Genes of the extinct Caucasian bison still roam the Białowieża Forest and are the source of genetic discrepances between Polish and Belarusian populations of the European bison,Bison bonasus

European bison (Bison bonasus) populations from both the Polish (PL) and the Belarusian (BY) sides of the Bia?owie?a Forest represent the Lowland genetic line (LB line) – progeny of the Lowland bison (Bison bonasus bonasus) that inhabited western, central, and south‐eastern Europe in historical times. During the species recovery, one of the founders was a descendant of the extinct Caucasian bison (Bison bonasus caucasicus) and its descendants formed the other genetic line – Lowland–Caucasian (LC). There have been justified suspicions that LB European bison in the former Soviet Union had undergone cross‐mating with the LC line. We performed a comparative genetic analyses on European bison from the BY and PL parts of the Bia?owie?a Forest, the LC line and extinct Caucasian bison, based on a set of 19 microsatellite markers and 1512 bovine single nucleotide polymorphism (SNP) markers, polymorphic in at least one of the studied populations. Although genetic variability (mean allele number and expected heterozygosity) for both populations were similar, the F_ST jack‐knifing and principal component analyses PCA revealed highly significant differences between PL and BY bison from the Bia?owie?a Forest. Examining DNA of the extinct Caucasian bison revealed that at least part of the genetic variants found in the BY, but not the PL, population were of Caucasian origin. The results indicate that the contemporary population of European bison from the BY part of the Bia?owie?a Forest should not be regarded as a LB line. The results also suggest that the actual global population size of the LB line European bison is only a half of its official status. Consideration of the presented results are crucial in determining management actions and policy decisions in order to conserve LB line bison within the Bia?owie?a Forest – its natural refuge. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 752–763.     

Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery

• 1 The European bison Bison bonasus went through a severe bottleneck and became extinct in the wild 90 years ago. The lowland subspecies B. b. bonasus is the only one of three original subspecies that exists today. The entire species derives from only 12 founders, including a bull of the Caucasian subspecies B. b. caucasicus. Due to its presence among founders, there are two geographically separated genetic lines of European bison: the pure lowland (Bia?owie?a) line and the hybrid lowland‐Caucasian line.
• 2 The lowland line of the European bison originates from only seven founders with an extremely varying genetic contribution. Approximately 80% of the genes in contemporary populations come from just two founders.
• 3 A variety of genetic markers (mtDNA, microsatellites, single nucleotide polymorphism microchips) were applied to studies of the level of depletion of genetic variability in European bison.
• 4 The lowland line of the European bison, the most extensively studied, shows very low levels of genetic variation, and has just half the microsatellite heterozygosity of the closely related American bison Bison bison. The effective population size (N_e) for the highly genetically homogenous lowland line in the Polish part of the Bia?owie?a Forest is estimated to be 23.5, far less than the census population size of 450.
• 5 The average inbreeding level in lowland bison is almost 50%, although no signs of inbreeding depression have been observed. In contrast, inbreeding effects have been noticed in the lowland‐Caucasian line, which has a much lower average inbreeding level (28%). In spite of the apparently high fitness of the lowland bison, the lack of genetic variation and high level of inbreeding may present substantial threats in the future, especially in the context of potential epizootics.

     

Movements of European bison (Bison bonasus) beyond the Białowieża Forest (NE Poland): range expansion or partial migrations?

