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.     

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.     

Polymorphism and divergence of multilocus DNA markers in sibling species Chironomus riparius Meigen and Chironomus piger Strenzke (Diptera, Chironomidae)

Intra- and interspecific variation and divergence of multilocus markers for genomic DNA of the sibling species from the thimmi group, Chironomus riparius and C. piger, were studied by PCR with arbitrary primers (RAPD). A high level of RAPD polymorphism was determined in both laboratory and natural populations of these species. The genetic distances were estimated between the C. riparius populations and between the sibling species C. riparius and C. piger. The genetic distance between C. riparius and C. piger was 4 to 5 times higher than that between the C. riparius populations. A comparison of the variation and divergence for the RAPD markers with those for other genomic markers--enzyme-coding genes and chromosomes (linked gene groups)--showed that different components of the genome differed in their contribution to the genome divergence.     

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。     

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.

     

Comparative analysis of genetic diversity of sesame (Sesamum indicum L.) from Vietnam and Cambodia using agro-morphological and molecular markers

The purpose of this study was to comparatively analyze the genetic diversity of sesame (Sesamum indicum L.) using agro-morphological and molecular markers. Twelve sesame populations collected from three regions in Cambodia and Vietnam were used in this study. A high genetic variation was revealed both by agro-morphological and RAPD markers within and among the 12 sesame populations. The range of agro-morphological trait based average taxonomic distance among populations (0.02 to 0.47) was wider than that of RAPD based genetic distance (0.06 to 0.27). The mean distance revealed by agro-morphological markers (0.23) and RAPD markers (0.22) was similar. RAPD based analysis revealed a relatively higher genetic diversity in populations from South Vietnam as compared to the other two regions. Interestingly, populations from this region also had higher values for yield related traits such as number of capsules per plant, number of seeds per capsule, and seed yield per plant suggesting positive correlation between the extent of genetic variation within population and yield related traits in sesame. A highly significant positive correlation (r = 0.88, P < 0.001) was found between agro-morphological and RAPD markers in estimating the genetic distance between populations. Both methods suggested the existence of a substantial amount of genetic diversity both in the Vietnamese and Cambodian populations. Although both agro-morphological and RAPD markers were found to be useful in genetic diversity analysis in sesame, their combined use would give superior results.     

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.     

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.     

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.     

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.     

林麝和马麝随机扩增多态DNA的研究

用随机扩增多态 DNA(RAPD)技术对饲养的林麝和马麝进行分子遗传标记研究。在选用的42 种随机引物中, 有25种引物产生了清晰稳定的条带, 单个引物获得标记数在1～14 之间,平均每个个体获得168个RAPD标记 , 其中林麝、马麝特异性标记各5个,个体特异性标记有3个, 这些标记可用来鉴定种或个体。平均遗传距离在林麝种内为0.27±0.023, 马麝为0.105±0.013, 种间为0.241±0.02 , 种间差异显著大于种内差异。分析表明饲养马麝种内遗传多样性低, 为增强饲养马麝的生存力, 最好从不同种群中引入种麝进行繁殖。     

Polymorphism and Divergence of Multilocus DNA Markers in Sibling Species Chironomus riparius Meigen and Chironomus piger Strenzke (Diptera,Chironomidae)

Intra- and interspecific variation and divergence of multilocus markers for genomic DNA of the sibling species from the thimmi group,Chironomus riparius and C. piger, were studied by PCR with arbitrary primers (RAPD). A high level of RAPD polymorphism was determined in both laboratory and natural populations of these species. The genetic distances were estimated between the C. riparius populations and between the sibling species C. riparius and C. piger. The genetic distance between C. riparius andC. piger was 4 to 5 times higher than that between the C. riparius populations. A comparison of the variation and divergence for the RAPD markers with those for other genomic markers—enzyme-coding genes and chromosomes (gene linkage groups)—showed that different components of the genome differed in their contribution to the genome divergence.     

Biochemical and DNA markers yield strikingly different results regarding variability and differentiation of roe deer (Capreolus capreolus, Artiodactyla: Cervidae) populations from northern Germany

Three mainland and two island roe deer ( Capreolus capreolus ) populations with a total sample size of 105 individuals from Schleswig–Holstein, northern Germany, were analysed with regard to genetic variability within and differentiation among populations as revealed by eight allozyme loci known to be polymorphic in roe deer, eight microsatellite loci and 404 bp of the mitochondrial control region. Surprisingly, the allozymes were completely monomorphic, but microsatellite and control region variability were high. Hypotheses as to demographic reasons for the variability patterns found, including bottlenecks, founder effects and translocations, are put forward. There were no statistically significant differences between the island and the mainland populations in terms of genetic variability as measured by expected heterozygosity, inbreeding coefficient and allelic richness. The correlations of the various variability indices were not statistically significant after Bonferroni correction. Nevertheless, there was a clear tendency for differentiation indices to yield concordant results for microsatellite and mitochondrial markers.     

Molecular phylogeny of Heritiera Ait on (Sterculiaceae), a tree mangrove: variations in RAPD markers and nuclear DNA content

Random amplified polymorphic DNA (RAPD) markers are used to estimate interspecific variation among mangrove and non-mangrove Heritiera fomes, H. littoralis and H. macrophylla. All the species have 2n = 38 chromosomes, with minute structural changes distinguishing the karyotype of each species. Significant variation of 4C DNA content occurs at the interspecific level. Interspecific polymorphism ranged from 14.09% between H. fomes and H. littoralis to 52.73% between H. fomes and H. macrophylla. H. macrophylla showed wide polymorphism in the RAPD marker with H. littoralis (51.23%) and H. fomes (52.73%). Two distinct RAPD products obtained from OPA-10 (1000 bp) and OPD-15 (900 bp) found characteristic molecular markers in H. macrophylla , a species from a non-mangrove habitat. H. macrophylla was more distantly related to H. fomes [genetic distance (1-F) = 0.305] than to H. littoralis [genetic distance (1-F) = 0.273]. H. littoralis was of a closer affinity to H. fomes [genetic distance (1-F) = 0.218] than to H. macrophylla.     

