Quantitative analysis of genetic parameters in populations of European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer with RAPD markers

A technique for obtaining unbiased estimates of genetic parameters (allelic frequencies of RAPD loci, heterozygosity (H), Wright's F statistic, and Nei's genetic distances) in populations of the European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer is presented. The technique employs jackknifing and multiple comparative analysis based on a modified Holmes's procedure for Bonferroni's test. It was demonstrated that samples from local groups of roe deer in the Trans-Ural region did not differ significantly in allelic frequencies (0.8, 0.81, and 0.78; P > 0.447) or Nei's genetic distances (0.0056, 0.0273, and 0.0218; P = 0.26), but they could be differentiated based on Wright's F statistic (0.0346, 0.0519, and 0.0450; P = 10(-9)). The parameters of intrapopulation heterozygosity (from 0.18 to 0.042) formed a gradient from the east to the west. Calibration estimates of molecular evolution rate in the family Cervidae obtained based on published data and Jukes-Cantor genetic distances estimated in this study demonstrated that the Siberian roe deer has split into two subspecies, C. pygargus pygargus Pall. and C. pygargus tianschanicus Satunin in the interval between 229 and 462.3 thousand years ago. The species formation of the Siberian and European roe deer was dated between 1.375 and 2.75 Myr ago. Based on the results obtained we recommend the approaches used in the study for analysis of population genetic structure and phylogenetic relationships between populations, subspecies, species, and higher taxa.     

Mitochondrial DNA Distinction of Northeastern China Roe Deer, Siberian Roe Deer, and European Roe Deer, to Clarify the Taxonomic Status of Northeastern China Roe Deer

Partial sequences of the mitochondrial control region of northeastern China roe deer were analyzed to determine the degree of genetic diversity. Fourteen haplotypes were observed. The haplotype diversity was high (h = 0.872), nucleotide diversity was medium (p _i = 0.0108), and the average Tamura–Nei nucleotide distance among them was 1.9%, indicating that genetic diversity of roe deer from northeastern China was relatively high and that the effective population size was large historically. To clarify the northeastern China roe deer's taxonomic status, these 14 haplotypes were compared with 31 haplotypes published in Genbank from Europe, Siberia, and Korea. The average genetic distance between haplogroups of northeastern China and European roe deer (5.8%) was more than twice that between northeastern China and Siberian roe deer (2.7%), indicating sufficient variation to consider roe deer of northeastern China and Siberia as a single species (Capreolus pygargus), distinct from European roe deer (Capreolus capreolus). This is the first presentation of mtDNA data for roe deer in northeastern China, which will be helpful in investigations of genetic diversity and clarifications of the taxonomic status of roe deer in the whole of China.     

Quantitative Analysis of Genetic Parameters in Populations of European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) Roe Deer with RAPD Markers

A technique for obtaining unbiased estimates of genetic parameters (allelic frequencies of RAPD loci, heterozygosity (H), Wright's Fstatistic, and Nei's genetic distances) in populations of the European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer is presented. The technique employs jackknifing and multiple comparative analysis based on a modified Holmes's procedure for Bonferroni's test. It was demonstrated that samples from local groups of roe deer in the Trans-Ural region did not differ significantly in allelic frequencies (0.8, 0.81, and 0.78; P > 0.447) or Nei's genetic distances (0.0056, 0.0273, and 0.0218; P = 0.26), but they could be differentiated based on Wright's F statistic (0.0346, 0.0519, and 0.0450; P = 10^–9). The parameters of within-population heterozygosity formed a gradient from the east to the west. Calibration estimates of molecular evolution rate in the family Cervidae obtained based on published data and Jukes–Cantor genetic distances estimated in this study demonstrated that the Siberian roe deer has split into two subspecies, C. pygargus pygargusPall. and C. pygargus tianschanicusSatunin in the interval between 229 and 462.3 thousand years ago. The species formation of the Siberian and European roe deer was dated between 1.375 and 2.75 Myr ago. Based on the results obtained we recommend the approaches used in the study for analysis of population genetic structure and phylogenetic relationships between populations, subspecies, species, and higher taxa.     

