A Molecular Genetic Study of Hybridization in Four Species of Ground Squirrels (Spermophilus: Rodentia,Sciuridae)

Four species of ground squirrel—yellow (Spermophilus fulvus), russet (S. major), small (S. pygmaeus), and spotted (S. suslicus)—occur in the Volga region. Between S. major and S. pigmaeus, S. major and S. fulvus, and S. major and S. suslicus, sporadic hybridization was reported. Using sequencing and restriction analysis, we have examined the mtDNA C region in 13 yellow, 60 russet, 61 small, 45 spotted ground squirrels, and 9 phenotypic hybrids between these species. It was shown that 43% of S. major individuals had alien mitotypes typical of S. fulvus and S. pygmaeus. Alien mitotypes occurred both within and outside sympatric zones. No alien mitotypes were found in 119 animals of the other three species, which suggests that only one parental species (S. major) predominantly participates in backcrosses. Phenotypic hybrids S. fulvus × S. major and S. major × S. pygmaeus) were reliably identified using RAPD–PCR of nuclear DNA. However, we could find no significant traces of hybridization in S. major with alien mitotypes. Analysis of p53 pseudogenes of S. major and S. fulvus that were for the first time described in the present study produced similar results: 59 out of 60 individuals of S. major (including S. major with S. fulvus mitotypes) had only the pseudogene variant specific for S. major. This situation is possible even at low hybridization frequencies (less than 1% according to field observations and 1.4 to 2.7% according to nuclear DNA analysis) if dispersal of S. major from the sympatric zones mainly involved animals that obtained alien mtDNA via backcrossing. The prevalence of animals with alien mitotypes in some S. major populations can be explained by the founder effect. Further studies based on large samples are required for clarifying the discrepancies between mitochondrial and nuclear DNA data.     

Study of hybridization in four species of ground squirrels (spermophilus: Rodentia,Sciuridae) by molecular genetic methods

Four species of ground squirrel--yellow (Spermophilus fulvus), russet (S. major), small (S. pygmaeus), and spotted (S. suslicus)--occur in the Volga region. Between S. major and S. pigmaeus, S. major and S. fulvus, and S. major and S. suslicus, sporadic hybridization was reported. Using sequencing and restriction analysis, we have examined the mtDNA C region in 13 yellow, 60 russet, 61 small, 45 spotted ground squirrels, and 9 phenotypic hybrids between these species. It was shown that 43% of S. major individuals had "alien" mitotypes typical of S. fulvus and S. pygmaeus. Alien mitotypes occurred both within and outside sympatric zones. No alien mitotypes were found in 119 animals of the other three species, which suggests that only one parental species (S. major) predominantly participates in backcrosses. Phenotypic hybrids S. fulvus x S. major and S. major x S. pygmaeus) were reliably identified using RAPD-PCR of nuclear DNA. However, we could find no significant traces of hybridization in S. major with alien mitotypes. Analysis of p53 pseudogenes of S. major and S. fulvus that were for the first time described in the present study produced similar results: 59 out of 60 individuals of S. major (including S. major with S. fulvus mitotypes) had only the pseudogene variant specific for S. major. This situation is possible even at low hybridization frequencies (less than 1% according to field observations and 1.4 to 2.7% according to nuclear DNA analysis) if dispersal of S. major from the sympatric zones mainly involved animals that obtained alien mtDNA via backcrossing. The prevalence of animals with alien mitotypes in some S. major populations can be explained by the founder effect. Further studies based on large samples are required for clarifying the discrepancies between mitochondrial and nuclear DNA data.     

