Chromosome studies in the mammalian subfamily Antilopinae

Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data

Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold-level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on synteny between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here, we present "sex assignment through coverage" (SATC), a method to assign sex to samples and identify sex-linked scaffolds from next generation sequencing (NGS) data. The method works for species with a homogametic/heterogametic sex determination system and only requires a scaffold-level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: (i) male and female individuals, and (ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is freely available at https://github.com/popgenDK/SATC as R code and a graphical user interface (GUI).

Meiotic behaviour of evolutionary sex-autosome translocations in Bovidae

The recurrent occurrence of sex-autosome translocations during mammalian evolution suggests common mechanisms enabling a precise control of meiotic synapsis, recombination and inactivation of sex chromosomes. We used immunofluorescence and FISH to study the meiotic behaviour of sex chromosomes in six species of Bovidae with evolutionary sex-autosome translocations (Tragelaphus strepsiceros, Taurotragus oryx, Tragelaphus imberbis, Tragelaphus spekii, Gazella leptoceros and Nanger dama ruficollis). The autosomal regions of fused sex chromosomes showed normal synapsis with their homologous counterparts. Synapsis in the pseudoautosomal region (PAR) leads to the formation of characteristic bivalent (in T. imberbis and T. spekii with X;BTA13/Y;BTA13), trivalent (in T. strepsiceros and T. oryx with X/Y;BTA13 and G. leptoceros with X;BTA5/Y) and quadrivalent (in N. dama ruficollis with X;BTA5/Y;BTA16) structures at pachynema. However, when compared with other mammals, the number of pachynema lacking MLH1 foci in the PAR was relatively high, especially in T. imberbis and T. spekii, species with both sex chromosomes involved in sex autosome translocations. Meiotic transcriptional inactivation of the sex-autosome translocations assessed by γH2AX staining was restricted to their gonosomal regions. Despite intraspecies differences, the evolutionary fixation of sex-autosome translocations among bovids appears to involve general mechanisms ensuring sex chromosome pairing, synapsis, recombination and inactivation.

Splitting or lumping? A conservation dilemma exemplified by the critically endangered dama gazelle (Nanger dama)

Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions.

The contribution of female meiotic drive to the evolution of neo-sex chromosomes

Sex chromosomes undergo rapid turnover in certain taxonomic groups. One of the mechanisms of sex chromosome turnover involves fusions between sex chromosomes and autosomes. Sexual antagonism, heterozygote advantage, and genetic drift have been proposed as the drivers for the fixation of this evolutionary event. However, all empirical patterns of the prevalence of multiple sex chromosome systems across different taxa cannot be simply explained by these three mechanisms. In this study, we propose that female meiotic drive may contribute to the evolution of neo-sex chromosomes. The results of this study showed that in mammals, the XY(1) Y(2) sex chromosome system is more prevalent in species with karyotypes of more biarmed chromosomes, whereas the X(1) X(2) Y sex chromosome system is more prevalent in species with predominantly acrocentric chromosomes. In species where biarmed chromosomes are favored by female meiotic drive, X-autosome fusions (XY(1) Y(2) sex chromosome system) will be also favored by female meiotic drive. In contrast, in species with more acrocentric chromosomes, Y-autosome fusions (X(1) X(2) Y sex chromosome system) will be favored just because of the biased mutation rate toward chromosomal fusions. Further consideration should be given to female meiotic drive as a mechanism in the fixation of neo-sex chromosomes.

The 34,XY1,der(13) chromosome constitution with loss of Y2 is associated with unilateral testicular hypoplasia in the endangered Indian blackbuck antelope (Antilope cervicapra)

The present study is the first report of unilateral testicular hypoplasia in 3 of 15 (20%) Indian blackbuck antelopes (Antilope cervicapra). Interestingly, the condition was restricted to only the right testis in all cases. Cytogenetic analysis revealed chromosomal aneuploidy in the affected individuals which had a 34,XY(1),der(13) karyotype with loss of the acrocentric (autosomal) Y(2) and an aberrant chromosome 13. We further determined that the semen output and the circulating testosterone levels were markedly low in the males with hypoplastic testes as compared to fertile males.