Skull variation in the Siberian roe deer <Emphasis Type="Italic">Capreolus pygargus</Emphasis> from the Far East: a revision of the distribution of the subspecies

Extremely widespread in the Palaearctic, roe deer are heterogeneous in many ways including their morphology. At present, two roe deer species and four basic subspecies are acknowledged. The taxonomic system of the Siberian roe deer is poorly developed compared to that of the European roe deer. One of the principal points of roe deer systematics is the determination of the boundaries of the ranges of the roe deer subspecies requiring a thorough study of the species’ diversity. By using craniometry, one of the most adequate systematics techniques, we have analyzed geographical distribution of the Suberian roe deer in the Russian Far East and adjacent areas. All studied specimens were separated into three groups, the distributions of craniometric parameters of two of which did not overlap. One of the groups corresponds to Capreolus pygargus pygargus Pallas, 1771, while the other two do not correspond to any of the Siberian roe deer subspecies presently acknowledged. We have shown that the C. pygargus pygargus range extends to the east to the Northern Primorye, i.e., it is 2,000 to 3,000 km wider than previously believed. The subspecies status of Capreolus pygargus tianschanicus Satunin, 1906 was not confirmed. The Southern Primorye and left bank of the Amur River are thus a part of the range of Capreolus pygargus melanotis Miller, 1911, penetrating here from the Northeastern China.     

Analysis of the variability of the control region and cytochrome b gene of mtDNA of Capreolus pygargus Pall

Analysis the of cytochrome b gene (1140 b.p.) polymorphism and polymorphism of 79 specimens of the control region (934 b.p.) of mtDNA of the Siberian roe deer Capreolus pygargus from 23 regions of Russia and Kazakhstan has been carried out. The combined alignment of two fragments of mitochondrial DNA revealed 36 haplotypes, which are distributed in three haplogroups. The net distance was 0.8, 1.3, and 1.3%. The specific pattern of haplogroups was described for roe deer of each region (Ural, trans-Ural, Eastern Siberia, Far East, Northeastern China). Unrelated haplogroups were found in populations of the Urals and Siberia. The variation pattern and spatial distribution of mitochondrial lines allowed us to suggest that a haplogroup that initially belongs to C. p. tianschanicus occurs secondarily in C. p. pygargus.     

Genetic diversity and genetic structure of the Siberian roe deer (<Emphasis Type="Italic">Capreolus pygargus</Emphasis>) populations from Asia

Background

The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia.

Results

Moderate levels of genetic diversity (H _E = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest?(H _E?= 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean F _ST = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (F _RT = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups.

Conclusions

Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an east-west gradient. The results suggest at least three distinct management units of roe deer in continental Asia, although genetic admixture is evident in some border areas. The insights obtained from this study shed light on management of Siberian roe deer in Asia and may be applied in conservation of local populations of Siberian roe deer.

     

东北地区狍种群的遗传多样性研究

狍为我国重要的经济动物,并且是国家一级保护动物东北虎的主要猎物之一。因此,深入了解狍各地理单元内种群的遗传变异,可以为我们制定保护管理策略提供依据,进而使珍稀濒危物种得到有效的保护和管理。本文对88个不同狍个体(来自8个不同地点)的线粒体DNA控制区的部分序列进行了测定和群体分析,获得了463bp的片断,并检测到59个变异位点,占分析长度的7.84%,且这59个变异位点皆为碱基置换,未出现碱基插入或缺失的现象,定义了30种单倍型,核苷酸多样性平均值为0.02641,种群总体遗传多样性较高。从Tajima’sD和FuandLi’sD值的估算结果来看,这8个狍种群相对于中性进化的歧异度并没有明显的偏离(P0.1),没有明显的证据显示这8个狍种群间存在很强的平衡选择。30个单倍型整体上将东北狍种群分为3个亚群,分子变异分析表明3个亚群间基因流Nm均大于1,说明这3个狍亚群间存在着基因流。     

Polymorphism of a short fragment of the mitochondrial genome control region (D-loop) in the Siberian roe deer <Emphasis Type="Italic">Capreolus pygargus</Emphasis> Pallas, 1771 (Artiodactyla,Cervidae) from the Russian Far East

Genetic diversity of Siberian roe deer Capreolus pygargus, 1771 from the Russian Far East was studied based on polymorphism analysis of a mtDNA control region fragment (390 bp). Three phylogenetic lines were found in the animals examined. The trend for change of haplotypes of different phylogroups was shown to occur from north to south in Sikhote-Alin. The haplotype distribution of Siberian roe deer in the Russian Far East correlated with data on morphologiocal variability.     

