Biology subjects

Weckstein, J. D.

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

4 recordsLinked to original sources

bioRxiv2025

The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

We use single genomes from seven tinamou species (Palaeognathae: Tinamidae) and apply a genome-architecture-aware phylogenomic approach to (1) quantify the landscape of introgression, (2) discriminate among conflicting genealogical signals in the genome, and (3) reconstruct evolutionary history. Using summary statistics and full likelihood, we detect pervasive asymmetric introgression between two sympatric Amazonian species clouding phylogenetic relationships in this group. However, these introgression results are sensitive to the assumed species tree. When assuming the Z-chromosome phylogeny as the species tree, the landscape of introgression is non-random; introgression is negatively associated with chromosome length, elevated at macrochromosome ends, and near zero for the Z-chromosome (the avian sex chromosome). A pseudo-autosomal region on the Z-chromosome, which recombines homologously with that of the W-chromosome, shows elevated introgression comparable to that of autosomes. Our results resolve the species tree of tinamous and imply a history of linked selection purging migrant alleles that are deleterious in the hybrid genome. This selection is countered in regions of the genome expected to experience elevated recombination, allowing introgressed alleles to accumulate across >20% of the genome. This work demonstrates a genome-architecture-aware approach to resolving the species tree in the face of introgression. As chromosome-level reference genomes spanning the tree of life become increasingly available, phylogenomic studies would benefit from the adoption of genome-architecture-aware approaches like ours. This is because the genomic landscapes of introgression and genealogy are largely predicted by chromosomal characteristics.

genomics↗

bioRxiv2024

Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression

As an old group that has diversified in South America over millions of years, the tinamous (Palaeognathae: Tinamidae) are of high interest for understanding the evolution of birds and the assembly of the Neotropical biota. However, there are currently no complete species-level phylogenies of this group. Most prior work has been based on either morphological data or a small number of molecular markers, each of which has limited capability for reconstructing the tinamou phylogeny. Therefore, the interrelationships of most tinamou species are uncertain. We analyzed 80 whole-genomes from a mix of historical study skins and frozen tissues, including all 46 recognized species of tinamous to (1) reconstruct their interrelationships, (2) estimate the timeframe of tinamou evolution, and (3) examine for the effects of incomplete lineage sorting (ILS) and ancestral introgression on genome evolution. We compared results for coding (BUSCO) and ultraconserved element (UCE) loci, as well as sex-linked and autosomal markers, and used fossil-calibrated tip-dating to estimate divergence times. Tinamous diverged from their sister-group, the extinct Moas, 50-60 mya, and their crown divergence occurred roughly 30-40 mya, followed by constant diversification rates until the present. Phylogenetic reconstructions were largely robust across methods and datasets. Only one clade in the genus Crypturellus displayed substantial species-tree discordance across the different data sets. To investigate the impacts of introgression on this discordance, we quantified introgression for 100kb non-overlapping windows across the genome, and identified pervasive genome-wide introgression. The distribution of this introgression across the genome was dependent on the assumed phylogeny applied to the f-branch model. When assuming one of these topologies in the f-branch model, patterns of introgression matched theoretical predictions about genome architecture. Overall, we present the most complete phylogeny for tinamous to date, identify an unrecognized species, and provide a case study for species-level phylogenomic analysis using whole-genomes.

genomics↗

bioRxiv2021

The interplay between host biogeography and phylogeny in structuring diversification of the feather louse genus Penenirmus

Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2,395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.

evolutionary biology↗

bioRxiv2018

Deeply conserved susceptibility in a multi-host, multi-parasite system

Variation in susceptibility is ubiquitous in multi-host, multi-parasite assemblages, and can have profound implications for ecology and evolution. The extent to which susceptibility is phylogenetically conserved among hosts is poorly understood and has rarely been appropriately tested. We screened for haemosporidian parasites in 3983 birds representing 40 families and 523 species, spanning ~4500 meters elevation in the tropical Andes. To quantify the influence of host phylogeny on infection status, we applied Bayesian phylogenetic multilevel models that included a suite of environmental, spatial, temporal, life history, and ecological predictors. We found evidence of deeply-conserved susceptibility across the avian tree; host phylogeny explained substantial variation in infection rate, and results were robust to phylogenetic uncertainty. Our study suggests that susceptibility is governed, in part, by conserved, latent aspects of anti-parasite defense. This demonstrates the importance of deep phylogeny for understanding the outcomes of present-day ecological interactions.\n\nStatement of authorshipLNB, SMM, NM, and CCW designed the study; SMM, SCG, HLL, HS, TV, JDW, and CCW collected the data; LNB and NM analyzed the data; LNB, NM, and CCW wrote the paper with input from all authors.\n\nData accessibility statementSpecimen information is available from the Arctos database (arctosdb.org) and in supplementary tables (Appendix S1). Files used for analysis will be archived in Dryad. DOI: XXX.

evolutionary biology↗