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15 results for “Tamias”
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks
<p>In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data.</p>
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks
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Data from: Effects of home range size and burrow fidelity on survival and reproduction in eastern chipmunks (Tamias striatus) across different environmental contexts
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Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
<p>Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the <i>Tamias quadrivittatus</i> group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (<i>T. canipes</i>, <i>T. cinereicollis</i>, <i>T. dorsalis</i>, <i>T. quadrivittatus</i>, <i>T. rufus</i>, and <i>T. umbrinus</i>) that show evidence for widespread mitochondrial introgression across species boundaries. Such evidence has historically derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.</p>
Exploration and relatedness of potential and realised mating pairs in Tamias striatus
<p><span>Individual exploration types are based on the cognitive speed-accuracy trade-off, which suggests that higher speed of information acquisition is done by sacrificing information quality</span><span>. In a mating context, fast exploration could thus increase the probability of finding mates at the cost of mating with kin or suboptimal partners. We tested this hypothesis by studying male mate choice patterns in a species with a scramble competition mating system. We used genotyping, localisation by radio-collar, trapping, and repeated exploration measures from a long-term study on wild Eastern chipmunks (<em>Tamias</em> <em>striatus</em>). We predicted that, according to the speed-accuracy trade-off hypothesis, slower-thorough explorers should be choosier than faster-superficial ones, and thus avoid inbreeding. We found that slower males reproduced more often with less related females, but only on one site where variance in relatedness and female density were high. Males showed no preference for their mates' exploration type. Our results suggest that superficial exploration decreases male choosiness and increases the risk of inbreeding, but only under decreased mate search costs due to high variance in relatedness among mates (at high density). Our findings reveal exploration-related, among-individual variance in inbreeding, highlighting the complexity of mate choice, and showing that many aspects of an individual's life contribute to animal decision-making.</span></p>
Data from: Age at first reproduction and senescence in Eastern chipmunks (Tamia striatus)
<p class="MsoNormal"><span>Senescence is the degradation of biological functions with </span><span>increasing </span><span>age. Its existence and relationship with life-history strategies remains poorly studied in short-lived wild vertebrate species. We investigated the relationships between age at first reproduction (AFR), reproductive senescence and longevity in an eastern chipmunk (<em>Tamias striatus</em>) population, where the first opportunity to breed is conditioned by pulses of seed production by trees (i.e., masts). </span><span>We used 11 years of data from a longitudinal study, in which females breed for the first time at seven, 15, or 22 months of age and males at seven or 15 months of age. We first assessed the effect of age on three traits associated with breeding performance, namely the number of offspring produced, and the probability of weaning or siring a litter. We then tested whether an earlier AFR accelerated reproductive senescence and reduced survival of both males and females. </span><span>We found sex-specific relationships between AFR and senescence. Females reproducing at 15 or 22 months of age showed reproductive senescence, but early-breeding females did not show any decline in reproductive performance at an older age. Also, although we observed reproductive senescence in males, it was not affected by AFR. </span><span>Our results are consistent with studies highlighting the existence of reproductive senescence in small, wild mammals. Importantly, we provide the first evidence that AFR can strongly influence the patterns of senescence in small short-lived species and does it in a sex-specific way. Our results highlight the importance of studying life-history strategies in both males and females when studying senescence in the wild.</span></p>
Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)
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Data from: Age at first reproduction and senescence in Eastern chipmunks (Tamia striatus)
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Sevilleta site, station Cerro Montosa Study Site, study of animal abundance of Tamias quadrivittatus in units of numberPerTrappingWeb on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Sevilleta (SEV) contains animal abundance of Tamias quadrivittatus measurements in numberPerTrappingWeb units and were aggregated to a yearly timescale.
Sevilleta site, station Two-22 Study Site, study of animal abundance of Tamias dorsalis in units of numberPerTrappingWeb on a yearly timescale
The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Sevilleta (SEV) contains animal abundance of Tamias dorsalis measurements in numberPerTrappingWeb units and were aggregated to a yearly timescale.
Data from: Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)
The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species' divergence.