The European bison is the largest terrestrial mammal in Europe. After extinction in the wild at the beginning of the twentieth century, it was re-introduced to Bia?owie?a Forest and other woodlands in Eastern Europe. In this paper, we analysed the movements of European bison beyond the continuous woodlands of the Bia?owie?a Forest (NE Poland) between 1964 and 2010. In total, 1,117 direct observations of bison were collected. The number of males moving out of the forest fluctuated during the study period, whilst the number of females steadily increased. The number of male observations outside of the forest per annum was dependent on the population size and snow depth, whilst the number of cows in mixed groups moving outside of the forest was correlated with the population size only. Males were observed mainly alone (50 % of observations) or in small groups of two to three individuals (25 %); however, distribution of group size differed from those observed in the population. There was a significant difference between the direction of movement of males and females out of the forest—males moved mainly west and southwest, whilst females moved to the north. This was also significantly different from the expected movement direction. The mean distance of bison observations from the forest border was 1.8?±?0.13 km and did not differ significantly between sexes. After 1990, males were observed significantly farther away from the forest (2.2 km) than in the previous years (0.9 km). Most observations (94 % of bulls and 93 % of cows) were up to 5 km from the forest edge. The range of bison in the vicinity of the Bia?owie?a Forest was strictly seasonal. Most observations (78 % in males and 88 % in females) were recorded from November to April. Increasing utilisation of areas beyond the forest habitats may be driven by different factors but most probably it is related to range expansion and the bison's preference for open habitats. The strong seasonal pattern of bison movements indicate that the partial seasonal migrations were initiated in the Bia?owie?a population.     

Paternally inherited markers in bovine hybrid populations

The genetic integrity of crossfertile bovine- or cattle-like species may be endangered by species hybridization. Previously, amplified fragment length polymorphism, satellite fragment length polymorphism and microsatellite assays have been used to analyze the species composition of nuclear DNA in taurine cattle, zebu, banteng and bison populations, while mitochondrial DNA reveals the origin of the maternal lineages. Here, we describe species-specific markers of the paternally transmitted Y-chromosome for the direct detection of male-mediated introgression. Convenient PCR-restriction fragment length polymorphism and competitive PCR assays are shown to differentiate the Y-chromosomes of taurine cattle, American bison and European bison, and to detect the banteng origin of Indonesian Madura and Bali cattle bulls.     

Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L.

A set of 33 cattle microsatellite primer pairs was tested with the DNA of American bison from a captive population in Belgium and evaluated for usefulness in parentage testing. Two primer sets did not amplify and three were monomorphic. Among the polymorphic markers, the number of alleles ranged from two to nine. Heterozygosity, polymorphism information content (PIC) and probability of exclusion (PE) values were low by comparison with those obtained with the same markers in cattle. Two methods of estimating PE were used, one which assumed equal allele frequencies between parental sexes and another which took into account differences in allele frequencies between parental sexes. An internationally accepted set of nine microsatellites gives cumulative PE values of 0·98 and 0·97, respectively, for the two methods. The potential of this marker set to identify bison × cattle hybrids is discussed. Because bison and cattle have a common ancestor, these microsatellites are a useful way to establish genetic distances and can lead to the construction of phylogenetic trees.     

微卫星DNA与生化标记分析对长爪沙鼠群体遗传分析的比较

目的比较生化标记和微卫星DNA标记方法对长爪沙鼠群体遗传分析的可靠性。方法应用27个生化位点和13个微卫星DNA位点,采用已建立的生化标记和微卫星DNA标记分析方法对国内2个长爪沙鼠群体进行遗传分析,计算并比较两种方法测得的各群体遗传参数。结果生化基因位点中有13个位点在整体中呈现遗传多态性,多态率为48.1%;微卫星位点中有11个位点在整体中表现出多态性,多态率均为84.6%。两种方法测得的平均有效等位基因数趋于一致,微卫星DNA的多态位点百分率和平均杂合度均明显高于生化标记方法。但生化标记和微卫星DNA检测对两个长爪沙鼠群体的遗传多样性差异反映一致,所反映的群体平衡状况也基本一致。结论生化标记分析和微卫星DNA方法均可较好地反映长爪沙鼠群体遗传结构。     

Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations

Introgressive hybridization is one of the major threats to species conservation, and is often induced by human influence on the natural habitat of wildlife species. The ability to accurately identify introgression is critical to understanding its importance in evolution and effective conservation management of species. Hybridization between North American bison (Bison bison) and domestic cattle (Bos taurus) as a result of human activities has been recorded for over 100 years, and domestic cattle mitochondrial DNA was previously detected in bison populations. In this study, linked microsatellite markers were used to identify domestic cattle chromosomal segments in 14 genomic regions from 14 bison populations. Cattle nuclear introgression was identified in five populations, with an average frequency per population ranging from 0.56% to 1.80%. This study represents the first use of linked molecular markers to examine introgression between mammalian species and the first demonstration of domestic cattle nuclear introgression in bison. To date, six public bison populations have been identified with no evidence of mitochondrial or nuclear domestic cattle introgression, providing information critical to the future management of bison genetic resources. The ability to identify even low levels of introgression resulting from historic hybridization events suggests that the use of linked molecular markers to identify introgression is a significant development in the study of introgressive hybridization across a broad range of taxa.     

