Genetic diversity and phylogeographic structure of Bactrian camels shown by mitochondrial sequence variations

The Bactrian camel includes various domestic (Camelus bactrianus) and wild (Camelus ferus) breeds that are important for transportation and for their nutritional value. However, there is a lack of extensive information on their genetic diversity and phylogeographic structure. Here, we studied these parameters by examining an 809‐bp mtDNA fragment from 113 individuals, representing 11 domestic breeds, one wild breed and two hybrid individuals. We found 15 different haplotypes, and the phylogenetic analysis suggests that domestic and wild Bactrian camels have two distinct lineages. The analysis of molecular variance placed most of the genetic variance (90.14%, P < 0.01) between wild and domestic camel lineages, suggesting that domestic and wild Bactrian camel do not have the same maternal origin. The analysis of domestic Bactrian camels from different geographical locations found there was no significant genetic divergence in China, Russia and Mongolia. This suggests a strong gene flow due to wide movement of domestic Bactrian camels.     

SNP discovery and population structure analysis in Lassi and Marecha camel breeds using a genotyping by sequencing method

Pakistani camels have been classified socio-geographically into 20 breeds, but they have not yet been subjected to substantial selective pressures and the genetic basis for these breeds is not understood. However, it should be possible to distinguish them by use of molecular data. This study investigated the genetic diversity and population structure within and between two major Pakistani camel breeds, Marecha and Lassi. As no SNP array is currently available, we first identified 63 619 SNPs using a genotyping by sequencing approach. After quality control, a panel of 36 926 SNPs was used in the analysis. Population structure was investigated with a principal coordinate analysis as well as a cluster analysis using NetView , and multilocus heterozygosity analysis to explore between- and within-breed genetic variation. In addition, between-breed variation was explored using the fixation index, F_ST. We also compared relationship matrices computed using the VanRaden SNP-based method and a method developed specifically for genotyping by sequencing data. Among the two camel breeds, Lassi showed a lower level of genetic diversity whereas Marecha showed a higher level. As a genotyping platform has not yet been developed for the camel, the SNPs discovered in this study will be useful in future genetic studies in camels.     

SNP discovery and genotyping using restriction‐site‐associated DNA sequencing in chickens

Single nucleotide polymorphisms (SNPs) are essential to the understanding of population genetic variation and diversity. Here, we performed restriction‐site‐associated DNA sequencing (RAD‐seq) on 72 individuals from 13 Chinese indigenous and three introduced chicken breeds. A total of 620 million reads were obtained using an Illumina Hiseq2000 sequencer. An average of 75 587 SNPs were identified from each individual. Further filtering strictly validated 28 895 SNPs candidates for all populations. When compared with the NCBI dbSNP (chicken_9031), 15 404 SNPs were new discoveries. In this study, RAD‐seq was performed for the first time on chickens, implicating the remarkable effectiveness and potential applications on genetic analysis and breeding technique for whole‐genome selection in chicken and other agricultural animals.     

Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus)

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro‐ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization.     

Old World camels in a modern world – a balancing act between conservation and genetic improvement

Old World camels have served humans in cross‐continental caravans, transporting people and goods, connecting different cultures and providing milk, meat, wool and draught since their domestication around 3000–6000 years ago. In a world of modern transport and fast connectivity, these beasts of burden seem to be out‐dated. However, a growing demand for sustainable milk and meat production, especially in countries affected by climate change and increasing desertification, brings dromedaries (Camelus dromedarius) and Bactrian camels (Camelus bactrianus) back onstage and into the focus of animal breeders and scientists. In this review on the molecular genetics of these economically important species we give an overview about the evolutionary history, domestication and dispersal of Old World camels, whereas highlighting the need for conservation of wild two‐humped camels (Camelus ferus) as an evolutionarily unique and highly endangered species. We provide cutting‐edge information on the current molecular resources and on‐going sequencing projects. We cannot emphasise enough the importance of balancing the need for improving camel production traits with maintaining the genetic diversity in two domestic species with specific physiological adaptation to a desert environment.     

Population structure of Atlantic mackerel inferred from RAD‐seq‐derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

Restriction‐site‐associated DNA sequencing (RAD‐seq) and related methods are revolutionizing the field of population genomics in nonmodel organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD‐seq data analyses rely on assumptions on nature and number of nucleotide variants present in a single locus, the choice of which may lead to an under‐ or overestimated number of SNPs and/or to incorrectly called genotypes. Using the Atlantic mackerel (Scomber scombrus L.) and a close relative, the Atlantic chub mackerel (Scomber colias), as case study, here we explore the sensitivity of population structure inferences to two crucial aspects in RAD‐seq data analysis: the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides insights into the effects of alternative RAD‐seq data analysis strategies on population structure inferences that are directly applicable to other species.     

