Genetic evaluation of the three captive mexican wolf lineages

The Mexican gray wolf appears to be extinct in the wild and exists now only in captivity. There are three captive putative Mexican wolf lineages: Certified, Ghost Ranch, and Aragón lineages. From pedigree analysis, the Certified lineage has the lowest level of inbreeding and has retained the most founder alleles. In contrast, the Ghost Ranch has a high level of inbreeding and fewest founder alleles. From molecular genetics data, particularly from microsatellite loci, it appears that all of the lineages consist of Mexican wolves, and none of them appear to have ancestry from dogs or coyotes. Further, the molecular data are consistent with the Certified lineage having three founders instead of the four previously assumed. From these findings, we recommend that the three lineages be combined to increase the number of founders and to postpone any inbreeding depression. The combination of pedigree analysis and molecular genetic data allowed us to resolve several long-standing concerns in Mexican wolves. Zoo Biol 16:47–69, 1997. © 1997 Wiley-Liss, Inc.     

Ancient origin and evolution of the Indian wolf: evidence from mitochondrial DNA typing of wolves from Trans-Himalayan region and Pennisular India

The two wolf types found in India are represented by two isolated populations and believed to be two sub-species of Canis lupus. One of these wolf, locally called Himalayan wolf (HW) or Tibetan wolf, is found only in the upper Trans-Himalayan region from Himachal Pradesh to Leh in Kasmir and is considered to be C. lupus chanco. The other relatively larger population is of Indian Gray wolf (GW) that is found in the peninsular India and considered to be C. lupus pallipes. Both these wolves are accorded endangered species status under the Indian Wildlife Protection Act. In 1998 for the first time in India, we initiated molecular characterization studies to understand their genetic structure and taxonomic status. Since then, we have analyzed the genetic variability in 18 of the total of 21 HW samples available in Zoological parks along with representative samples of GW, wild dogs and jackals. Our study of mitochondrial DNA diversity across three different taxonomically informative domains i.e., cytochrome-B gene, 16S rDNA and hypervariable d-loop control region revealed HW to be genetically distinct from the GW as well as from all other wolves of the world, including C. lupus chanco from China. Most importantly, d-loop haplotypic diversity revealed both HW and GW from India to be significantly diverse from other wolf populations globally and showed that these represent the most ancient lineages among them. Phylogenetic analysis revealed the Indian wolves as two independent lineages in a clade distinct and basal to the clade of all wolves from outside of India. Conservative estimate of evolutionary time-span suggests more than one million years of separation and independent evolution of HW and GW. We hypothesize that Indian wolves represent a post-jackal pre-wolf ancestral radiation that migrated to India about 1-2 mya and underwent independent evolution without contamination from other wolf like canids. The study thus, suggests that Indian subcontinent had been one major center of origin and diversification of the wolf and related canids. Further, the significant degree of genetic differentiation of HW from GW and of these two from other wolves, suggest the interesting possibility of them to be new wolf species/subspecies in evolution that may need to be described possibly as C. himalayaensis and C. indica (or as C. lupus himalyaensis and C. lupus indica), respectively. Thus for the first time, the study reveals new ancient wolf lineages in India and also highlights the need to revisit the origin, evolution and dispersion of wolf populations in Asia and elsewhere. Simultaneously, it increases the conservation importance of Indian wolves warranting urgent measures for their effective protection and management, especially of the small HW population that at present is not even recognized in the canid Red List.     

Paleogenomics reveals independent and hybrid origins of two morphologically distinct wolf lineages endemic to Japan

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Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses

Multiple geographical regions have been proposed for the domestication of Equus caballus . It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.     

Incongruous nuclear and mitochondrial phylogeographic patterns in two sympatric lineages of the wolf spider Pardosa astrigera (Araneae: Lycosidae) from China

We investigated the genetic structure of mitochondrial DNA (COI and 16S rRNA-tRNA(Leu(CUN))-ND1) and nuclear DNA (ITS2) variations among and within populations of Pardosa astrigera in China. Two phenotypes of males were recognized. They differed genetically also in the presence (type A) or absence (type B) of common insertions and deletions in ITS2. The concordance between mtDNA based phylogeny and the phenotypic variations of P. astrigera was weak. Haplotypes of type A did not form a monophyletic group. Instead they were found in three clades, in one of them mixed with type B haplotypes, most likely as a result of long-term and ongoing gene flow of mtDNA between the two phenotypic groups (M = 0.69). Pairwise sequence divergences of all data sets indicated that the genetic divergences between the two phenotypes fall within intraspecific range. Our results indicated that the P. astrigera populations in China consist of two sympatric lineages with male phenotypic variations. Patterns of mismatch distribution within lineages suggested long-term demographic stability in the lineage A, and growth in lineage B that expanded rapidly and recolonized from a southern refuge to the northern parts of China during the late-Pleistocene. On the basis of the estimated divergence time between the two lineages (0.18-0.41 Ma), we suggest that the dry-cold climate and the uplift of the Tibetan plateau during the mid-Pleistocene appear to have a determinating impact on the evolutionary history of P. astrigera in China.     

