Biology subjects

Linck, E.

Publications and source records attributed to Linck, E..

4 recordsLinked to original sources

bioRxiv2025

A chromosome-scale genome assembly for Clark's Nutcracker (Nucifraga columbiana)

Focal and intelligent passerine songbirds, corvids (Aves: Corvidae) have served as models for research on the genomics of hybridization and cognition. Clarks Nutcracker (Nucifraga columbiana), the sole North American member of its genus, is distributed in mountain forests from northern Mexico to northern British Columbia. A seed predator, N. columbiana is highly reliant on pine nuts from Pinus spp. conifers, which it both consumes directly from cones and caches for future use. Because cached seeds are often forgotten or abandoned, it is a major seed disperser for high elevation pines--in particular Whitebark Pine P. albicaulis. Previous studies of genetic variation in Clarks Nutcracker found range-wide panmixia and generally high levels of heterozygosity at a handful of nuclear and mitochondrial loci, potentially due to seasonal elevational movements and long term dispersal. An earlier genome assembly from low-coverage short read data was highly fragmented and has not to date been used as the basis for population-level resequencing. Here we report on the first chromosome-scale genome assembly for N. colombiana. We generated long-read sequencing and genome conformation mapping data from tissues sampled from a male N. columbiana individual in Wyoming, USA. These data were assembled into a highly contiguous and complete assembly, which showed strong chromosomal synteny with New Caledonian crow (Corvus moneduloides). This genome has relatively low heterozygosity compared to other Corvid genomes and to previous population-level heterozygosity estimates for the species. We also found evidence of a long-term decline in effective population size dating back to the Pleistocene, after accounting for a technical artifact common to demographic inference using the pairwise sequential Markovian coalescent. These findings raise concerns about the future viability of the species and its mutualist P. albicaulis; we hope the assembly will motivate further comparative and conservation genomics research.

genomics↗

bioRxiv2019

On the relative ease of speciation with periodic gene flow

AO_SCPLOWBSTRACTC_SCPLOWCommon models of speciation with gene flow consider constant migration or admixture on secondary contact, but earths recent climatic history suggests many populations have experienced cycles of isolation and contact over the last million years. How does this process impact the rate of speciation, and how much can we learn about its dynamics by analyzing the genomes of modern populations? Here we develop a simple model of speciation through Bateson-Dobzhansky-Muller incompatibilities in the face of periodic gene flow and validate our model with forward time simulations. We then use empirical atmospheric CO2 concentration data from the Vostok Ice Cores to simulate cycles of isolation and secondary contact in a tropical montane landscape, and ask whether they can be distinguished from a standard isolation-with-migration model by summary statistics or joint site frequency spectrum-based demographic inference. We find speciation occurs much faster under periodic than constant gene flow with equivalent effective migration rates (Nm). These processes can be distinguished through combinations of summary statistics or demographic inference from the site frequency spectrum, but parameter estimates appear to have little resolution beyond the most recent cycle of isolation and migration. Our results suggest speciation with periodic gene flow is a common force in generating species diversity through Pleistocene climate cycles, and highlight the limits of current inference techniques for demographic models mimicking the complexity of earths recent climatic history.

evolutionary biology↗

bioRxiv2019

Speciation with gene flow across an elevational gradient in New Guinea kingfishers

Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks, and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high elevation and low elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modeling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that while in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.

evolutionary biology↗

bioRxiv2018

Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

Incomplete or geographically biased sampling poses significant problems for research in phylogeog-raphy, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of a widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or \"sibling\") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the groups range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

evolutionary biology↗