Phylogeographic and population genetic structure of bighorn sheep (Ovis canadensis) in North American deserts

Abstract

Fossil data are ambiguous regarding the evolutionary origin of contemporary desert bighorn sheep ( Ovis canadensis subspecies). To address this uncertainty, we conducted phylogeographic and population genetic analyses on bighorn sheep subspecies found in southwestern North America. We analyzed 515 base pairs of mtDNA control region sequence and 39 microsatellites in 804 individuals from 58 locations. Phylogenetic analyses revealed 2 highly divergent clades concordant with Sierra Nevada ( O. c. sierrae ) and Rocky Mountain ( O. c. canadensis ) bighorn and showed that these 2 subspecies both diverged from desert bighorn prior to or during the Illinoian glaciation (~315–94 thousand years ago [kya]). Desert bighorn comprised several more recently diverged haplogroups concordant with the putative Nelson ( O. c. nelsoni ), Mexican ( O. c. mexicana ), and Peninsular ( O. c. cremnobates ) subspecies. Corresponding estimates of effective splitting times (~17–3 kya), and haplogroup ages (~85–72 kya) placed the most likely timeframe for divergence among desert bighorn subspecies somewhere within the last glacial maximum. Median-joining haplotype network and Bayesian skyline analyses both indicated that desert bighorn collectively comprised a historically large and haplotype-diverse population, which subsequently lost much of its diversity through demographic decline. Using microsatellite data, discriminant analysis of principle components (DAPC) and Bayesian clustering analyses both indicated genetic structure concordant with the geographic distribution of 3 desert subspecies. Likewise, microsatellite and mitochondrial-based FST comparisons revealed significant fixation indices among the desert bighorn genetic clusters. We conclude these desert subspecies represent ancient lineages likely descended from separate Pleistocene refugial populations and should therefore be managed as distinct taxa to preserve maximal biodiversity. Los datos de fósiles sobre el origen evolutivo de las ovejas del desierto ( Ovis canadensis subespecies) contemporáneas son ambiguos. Para dilucidar esta incertidumbre, llevamos a cabo análisis filogeográficos y de genética de poblaciones entre cinco subespecies de ovejas del suroccidente de Norteamérica. Analizamos 515 pb de secuencia de la región control del ADN mitocondrial y 39 microsatélites en 804 ovejas de 58 localidades. Los análisis filogenéticos revelaron 2 clados altamente divergentes concordantes con ovejas de la Sierra Nevada ( O. c. sierrae ) y de las Montañas Rocosas ( O. c. canadensis ), y demostraron que estas dos subespecies divergieron antes o durante la glaciación de Illinois (315,000–94,000 años). Las ovejas del desierto formaron varios haplogrupos recientemente derivados concordantes con las subespecies de Nelson ( O. c. nelsoni ), México ( O. c. mexicana ) y peninsular ( O. c. cremnobates ). Las estimaciones correspondientes al tiempo de separación efectiva (17,000–3,000 años) y edades de haplogrupos (85,000–72,000 años) son los plazos más probables para las divergencia...

Discovering variation of secondary metabolite diversity and its relationship with disease resistance inCornus floridaL.

“…We conducted DAPC both by defining groups by collection sites and by allowing the program clustering algorithm to find optimal cluster number (K) without priors. Discriminant analyses of principal components does not require assumptions on a population genetic model (e.g., linkage equilibrium of markers) in contrast to programs like STRUCTURE (Pritchard, Stephens, & Donnelly, 2000) so DAPC has been widely adopted in recent population genetic studies (Buchalski et al, 2016;Cahill & Levinton, 2016;Grünwald & Goss, 2011). Its use for metabolic study is recent, but its efficacy in discriminating different biologically meaningful chemotype classes has been demonstrated and favored over other discriminant analysis methods under certain circumstances (Gromski et al, 2015;Scheitz et al, 2013).…”

Assessing polar bear (Ursus maritimus) population structure in the Hudson Bay region using SNPs

“…For DAPCs without prior information, the function find.clusters() in adegenet was used to determine the optimal number of clusters in our dataset. Specifically, we ran successive k-means clustering with increasing number of clusters (K = 1-15 clusters) and used the diffNgroup option to identify the sharp changes in fit of models (measured using the Bayesian information criterion (BIC)) with different number of clusters (e.g., Buchalski et al, 2016;Vallejo-Marin & Lye, 2013). We conducted 20 iterations to assess the stability in detection of the number of clusters.…”

A legacy of geo‐climatic complexity and genetic divergence along the lower Colorado River: Insights from the geological record and 33 desert‐adapted animals

“…The Gila River marks either the geographical limit or site of genetic divergence in lizards ( Crotaphytus nebrius , McGuire et al, ; Uma rufopunctatus , U. cowlesi , and U. sp ., Gottscho et al, ), snakes ( Lichanura trivirgata , Wood, Fisher, & Reeder, ), rodents ( Chaetopidus penicillatus , Jezkova et al, ) and scorpions (haplotype groups 5 and 6 of Hadrurus arizonensis , Graham et al, ). The Bill Williams river marks a similar pattern for snakes ( Chionactis annulatus and C. occipitalis , Wood et al, ), toads (haplogroups within Anaxyrus punctatus , Jaeger et al, ), lizards ( Sceloporus magister , S. “uniformis” , Leaché & Mulcahy, ; Uma spp, Gottscho et al, ), mammals (Nelson and Mexican groups of Ovis canadensis , Buchalski et al, ) and arachnids (haplotype group 3 of Aphonopelma mojave , Graham et al, ). Geomorphic studies show that the Colorado and Gila rivers experienced increased discharge and gravel transport during Pleistocene glacial periods of higher rainfall, and channel deposits were incised by erosion during the drier interglacial periods (Anders et al, ; Chadwick, Hall, & Phillips, ; Sharp, Ludwig, Chadwick, Amundson, & Glaser, ; Waters, ; Waters & Haynes, ).…”

“…There is complete differentiation observed for the turret‐building tarantula ( Aphonopelma prenticei ; Graham, Hendrixson, Hamilton, & Bond, ), round‐tailed ground squirrel ( Xerospermophilus tereticaudus ; Bell, Hafner, Leitner, & Matocq, ) and leopard frogs ( Lithobates onca & L. yavapaiensis ; Oláh‐Hemmings et al, ). In contrast, there is little river‐based differentiation in the desert pocket mouse ( Chaetodipus penicillatus ; Jezkova, Jaeger, Marshall, & Riddle, ), Arizona hairy scorpion ( Hadrurus arizonensis ; Graham, Jaeger, Prendini, & Riddle, ), and bighorn sheep ( Ovis canadensis , Nelson; Buchalski et al, ), among others. This disparity may reflect species‐specific differences in dispersal ability or niche specificity, but there is not good evidence for such patterns at this time.…”