High mitochondrial differentiation levels between wild and domestic Bactrian camels: a basis for rapid detection of maternal hybridization

Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804‐base‐pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR‐RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR‐RFLP system was effective for both traditional (blood, skin) and non‐invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR‐RFLP system.     

采用微卫星标记分析10个双峰驼群体的遗传变异和群体间的遗传关系

为从分子水平上对我国双峰驼(Camelus bactrianus)群体的遗传多样性、群体间遗传关系、群体遗传分化及近交情况进行全面、系统地研究,为双峰驼种质资源保护和新品种培育提供基础数据,本文利用18对微卫星引物,分析了我国9个双峰驼群体和1个蒙古双峰驼群体的遗传多样性和遗传关系。结果显示:10个群体均具有较高的遗传多样性,共检测到242个等位基因,平均等位基因数为13.44,平均有效等位基因数为4.18,平均观察杂合度(Ho)为0.5528。10个群体间存在显著的遗传分化,有9.6%的遗传变异来自群体间,90.4%的遗传变异来自群体内部的个体间。聚类分析、主成分分析和群体遗传结构分析结果都表明10个群体被分成2个明显的分支,新疆4个群体单独聚为一类,剩下的6个群体聚为一类。这一结果可能与它们的地理分布和群体间的地理屏障有关。     

Y-chromosome polymorphisms of the domestic Bactrian camel in China

Single-nucleotide polymorphisms (SNPs), microsatellites and copy number variation (CNV) were studied on the Y chromosome to understand the paternal origin and phylogenetic relationships for resource protection, rational development and utilization of the domestic Bactrian camel in China. Our sample set consisted of 94 Chinese domestic Bactrian camels from four regions (Inner Mongolia, Gansu, Qinghai and Xinjiang), we screened 29 Y-chromosome-specific loci for SNPs, analysed 40 bovine-derived microsatellite loci and measured CNVs of HSFY and SRY through Sanger sequencing, automated fluorescence-based microsatellite analysis and quantitative real-time PCR, respectively. A multicopy gene, SRY, was first found, and sequence variation was only detected in SRY in a screen of 29 loci in 13 DNA pools of individual camels. In addition, a TG repeat in the USP9Y gene was identified as the first polymorphic microsatellite in the camel Y chromosome, whereas microsatellite based on bovine sequences were not detected. The frequency of each allele varied among different populations. For the Nanjiang, Hexi and Alashan populations, a 243-bp allele was found. For the Sunite population, 241-bp, 243-bp and 247-bp alleles were detected, and the frequencies of these alleles were \(22.2\%\), \(44.5\%\) and \(33.3\%\), respectively; 241-bp and 243-bp alleles were found in other populations. Finally, CNVs in two Y-chromosomal genes were detected; CNV for HSFY and SRY ranged from 1 to 3 and from 1 to 9, respectively.     

Diversity and distribution of CYP gene family in Bactrian camel

Cytochrome P450 (CYP) enzymes belong to a superfamily of monooxygenases which are phase I enzymes responsible for the first pass metabolism of about 90% of drugs in animals. However, these enzymes are often polymorphic and metabolism of the same drug in different species or different individuals is influenced by genetic and non-genetic factors. Bactrian camels are capable of survival in harsh living environments, being able to consume diets that are often toxic to other mammals and can tolerate extreme water and food deprivation. The aim of this study was to investigate whether the Bactrian camel’s special metabolic pathways and unique detoxification capabilities are attributable to particularities of the CYP gene family. The Bactrian camel’s whole genome sequencing data were systemically analyzed and annotated, and then, CYP gene family was searched from the whole protein database and compared with CYP gene families of cattle, horse, chicken, and human. The total of 63 CYP gene copies were found in Bactrian camel’s whole genome and were classified into 17 families and 38 subfamilies. Among them, 9 multi-gene families were found, and CYP2, CYP3, and CPY4 have 27, 6, and 7 subfamilies, accounting for 43, 10, and 11% in camel CYP gene, respectively. In comparison with cattle, chicken, horse, and human, the distribution of CYP gene subfamilies in camel is different, with more CYP2J and CYP3A copies in the Bactrian camel, which may contribute to the Bactrian camel’s specific biological characteristics and metabolic pathways. Comparing to the cow, horse, chicken, and human CYP genes, the distribution of CYP gene subfamilies is distinct in the Bactrian camel. The higher copy number of CYP2J gene and CYP3A gene in Bactrian camel may be the important factors contributing to the distinct biological characteristics and metabolic pathways of Bactrian camels for adaptation to the harsh environments.     