On the Gene Pool of Roe Deer (<Emphasis Type="Italic">Capreolus</Emphasis>) of Eastern Europe: Analysis of the Cyt <Emphasis Type="Italic">b</Emphasis> Gene Sequence Variability

Sequence analysis of the mtDNA cytochrome b gene (974 bp) was performed using 139 roe deer specimens from different regions of the European part of Russia and Ukraine. The data obtained showed that, at present, both European and Siberian roe deer inhabit this part of the range with predominance of the later: about 60% of individuals carry various Siberian haplotypes, most of which are similar to those in the populations of Capreolus pygargus from the Urals, Siberia, and the Far East. A great variety of mtDNA haplotypes of Siberian roe deer in Eastern Europe is undoubtedly caused by the heterogeneity of founder individuals (immigrants) that were imported from different parts of Asia. Some problems of coexistence of closely related species are discussed.     

Phylogeography of roe deer (Capreolus capreolus) populations: the effects of historical genetic subdivisions and recent nonequilibrium dynamics

We sequenced 704 mitochondrial DNA (mtDNA) control-region nucleotides and genotyped 11 autosomal microsatellites (STR) in 617 European roe deer (Capreolus capreolus) samples, aiming to infer the species' phylogeographical structure. The mtDNA sequences were split in three distinct haplogroups, respectively, named: Clade West, sampled mainly in Iberia; Clade East, sampled mainly in Greece and in the Balkans; and Clade Central, which was widespread throughout Europe, including the eastern countries and Iberia, but not Greece. These clades might have originated in distinct Iberian and Balkanic refuges during the penultimate or the last glaciations. Clades East and West contributed little to the current postglacial mtDNA diversity in central Europe, which apparently was recolonized mainly by haplotypes belonging to Clade Central. A unique subclade within Clade Central grouped all the haplotypes sampled from populations of the Italian subspecies C. c. italicus. In contrast, haplotypes sampled in central and southern Spain joined both Clade Central and Clade West, suggesting that subspecies C. c. garganta has admixed origin. STR data support a genetic distinction of peripheral populations in north Iberia and southern Italy, and show the effects of anthropogenic disturbance in fragmented populations, which were recently reintroduced or restocked and not may be in mutation-drift equilibrium. Roe deer in central Europe are mainly admixed, while peripheral populations in north Portugal, the southern Italian Apennines and Greece represent the remains of refugial populations and should be managed accordingly.     

Variability of multilocus DNA markers in populations of the Siberian (Capreolus pygargus Pall.) and European (C. capreolus L.) roe deer

Two types of nuclear DNA markers, M13 minisatellites and RAPD, were used to examine intraspecific and interspecific variation in closely related roe deer species, Capreolus capreolus L. and C. pygargus Pall. The roe deer populations studied were highly polymorphic for minisatellite DNA markers (S = 0.12-0.36). Heterozygosities of the RAPD loci were 0.185 (Russian Far East), 0.145, 0.131, 0.088 (Cis-Ural), and 0.06 (France). They correlated with karyotypic variation of B chromosomes (r = 0.975, P < 0.02; Spearman's correlation coefficient r = 1, P = 0.1 x 10(-5)), which indicated a contribution of microchromosomes to genetic variation of the species. The genetic distance D between the closely related species C. capreolus and C. pygargus was 50 times greater than the distance between populations within a species. The estimates of heterozygosity and genetic distance between local populations of Cis-Ural and the Far East suggest their specific spatial organization within this geographical range and reveal features of their historical development.     

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations

Background

The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved.