Molecular insights into X;BTA5 chromosome rearrangements in the tribe Antilopini (Bovidae)

For a clade that includes Antilope, Gazella,Nanger and Eudorcas (Antilopinae), X;BTA5 translocation is a synapomorphy. Using a combination of fluorescence in situ hybridization (FISH) probes and polymerase chain reaction techniques, we provide (i) the first insight into the X;BTA5 architecture which differs in the species under study: Antilope cervicapra (genus Antilope), Gazella leptoceros (genus Gazella) and Nanger dama ruficollis (genus Nanger), (ii) determination of interstitial satellite DNA at the X;BTA5 junctions, and (iii) determination of repetitive sequences occupying constitutive heterochromatin of Xp arms in the studied species. The distribution of 2 repetitive DNA families in the centromeric regions of all chromosomes has been investigated by FISH with probes representing satellite I and satellite II DNA in all studied species. In this context, we discuss a markedly smaller centromere in the BTA5 (Y2) unfused chromosomes in males in the XY1Y2 determining system in comparison with other acrocentrics. An analysis of karyotypic data described in current published studies revealed a disparity with the data determined by FISH. In this report, we document chromosomal fusions in the 3 species mentioned resulting from FISH with painting probes prepared from cattle (Bos taurus). The number and chromosomal location of nucleolus organizer regions were determined by FISH. In the present study, we emphasize the importance of chromosomal rearrangement verification, particularly, if they are used for phylogenetic analysis.

A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants

This paper presents the first complete estimate of the phylogenetic relationships among all 197 species of extant and recently extinct ruminants combining morphological, ethological and molecular information. The composite tree is derived by applying matrix representation using parsimony analysis to 164 previous partial estimates, and is remarkably well resolved, containing 159 nodes (> 80 % of the potential nodes in the completely resolved phylogeny). Bremer decay index has been used to indicate the degree of certainty associated with each clade. The ages of over 80% of the clades in the tree have been estimated from information in the literature. The supertree for Ruminantia illustrates which areas of ruminant phylogeny are still only roughly known because of taxa with controversial relationships (e.g. Odocoileini, Antilopinae) or not studied in great detail (e.g. Muntiacus). It supports the monophyly of the ruminant families and Pecora. According to this analysis Antilocapridae and Giraffidae constitute the superfamily Giraffoidea, which is the sister group of a clade clustering Bovoidea and Cervoidea. The position of several taxa whose systematic positions have remained controversial in the past (Saiga, Pelea, Aepycerus, Pantholops, Ammotragus, Pseudois) is unambiguously established. Nevertheless, the position of Neotragus and Oreotragus within the original radiation of the non-bovine bovids remains unresolved in the present analysis. It also shows that six successive rapid cladogenesis events occurred within the infraorder Pecora during the Oligocene to middle Pliocene, which coincided with periods of global climatic change. Finally, the presented supertree will be a useful framework for comparative and evolutionary biologists interested in studies involving the ruminants.

The karyotype of the addax and its comparison with karyotypes of other species of Hippotraginae antelopes

The karyotype of the addax (Addax nasomaculatus, 2n = 58) has been investigated by RBG and CBG banding techniques. All chromosomes are acrocentric except the first pair of autosomes, which is submetacentric. The X chromosome is the largest acrocentric, and the Y chromosome is a medium sized acrocentric. According to the standard conventions used for cattle and goat, p- and q-arms of the pair of submetacentric autosomes correspond, respectively, to chromosomes # 27 # 1. The comparison of banding patterns of chromosomes in addax and four other species of the subfamily Hippotraginae reveals several common features and a high degree of homoeology with caprine and bovine karyotypes.

Phylogenetic relationships in the bovid subfamily Antilopinae based on mitochondrial DNA sequences

A molecular phylogeny of the subfamily Antilopinae was determined using the two mitochondrial DNA (mtDNA) genes cytochrome b and cytochrome c oxidase III. The tribe Antilopini is monophyletic with Antidorcas marsupialis and Litocranius walleri basal to the large genus Gazella. Antilope cervicapra falls within Gazella. This placement would either make Gazella paraphyletic or require that the genus name Gazella be changed to Antilope. Gazella thomsonii is supported as a subspecies of G. rufifrons. Most members of the tribe Neotragini are sister species to the Antilopini, but the Neotragini is rendered paraphyletic by a deep placement of Neotragus moschatus.

Chromosomes of Damaliscus (Artiodactyla, Bovidae): simple and complex centric fusion rearrangements

G- and C-banded karyotypes of Damaliscus hunteri, D. lunatus and D. pygargus were compared using the standard karyotype of Bos taurus. Chromosomal complements were 2n = 36 in D. lunatus jimela, 2n = 38 in D. pygargus phillipsi and D. p. pygargus, and 2n = 44 in D. hunteri. The fundamental number in all karyotypes was 60. Among the three species of Damaliscus, seven autosomal pairs and the X chromosomes were conserved. Y-chromosome differences were attributed to heterochromatic additions or deletions. Banded karyotypes of the two subspecies of D. pygargus exhibited complete homology. Chromosomal complements of D. pygargus and D. lunatus differed by a simple centric fusion. However, karyotypes of D. pygargus and D. lunatus differed from D. hunteri by numerous centric fusions, several of which were related by monobrachial chain complexes. Between the karyotypes of D. hunteri and D. pygargus or D. lunatus, there were two chain complexes, one involving five chromosomes (chain V) and the other involving 12 in pygargus (chain XII) or 13 in lunatus (chain XIII). There were also two simple centric fusions between D. hunteri and D. lunatus/D. pygargus; acrocentric chromosomes 13, 15, 20 and 22 in D hunteri were fused as 13;15 and 20;22 in D. lunatus and D. pygargus.

