIVERSIFICATION

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

evolutionary biology↗