Methodology/Principal Findings

We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples.

Conclusion/Significance

Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer represent a complex and heterogeneous species with high migration rates and without evident subspecies structure. Low genetic diversity of the West Siberian Plain population indicates a recent bottleneck or founder effect.     

Irreversible microevolutionary changes in genotypic composition of sika deer <Emphasis Type="Italic">Cervus nippon</Emphasis> populations in response to vegetation degradation and food shortage

The present study deals with changes in important skull characteristics of the sika deer Cervus nippon Temminck, 1838 in response to changes in food supply. Moderate food shortage results mainly in a linear reduction in skull size, while severe food shortage results in changes in skull shape. In the deer that returned to habitats with sufficient food supply, some skull parameters recovered to, or even exceeded, normal values, whereas other parameters remained stressed resulting in retention or enhancement of skull distortions. Differences in skull parameters among the populations studied were comparable to those between some cervid species, eg, the Siberian roe deer Capreolus pigargus Pallas, 1771 and European roe deer Capreolus capreolus Linnaeus, 1758 and other deer subspecies. In the introduced sika deer populations, skull distortions were apparently caused by interspecific hybridization. Descendants of the escaped deer have not reverted to the normal phenotype, even over several generations, providing a recent case of true evolutionary changes. This occurred by a change in the ratio of different morphotypical groups, probably due to their different responses to food shortage. Thus sufficient food supply may account for changes in a population’s genotypic composition through selection of characteristics that favour passing on genetic material when food is limited.     

Microsatellite investigation of roe deer (Capreolus capreolus) in Scandinavia reveals genetic differentiation of a Baltic Sea Island population

After a decline in the early 19th century, a remnant population of the Scandinavian roe deer (Capreolus capreolus) was protected in southern Sweden around 1840. The roe deer quickly recovered and recolonized most of the Scandinavian Peninsula. In this study, I analyze microsatellite variation in 14 roe deer populations in Scandinavia to (1) investigate if all Swedish roe deer trace their ancestry to southern Sweden, (2) define other areas where roe deer may have remained during the population decline, and (3) examine if the large geographic distances during the expansion phase have influenced the degree and sorting of genetic variation. The results show that the mainland roe deer most likely trace their ancestry to southern Sweden, but interestingly, the two neighboring populations Övedskloster and Wittskövle in the south are significantly different from each other (p<0.01). Furthermore, the population in Wittskövle and roe deer from Köpingsvik at the Baltic Sea Island Öland are significantly different from all other populations (p<0.1). Thus, potentially, there are more than one founder population that contributed to the current Swedish population. The particular differentiation of roe deer from Öland might be an effect of random population genetic processes during the population expansion phase, potentially in combination with introductions of roe deer from other areas than the Swedish mainland. The results are discussed in relation to management of roe deer in Sweden.     

Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer

Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness‐related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex‐linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex‐specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8–10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human‐mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.     

Fluctuating asymmetry in populations of British roe deer (Capreolus capreolus) following historical bottlenecks and founder events

The potential impact of population bottlenecks and founder events on genetic diversity and indirect measures of fitness (such as fluctuating asymmetry; FA) has important conservation implications. Here we take advantage of historical events that generated a remnant roe deer (Capreolus capreolus) population in the north of the British Isles that retained diversity, while populations in the south were apparently extirpated during the early mediaeval era. The southern population was later re-established from small founder populations of introduced European roe deer starting in the 19th century. We assess the impact of these events, using the northern remnant population as a reference, based on measures of FA at 16 bilateral cranial traits. Comparing the northern and southern populations we find evidence of differential impact on both the level of FA and the relationship between FA and levels of genetic diversity.     

