Comparative genomic analysis of high-altitude adaptation for Mongolia Mastiff,Tibetan Mastiff,and Canis Lupus

Tibetan Mastiff has adapted to the extreme environment of the Qinghai-Tibetan Plateau. Yet, the underlying mechanisms of its high-altitude-adaptation and origin remains elusive. Here, we generated the draft genomes of Mongolia Mastiff, Tibetan Mastiff, and Canis Lupus. The phylogenetic tree uncovered that Tibetan Mastiff and Mongolia Mastiff were derived from Canis Lupus species. The comparative genomic analyses identified that the expansion of gene families related to DNA repair and damage response, and contraction related to ATPase activity revealed the genetic adaptations of Tibetan Mastiff and Canis Lupus to high altitude. In addition, the Tibetan Mastiff and Canis Lupus had signals of positive selection for genes involved in fatty-acid α/β- oxidation for highland adaptation. Notably, the positively selected TERT of Tibetan Mastiff should be an adaptive trait for correcting DNA damage. These findings suggested that the Tibetan Mastiff and Canis Lupus evolves basic strategies for adaptation to high altitude.     

周口店变异狼(Canis lupus variabilis)在家畜狗(Canis familiaris)祖先系列中的位置

本文作者对周口店第一、第三及第十三地点的一种化石犬类——变异狼(Canis lupus uariadilis)进行了观察和测量。根据其头骨大小、形态特征以及与中国早期人类共生的情况来看,认为它有可能是从驯化的野生狼导致家畜狗出现的一种祖先类型。     

Does interference competition with wolves limit the distribution and abundance of coyotes?

Interference competition with wolves Canis lupus is hypothesized to limit the distribution and abundance of coyotes Canis latrans, and the extirpation of wolves is often invoked to explain the expansion in coyote range throughout much of North America. We used spatial, seasonal and temporal heterogeneity in wolf distribution and abundance to test the hypothesis that interference competition with wolves limits the distribution and abundance of coyotes. From August 2001 to August 2004, we gathered data on cause-specific mortality and survival rates of coyotes captured at wolf-free and wolf-abundant sites in Grand Teton National Park (GTNP), Wyoming, USA, to determine whether mortality due to wolves is sufficient to reduce coyote densities. We examined whether spatial segregation limits the local distribution of coyotes by evaluating home-range overlap between resident coyotes and wolves, and by contrasting dispersal rates of transient coyotes captured in wolf-free and wolf-abundant areas. Finally, we analysed data on population densities of both species at three study areas across the Greater Yellowstone Ecosystem (GYE) to determine whether an inverse relationship exists between coyote and wolf densities. Although coyotes were the numerically dominant predator, across the GYE, densities varied spatially and temporally in accordance with wolf abundance. Mean coyote densities were 33% lower at wolf-abundant sites in GTNP, and densities declined 39% in Yellowstone National Park following wolf reintroduction. A strong negative relationship between coyote and wolf densities (beta = -3.988, P < 0.005, r(2) = 0.54, n = 16), both within and across study sites, supports the hypothesis that competition with wolves limits coyote populations. Overall mortality of coyotes resulting from wolf predation was low, but wolves were responsible for 56% of transient coyote deaths (n = 5). In addition, dispersal rates of transient coyotes captured at wolf-abundant sites were 117% higher than for transients captured in wolf-free areas. Our results support the hypothesis that coyote abundance is limited by competition with wolves, and suggest that differential effects on survival and dispersal rates of transient coyotes are important mechanisms by which wolves reduce coyote densities.     

Widespread occurrence of a domestic dog mitochondrial DNA haplotype in southeastern US coyotes

Sequence analysis of the mitochondrial DNA control region from 112 southeastern US coyotes (Canis latrans) revealed 12 individuals with a haplotype closely related to those in domestic dogs. Phylogenetic analyses grouped this new haplotype in the dog/grey wolf (Canis familiaris/Canis lupus) clade with 98% bootstrap support. These results demonstrate that a male coyote hybridized with a female dog, and female hybrid offspring successfully integrated into the coyote population. The widespread distribution of this haplotype from Florida to West Virginia suggests that the hybridization event occurred long ago before the southeastern USA was colonized by coyotes. However, it could have occurred in the southeastern USA before the main front of coyotes arrived in the area between male coyotes released for sport and a local domestic dog. The introgression of domestic dog genes into the southeastern coyote population does not appear to have substantially affected the coyote's genetic, morphological, or behavioural integrity. However, our results suggest that, contrary to previous reports, hybridization can occur between domestic and wild canids, even when the latter is relatively abundant. Therefore, hybridization may be a greater threat to the persistence of wild canid populations than previously thought.     