A search for Y-chromosomal species-specific markers and their use for hybridization analysis in ground squirrels (Spermophilus: Rodentia, sciuridae)

In four ground squirrel species from the Volga region—yellow (Spermophilus fulvus), russet (S. major), little (S. pygmaeus), and speckled (S. suslicus)—four hybridization variants (major/fulvus, major/pygmaeus, major/suslicus, and pygmaeus/suslicus) have been reliably described. Earlier we have shown that populations of S. major from the Volga region were characterized by wide introgression of mtDNA from S. fulvus and S. pygmaeus, which probably, resulted from ancient hybridization [5]. In this study, the same populations were used to analyze the introgression of the Y chromosome, which (unlike mtDNA) is paternally inherited. Three genes, ZfY, SRY, and SmcY were tested as Y-chromosomal candidate markers. It was demonstrated that Y chromosome of ground squirrels lacked the ZfY gene, while its homologous structure, ZfY(X), was presumably linked to the X chromosome. The SRY region examined was rather conservative. In particular, the sequences determined in S. major and S. fulvus were identical, while three out of four substitutions found in S. pygmaeus were located in the coding region. The SmcY gene was found to be the most suitable marker, providing distinguishing of all of the four ground squirrel species by nine nucleotide substitutions. Introgression at the Y chromosome was observed only in two cases: in one S. major individual (out of 51 phenotypically pure animals) caught in the major/fulvus sympatry zone, and in four (one litter) out of fourteen S. fulvus individuals caught in close vicinity of the sympatry zone of these two species. Among 28 S. pymaeus and 9 S. suslicus individuals, no foreign SmcY genes were detected. Two colonies of the “hybrid swarm” type were examined with eight major/suslicus hybrids analyzed in the first and seventeen major/fulvus hybrids in the second colony. The prevalence of the S. major paternal lineages was observed in both colonies (87.5 and 82.4%, respectively). The data obtained suggest that compared to wide mtDNA introgression, introgression of Y chromosome in the Volga region ground squirrels is statistically significantly less frequent event.     

Genetic analysis of sable (<Emphasis Type="Italic">Martes zibellina</Emphasis>) and pine marten (<Emphasis Type="Italic">M. martes</Emphasis>) populations in sympatric part of distribution area in the northern Urals

Analysis of nucleotide sequences of the mitochondrial DNA (mtDNA) control region (495 bp) of sables (Martes zibellina) and pine martens (M. martes) from allopatric parts of the species ranges has shown a considerable interspecific genetic distance (>3%). In sympatric populations of these species in the northern Urals, differences between two species-specific mtDNA lineages are still large; however, classification of each individual nucleotide sequence with one of the two lineages is not correlated with whether the given animal is phenotypically a sable, a pine marten, or a potential hybrid (the so-called “kidas”). This indicates a high degree of reciprocal introgression of the sable and pine marten mtDNA in the northern Urals and suggests that their interspecific hybridization is common in the sympatric zone.     

Molecular genetic relationships among east Palaerctic ground squirrels of the genus <Emphasis Type="Italic">Spermophilus</Emphasis> (Sciuridae,Rodentia)

Abstact  Genetic diversity in the four east Palearctic ground squirrel species of the genus Spermophilus—S. undulatus, S. parryi (subgenus Urocitellus), S. dauricus, and S. relictus (subgenus Citellus)—was investigated using RAPD PCR with ten random primers. Siberian chipmunk, Tamias sibiricus, was used as an out-group. Molecular markers for different taxonomic ranks were identified, including those for the genera Spermophilus and Tamias, subgenera Urocitellus and Citellus, as well as for each of the four species, S.undulatus, S. parryi, S. dauricus, and S. relictus. For the ground squirrel species and subgenera, genetic differentiation indices (H _t, H _s, D _st, G _st,Nm, and D) were calculated. In addition, for these groups the NJ phylogenetic reconstructions and UPGMA dendrograms of genetic similarity of the individuals and combined populations were constructed. Comparative molecular genetic analysis revealed a high genetic differentiation between S. undulatus, S. dauricus, S. relictus, and S. parryi (G _st= 0.58 to 0.82; D= 0.53 to 1.06), along with a low level of genetic differentiation of the subgenera Citellus and Urocitellus (G _st = 0.33; D= 0.27), distinguished in accordance with the existing taxonomic systems of the genus Spermophilus Original Russian Text ? M.V. Tsvirka, L.N. Spiridonova, V.P. Korablev, 2008, published in Genetika, 2008, Vol. 44, No. 8, pp. 1108–1116.     

