Genetic diversity and phylogeography of Siberian roe deer,Caproulus pygargus,in central and peripheral populations

Current understanding of phylogeographical structure and genetic diversity of Siberian roe deer remains limited mainly due to small sample size and/or low geographical coverage in previous studies. Published data suggest at least two phylogroups: western (Ural Mountains and Western Siberia) and eastern (east from lake Baikal, including the Korean peninsula), but their phylogenetic relationship remains unclear. Combined sequences of cytochrome b (1140 bp) and the mtDNA control region (963 bp) were analyzed from 219 Siberian roe deer from 12 locations in Russia, Mongolia, and South Korea, which cover a large part of its range, to assess genetic diversity and phylogeographical status. Special emphasis was placed on the demographic history and genetic features of central, peripheral, and isolated populations. Results of median‐joining network and phylogenetic tree analyses indicate that Siberian roe deer from the Urals to the Pacific Ocean are genetically diverse and that geographical distribution and composition of haplogroups coincide with previously described ranges of the subspecies Capreolus pygargus pygargus and Capreolus pygargus tianschanicus. We found that peripheral populations in the northwestern parts of the species range (Urals), as well as the isolated population from Jeju Island, are genetically distinct from those in the core part of the range, both in terms of genetic diversity and quantitative composition of haplogroups. We also found that northwestern (Urals) and northern (Yakutia) peripheral populations share the same haplogroup and fall into the same phylogenetic clade with the isolated population from Jeju Island. This finding sheds light on the taxonomic status of the Jeju Island population and leads to hypotheses about the discordance of morphological and genetic evolution in isolated populations and specific genetic features of peripheral populations.     

Multi-Scale Foraging Habitat Use and Interactions by Sympatric Cervids in Northeastern China

Abstract: Moose (Alces alces) and roe deer (Capreolus pygargus) are sympatric in the forest region of northeastern China. Using univariate analyses of feeding sign data, we found the 2 species were positively associated, but there were distinctions between their use of forage resources across landscape, patch, and microhabitat scales. We used resource selection function models to predict the influence of environmental covariates on moose and roe deer foraging; we detected covariate effects at the landscape and microhabitat scales but not at the patch scale. Forage resources used by the 2 species were similar, but moose used wetter areas and more low-visibility habitats than did roe deer, which strongly avoided areas with sparse vegetation. Both species were influenced by forage abundance and distribution at the microhabitat scale but exhibited differences in intensity of use of plant species and microhabitats. Moose used areas with deeper snow and avoided hiding cover; roe deer avoided areas with higher total basal areas of tree stems and preferred areas with high plant species richness. For moose, there was a trade-off in the use of concealment cover between the landscape and microhabitat scales. We detected avoidance by moose of roads where roe deer occurred. Roe deer exhibited more capacity for coping with human disturbance and interspecific interaction. In areas similar to our study area, road closures and suppression of roe deer near roads within 3–5 years postlogging may benefit moose. Furthermore, a mosaic of areas with different logging intervals may contribute to spatial separation of moose and roe deer and promote their coexistence.     

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.     

Vulnerability of Domestic Sheep to Lynx Depredation in Relation to Roe Deer Density

Abstract The Eurasian lynx (Lynx lynx) causes large loss of free-ranging domestic sheep in Norway. We tested whether the observed higher kill rates by male lynx than female lynx were related to an association between the availability of the main natural prey, as measured by roe deer (Capreolus capreolus) habitat suitability, presence of sheep, and habitat selection of male and female lynx. We found that lynx selected areas with high roe deer suitability during summer and winter. Moreover, during summer, compared to male lynx, females had greater selection for roe deer areas and a stronger avoidance for sheep grazing areas, which suggests that previously observed differences in kill rates between male and female lynx can be attributed to sex-specific habitat use during summer. The connection between lynx habitat use and roe deer also was reflected in a positive relationship between the roe deer suitability of a sheep grazing area and the total loss of lambs, which suggests that livestock, rather than being actively selected, are mainly killed by lynx incidentally when encountered during other lynx activities (e.g., searching for natural prey species). Therefore, any management practice that separates lynx and sheep, such as concentrating livestock into small patches or less preferred habitats, may reduce depredation.     