PMERGE: Computational filtering of paralogous sequences from RAD‐seq data

Restriction‐site associated DNA sequencing (RAD‐seq) can identify and score thousands of genetic markers from a group of samples for population‐genetics studies. One challenge of de novo RAD‐seq analysis is to distinguish paralogous sequence variants (PSVs) from true single‐nucleotide polymorphisms (SNPs) associated with orthologous loci. In the absence of a reference genome, it is difficult to differentiate true SNPs from PSVs, and their impact on downstream analysis remains unclear. Here, we introduce a network‐based approach, PMERGE that connects fragments based on their DNA sequence similarity to identify probable PSVs. Applying our method to de novo RAD‐seq data from 150 Atlantic salmon (Salmo salar) samples collected from 15 locations across the Southern Newfoundland coast allowed the identification of 87% of total PSVs identified through alignment to the Atlantic salmon genome. Removal of these paralogs altered the inferred population structure, highlighting the potential impact of filtering in RAD‐seq analysis. PMERGE is also applied to a green crab (Carcinus maenas) data set consisting of 242 samples from 11 different locations and was successfully able to identify and remove the majority of paralogous loci (62%). The PMERGE software can be run as part of the widely used Stacks analysis package.     

Characterization of heavy-chain antibody gene repertoires in Bactrian camels

Camelids are the only mammals that can produce functional heavy-chain antibodies (HCAbs). Although HCAbs were discovered over 30 years ago, the antibody gene repertoire of Bactrian camels remains largely underexplored. To characterize the diversity of variable genes of HCAbs (VHHs), germline and rearranged VHH repertoires are constructed. Phylogenetics analysis shows that all camelid VHH genes are derived from a common ancestor and the nucleotide diversity of VHHs is similar across all camelid species. While species-specific hallmark sites are identified, the non-canonical cysteines specific to VHHs are distinct in Bactrian camels and dromedaries compared with alpacas. Though low divergence at the germline repertoire between wild and domestic Bactrian camels, higher expression of VHHs is observed in some wild Bactrian camels than that of domestic ones. This study not only adds our understanding of VHH repertoire diversity across camelids, but also provides useful resources for HCAb engineering.     

Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

Here, we present an adaptation of restriction‐site‐associated DNA sequencing (RAD‐seq) to the Illumina HiSeq2000 technology that we used to produce SNP markers in very large quantities at low cost per unit in the Réunion grey white‐eye (Zosterops borbonicus), a nonmodel passerine bird species with no reference genome. We sequenced a set of six pools of 18–25 individuals using a single sequencing lane. This allowed us to build around 600 000 contigs, among which at least 386 000 could be mapped to the zebra finch (Taeniopygia guttata) genome. This yielded more than 80 000 SNPs that could be mapped unambiguously and are evenly distributed across the genome. Thus, our approach provides a good illustration of the high potential of paired‐end RAD sequencing of pooled DNA samples combined with comparative assembly to the zebra finch genome to build large contigs and characterize vast numbers of informative SNPs in nonmodel passerine bird species in a very efficient and cost‐effective way.     

野双峰驼各分布区的生存环境差异及评价

世界上野双峰驼(Camelus bactrianus ferus)目前仅分布于中国新疆境内及中蒙边境,即：中国新疆的塔克拉玛干沙漠、阿尔金山北麓、戛顺戈壁、中蒙边境及蒙古国西部的外阿尔泰戈壁。总数共计730～880头。目前已为极度濒危物种。本文对野驼在不同分布区由于生境及人类活动影响所造成的差异加以对比研究并进行评价,为野骆驼保护提供依据。     

Cloning and Molecular Characterization of HSL and Its Expression Pattern in HPG Axis and Testis during Different Stages in Bactrian Camel

Hormone-sensitive lipase (HSL) is a key enzyme in animal fat metabolism and is involved in the rate-limiting step of catalyzing the decomposition of fat and cholesterol. It also plays an important regulatory role in maintaining seminiferous epithelial structure, androgen synthesis and primordial germ cell differentiation. We previously reported that HSL is involved the synthesis of steroids in Bactrian camels, although it is unclear what role it plays in testicular development. The present study was conducted to characterize the biological function and expression pattern of the HSL gene in the hypothalamic pituitary gonadal (HPG) axis and the development of testis in Bactrian camels. We analyzed cloning of the cDNA sequence of the HSL gene of Bactrian camels by RT-PCR, as well as the structural features of HSL proteins, using bioinformatics software, such as ProtParam, TMHMM, Signal P 4.1, SOPMA and MEGA 7.0. We used qRT-PCR, Western blotting and immunofluorescence staining to clarify the expression pattern of HSL in the HPG axis and testis of two-week-old (2W), two-year-old (2Y), four-year-old (4Y) and six-year-old (6Y) Bactrian camels. According to sequence analysis, the coding sequence (CDS) region of the HSL gene is 648 bp in length and encodes 204 amino acids. According to bioinformatics analysis, the nucleotide and amino acid sequence of Bactrian camel HSL are most similar to those of Camelus pacos and Camelus dromedarius, with the lowest sequence similarity with Mus musculus. In adult Bactrian camel HPG axis tissues, both HSL mRNA and protein expression were significantly higher in the testis than in other tissues (hypothalamus, pituitary and pineal tissues) (p < 0.05). The expression of mRNA in the testis increased with age and was the highest in six-year-old testis (p < 0.01). The protein expression levels of HSL in 2Y and 6Y testis were clearly higher than in 2W and 4Y testis tissues (p < 0.01). Immunofluorescence results indicate that the HSL protein was mainly localized in the germ cells, Sertoli cells and Leydig cells from Bactrian camel testis, and strong positive signals were detected in epididymal epithelial cells, basal cells, spermatocytes and smooth muscle cells, with partially expression in hypothalamic glial cells, pituitary suspensory cells and pineal cells. According to the results of gene ontology (GO) analysis enrichment, HSL indirectly regulates the anabolism of steroid hormones through interactions with various targets. Therefore, we conclude that the HSL gene may be associated with the development and reproduction of Bactrian camels in different stages of maturity, and these results will contribute to further understanding of the regulatory mechanisms of HSL in Bactrian camel reproduction.     