Distribution, status and conservation of Indian gray wolf (Canis lupus pallipes) in Karnataka, India

The Indian gray wolf Canis lupus pallipes is the major large carnivore in the plains of Karnataka, India. We carried out a study on its distribution and status from November 2001 to July 2004. We estimated 555 wolves occupying about 123 330 km² of the state. In the past 40 years, wolves have disappeared from the southern plateau from an area of about 31 801 km². Their distribution is now largely restricted to the north-eastern dry plains. The wolf has also disappeared in recent years from some 'protected areas' such as Melkote Temple Wildlife Sanctuary, and their present population is largely found in 'non-protected' areas. Blackbucks are the only natural prey of wolves in Karnataka, but their density in most parts of the state is extremely low. The major prey species is domestic livestock, especially sheep. The available 'remote area' (forests or rocky terrains) in the wolf-occupied regions determined the status of the wolf. Killing of adult wolves and pups was common throughout the range of the wolf. However, such killings were made largely by local sheepherders with small sheep holdings and not by nomadic shepherds who maintained large sheep herds. The forests in the north-eastern parts of the state exist in small patches every few kilometers. Because each wolf pack ranges over large distances and is by and large a commensal species, we propose that the management of these small forest patches, considering them as components of a larger landscape, is the only effective conservation practice for the wolf. Although existing locally in low densities, because of a large ranging area of a single pack, the seemingly isolated wolf packs can become parts of a large metapopulation, providing a sustainable population.     

Splitting the Difference: Gender and Myth in Ancient Greece and India

Splitting the Difference: Gender and Myth in Ancient Greece and India. Wendy Doniger. Chicago, EL: University of Chicago Press, 1999. 376 pp.     

Estimating fitness by competition assays between drug susceptible and resistant Mycobacterium tuberculosis of predominant lineages in Mumbai, India

Background

Multi Drug Resistant Tuberculosis (MDR TB) is a threat to global tuberculosis control. A significant fitness cost has been associated with DR strains from specific lineages. Evaluation of the influence of the competing drug susceptible strains on fitness of drug resistant strains may have an important bearing on understanding the spread of MDR TB. The aim of this study was to evaluate the fitness of MDR TB strains, from a TB endemic region of western India: Mumbai, belonging to 3 predominant lineages namely CAS, Beijing and MANU in the presence of drug susceptible strains from the same lineages.

Methodology

Drug susceptible strains from a single lineage were mixed with drug resistant strain, bearing particular non synonymous mutation (rpoB D516V; inhA, A16G; katG, S315T1/T2) from the same or different lineages. Fitness of M.tuberculosis (M.tb) strains was evaluated using the difference in growth rates obtained by using the CFU assay system.

Conclusion/Significance

While MANU were most fit amongst the drug susceptible strains of the 3 lineages, only Beijing MDR strains were found to grow in the presence of any of the competing drug susceptible strains. A disproportionate increase in Beijing MDR could be an alarm for an impending epidemic in this locale. In addition to particular non synonymous substitutions, the competing strains in an environment may impact the fitness of circulating drug resistant strains.     

Echinococcus granulosus in the wolf in Italy

During the period 1987-1999, 119 wolf cadavers were examined and checked for the presence of Echinococcus granulosus. All the animals were retrieved along the whole Apennines range of distribution of the species in Italy and most of them were illegally killed. Eighteen wolves resulted positive (15%). The mean intensity was 697.5. The force of infection for prevalence was 8.2 year(-1). The prevalence of the parasite was significantly and positively influenced by the local prevalence of cystic echinococcosis (CE) in sheep. Mean intensity was significantly and positively influenced by both the age of the wolf and the prevalence of CE in sheep. A deterministic model was used in order to simulate a purely theoretical sylvatic cycle of the parasites having the wolf as the only definitive host with 15% of prevalence. The expected prevalence of CE in wild intermediate species ranges between 10% and 25%. This prevalence overlaps the one observed in sheep. Even if both the wolf and the wild ungulate populations are increasing, the wolf still acts as a part of the main dog-sheep cycle of the parasite.     

Yersinia pestis lineages in Mongolia

Background

Whole genome sequencing allowed the development of a number of high resolution sequence based typing tools for Yersinia (Y.) pestis. The application of these methods on isolates from most known foci worldwide and in particular from China and the Former Soviet Union has dramatically improved our understanding of the population structure of this species. In the current view, Y. pestis including the non or moderate human pathogen Y. pestis subspecies microtus emerged from Yersinia pseudotuberculosis about 2,600 to 28,600 years ago in central Asia. The majority of central Asia natural foci have been investigated. However these investigations included only few strains from Mongolia.

Methodology/Principal Findings

Clustered Regularly Interspaced Short Prokaryotic Repeats (CRISPR) analysis and Multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) with 25 loci was performed on 100 Y. pestis strains, isolated from 37 sampling areas in Mongolia. The resulting data were compared with previously published data from more than 500 plague strains, 130 of which had also been previously genotyped by single nucleotide polymorphism (SNP) analysis. The comparison revealed six main clusters including the three microtus biovars Ulegeica, Altaica, and Xilingolensis. The largest cluster comprises 78 isolates, with unique and new genotypes seen so far in Mongolia only. Typing of selected isolates by key SNPs was used to robustly assign the corresponding clusters to previously defined SNP branches.

Conclusions/Significance

We show that Mongolia hosts the most recent microtus clade (Ulegeica). Interestingly no representatives of the ancestral Y. pestis subspecies pestis nodes previously identified in North-western China were identified in this study. This observation suggests that the subsequent evolution steps within Y. pestis pestis did not occur in Mongolia. Rather, Mongolia was most likely re-colonized by more recent clades coming back from China contemporary of the black death pandemic, or more recently in the past 600 years.