The intraspecies variability of <Emphasis Type="Italic">Spermophilus relictus</Emphasis> sensu lato Kaschkarov 1923 (Sciuridae,Rodentia)

The intraspecies variability of Spermophilus relictus sensu lato was studied based on 27 measurements of skulls from 67 specimens of relict ground squirrels (S. relictus) and 66 specimens of Tien Shan ground squirrels (S. ralli), as well as six specimens of the relict ground squirrel from the Gissar Ridge (Tien Shan). A colorimetric analysis of skins of relict ground squirrels (19 specimens, including three individuals from the Gissar Ridge) and Tien Shan ground squirrels (19 specimens) was made. Significant intraspecies variability was found in the relict and Issyk-Kul ground squirrels, whereas the interspecies differences were small, raising questions about the species independence of the Tien Shan ground squirrel (S. ralli).     

Genetic divergence of populations of the white char <Emphasis Type="Italic">Salvelinus Albus</Emphasis>, northern and southern forms of malma <Emphasis Type="Italic">S. malma</Emphasis> (Salmonidae), by microsatellite loci of DNA

A very small but statistically significant genetic differentiation by allele frequencies (in the Kamchatka basin F _ST = 0.016 and in Kronotskoe Lake F _ST = 0.063) is revealed between sympatric populations of the northern malma Salvelinus malma malma and of the white char S. albus by analysis of nine microsatellite loci. Factor analysis and clusterization of individual multilocal genotypes in the sum sample of sympatric S. malma malma and S. albus also demonstrate their extremely weak genetic differentiation. Divergence between geographically isolated (allopatric) populations of each of these chars exceeds by two-three times the interspecies differentiation in the zones of sympatry. Samples from allopatric populations clusterize by the geographic principle but not by the taxonomic principle. Such a situation may be explained by the absence of reproductive isolation and presence of hybridization between sympatric S. malma malma and S. albus with the simultaneous existence of some limitations of genetic exchange related to the ecological specialization of these chars. Analysis of microsatellite loci revealed highly significant genetic differences between the northern and southern forms of malma S. malma krascheninnikovi by many times exceeding genetic differences between S. malma malma and S. albus. The obtained data do not confirm the independent species status of S. albus but support the opinion of the species level of differences between the northern and southern forms of malma.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

Some notes on fig-eating by arboreal mammals in Malaysia

During a study of avian fig-eating at Kuala Lompat, Malaysia, observations were also made of fig-eating by mammals. Four species of primate, seven species of squirrel, and two species of civet consumed figs. Twenty-six species ofFicus were of importance to arboreal mammals. Observations suggest that there were differences in the importance of figs in the diets of sympatric langurs (Presbytis) and congeneric squirrels. Dusky langursPresbytis obscura ate carbohydrate-rich ripe figs despite their ruminant-like digestive system and the danger of bloat.     

Directional mitochondrial introgression and character displacement due to reproductive interference in two closely related Pterostichus ground beetle species

Reproductive interference due to interspecific hybridization can lead to character displacement among related species with overlapping ranges. However, no studies have examined which reproductive traits are most important in reducing reproductive interference. We conducted molecular analyses of two nuclear genes (28S and Wingless) and a mitochondrial gene (COI) from two closely related ground beetle species, Pterostichus thunbergi and Pterostichus habui (Coleoptera: Carabidae), with overlapping distributions. In addition, we examined four reproductive traits (body size, organ morphologies of intromittent and non‐intromittent male genital organs, and female reproductive period) in sympatric and allopatric habitats. We compared male genital morphology using geometric morphometric analysis. The species determined by morphology were classified into separate groups based on the phylogenetic tree constructed by the nuclear gene (Wingless). However, according to the mitochondrial genes examined, P. thunbergi was not monophyletic, whereas at the sympatric sites, these species formed a monophyletic clade. This incongruence suggests that interspecific hybridization and subsequent mitochondrial introgression from P. habui to P. thunbergi have occurred. Concerning genital morphology, both of the intromittent and nonintromittent organs of P. thunbergi differed more from P. habui at the sympatric sites than between allopatric sites, suggesting reproductive character displacement. Pterostichus thunbergi, which likely arrived in P. habui habitat in small numbers, would have experienced stronger selection pressures than P. habui.     

