Biology subjects

Kimball, R. T.

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

11 recordsLinked to original sources

bioRxiv2026

Recombination and incomplete lineage sorting resolve the enigma of lysozyme evolution

Lysozyme has long been a model for understanding enzyme structure, function, and evolution. Early studies revealed a conflict between organismal phylogeny and the distribution of three functionally important amino acid residues in galliform birds. Lysozymes differing at all three amino acids appear functionally equivalent, but intermediates exhibit reduced stability and have not been observed in nature. However, the phylogeny suggests two independent occurrences of the three mutations, requiring two separate transitions through low fitness intermediates. We reexamined this apparent paradox using phylogenomic methods, accounting for incomplete lineage sorting and intralocus recombination. The lysozyme locus tree conflicts with an estimated species tree, but the conflict involves a short branch in coalescent units, consistent with incomplete lineage sorting. We also found evidence for recombination, with different parts of the lysozyme locus supporting alternative relationships. The three amino acids are encoded by exons located in different recombination-defined segments with different evolutionary histories. These results support a model where ancestral polymorphism, coupled with recombination between independently arising mutations, allowed rapid transitions between peaks in the fitness landscape without fixation of deleterious intermediates. Our findings resolve this long-standing question in lysozyme evolution and highlight the importance of considering complex genealogical processes such as incomplete lineage sorting and recombination when reconstructing ancestral proteins and interpreting apparent cases of molecular convergence.

evolutionary biology↗

bioRxiv2025

The phylogenetic position of the extinct Hawaiian honeyeaters: Overcoming the limitations of antique DNA

Mohoidae, the Hawaiian honeyeaters, are a group of extinct birds that once inhabited the Hawaiian Islands. Their genetic data are only available from historical museum specimens, so it is based on highly fragmented and damaged DNA. Poor sequence recovery in these "antique" samples can bias phylogenetic inference which often results in exceptionally long terminal branches in the phylogeny. These long branches can distort estimates of phylogeny, an artifact known as long branch attraction. However, the best way to analyze this data is unclear because these long branches are typically artifactual, reflecting DNA quality. We investigated the position of Mohoidae within the superfamily Bombycilloidea using published alignments of ultraconserved elements (UCEs) and re-assembled UCEs from raw sequencing reads. The uncertainty involves two monotypic families (Hypocoliidae and Hylocitreidae). Re-aligning UCEs using a smaller taxon set closely related to Mohoidae, along with edge trimming and re-assembly, eliminated the long branches of Mohoidae and Hypocoliidae (also represented by an antique sample). The sister relationship of these two families in previous studies appears to be artifactual; our new analyses yielded congruent topologies that placed Mohoidae as sister to a clade comprising Hypocoliidae and Hylocitreidae. We also found that different assemblers (SPAdes vs Trinity) yielded sequences with conflicts towards the ends of the UCEs, especially for the antique samples, although this did not alter the topology. Finally, combining the UCEs with legacy data allowed us to produce a strongly supported complete phylogeny of Bombycilloidea the included all extant species as well as the extinct Mohoidae.

evolutionary biology↗

bioRxiv2025

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

evolutionary biology↗

bioRxiv2024

Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

The evolutionary histories of different genomic regions typically differ from each other and from the underlying species phylogeny. This makes species tree estimation challenging. Here, we examine the performance of phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, the species tree of living birds. We compared trees generated by maximum likelihood (ML) analysis of concatenated data, gene tree summary methods, and SVDquartets. We also conduct the first empirical test of a "new" method called METAL (Metric algorithm for Estimation of Trees based on Aggregation of Loci), which is based on evolutionary distances calculated using concatenated data. We conducted this test using a novel dataset comprising more than 4,000 ultraconserved element (UCE) loci from almost all bird families and two existing UCE and intron datasets sampled from almost all avian orders. We identified "reliable clades" very likely to be present in the true avian species tree and used them to assess method performance. ML analyses of concatenated data recovered almost all reliable clades with less data and greater robustness to missing data than other methods. METAL recovered many reliable clades, but only performed well with the largest datasets. Gene tree summary methods (weighted ASTRAL and weighted ASTRID) performed well; they required less data than METAL but more data than ML concatenation. SVDquartets exhibited the worst performance of the methods tested. In addition to the methodological insights, this study provides a novel estimate of avian phylogeny with almost 99% of the currently recognized avian families. Only one of the 181 reliable clades we examined was consistently resolved differently by ML concatenation versus other methods, suggesting that it may be possible to achieve consensus on the deep phylogeny of extant birds.