A karyotypic analysis of the lesser Malay chevrotain, Tragulus javanicus (Artiodactyla: Tragulidae)

Chevrotains are small forest-dwelling ruminants of the family Tragulidae. The chromosome number of the lesser Malay chevrotain was determined to be 2n = 32, NF = 64, G- and Q-banding allowed the identification of homologous chromosomes, and C-banding demonstrated the presence of pericentromeric, telomeric and interstitial constitutive heterochromatin. Q-band comparisons with domestic cattle revealed relatively few monobrachial chromosome band homologies. However, the smallest biarmed autosome of the chevrotain, chromosome 15, was determined to be cytogenetically homologus with the acrocentric chromosome 19 of cattle. A molecular cytogenetic analysis confirmed this putative chromosomal homology. In fact, molecular cytogenetic analyses indicate complete conservation of synteny among mouse deer chromosome 15, domestic cattle chromosome 19, domestic pig chromosome 12 and human chromosome 17. In the light of these molecular cytogenetic data and since mouse deer chromosome 15 is submetacentric and appears homologous in banding to submetacentric chromosome 12 of the domestic pig, these outgroup comparisons indicate that the acrocentric condition of cattle chromosome 19 has been derived by inversion. Since this derivative condition is present in the Antilocapridae, Bovidae, Cervidae and Giraffidae, it is a chromosomal synapomorphy that unites these advance ruminant families within the Artiodactyla.

Evolutionary histories of highly repeated DNA families among the Artiodactyla (Mammalia)

Six highly repeated DNA families were analyzed using Southern blotting and fluorescence in situ hybridization in a comparative study of 46 species of artiodactyls belonging to seven of the eight extant taxonomic families. Two of the repeats, the dispersed bovine-Pst family and the localized 1.715 component, were found to have the broadest taxonomic distributions, being present in all pecoran ruminants (Giraffidae, Cervidae, Antilocapridae, and Bovidae), indicating that these repeats may be 25-40 million years old. Different 1.715 restriction patterns were observed in different taxonomic families, indicating that independent concerted evolution events have homogenized different motifs in different lineages. The other four satellite arrays were restricted to the Bovini and sometimes to the related Boselaphini and Tragelaphini. Results reveal that among the two compound satellites studied, the two components of the 1.711a originated simultaneously, whereas the two components of the 1.711b originated at two different historical times, perhaps as many as 15 million years apart. Systematic conclusions support the monophyly of the infraorder Pecora, the monophyly of the subfamily Bovinae (containing the Boselaphini, Bovini, and Tragelaphini), an inability to resolve any interrelationships among the other tribes of bovids, paraphyly of the genus Bos with respect to Bison, and a lack of molecular variation among two morphologically and ecologically distinct subspecies of African buffaloes (Syncerus caffer cafer and S. c. nanus). Cytogenetically, a reduction in diploid chromosome numbers through centric fusion in derived karyotypes is accompanied by a loss of centromeric satellite DNA. The nilgai karyotype contains an apparent dicentric chromosome as evidenced by the sites of 1.715 hybridization. Telomeric sequences have been translocated to the centromeres without concomitant chromosomal rearrangement in Thompson's gazelle.

Meiosis in chromosomally heteromorphic goitered gazelle, Gazella subgutturosa (Artiodactyla, Bovidae)

Chromosomal-pairing behaviour was studied in the spermatocytes of individual goitered gazelles which were heteromorphic for a 14/15 Robertsonian translocation and which possessed an autosome-to-X translocation. Both translocations exhibited trivalent pairing configurations in pachytene and diakinesis/metaphase I nuclei. Synapsis of the sex chromosomes during pachynema was followed by end-to-end association of the X and Y during diakinesis/metaphase I. The only univalents identified were of the Y chromosome; Y univalency ranged from 15.9% at pachynema to 5.7% at diakinesis/metaphase I. Robertsonian trivalents exhibited evidence of synaptic adjustment in the paracentromeric region. Chiasmata were formed in most bivalents and trivalents; chiasmata were restricted to the autosomal portion of the autosome-to-XY trivalent. Analysis of metaphase II configurations (secondary spermatocytes) revealed no nondisjunction in individuals homozygous or heterozygous for the Robertsonian translocation. These data are consistent with the hypothesis that neither the autosomal nor the gonosomal heteromorphism reduces the meiotic fitness of male goitered gazelles.