Divergence with gene flow within the recent chipmunk radiation (Tamias)

Abstract

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para-and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.

Insights on the host associations and geographic distribution of Hymenolepis folkertsi (Cestoda: Hymenolepididae) among rodents across temperate latitudes of North America

“…Genetic divergence revealed across localities for H. folkertsi suggests historically isolated populations, consistent with extended evolutionary and biogeographic histories for species of Peromyscus and Tamias in North America (Kurtén and Anderson 1980). Drivers for parasite and host diversification and faunal assembly are evident through recurring episodes of climatological change, ecological perturbation, and geographic fragmentation over about the last three million years from the late Pliocene through the Quaternary (Dragoo et al 2006; Hoberg et al 2012; Makarikov et al 2015; Sullivan et al 2014; Galbreath and Hoberg 2015; Bell et al 2016). Divergence documented among putative populations of H. folkertsi may indicate poorly differentiated species or a mosaic of discrete genetic variation across spatial scales reflecting local conditions or assemblages.…”

“…Considering only recognized cricetid and sciurid host groups, there are 56 species of Peromyscus , the monotypic O. nuttalli , 23 species of Tamias ( Neotamias ), 2 species of Ictidomys , and 10 species of Sciurus across North America (Musser and Carelton 2005; Thorington and Hoffmann 2005; Helgen et al 2009; Sullivan et al 2014). Minimal synoptic information for parasite diversity has been documented in these assemblages.…”

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

“…There is an emerging consensus that gene flow frequently occurs following speciation despite the establishment of reproductive barriers that otherwise maintain species-level distinctiveness (Roca et al 2005;Good et al 2008;Ellegren et al 2012;Garrigan et al 2012;Toews and Brelsford 2012;Cahill et al 2013Cahill et al , 2014Cui et al 2013;Martin et al 2013;Kutschera et al 2014;Sullivan et al 2014). However, incomplete lineage sorting (ILS) is assumed by default to underpin most cases of phylogenetic discordance.…”

Complex within a Complex: Integrative Taxonomy Reveals Hidden Diversity in Cicadetta brevipennis (Hemiptera: Cicadidae) and Unexpected Relationships with a Song Divergent Relative

“…Increasingly, new studies indicate that speciation can occur in the presence of intermittent or continuous gene flow between diverging populations (e.g. [5–8]) and that species contain genes assembled from multiple semi-independently evolving lineages [9]. A useful new way of thinking about speciation was suggested by Butlin et al .…”