On following pages: 165. Unstriped Ground Squirrel (Xerus rutilus); 166. Damara Ground Squirrel (Geosciurus princeps davidianus); 169. Forrest's Rock Squirrel (Sciurotamias forresti); 170. Siberian Chipmunk (Tamias sibiricus); 171. Least (Tamias townsendii); 174. Red-tailed Chipmunk (Tamias ruficaudus); 175. Shadow Chipmunk (Tamias senex); 176.); 167. South African Ground Squirrel (Geosciurus inauris); 168. Pere David's Rock Squirrel (Sciurotamias Chipmunk (Tamias minimus); 172. Yellow-pine Chipmunk (7Tamias amoenus); 173. Townsend's Chipmunk Uinta Chipmunk (Tamias umbrinus). in Sciuridae
On following pages: 165. Unstriped Ground Squirrel (Xerus rutilus); 166. Damara Ground Squirrel (Geosciurus princeps davidianus); 169. Forrest's Rock Squirrel (Sciurotamias forresti); 170. Siberian Chipmunk (Tamias sibiricus); 171. Least (Tamias townsendii); 174. Red-tailed Chipmunk (Tamias ruficaudus); 175. Shadow Chipmunk (Tamias senex); 176.); 167. South African Ground Squirrel (Geosciurus inauris); 168. Pere David's Rock Squirrel (Sciurotamias Chipmunk (Tamias minimus); 172. Yellow-pine Chipmunk (7Tamias amoenus); 173. Townsend's Chipmunk Uinta Chipmunk (Tamias umbrinus).
On following pages: 180. Yellow-cheeked Chipmunk (Tamias ochrogenys); 181. Long-eared Chipmunk (Tamias quadrimaculatus 184. Hopi Chipmunk (Tamias rufus); 185. Colorado Chipmunk (Tamias quadrivittatus); 186. Merriam''s Chipmunk (Tamias California Chipmunk (Tamias obscurus); 190. Gray-collared Chipmunk (Tamias cinereicollis); 191. Gray-footed Chipmunk 194. Eastern Chipmunk (Tamias striatus); 195. White-tailed Antelope Squirrel (Ammospermophilus leucurus); 196 harrisii); 198. Texas Antelope Squirrel (Ammospermophilus interpres). ); 182. Lodgepole Chipmunk (Tamias speciosus); 183. Panamint Chipmunk (Tamias panamintinus), merriami); 187. Alpine Chipmunk (Tamias alpinus); 188. Palmer's Chipmunk (Tamias palmeri); 189. (Tamias canipes); 192. Durango Chipmunk (Tamias durangae); 193. Buller's Chipmunk (Tamias bulleri),. Nelson's Antelope Squirrel (Ammospermophilus nelsoni); 197. Harris's Antelope Squirrel (Ammospermophilus in Sciuridae
On following pages: 180. Yellow-cheeked Chipmunk (Tamias ochrogenys); 181. Long-eared Chipmunk (Tamias quadrimaculatus 184. Hopi Chipmunk (Tamias rufus); 185. Colorado Chipmunk (Tamias quadrivittatus); 186. Merriam''s Chipmunk (Tamias California Chipmunk (Tamias obscurus); 190. Gray-collared Chipmunk (Tamias cinereicollis); 191. Gray-footed Chipmunk 194. Eastern Chipmunk (Tamias striatus); 195. White-tailed Antelope Squirrel (Ammospermophilus leucurus); 196 harrisii); 198. Texas Antelope Squirrel (Ammospermophilus interpres). ); 182. Lodgepole Chipmunk (Tamias speciosus); 183. Panamint Chipmunk (Tamias panamintinus), merriami); 187. Alpine Chipmunk (Tamias alpinus); 188. Palmer's Chipmunk (Tamias palmeri); 189. (Tamias canipes); 192. Durango Chipmunk (Tamias durangae); 193. Buller's Chipmunk (Tamias bulleri),. Nelson's Antelope Squirrel (Ammospermophilus nelsoni); 197. Harris's Antelope Squirrel (Ammospermophilus
Data from: Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)
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Data from: Divergence-with-gene-flow within the recent chipmunk radiation (Tamias)
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