Effects of human activities on the spatial distribution of eastern roe deerCapreolus pygargus bedfordi in the Lesser Khingan Mountains, northeastern China

Eastern roe deerCapreolus pygargus bedfordi Thomas, 1908 occurred throughout China historically, but today are only found in 7 provinces. Their populations in China have been greatly impacted by human disturbances. Little is known about what kinds of human disturbances impact their distribution and resource requirements for survival. A survey was conducted over 20 661 ha located at the Erkehe Forestry Farm in the Lesser Khingan Mountains, northeastern China. Field work lasted from January to March, 2006 and January to March, 2007, and a total of 613 plots were visited along 28 sampling transects. Predictive models of easter roe deer resource selection were developed with or without the inclusion of human disturbance factors. Whether human disturbance exists or not, eastern roe deer retained strong links to patch size and patch density of low shrub and swamp, and the probability of moose occurrence. Low shrub and swamps created after logging provide more abundant annual shoots for food, and were vital for survival in harsh winters. When human disturbance was not modeled, eastern roe deer avoided higher density of bothBetula platyphylla andLarix gmelinii patches at a landscape scale, and larger mixed coniferous and broad-leaf patchs at local scales. Once human disturbances existed, eastern roe deer occurred in areas with higher NDVI and they had a considerably lower probability of presence in areas associated with roads and with a forest harvest interval of 4 years. Consequently, to predict effects of human disturbance on eastern roe deer spatial distribution, models need to incorporate effects of other competitive species, multiple spatial scale resource variables respectively, which will provide more value information for management and use of eastern roe deer population.     

Immunogenetic heterogeneity in a widespread ungulate: the European roe deer (Capreolus capreolus)

Understanding how immune genetic variation is shaped by selective and neutral processes in wild populations is of prime importance in both evolutionary biology and epidemiology. The European roe deer (Capreolus capreolus) has considerably expanded its distribution range these last decades, notably by colonizing agricultural landscapes. This range shift is likely to have led to bottlenecks and increased roe deer exposure to a new range of pathogens that until recently predominantly infected humans and domestic fauna. We therefore investigated the historical and contemporary forces that have shaped variability in a panel of genes involved in innate and acquired immunity in roe deer, including Mhc‐Drb and genes encoding cytokines or toll‐like receptors (TLRs). Together, our results suggest that genetic drift is the main contemporary evolutionary force shaping immunogenetic variation within populations. However, in contrast to the classical view, we found that some innate immune genes involved in micropathogen recognition (e.g. Tlrs) continue to evolve dynamically in roe deer in response to pathogen‐mediated positive selection. Most studied Tlrs (Tlr2, Tlr4 and Tlr5) had similarly high levels of amino acid diversity in the three studied populations including one recently established in southwestern France that showed a clear signature of genetic bottleneck. Tlr2 implicated in the recognition of Gram‐positive bacteria in domestic ungulates, showed strong evidence of balancing selection. The high immunogenetic variation revealed here implies that roe deer are able to cope with a wide spectrum of pathogens and to respond rapidly to emerging infectious diseases.     

Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein‐coding genes are extremely conserved; however, some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species‐specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein‐coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost four‐fold higher d_N/d_S ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well‐preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.     

Demography and adaptation promoting evolutionary transitions in a mammalian genus that diversified during the Pleistocene

Species that evolved in temperate regions during the Pleistocene experienced periods of extreme climatic transitions. Consequent population fragmentation and dynamics had the potential to generate small, isolated populations where the influence of genetic drift would be expected to be strong. We use comparative genomics to assess the evolutionary influence of historical demographics and natural selection through a series of transitions associated with the formation of the genus Capreolus, speciation within this genus during the Quaternary and during divergence among European roe deer (C. capreolus) populations. Our analyses were facilitated by the generation of a new high‐coverage reference genome for the Siberian roe deer (C. pygargus). We find progressive reductions in effective population size (N_e), despite very large census sizes in modern C. capreolus populations and show that low N_e has impacted the C. capreolus genome, reducing diversity and increasing linkage disequilibrium. Even so, we find evidence for natural selection shared among C. capreolus populations, including a historically documented founder population that has been through a severe bottleneck. During each phylogenetic transition there is evidence for selection (from dN/dS and nucleotide diversity tests), including at loci associated with diapause (delayed embryonic development), a phenotype restricted to this genus among the even‐toed ungulates. Together these data allow us to assess expectations for the origin and diversification of a mammalian genus during a period of extreme environmental change.