Biology subjects

Kimball, R. T.

Publications and source records attributed to Kimball, R. T..

5 recordsLinked to original sources

bioRxiv2022

Molecular early burst associated with the diversification of birds at the K-Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K- Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

evolutionary biology↗

bioRxiv2022

Improved target capture with lower hybridization temperatures for invertebrate loci with different baiting strategies: a case study of the leaf-footed bugs and allies (Hemiptera: Coreoidea)

Target capture approaches are widely used in phylogenomic studies, yet only four experimental comparisons of a critical parameter, hybridization temperature, have been published. These studies provide conflicting conclusions regarding the benefits of lower temperatures during target capture, and none include invertebrates where bait-target divergences may be higher than seen in vertebrate capture studies. Most capture studies use a fixed hybridization temperature of 65{degrees}C to maximize the proportion of on-target data, but many invertebrate capture studies report low locus recovery. Lower hybridization temperatures, which might improve locus recovery, are not commonly employed in invertebrate capture studies. We used leaf-footed bugs and relatives (Hemiptera: Coreoidea) to investigate the effect of hybridization temperature on capture success of ultraconserved elements (UCE) targeted by previously published baits derived from divergent hemipteran genomes and other loci targeted by newly designed baits derived from less divergent coreoid transcriptomes. We found touchdown capture approaches with lower hybridization temperatures generally resulted in lower proportions of on-target reads and lower read depth but were associated with more contigs and improved recovery of UCE loci. Low temperatures were also associated with increased numbers of putative paralogs of UCE loci. Hybridization temperatures did not generally affect recovery of newly targeted loci, which we attributed to their lower bait-target divergences (compared to higher divergences between UCE baits and targets) and greater bait tiling density. Thus, optimizing in vitro target capture conditions to accommodate low hybridization temperatures can provide a cost-effective, widely applicable solution to improve recovery of protein-coding loci in invertebrates.

genomics↗

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↗

bioRxiv2021

Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.

evolutionary biology↗

bioRxiv2020

Phylogenomics of the leaf-footed bug subfamily Coreinae (Hemiptera: Coreidae): applicability of ultraconserved elements at shallower depths

Baits targeting invertebrate ultraconserved elements (UCEs) are becoming more common for phylogenetic studies. Recent studies have shown that invertebrate UCEs typically encode proteins -- and thus, are functionally different from more conserved vertebrate UCEs --can resolve deep divergences (e.g., superorder to family ranks). However, the ability of the invertebrate UCE baits to robustly resolve relationships at shallower phylogenetic scales (i.e., tribes and congeners) has been generally limited to Coleoptera and Hymenoptera. Here, we assessed the ability of a recently designed Hemiptera UCE bait set to reconstruct more recent phylogenetic relationships in the largest leaf-footed bug subfamily, the Coreinae (Hemiptera: Coreidae), using a taxon-rich sample representing 21 of the 32 coreine tribes. Many well-supported, novel relationships were congruent in maximum likelihood and summary coalescent analyses. We also found evidence for the para- and polyphyly of several tribes and genera of Coreinae, as well as the subfamilies Coreinae and Meropachyinae. Our study, along with other recent UCE studies, provides evidence that UCEs can produce robust and novel phylogenetic hypotheses at various scales in invertebrates. Additionally, we used different DNA extraction and target enrichment protocols and recovered more UCE data using a touch-down hybridization approach.

evolutionary biology↗