evolutionary biology↗

bioRxiv2023

Interspecific Aggression Of Two Wrens Along An Environmental Gradient In Western Ecuador

Interspecific territoriality is a prevalent form of interference competition among animals. However, the connections between hybridization, climate, and interspecies territorial aggression in tropical regions remain largely unexplored. Here, we investigated territorial aggression in two hybridizing tropical bird species, C. z. brevirostris and C. f. pallescens, in western Ecuador using playback experiments. We tested three hypotheses: 1) hybridizing species exhibit comparable intra- and inter-specific territorial aggression; 2) asymmetrical aggression driven by C. z. brevirostris dominance determines gene flow patterns; and 3) precipitation influences territorial aggression. Supporting hypothesis 1, the admixed C. f. pallescens North showed no difference in intra-vs inter-specific aggression. However, the non-admixed C. f. pallescens South exhibited greater inter-specific aggression, providing partial support for hypothesis 1. Contrary to hypothesis 2, C. f. pallescens South displayed significantly higher aggression than C. z. brevirostris and C. f. pallescens North. Furthermore, precipitation models outperformed null models, supporting hypothesis 3 that precipitation influences Campylorhynchus territorial aggression. Collectively, these findings suggest hybridization can stabilize coexistence via territoriality, and precipitation strongly affects aggression, potentially through resource availability. Unexpectedly, C. z. brevirostris dominance did not appear to drive asymmetric introgression between species, warranting further investigation into the underlying mechanisms. Complex factors shape territorial aggression in tropical birds, including genetic admixture, group size, latitude, and climate. This study highlights the need for additional research elucidating the relationships between hybridization, territoriality, and environmental stressors in tropical avian communities. We discuss possible mechanisms explaining the detected effects of precipitation on aggression and the lack of C. z. brevirostris dominance in determining introgression patterns.

ecology↗

bioRxiv2023

Exploring The Role Of Isolation By Distance, Isolation By Environment, And Hybridization In Campylorhynchus Wrens Along A Precipitation Gradient In Western Ecuador

Climate variability can cause genetic and phenotypic diversity within species, which affects the evolution of biodiversity. A balance between gene flow and selection maintains changes in the frequency of genetic and phenotypic variants along an environmental gradient. In this study, we investigated a hybrid zone in western Ecuador involving two species of wrens (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus, and their admixed populations. We hypothesized that isolation by distance (IBD) and different ecological preferences, isolation by environment (IBE), result in limited dispersal between populations along the precipitation gradient in western Ecuador. We asked two main questions: (1) What is the relative contribution of IBD and IBE to patterns of genetic differentiation of these species along the environmental gradient in western Ecuador? And (2) Is there evidence of genetic admixture and introgression between these taxa in western Ecuador? We analyzed 4,409 SNPs from the blood of 112 individuals sequenced using ddRadSeq. The most likely clusters ranged from K=2-4, corresponding to categories defined by geographic origins, known phylogenetics, and physical or ecological constraints. Evidence for IBD was strong across all models, and evidence for IBE was less strong but still significant for annual mean precipitation and precipitation seasonality. We observed gradual changes in genetic admixture between C. f. pallescens and C. zonatus along the environmental gradient. Genetic differentiation of the two populations of C. f. pallescens could be driven by a previously undescribed potential physical barrier near the center of western Ecuador. Lowland habitats in this region may be limited due to the proximity of the Andes to the coastline, limiting dispersal and gene flow, particularly among dry-habitat specialists. We do not propose taxonomic changes, but the admixture observed in C. f. pallescens suggests that this described subspecies could be a hybrid between C. z. brevirostris and C. fasciatus, with different degrees of admixture along western Ecuador and northwestern Peru. This study contributes to the knowledge of avian population genomics in the tropics.

evolutionary biology↗

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↗