Nest site availability and niche differentiation between two cavity‐nesting birds in time and space

Niche differentiation is a key concept in the field of ecology and refers to the process by which competing species within an ecological community partition utilization of environmental resources to achieve coexistence. The existence of niche differentiation is uniquely difficult to prove on account of the fact that historical interaction among species, which plays a key role in elucidating the current state of coexistence among species, is not well known. We created continuous niche gradients in nest‐site resources between two sympatric secondary cavity‐nesting birds, the green‐backed tit (Parus monticolus) and the russet sparrow (Passer cinnamomeus), and investigated whether nesting site is a factor contributing to limiting breeding overlap by regular inspection and 388,160 min of film recording. Our results indicate that although we manipulated nest site availability to be uniformly high along the habitat gradient, the two bird species have little overlap in nest sites and rarely compete for them. Furthermore, the green‐backed tit possessed a wide range of fundamental niche that covered that of the russet sparrow, while their reproductive time was largely segregated. The sparrow was more aggressive and outcompeted the tit in their overlapped range. These results suggest that even though nesting sites are crucial to the reproduction of cavity‐nesting birds, some other factor plays a more important role in limiting niche overlap between sparrows and tits in space and time. Given that these two cavity‐nesting birds continued to use different habitats and breed in segregated time after our manipulation, their relationship is better explained by the ghost of competition past theory.     

Dynamics of colonies of the speckled ground squirrel (<Emphasis Type="Italic">Spermophilus suslicus</Emphasis> Guld., 1770) on the northern boundary of the habitat

Results of studies in 1999–2009 of the dynamics of five isolated colonies of the speckled ground squirrel (Spermophilus suslicus) at the northern boundary of the habitat of this species (Zaraiskii area, Moscow oblast) are given. An abrupt decrease in the number of this species in colonies was established, as was a multifold decrease (up to 70–90%) in suitable habitats due to the plowing of meadows and build-up of the area. The fragmentation of the optimum habitat of ground squirrels reached a stage where colonies can no longer exist as a stable autonomous system. The process of their extinction unfolds quickly: the number of animals in some colonies decreased five-six times over the last ten years. To preserve this species, it is necessary to create areas of steppefied meadows with regulated agricultural use.     

Morphological and molecular evidence of natural hybridization in Shorea (Dipterocarpaceae)

Shorea (Dipterocarpaceae) is a large genus in which many closely related species often grow together in Southeast Asian lowland tropical rain forests. Many Shorea species share common pollinators, and earlier studies suggested occurrence of interspecific hybridization and introgression. Here, we show morphological and molecular evidence of hybridization between Shorea species. In the census of all the trees of Shorea curtisii, Shorea leprosula, and Shorea parvifolia (>30 cm dbh) within the 164-ha area of Bukit Timah Nature Reserve in Singapore, we found 21 morphologically recognizable hybrid individuals. All of the putative hybrids could be distinguished obviously from the parental species on the basis of vegetative characters. Population genetic analysis of DNA sequences of two nuclear (GapC and PgiC) and chloroplast (trnL-trnF) regions demonstrated that each of the three species had several species-specific mutations. The nuclear sequences of the putative hybrids were heterozygote at all the species-specific sites between two parental species. Hybrid between S. curtisii and S. leprosula was found most, while S. curtisii × S. parvifolia and S. leprosula × S. parvifolia hybrids were also found. Almost no shared polymorphism between populations of the parental species suggests rarity of introgression. The study indicated that natural hybridization between sympatric Shorea species should not be uncommon, but all of the hybrid individuals were F₁, and the post-F₁ hybrids were considerably rare.     