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.     

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。     

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.     

Thirty‐four polymorphic microsatellites for European roe deer

The European roe deer (Capreolus capreolus) is an interesting model for molecular ecology studies because of its abundance and adaptability across a range of environments (including human‐modified habitats), and because of its increasing impacts on agricultural crops and on regenerating forests. We identify polymorphic microsatellites in two managed populations of roe deer in France by using cross‐species amplification of primers from other Cervids and from Bovids. Of the 62 primer pairs tested, 45 amplified microsatellites in roe deer, and 34 were polymorphic. Eleven primer pairs were selected for multiplex gel‐loading for routine genotyping of the studied populations.     

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.     

Siberian Roe Deer (<Emphasis Type="Italic">Capreolus pygargus</Emphasis> Pallas, 1771) in Ukraine: Analysis of the Mitochondrial and Nuclear DNA

A molecular-genetic analysis of the nucleotide sequences of the cytochrome b gene (1140 base pairs) of the mitochondrial DNA and 17 microsatellite loci of eight samples of roe deer from the Samara forest of Dnipropetrovsk oblast (Ukraine) was carried out. For comparison, 212 corresponding mtDNA sequences of the Siberian and European roe deer and data on the variability of microsatellite markers in 49 representatives of these species were included in the study. It was noted that all the analyzed mitochondrial sequences of individuals from the Samara forest are characteristic of the Siberian roe Capreolus pygargus Pallas, 1771. Four haplotypes were described, all of which belonged to the haplogroup typical for the western part of the range of C. pygargus. A fragment analysis of the microsatellite loci of nuclear DNA confirmed the identification of the investigated group with the Siberian species.     

Hypoderma actaeon: an emerging myiasis in roe deer (Capreolus capreolus)

Subcutaneous larvae of Hypoderma spp. (Diptera: Oestridae) were detected in the dorsal region in 10 roe deer, Capreolus capreolus (Artiodactyla: Cervidae), hunted in central Spain between January and March 2016. All larvae were found in the inner side of the hide during the skinning of the animals. The study of the morphological features of eight larvae of different stages collected from two animals allowed the identification of Hypoderma actaeon Brauer. The small size (4–5 mm) of some of the first instars suggests that the internal lifecycle of H. actaeon may be exclusively subcutaneous. This is the first confirmation of H. actaeon in roe deer; however, further studies to assess the spread of the parasite and to follow the evolution of this myiasis in roe deer are needed.     

Temporal shifts of DNA‐microsatellite allele profiles in roe deer (Capreolus capreolus L.) within three decades

DNA‐microsatellite polymorphism (four loci) was studied in 56 male roe deer (Capreolus capreolus) from a 900‐ha hunting territory in the Vosges du Nord Mountains (France), culled over 34 years (1956–1990). Changed allele frequencies at two loci within this period, and increased allelic diversity, were traced to a phase of reduced population density and subsequent immigration. Decadic population samples collected within 900‐ha were distinguished by higher genetic variability measures than were certain geographical samples across Central Europe (4–900 km). On average, the decadic cohorts were distinguished by a gene diversity index of G_ST = 0.0286, and a genetic distance of D = 0.0938, which reflect 54% (G_ST) and 69% (D) of the respective geographic (350 km) differentiation indices of roe deer in Central Europe. The importance of demography and population ecology effects for microevolution in a large mammal is demonstrated, as is the risk of artefact by composing population samples of deer over several years. Population genetic screening should cover various demes of roe deer from the same general region, and be based on many unlinked polymorphic loci, to minimize the distorting effects of genetic dynamics at the small spatial scale.     

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.     

The genetic structure of natural and reintroduced roe deer (Capreolus capreolus) populations in the Alps and central Italy,with reference to the mitochondrial DNA phylogeography of Europe

The first hypervariable fragment (HVI) of the mitochondrial DNA control region was sequenced in 90 individuals of the European roe deer (Capreolus capreolus) from the Alps, central Italy and Spain. Pooling these data with 70 published sequences from several European regions, we were able to identify patterns of divergence within the Italian peninsula, and in Europe in general. The results we obtained can be summarized as follows. First, the genetic structure of European roe deer populations is substantial (PhiST values around 0.6). Second, the divergence between some central Italian populations, the Alpine group (which is genetically close to the French, the Spanish and the Norwegian samples) and the Eastern European populations seems to reflect Upper Pleistocene subdivisions, possibly related to three southern European refugia. Third, a different group of central Italian individuals probably diverged more recently from the Alpine group, and their attribution to the subspecies C. c. italicus does not appear justified. Fourth, the analysis of mitochondrial DNA in the roe deer can be used to identify recently reintroduced animals in the western Alps which clearly cluster within the Eastern European group, thus providing an important tool for conservation and management strategies for this species.     