Genetic variability among Polish Red, Hereford and Holstein-Friesian cattle raised in Poland based on analysis of microsatellite DNA sequences

Polymorphism of 11 microsatellite DNA loci was analysed in Polish Red (PR), Hereford and Holstein-Friesian (HF) cattle raised in Poland and genetic distance among these breeds was determined. At the 11 loci (TGLA227, BM2113, TGLA53, ETH10, SPS115, TGLA126, TGLA122, INRA23, ETH3, ETH225 and BM1824) analysed with automated DNA sizing technology, a total of 213 alleles were identified: 76 in PR, 76 in HF, and 61 in Hereford. All the microsatellite DNA markers showed high polymorphism. Polymorphism information content (PIC) calculated for each marker exceeded 0.5, except for the ETH3 locus in Hereford cattle (PIC=0.475), and heterozygosity (H) ranged from 54.1% to as much as 85.2%. The coefficient of genetic distance was 0.354 between PR and Hereford, 0.414 between HF and Hereford, and 0.416 between PR and HF cattle.     

Resting site selection by large herbivores – The case of European bison (Bison bonasus) in Białowieża Primeval Forest

Resting site selection by European bison (Bison bonasus, L., 1758), the largest terrestrial mammal of Europe, was studied in the free-ranging population in Bia?owie?a Primeval Forest (Poland) in 2009–2010. In total, 104 sites of 21 bison (both collared and uncollared) were analysed to determine the most important microhabitat characteristics selected by resting bison during summer and winter and to study the influence of supplementary feeding on resting behaviour of this herbivore. Resting sites were identified on the basis of GPS locations and activity records collected by GPS collars, as well as direct observations of bison, and were compared with control sites. Microhabitat selection by bison did not differ significantly between the sexes. During summer and winter, bison resting sites displayed a high tree density, low visibility and high complexity (structures providing cover). Summer resting sites were also characterised by a significantly lower abundance of blood-sucking insects and denser canopy than control sites. Winter resting sites showed a lower complexity and higher visibility than summer sites, and were less often located in mixed forest habitats. During winter, bison rested more frequently in forest below 50 years of age than in older forest. Resting sites of non-fed bison were more often located in young coniferous forests, were lower in visibility and situated closer to open areas than sites of bison using supplementary winter feeding, suggesting a trade-off between food and cover. The results indicate that European bison select their resting sites in areas of mosaic habitat structure providing cover from disturbances with access to profitable natural forage grounds.     

Development of microsatellite markers for the neotropical tree species Dipteryx alata (Fabaceae)

? Premise of the study: Microsatellite markers were developed for the population genetic analyses of the neotropical tree Dipteryx alata (Fabaceae). ? Methods and Results: Microsatellites were developed from a genomic shotgun library. Polymorphism at each microsatellite loci was analyzed based on 94 individuals from three populations. Eight loci amplified successfully and presented one to 10 alleles, and expected heterozygosities ranged from 0.097 to 0.862. Four loci also amplified in Pterodon emarginatus and presented similar polymorphism. ? Conclusion: The eight microsatellite primer pairs are potentially suitable for population genetic studies and successfully amplified in another Fabaceae species.     

Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.     