A search for Y-chromosomal species-specific markers and their use for hybridization analysis in ground squirrels

In four ground squirrel species from the Volga region-yellow (Spermophilus fulvus), russet (S. major), little (S. pygmaeus), and speckled (S. suslicus)--four hybridization variants (major/fulvus, major/pygmaeus, major/suslicus, and pygmaeus/suslicus) have been reliably described. Earlier we have shown that populations of S. major from the Volga region were characterized by wide introgression of mtDNA from S. fulvus and S. pygmaeus, which probably, resulted from ancient hybridization. In this study, the same populations were used to analyze the introgression of the Y chromosome, which (unlike mtDNA) is paternally inherited. Three genes, ZfY, SRY, and SmcY were tested as Y-chromosomal candidate markers. It was demonstrated that Y chromosome of ground squirrels lacked the ZfY gene, while its homologous structure, ZfY(X), was presumably linked to the X chromosome. The SRY region examined was rather conservative. In particular, the sequences determined in S. major and S. fulvus were identical, while three out of four substitutions found in S. pygmaeus were located in the coding region. The SmcY gene was found to be the most suitable marker, providing distinguishing of all of the four ground squirrel species by nine nucleotide substitutions. Introgression at the Y chromosome was observed only in two cases: in one S. major individual (out of 51 phenotypically pure animals) caught in the major/fulvus sympatry zone, and in four (one litter) out of fourteen S. fulvus individuals caught in close vicinity of the sympatry zone of these two species. Among 28 S. pymaeus and 9 S. suslicus individuals, no foreign SmcY genes were detected. Two colonies of the "hybrid accumulation" type were examined with eight major/suslicus hybrids analyzed in the first and seventeen major/fulvus hybrids in the second colony. The prevalence of the S. major paternal lineages was observed in both colonies (87.5 and 82.4%, respectively). The data obtained suggest that compared to wide mtDNA introgression, introgression of Y chromosome in the Volga region ground squirrels is statistically significantly less frequent event.     

Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial‐genetic patterns of connectivity

Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within‐species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population‐level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G”_ST) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G”_ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species.     

Rats are not the only introduced rodents producing ecosystem impacts on islands

In addition to rats, nutria (Myocastor coypus) and the North American beaver (Castor canadensis) have certainly caused damage at an ecosystem level when introduced to islands, in both cases primarily by ecosystem engineering. Of other introduced rodents successfully established on islands, the gray squirrel (Sciurus carolinensis) may be in the process of damaging entire forest ecosystems, particularly by bark-stripping. Though introduced muskrats (Ondatra zibethicus) have had ecosystem-level impacts in continental Europe, their impact on islands worldwide to which they have been introduced has been very limited. The North American red squirrel (Tamiasciurus hudsonicus) and Barbary ground squirrel (Atlantoxerus getulus) have each had substantial impacts when introduced to particular islands, but for neither species have these impacts yet been demonstrated to spread through an entire ecosystem. Introduced house mice (Mus musculus) may well generate ecosystem impacts on remote islands lacking rats, and it is possible that explosions of house mice on islands after rat eradication, a common occurrence, will lead in some instances to ecosystem impacts.     

Range‐wide genetic analysis reveals limited structure and suggests asexual patterns in the rare forb Senecio macrocarpus

Genetic diversity and recombination underlie the long‐term persistence and evolution of species and are strongly influenced by population size, breeding system and plant longevity. Here, we study genetic structure in the rare Senecio macrocarpus in southeastern Australia to guide current conservation practices. Thirteen neutral microsatellite markers and two chloroplast regions were used to survey the 20 known S. macrocarpus populations and one sympatric S. squarrosus population, a morphologically similar species. All markers showed severe excess or deficit of heterozygotes and linkage disequilibrium was significant. Microsatellite markers revealed 100 multi‐locus genotypes (MLGs) from 523 S. macrocarpus individuals and a further 4 MLGs from 27 S. squarrosus individuals. MLGs varied in frequency and distribution. At the extremes, one MLG was found 108 times across the sampling region and 66 MLGs were found once. The MLGs of all 38 seedlings genotyped were identical to their seed parents implying an asexual origin. Chloroplast regions showed little variation within S. macrocarpus but differed from S. squarrosus. Chromosome counts for S. macrocarpus revealed the same ploidy level as S. squarrosus (2n = 6x = 60) and pollen–ovule ratios were typical of erechthitoid Senecio species showing self‐compatibility. Results suggest that establishment of small populations occur primarily from one extensive source population with indications that both apomixis and selfing may be contributing to its reproduction cycle. We suggest that this species may contribute to future evolutionary processes despite limited genotypic variation and restricted distribution. Its conservation will safeguard evolutionary processes that might occur through occasional outcrossing and hybridization events between sympatric species. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 256–269.     