圈养条件下狍繁殖行为的研究

本试验研究了狍(东北亚种)在人工饲养条件下的繁殖行为。研究结果表明:(1)在交配季节,雄狍具有卷唇嗅闻、扒土等行为;雄狍与雌狍的卧息、冲突行为差异显著,尾阴探究差异极显著。(2)妊娠雌狍选择隐蔽处分娩产仔。(3)在临产前,雌狍有临产表现,采取侧卧分娩姿势,仔狍娩出后,舔食仔狍的胎水和胎膜。     

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.     

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.     

同域分布的野猪与狍活动节律及与月光周期的关系

完全的竞争者不能共存,物种间生态位分化是同域物种长期稳定共存的基础。不同物种在同一分布区时间生态位的分化对其共存至关重要。为研究同域分布物种的共存机制,在2018年11月到2021年7月利用远红外相机监测技术对穆棱东北红豆杉国家级自然保护区同域分布的野猪(Sus scrofa)和狍(Capreolus pygargus)进行了野外监测研究,并利用核密度估计方法和雅各布斯选择指数(JSI)对日活动节律和一段时间内的活动周期选择进行了评估,同时还利用非参数检验评估了2个物种的活动与月光周期的关系。研究结果表明,狍不管在全年还是在不同的季节,日活动节律均为双峰模式,而野猪的活动模式表现出明显的可塑性,在全年和冷季为单峰型,暖季为双峰型,二者在日活动节律上的重叠程度较高(Dhat>0.59),在暖季的重叠系数最高(Dhat=0.65)。此外,在时间段的选择上,狍在全年和冷季更喜欢在黎明和黄昏活动(0.170.32),而野猪活动在全年和冷季对白天和黄昏的选择更多(JSI>0.3),暖季则更喜欢在白天活动(J...     

老爷岭南部狍冬季移动、卧息生境选择及其适宜性评价

在动物生境研究中,移动生境和卧息生境是生境研究的焦点。开展移动生境和卧息生境选择,并在此基础上进行生境评价,有利于深入了解动物对移动和卧息生境条件的需求,制定科学合理的栖息地保护计划。以东北虎（Panthera tigris altaica）的主要猎物物种之一-狍（Capreolus pygargus）为研究对象,于2017-2019年冬季积雪覆盖期在老爷岭南部通过随机布设28个大样方和84条用于足迹链跟踪的样线收集狍的移动点和卧息点信息,再结合近年来收集的东北虎出现点,利用广义可加模型（GAM）和最大熵模型（MaxEnt）进行狍移动、卧息生境选择及评价研究。移动生境选择研究表明,狍在移动的过程中偏好选择坡度小、距农田距离>500 m、远离道路、居民点和低海拔或较高海拔的区域;移动生境评价分析表明,移动适宜和次适宜生境面积之和为1318.16 km²,占研究区域面积的51.28%,当加入虎活动点影响因子后,狍移动适宜和次适宜生境面积之和为901.52 km²,适宜和次适宜生境面积之和减少了31.61%。狍卧息生境选择研究表明,水源、农田、道路和雪深是影响狍卧息的关键因素,其中雪深对狍卧息生境选择的贡献率达到70.13%;卧息生境评价表明,卧息适宜和次适宜生境面积之和为1243.77 km²,占研究区域面积的48.39%,当加入虎出现点因子后,适宜生境和次适宜生境面积之和减少了61.00%,仅为485.02 km²。研究认为,虎的出现对狍移动和卧息生境选择均产生影响,虎的活动及捕食行为可能会减少狍的活动范围和频次,狍远离虎活动区域卧息休息,压缩了狍适宜卧息的空间。