Low level of genetic variability in European bisons (Bison bonasus) from the Bialowieza National Park in Poland

Nuclear DNA markers (microsatellites) were used to screen the genetic variability in the European bison population of the Bialowieza National Park, Poland. The species is listed as endangered and the Bialowieza population is the largest one worldwide. Many other herds were founded by individuals from Bialowieza. Out of 18 microsatellites, nine were polymorphic, five were found to be homozygous, and four loci did not amplify. No significant deviation from Hardy–Weinberg-equilibrium (HWE) was observed, and the average number of alleles was 2.3 per locus. Thus, the European bison is characterized by a very low level of genetic diversity, most likely resulting from the population decline in the nineteenth century. Nevertheless, allelic variability derived from the nine polymorphic loci established in this study allowed to identify each individual by its genotypic profile. This data is valuable for conservation plans of this impressive species, especially for the control of breeding success in these animals.     

A search for genetic markers associated with egg production in the ostrich (Struthio camelus)

The aim of the current study was to search for genetic markers, microsatellite loci associated with laying performance in ostriches. The material consisted of two groups of ostrich hens characterized by high or low laying performance (over 75 and less than 25 eggs per season, respectively). The investigation covered 30 microsatellite loci characteristic for the ostrich (the CAU group) and led to identification of significant differences in allele and genotype frequencies between the two groups of hens considered. Out of a total of 30 microsatellite loci examined, 28 showed different alleles in relation to analyzed performance groups. In hens of high laying performance (HP group, n = 12), specific alleles occurred in 23 microsatellite loci (40 alleles of 243 identified), while in those of low egg production (LP group, n = 12), they occurred in 22 (51 alleles of 243 identified). The results indicate the usefulness of the microsatellite loci as the potential genetic markers associated with laying performance that can be applied for genetic improvement of ostrich flocks.     

食蟹猴微卫星DNA标记遗传监测及多态性分析

目的研究国内食蟹猴种群的遗传背景特性,建立食蟹猴种群遗传质量监测方法。方法采用微卫星DNA遗传标记技术对50只食蟹猴种群个体进行遗传质量监测及DNA多态性分析。结果从100个微卫星DNA位点中筛选出20个多态性高的位点,其食蟹猴种群个体的等位基因数目为5-10条,个体间均呈现高度的多态性;其观察等位基因数（Na）为5.0～10.0,有效等位基因数（Ne）为4.6118～8.3404,基因多样性（H）为0.7832～0.8801和香隆信息指数（I）为1.5651～2.1592。结论本实验有效地分析了食蟹猴种群的遗传多态性,为今后筛选特异性微卫星位点来建立食蟹猴种群遗传质量监测方法提供了理论依据。     

Cloning and characterization of microsatellite loci in channel catfish, Ictalurus punctatus

Short tandem repeat (microsatellite) loci were cloned from the channel catfish, Ictalurus punctatus , genome for use as molecular markers for genetic improvement of this important agricultural species. Plasmid clones containing catfish genomic DNA inserts were identified, by hybridization with tandem repeat DNA probes, and sequenced using automated laser fluorescence. A feral population of catfish displayed levels of heterozygosity greater than 0·7 for 13 of 22 loci and heterozygosity greater than 0·5 for 20 of 22 loci. Allelic polymorphism ranged from three to 17 alleles per locus in the feral population. Populations of domestic, farm-raised catfish and a research strain displayed levels of heterozygosity similar to the feral population. Non-invasive tissue sampling provided abundant material for the polymerase chain reaction-based genotype assay. The microsatellite loci will be useful in the molecular characterization and genetic improvement of channel catfish populations.     

Isolation and Characterization of Microsatellite Loci for Striped Bass (Morone saxatilis)

Genetic variation has been difficult to detect in striped bass (Morone saxatilis). Therefore, we identified and characterized 13 microsatellite loci to provide additional genetic markers for striped bass. Microsatellites were identified by screening a striped bass genomic library or by using primers developed for European sea bass (Dicentrarchus labrax) microsatellite loci. We found that 6 of the 13 microsatellite loci were polymorphic in DNA samples obtained from wild populations of striped bass. The number of alleles per locus varied from 3 to 12, and the observed heterozygosities ranged from 0.55 to 0.78. These results indicate that microsatellite loci provide more alleles and higher heterozygosities than other genetic markers developed for striped bass. Received November 9, 1999; accepted February 11, 2000.     

