Phylogeography of Cedros and Tiburón Island Mule Deer in North America's Desert Southwest

Speciation without gene-flow in hybridizing deer

Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Hybridisation is part of this continuum and can both promote and inhibit the speciation process. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridizing sister species. We quantified genome-wide historical introgression and performed genome scans to look for signatures of four different selection scenarios. Despite ample modern evidence of hybridisation, we found negligible patterns of ancestral introgression and no signatures of divergence with gene flow, rather localized patterns of allopatric and balancing selection were detected across the genome. Genes under balancing selection were related to immunity, MHC and sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of historical gene-flow suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene and genome wide differentiation accrued via genetic drift. Dobzhansky-Muller incompatibilities and selection against hybrids are hypothesised to be acting, and diversity correlations to recombination rates suggests these sister species are far along the speciation continuum.

Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification

Biodiversity can be boosted by colonization of new habitats such as remote islands and separated continents. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over the Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus Eptesicus (Chiroptera, Vespertilionidae). Previous molecular studies have found New World Eptesicus more closely related to Histiotus, a Neotropical endemic lineage with enlarged ears, than to Old World Eptesicus. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World Eptesicus and Histiotus using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where E. fuscus and Histiotus are sister clades that together diverged from two sister clades of Neotropical Eptesicus. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.

Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure

Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the principal component analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (Eptesicus fuscus) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to (1) plot PCA with a colour gradient showing per sample missingness, (2) interpret samples close to the PCA origin with extra caution, (3) explore filtering parameters with and without the missingness-biased samples, and (4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.