skip to main content

Search for: All records

Creators/Authors contains: "Thom, Gregory"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Hancock, Angela (Ed.)

    Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how variation in genomic characteristics (e.g. recombination rate) impacts our ability to reconstruct general patterns of differentiation between species that cooccur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in genomic regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations toward lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate spatial patterns of population differentiation.

    more » « less
    Free, publicly-accessible full text available January 1, 2025
  2. Abstract

    Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within data sets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade’s species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of the genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower-quality samples. Most instances of topological conflict and nonmonophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, the noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many data sets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology. [Historical DNA; machine learning; museomics; Psittaciformes; species tree.]

    more » « less
  3. Abstract Aim

    We aim to test the biogeographic drivers of diversification and gene‐flow at the Isthmus of Panama using a species complex of suboscine birds as a case study. We specifically evaluate whether diversification in these birds is better explained by continuous parapatry or a Refuge Model of periodic isolation and gene‐flow due glacial cycling.


    The Isthmus of Panama (Neotropics).


    Pachyramphus aglaiaeandPachyramphus homochrous(Aves: Tityridae).


    We develop an approach to distinguish among the two biogeographic hypotheses—parapatric ecological speciation versus climatically mediated speciation—by making explicit predictions for demographic history, niche evolution and change in geographic connectivity over time. We sequenced genome‐wide markers (ultraconserved elements) to estimate the evolutionary and demographic history of this group. We applied both phylogenomic network analyses and demographic modelling using a supervised machine learning approach. These genetic analyses were combined with a novel distribution modelling method that estimates the probability of interspecies contact as a function of climatic conditions through time.


    We found that both spatial and genetic analyses revealed concordant results. All speciation events occurred during the Pleistocene and were characterized by non‐continuous gene‐flow, supporting a scenario of climate‐mediated diversification. Spatial connectivity was highest at present, consistent with our best demographic model of secondary contact.

    Main conclusions

    This study exemplifies a mechanism by which speciation, dispersal and introgression unfold in an important region for Neotropical diversification—the Isthmus of Panama—where periods ofbothisolation and introgression probably drive diversification. Overall, our results are consistent with the Refuge Model of biotic diversification, but suggest that introgression may be a crucial yet underappreciated component of this classic paradigm.

    more » « less