Genetic diversity and bottleneck analysis of Indian bellary sheep by microsatellite markers

Bellary sheep population variability and structure was investigated genetically utilizing FAO recommended microsatellite markers. Genetic variation at 20 microsatellite loci, population structure, and genetic bottleneck hypothesis were examined. Estimates of genetic variability such as effective number of alleles and gene diversities revealed substantial genetic variation frequently displayed by microsatellite markers. A total of 133 alleles were detected. Average polymorphism across the studied loci and expected gene diversity in the population were 1.419 +/- 0.405 and 0.684 +/- 0.140, respectively. No significant genotypic linkage disequilibrium was detected across population, suggesting no evidence of linkage between loci. The population was observed to be significantly differentiated into different groups, showed fairly high level of inbreeding (f = 0.253 +/- 0.050) and global heterozygote deficit. Population structure analysis indicated the intermixing/introduction of unique/rare alleles in these migrating flocks. A normal L-shaped distribution of mode-shift test, non-significant heterozygosity excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests suggested that there was no recent bottleneck. The study revealed that even breed with increasing population trend needs genetic management for the conservation and improvement.     

PERMANENT GENETIC RESOURCES: Development and characterization of 14 polymorphic microsatellite loci in the endangered tree Euptelea pleiospermum (Eupteleaceae)

Fourteen polymorphic microsatellite loci were developed and characterized for the endangered and tertiary relict tree, Euptelea pleiospermum. A genomic DNA enrichment protocol was used to isolate microsatellite loci and polymorphism was explored using 32 individuals from one natural population. The observed number of alleles ranged from two to nine. The ranges of observed and expected heterozygosities were 0.25-1.00 and 0.22-0.85, respectively. These microsatellite markers provide powerful tools for the ongoing conservation genetic studies of E. pleiospermum.     

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae

Genetic polymorphism was investigated in Thlaspi caerulescens J. & C. Presl at 15 gene regions, of which seven have been identified to putatively play a role in heavy-metal tolerance or hyperaccumulation. Single nucleotide and length polymorphisms were assessed at four cleaved amplified polymorphic sequences (CAPS) and 11 simple sequence repeat (microsatellite) loci, respectively. The utility of these loci for genetic studies in T. caerulescens was measured among seven natural populations (135 individuals). Fourteen loci rendered polymorphism, and the number of alleles per locus varied from 2 to 5 and 1 to 27 for CAPS and microsatellites, respectively. Up to 12 alleles per locus were detected in a population. The global observed heterozygosity per population varied between 0.01 and 0.31. Additionally, cross-species/genera amplification of loci was investigated on eight other Brassicaceae (five individuals per population). Overall, 70% of the cross-species/genera amplifications were successful, and among them, more than 40% provided intraspecific polymorphisms within a single population. This indicates that such markers may, as well, allow comparative population genetic or mapping studies between and within several Brassicaceae, particularly for genes involved in traits such as heavy-metal tolerance and/or hyperaccumulation.     

青鱼微卫星标记的开发与特性分析

青鱼(Mylopharyngodon piceus)是中国最为重要的淡水养殖鱼类。开发青鱼的微卫星标记能为青鱼的遗传多样性分析提供更多工具。本研究使用磁珠富集法,利用生物素探针(CA)10和(GACA)6,富集得到青鱼基因组微卫星片段,进一步通过设计微卫星引物检验其在青鱼原种群体中的有效性和多态性水平。结果显示,所构建文库中849个克隆含有微卫星序列,通过利用PCR技术在吴江原种青鱼36个个体中进行多态性筛选,获得了25个多态性微卫星位点。其平均等位基因数(Na)和有效等位基因数(Ne)分别为7.08和3.526,平均观测杂合度(Ho)和期望杂合度(He)分别为0.602和0.619,平均多态信息含量(PIC)为0.568。其中,Mp23、Mp27和Mp35这3个位点极显著偏离哈迪-温伯格平衡(P 0.01)。本研究开发的微卫星标记能为青鱼种质资源的评价和保护等研究提供工具。