Small‐ and large‐scale heterogeneity in genetic variation across the collard flycatcher genome: implications for estimating genetic diversity in nonmodel organisms

Population genetic studies in nonmodel organisms are often hampered by a lack of reference genomes that are essential for whole‐genome resequencing. In the light of this, genotyping methods have been developed to effectively eliminate the need for a reference genome, such as genotyping by sequencing or restriction site‐associated DNA sequencing (RAD‐seq). However, what remains relatively poorly studied is how accurately these methods capture both average and variation in genetic diversity across an organism's genome. In this issue of Molecular Ecology Resources, Dutoit et al. (2016) use whole‐genome resequencing data from the collard flycatcher to assess what factors drive heterogeneity in nucleotide diversity across the genome. Using these data, they then simulate how well different sequencing designs, including RAD sequencing, could capture most of the variation in genetic diversity. They conclude that for evolutionary and conservation‐related studies focused on the estimating genomic diversity, researchers should emphasize the number of loci analysed over the number of individuals sequenced.     

A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

Reduced representation genome sequencing such as restriction‐site‐associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome.     

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

The KwaZulu‐Natal yellowfish (Labeobarbus natalensis) is an abundant cyprinid, endemic to KwaZulu‐Natal Province, South Africa. In this study, we developed a single‐nucleotide polymorphism (SNP) dataset from double‐digest restriction site‐associated DNA (ddRAD) sequencing of samples across the distribution. We addressed several hidden challenges, primarily focusing on proper filtering of RAD data and selecting optimal parameters for data processing in polyploid lineages. We used the resulting high‐quality SNP dataset to investigate the population genetic structure of L. natalensis. A small number of mitochondrial markers present in these data had disproportionate influence on the recovered genetic structure. The presence of singleton SNPs also confounded genetic structure. We found a well‐supported division into northern and southern lineages, with further subdivision into five populations, one of which reflects north–south admixture. Approximate Bayesian Computation scenario testing supported a scenario where an ancestral population diverged into northern and southern lineages, which then diverged to yield the current five populations. All river systems showed similar levels of genetic diversity, which appears unrelated to drainage system size. Nucleotide diversity was highest in the smallest river system, the Mbokodweni, which, together with adjacent small coastal systems, should be considered as a key catchment for conservation.     

Microscopic and molecular detection of Deraiophoronema evansi (Lewis, 1882) in domestic Bactrian camels (Camelus bactrianus) of Mongolia

Cameline filarosis is an important parasitic disease having an economic impact on the camel industry around the world. However, there has been no study on filarosis in Bactrian camels of Mongolia. Therefore, the aim of the present study was to detect and identify microfilariae of Deraiophoronema evansi (D. evansi) in Bactrian camels from three provinces, located in southern and southwestern Mongolia. Blood samples were obtained from 400 healthy two-humped camels of different ages and both sexes. All blood samples were analysed using a variety of diagnostic techniques. Microfilariae were detected in 30 Bactrian camels (7.5%) by the Knott technique, while 13 Bactrian camels (3.3%) tested positive in a direct smear test. D. evansi was detected in 18 Bactrian camels (4.5%) by PCR assay. Prevalence was shown to be high among Bactrian camels in the age group up to 5 years, while the lowest positive results were obtained for Bactrian camels in the 5–10-year age group and the over 10-year age group. To confirm the morphological identification, D. evansi–COI gene sequences were subjected to phylogenetic analyses. The D. evansi–COI gene sequences from Mongolian two-humped camels were identical to sequences from Iranian one-humped camels and were clustered together with these sequences in the phylogeny. This is the first report of molecular detection and identification of microfilariae of D. evansi in Bactrian camels of Mongolia.