Biology subjects

Lovette, I.

Publications and source records attributed to Lovette, I..

4 recordsLinked to original sources

bioRxiv2025

History of divergence and gene flow shaping geographic variation in Andean warblers (Myioborus)

Studying how genetic variation is structured across space, and how it relates to divergence in phenotypic traits relevant to reproductive isolation, is important for our overall understanding of the speciation process. We used reduced-representation genomic data (ddRAD-seq) to examine patterns of genetic variation across the full distribution of an Andean warbler species complex (Myioborus ornatus-melanocephalus), which includes a known hybrid zone between two strikingly different plumage forms. Genetic structure largely reflects geographic variation in head plumage, some of which corresponds to major topographic barriers in the Andes. We also found evidence of isolation by distance shaping genetic patterns across the groups broad latitudinal range. We found that chrysops and bairdi, two taxa with marked plumage differences that have a known hybrid zone, were characterized by low overall genetic divergence. Based on our cline analyses of both plumage and genomic hybrid indices, this hybrid zone extends for approximately 250 km, where advanced generation hybrids are likely most common. We also identified a slight difference in the centers of the plumage and genomic clines, potentially suggesting the asymmetric introgression of chrysops-like plumage traits. By studying genetic variation in a phenotypically complex group distributed across a topographically complex area, which includes a hybrid zone, we were able to show how both geographic features and potentially sexually selected plumage traits may play a role in species formation in tropical mountains

evolutionary biology↗

bioRxiv2019

Genomic phylogeography of the White Crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

The complex landscape history of the Neotropics has generated opportunities for population isolation and diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow reveals a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last [~]2.5 Ma.

evolutionary biology↗

bioRxiv2018

Low genomic divergence and high gene flow between locally adapted populations of the swamp sparrow

Populations that have recently diverged across sharp environmental gradients provide an opportunity to study the mechanisms by which natural selection drives adaptive divergence. Inland and coastal populations of the North American swamp sparrow have become an emerging model system for studies of natural selection because they are morphologically and behaviourally distinct despite a very recent divergence time (<15,000 years), yet common garden experiments have demonstrated a genetic basis for their phenotypic differences. We characterized genomic patterns of variation within and between inland and coastal swamp sparrows via reduced representation sequencing in order to reconstruct the contributions of demography, gene flow and selection to this case of recent adaptive divergence. Compared to inland swamp sparrows, coastal swamp sparrows exhibited fewer polymorphic sites and reduced nucleotide diversity at those sites, indicating that a bottleneck and/or recent selective sweeps occurred in that population during coastal colonization and local adaptation. Estimates of genome-wide differentiation (FST=0.02) and sequence divergence ({Phi}ST=0.05) between inland and coastal populations were very low, consistent with postglacial divergence. A small number of SNPs were strongly differentiated (max FST=0.8) suggesting selection at linked sites. Swamp sparrows sampled from breeding sites at the habitat transition between freshwater and brackish marshes exhibited high levels of genetic admixture. Such evidence of active contemporary gene flow makes the evolution and maintenance of local adaptation in these two populations even more notable. We summarize several features of the swamp sparrow system that may facilitate the maintenance of adaptive diversity despite gene flow, including the presence of a magic trait.

evolutionary biology↗

bioRxiv2018

Whole genome scan reveals the multigenic basis of recent tidal marsh adaptation in a sparrow

Natural selection acts on functional molecular variation to create local adaptation, the \"good fit\" we observe between an organisms phenotype and its environment. Genomic comparisons of lineages in the earliest stages of adaptive divergence have high power to reveal genes under natural selection because molecular signatures of selection on functional loci are maximally detectable when overall genomic divergence is low. We conducted a scan for local adaptation genes in the North American swamp sparrow (Melospiza georgiana), a species that includes geographically connected populations that are differentially adapted to freshwater vs. brackish tidal marshes. The brackish tidal marsh form has rapidly evolved tolerance for salinity, a deeper bill, and darker plumage since colonizing coastal habitats within the last 15,000 years. Despite their phenotypic differences, background genomic divergence between these populations is very low, rendering signatures of natural selection associated with this recent coastal adaptation highly detectable. We recovered a multigenic snapshot of ecological selection via a whole genome scan that revealed robust signatures of selection at 31 genes with functional connections to bill shape, plumage melanism and salt tolerance. As in Darwins finches, BMP signaling appears responsible for changes in bill depth, a putative magic trait for ecological speciation. A signal of selection at BNC2, a melanocyte transcription factor responsible for human skin color saturation, implicates a shared genetic mechanism for sparrow plumage color and human skin tone. Genes for salinity tolerance constituted the majority of adaptive candidates identified in this genome scan (23/31) and included vasoconstriction hormones that can flexibly modify osmotic balance in tune with the tidal cycle by influencing both drinking behavior and kidney physiology. Other salt tolerance genes had potential pleiotropic effects on bill depth and melanism (6/31), offering a mechanistic explanation for why these traits have evolved together in coastal swamp sparrows, and in other organisms that have converged on the same \"salt marsh syndrome\". As a set, these candidates capture the suite of physiological changes that coastal swamp sparrows have evolved in response to selection pressures exerted by a novel and challenging habitat.

evolutionary biology↗