Comparative Molecular Phylogeny and Evolution of Sex Chromosome DNA Sequences in the Family Canidae (Mammalia: Carnivora)

Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)

Deciphering the origins of phenotypic variations in natural animal populations is a challenging topic for evolutionary and conservation biologists. Atypical morphologies in mammals are usually attributed to interspecific hybridisation or de-novo mutations. Here we report the case of four golden jackals (Canis aureus), that were observed during a camera-trapping wildlife survey in Northern Israel, displaying anomalous morphological traits, such as white patches, an upturned tail, and long thick fur which resemble features of domesticated mammals. Another individual was culled under permit and was genetically and morphologically examined. Paternal and nuclear genetic profiles, as well as geometric morphometric data, identified this individual as a golden jackal rather than a recent dog/wolf-jackal hybrid. Its maternal haplotype suggested past introgression of African wolf (Canis lupaster) mitochondrial DNA, as previously documented in other jackals from Israel. When viewed in the context of the jackal as an overabundant species in Israel, the rural nature of the surveyed area, the abundance of anthropogenic waste, and molecular and morphological findings, the possibility of an individual presenting incipient stages of domestication should also be considered.

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

Phylogenetic relationships between different raccoon dog (Nyctereutes procyonoides) populations based on four nuclear and Y genes

BACKGROUND

The raccoon dog (Nyctereutes procyonoides), endemic to East Asia, is classified as six subspecies according to their geographical distribution including a population introduced to Europe. Studies on phylogenetic relationship or population genetics in both native and introduced areas have been carried out recently. Lately, opinions that Japanese raccoon dogs should be classified as a different species were asserted based on several studies using karyotypes, morphometric characters, mtDNA, and microsatellites analysis. However, no data pertaining to the nuclear DNA (nDNA) or Y chromosome are available.

OBJECTIVE

To estimate the relationship among the species using different genes is necessary in understanding of the history of this species.

METHOD

Therefore, we investigated nDNA and Y chromosomes in our study to define relationships: (1) between continental raccoon dog populations, (2) between original and introduced groups, and (3) between continental and Japanese groups.

RESULTS

The analysis of four nuclear (CHRNA1, VTN, TRSP, WT1) and ZFY genes indicated that there had been no genetic differentiation among the continental populations. However, significant differences were observed between continental and Japanese raccoon dogs in VTN and ZFY genes implying genetic differentiation has been going between them.

CONCLUSION

To better understand the phylogenetic relationship among raccoon dog populations, further study will be necessary.

Comparative Study of the Bush Dog (Speothos venaticus) Karyotype and Analysis of Satellite DNA Sequences and Their Chromosome Distribution in Six Species of Canidae

The bush dog (Speothos venaticus, 2n = 74) is a near threatened species taxonomically classified among South American canids. We revised the bush dog karyotype and performed a comparative sequence analysis of satellite and satellite-like DNAs in 6 canids: the bush dog, domestic dog (Canis familiaris, 2n = 78), grey wolf (C. lupus, 2n = 78), Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54+B), red fox (Vulpes vulpes, 2n = 34+B), and arctic fox (V. lagopus, 2n = 48-50) to specify the species position among Canidae. Using FISH with painting and BAC probes, we found that the distribution of canid evolutionarily conserved chromosome segments in the bush dog karyotype is similar to that of the domestic dog and grey wolf. The bush dog karyotype differs by 2 acrocentric chromosome pairs formed by tandem fusions of the canine (29;34) and (26;35) orthologues. An interstitial signal of the telomeric probe was observed in the (26;35) fusion site in the bush dog indicating a recent evolutionary origin of this rearrangement. Sequences and hybridisation patterns of satellite DNAs were compared, and a phylogenetic tree of the 6 canid species was constructed which confirmed the bush dog position close to the wolf-like canids, and apart from the raccoon dog and foxes.

Phylogenetic evidence for the ancient Himalayan wolf: towards a clarification of its taxonomic status based on genetic sampling from western Nepal

Wolves in the Himalayan region form a monophyletic lineage distinct from the present-day Holarctic grey wolf Canis lupus spp. (Linnaeus 1758) found across Eurasia and North America. Here, we analyse phylogenetic relationships and the geographic distribution of mitochondrial DNA haplotypes of the contemporary Himalayan wolf (proposed in previous studies as Canis himalayensis) found in Central Asia. We combine genetic data from a living Himalayan wolf population collected in northwestern Nepal in this study with already published genetic data, and confirm the Himalayan wolf lineage based on mitochondrial genomic data (508 bp cytochrome b and 242 bp D-loop), and X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences. We then compare the genetic profile of the Himalayan wolf lineage found in northwestern Nepal with canid reference sequences from around the globe with maximum likelihood and Bayesian phylogeny building methods to demonstrate that the Himalayan wolf forms a distinct monophyletic clade supported by posterior probabilities/bootstrap for D-loop of greater than 0.92/85 and cytochrome b greater than 0.99/93. The Himalayan wolf shows a unique Y-chromosome (ZFY) haplotype, and shares an X-chromosome haplotype (ZFX) with the newly postulated African wolf. Our results imply that the Himalayan wolf distribution range extends from the Himalayan range north across the Tibetan Plateau up to the Qinghai Lakes region in Qinghai Province in the People's Republic of China. Based on its phylogenetic distinction and its older age of divergence relative to the Holarctic grey wolf, the Himalayan wolf merits formal classification as a distinct taxon of special conservation concern.

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.