采用RAPD标记探讨瓣蕊唐松草(毛茛科唐松草属)的遗传多样性及其地理分布格局(英文)

Random amplified polymerphic DNA(RAPD)method was applied to assessg enetic variation and population structure of Thahctrum petalotdeum L(Ranunoulaceae),Two hundred and forty-six individuals from 11 populations of the species were investigated by RAPD profiles Twenty selected RAPD primers generated 125 bands．in which 120 were polymorphic Ther esults revealed a high level of genetic variation(ercentage of polymorphIc bands(PPB was 96％．Nei’s gene diversity(りwas 03502 and shannon’s information index(I) was 0．5199 at the species level) The differentiation among the populations was high(Gst=0．3511)in this species．Result of analyzing of molecularvariance(AMOVA)showedthat38．88％of genetic variance was found among the populations Positive correlation withr r=01945(P=00002)was found between genetic distance and geographic distance amongpo pulations Two populations distributed in the drainage basin of YanELz River affined genedcally and formed one clada and the rest nine populations formed the other clade in both unweighted pair-group method using arithmetic average(UPGMA)trees made by two different method different methods. It was yen/clear that these two populations were very special, andmust be closely related in history, despite the fact that they now share quite weak link to the restpopulations through gene communication.     

采用RAPD标记探讨瓣蕊唐松草(毛茛科唐松草属)的遗传多样性及其地理分布格局

采用随机扩增多态DNA(RAPD)标记对瓣蕊唐松草(Thalictrum petaloideum L.)(毛莨科)11个居群246个体的遗传多样性及居群遗传结构进行了检测.20个随机引物扩增出125个用于分析的条带.结果表明:瓣蕊唐松草在物种水平上具有极高的遗传多样性,多态条带比率(PPB)为96%,Nei的基因多样度(h)为0.3502,Shannon多样性指数(I)为0.519 9;居群间分化比较明显,基因分化系数(GsT)为0.351 1,分子方差分析(AMOVA)表明居群间遗传变异占总遗传变异的38.88%;根据条带频率与平均分类距离和Nei遗传距离分别进行UPGMA聚类,结果基本一致,并且反映出与该种地理分布有一定相关性;长江流域分布的两个居群表现出较高的相似性,并与北方分布的各居群构成独立的两支,显示出这两个居群的特殊性,从而对该物种独特分布区成因是由于冰退回迁造成的观点提供了一定的支持.     

Molecular identification and prevalence of Dictyocaulus spp. (Trichostrongyloidea: Dictyocaulidae) in Swedish semi-domestic and free-living cervids

Lungs of 102 roe deer (Capreolus capreolus), 136 moose (Alces alces), 68 fallow deer (Dama dama), and six red deer (Cervus elaphus) were examined during hunting seasons from 16 September 1997 to 1 March 2000. The aim was to determine the species composition and prevalence of Dictyocaulus lungworms in these hosts in Sweden. Worms were identified following polymerase chain reaction (PCR) amplification of the internal transcribed spacer of ribosomal DNA (ITS2), followed by hybridization with four species-specific oligonucleotides. In addition, 50 lungworms from five reindeer (Rangifer tarandus) from Norway were similarly analyzed. A total of 399 worms were recovered and analyzed representing a range of 29-128 worms per host species. All specimens from roe deer were identified as Dictyocaulus capreolus, whereas those from red deer and reindeer were identical with D. eckerti. From moose, 73 (81.1%) of the worms were identified as D. capreolus whereas 17 (18.9%) were D. eckerti. The ITS2 sequence of fallow deer lungworms differed significantly when compared with the ITS2 of D. viviparus, D. capreolus, and D. eckerti. This indicated that fallow deer in Sweden may be infected with a new genotype of Dictyocaulus spp. Consequently, a specific probe designed for the ITS2 from this Dictyocaulus sp. hybridized exclusively with samples from lungworms of fallow deer. Interestingly, no D. viviparus were found in any of these hosts. The prevalence of infection in each host was as follows: D. capreolus in roe deer (14.7%) and moose (10.6%); D. eckerti in moose (0.7%) and red deer (33.3%); and Dictyocaulus sp. in fallow deer (10.3%). Regardless of lungworm species, the overall prevalence of Dictyocaulus spp. in these hosts was 12.2%. Prevalence between male and female animals and among the different age groups did not differ significantly. Finally an enzyme linked immunosorbent assay (ELISA) specific for patent D. viviparus infection in cattle was utilized to analyze lung tissue fluids from infected animals. All samples from roe deer, red deer, and fallow deer were negative in the ELISA. However, three out of twelve (25%) samples from moose and 17 of 40 (43%) samples from cattle were positive. This indicated that moose anti-D. capreolus antibodies recognized the D. viviparus antigen and that anti-cattle immunoglobulin cross-reacted with moose antibodies.     

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.     

Assessment of genetic diversity of wild soybean (Glycine soja Siebold et Zucc.) in the far eastern region of Russia

Polymorphism of RAPD markers was analyzed in the wild soybean populations from the Far East region of Russia. The level of RAPD marker polymorphism was significantly higher in the wild than in the cultivated soybean. The results obtained suggest active development of genetically different groups of wild soybean. Geographically isolated subpopulations showed maximum distance from the main population of wild soybean.