Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii)

Abstract

The Bell's Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell's Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell's Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11-2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell's Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell's Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell's Vireo throughout its range.

Phylogeography of a widespread small carnivore, the western spotted skunk (Spilogale gracilis) reveals temporally variable signatures of isolation across western North America

“…These two regions would have supported two isolated populations of S. gracilis with limited gene flow during glacial maxima, leading to East‐Central and West genetic clades, respectively. A similar pattern, although with much less suitable areas along the west coast, was recently recovered for Bell's Vireo, Vireo belleii (Klicka, Kus, Title, & Burns, ), providing additional support for similar refugial patterns in other codistributed taxa. Using ENM reprojections to the LGM, Klicka et al.…”

“…Using ENM reprojections to the LGM, Klicka et al. () found support for two or potentially three Pleistocene refugia (i.e., central California, northwest Mexico, and northeast Mexico) that corresponded with phylogeographic breaks in mtDNA clades observed in S. gracilis .…”

“…This barrier resulted in separation of desert lowland fauna throughout the Pleistocene, although oscillating climate cycles often led to expansion and contraction of grassland habitat which could explain why some species and not others show phylogeographic signatures associated with this barrier (Morafka, ). Phylogeographic breaks along this barrier have been recovered for bats (Weyandt & Van Den Bussche, ), birds (Klicka et al., ; Zink, Kessen, Line, & Blackwell‐Rago, ), small mammals, plants, and reptiles (Hafner & Riddle, ; Riddle & Hafner, ). Mitochondrial DNA indicates that the Cochise filter barrier could have helped to separate Arizona and East‐Central populations of S. gracilis throughout the Pleistocene (Figure ).…”

“…Although patterns associated with the Arizona clade appear to support the potential impacts of PPD on S. gracilis genetic structure, phylogeographic patterns at the intraspecific level appear to have resulted more from QCC than PPD according to data from divergence estimates, de- Our ENM for the LGM supported the presence of two and possibly three refugia for S. gracilis during the Quaternary (Figure 3b). LGM, Klicka et al (2016) found support for two or potentially three (Rzedowski, 1978 (Figure 3).…”

Identifying evolutionarily significant units for conservation of the endangered Malus sieversii using genome‐wide RADseq data

“…Genome-wide SNPs can be used to explore deeper-level intraspecies phylogenetic structures than those assessed using a limited numbers of neutral loci (Emerson et al 2010, Jeffries et al 2016. Genomic methods have also been applied in biological conservation to identify distinct genetic clusters and to infer effective population sizes for endangered species (Klicka et al 2016). The ability of genome-wide SNPs to identify distinct genetic clusters may mean that they are more suitable that traditional markers for identifying ESUs for endangered species.…”