Biology subjects

Manthey, J. D.

Publications and source records attributed to Manthey, J. D..

4 recordsLinked to original sources

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

Waves of Colonization and Gene Flow in a Great Speciator

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones--where reproductive isolation can further develop via reinforcement or phenotypic displacement--or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayrs foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.

evolutionary biology↗

bioRxiv2023

Library preparation method and DNA source influence endogenous DNA recovery from 100-year-old avian museum specimens

Museum specimens collected prior to cryogenic tissue storage are increasingly being used as genetic resources, and though high throughput sequencing is becoming more cost-efficient, whole genome sequencing (WGS) of historical DNA (hDNA) remains inefficient and costly due to its short fragment sizes and high loads of exogenous DNA, among other factors. It is also unclear how sequencing efficiency is influenced by DNA source. We aimed to identify the most efficient method and DNA source for collecting WGS data from avian museum specimens. We analyzed low-coverage WGS from 60 DNA libraries prepared from four American Robin (Turdus migratorius) and four Abyssinian Thrush (Turdus abyssinicus) specimens collected in the 1920s. We compared DNA source (toepad versus incision-line skin clip) and three library preparation methods: 1) double-stranded, single tube (KAPA); 2) single-stranded, multi-tube (IDT); and 3) single-stranded, single-tube (Claret Bioscience). We found that the multi-tube ssDNA method resulted in significantly greater endogenous DNA content, average read length, and sequencing efficiency than the other tested methods. We also tested whether a predigestion step reduced exogenous DNA in libraries from one specimen per species and found promising results that warrant further study. The ~10% increase in average sequencing efficiency of the best performing method over a commonly implemented dsDNA library preparation method has the potential to significantly increase WGS coverage of hDNA from bird specimens. Future work should evaluate the threshold for specimen age at which these results hold and how the combination of library preparation method and DNA source influence WGS in other taxa.

genomics↗

bioRxiv2022

Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana)

The nonrandom distribution of chromosomal characteristics and functional elements--genomic architecture--impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure--ordination, clustering, and phylogenetic methods-- we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of linked selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.

evolutionary biology↗