Genetic connectivity between sympatric populations of closely related char species,Dolly Varden <Emphasis Type="Italic">Salvelinus malma</Emphasis> and white char <Emphasis Type="Italic">Salvelinus albus</Emphasis>

The closely related chars Salvelinus malma and Salvelinus albus, which sympatrically inhabit the Kamchatka River basin and Kronotsky Lake (Kamchatka), attract the attention of the researchers because of their debated origin and taxonomic status. Previous studies of sympatric populations of these chars revealed small but statistically significant genetic differences between these species at a number of molecular markers, suggesting the presence of the genetic exchange and hybridization. In this study, based on genotypic characterization of nine microsatellite loci, a considerable level of historical and contemporary genetic migration between sympatric populations of these chars was demonstrated. At the individual level, a high degree of hybridization was observed, mainly among the Dolly Varden individuals from the studied populations. The obtained evidences on the genetic connectivity between sympatric S. malma and S. albus do not support the separate species status of S. albus.     

Daily rhythmicity and hibernation in the Anatolian ground squirrel under natural and laboratory conditions

We studied daily rhythmicity of body temperature (T _b) before and during hibernation in Anatolian ground squirrels (Spermophilus xanthoprymnus) under natural and laboratory conditions using surgically implanted temperature loggers. Under both conditions, robust daily T _b rhythmicity with parameters comparable to those of other ground squirrel species was observed before but not during hibernation. Euthermic animals had robust daily T _b rhythms with a mean of 37.0°C and a range of excursion of approximately 4°C. No T _b rhythm was detected during torpor bouts, either because T _b rhythmicity was absent or because the daily range of excursion was smaller than 0.2°C. The general patterns of hibernation that we observed in Anatolian ground squirrels were similar to those previously observed by other investigators in other species of ground squirrels.     

Genetic diversity and population divergence in fragmented habitats: Conservation of Idaho ground squirrels

The Idaho ground squirrel, which consists of a northern (Spermophilus brunneus brunneus) and a southern subspecies (S. b. endemicus), has suffered from habitat loss and fragmentation, resulting in a reduction in both numbers and geographic range of the species. The northern Idaho ground squirrel (NIDGS) is listed as a threatened subspecies under the Endangered Species Act, and the southern Idaho ground squirrel (SIDGS) is a candidate. Because Idaho ground squirrel populations are small and often isolated, they are susceptible to inbreeding and loss of genetic diversity through drift. This research evaluates levels of genetic diversity and patterns of population divergence in both subspecies of Idaho ground squirrels. We hypothesized that NIDGS would exhibit lower genetic diversity and greater population divergence due to a longer period of population isolation relative to most SIDGS populations. Genetic diversity and divergence were quantified using 8 microsatellite loci. Contrary to expectations, SIDGS populations exhibited consistently lower levels of microsatellite diversity. Additionally, NIDGS exhibited only modest divergence among populations, while divergence levels among SIDGS populations were highly varied. Preliminary evaluations of mitochondrial DNA diversity and structure revealed lower diversity in NIDGS and some differences in gene flow that warrant further study. Based on our results, we suggest different management strategies for the two subspecies. Habitat restoration appears to be the most desirable conservation strategy for NIDGS populations. In contrast, low genetic diversity observed in SIDGS may warrant supplementation of isolated populations through translocations or captive breeding to mitigate further loss of genetic variability.