Using faecal DNA sampling and GIS to monitor hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)

The US Fish and Wildlife Service's (USFWS) Red Wolf Recovery Program recognizes hybridization with coyotes as the primary threat to red wolf recovery. Efforts to curb or stop hybridization are hampered in two ways. First, hybrid individuals are difficult to identify based solely on morphology. Second, managers need to effectively search 6000 km(2) for the presence of coyotes and hybrids. We develop a noninvasive method to screen large geographical areas for coyotes and hybrids with maternal coyote ancestry by combining mitochondrial DNA sequence analysis of faeces (scat) and geographic information system (GIS) technology. This method was implemented on the Alligator River National Wildlife Refuge (1000 km(2)) in northeastern North Carolina. A total of 956 scats were collected in the spring of 2000 and 2001 and global positioning system (GPS) coordinates were recorded. Seventy-five percent of the scats were assigned to species and five coyote/hybrid scats were detected. Placement of scat location coordinates on a map of the experimental population area revealed that four of the coyote/hybrid scats were detected within the home ranges of sterilized hybrids. The other coyote/hybrid scat indicated the presence of a previously unknown individual. We suggest this method be expanded to include more of the experimental population area and be optimized for use with nuclear markers to improve detection of hybrid and back-crossed individuals.     

Origin and status of the Great Lakes wolf

An extensive debate concerning the origin and taxonomic status of wolf-like canids in the North American Great Lakes region and the consequences for conservation politics regarding these enigmatic predators is ongoing. Using maternally, paternally and biparentally inherited molecular markers, we demonstrate that the Great Lakes wolves are a unique population or ecotype of gray wolves. Furthermore, we show that the Great Lakes wolves experienced high degrees of ancient and recent introgression of coyote and western gray wolf mtDNA and Y-chromosome haplotypes, and that the recent demographic bottleneck caused by persecution and habitat depletion in the early 1900s is not reflected in the genetic data.     

Captive breeding and the reintroduction of Mexican and red wolves

Mexican and red wolves were both faced with extinction in the wild until captive populations were established more than two decades ago. These captive populations have been successfully managed genetically to minimize mean kinship and retain genetic variation. Descendants of these animals were subsequently used to start reintroduced populations, which now number about 40-50 Mexican wolves in Arizona and New Mexico and about 100 red wolves in North Carolina. The original captive Mexican wolf population was descended from three founders. Merging this lineage with two other captive lineages, each with two founders, has been successfully carried out in the captive population and is in progress in the reintroduced population. This effort has resulted in increased fitness of cross-lineage wolves, or genetic rescue, in both the captive and reintroduced populations. A number of coyote-red wolf hybrid litters were observed in the late 1990s in the reintroduced red wolf population. Intensive identification and management efforts appear to have resulted in the elimination of this threat. However, population reintroductions of both Mexican and red wolves appear to have reached numbers well below the generally recommended number for recovery and there is no current effort to re-establish other populations.     

中国狼研究进展

狼(Canis lupus)是公众印象中凶残、狡猾动物的代表,国际上关于狼的研究很多,但中国狼的研究较少。本文在国内文献和作者自己的研究工作基础上,综述了中国狼的分类、遗传、分布、种群密度、解剖、生理、生态等方面的研究进展,为中国狼的保护和管理提供参考。     

Activity patterns of gray wolves housed in small vs. large enclosures

Free-ranging gray wolves (Canis lupus) generally inhabit large home ranges, yet they are housed in a variety of restricted spaces when in captivity. There is continual debate as to whether space restrictions alter a wolf's behavior. The purpose of these studies was to remotely measure and then compare the amount and frequency of activity of gray wolves housed in small, artificial enclosures vs. large, more natural enclosures. Test animals comprised three adult wolves housed in kennels and three and four wolves housed in separate natural enclosures. Kenneled wolves had 2.8 m² of surface area per wolf, and wolves in natural enclosures had 466.6 m² (South Pack) and 349.9 m² (North Pack) per wolf. Wolves were fitted with radiotelemetry collars containing activity sensors. Activity data were recorded every 20 min for 57 continuous hr. The amount of activity for each wolf was calculated using areas under the curve (AUCs), and the frequency of activity was analyzed by spectral analysis. There was no difference (P ≥ 0.22) in AUCs between kenneled wolves (1.399 ± 0.214 x 10⁵ radians) and South Pack wolves (1.564 ± 0.139 X 10⁵ radians) or North Pack wolves (1.617 ± 0.192 x 10⁵ radians). All three groups had similar peak spectral values at frequencies that were close to daily cycles (i.e., ω = 0.12–0.17 cycles per unit time). Peaks in coherence near the dominant spectral frequency were most significant between the natural enclosures and the least significant between the kenneled wolves and the South Pack wolves. Based on these criteria of activity and under these circumstances, enclosure size appeared to have no effect on wolf activity. However, small sample sizes and variation in the data do not make these results definitive. © 1996 Wiley-Liss, Inc.     

Comparison of Mexican Wolf and Coyote Diets in Arizona and New Mexico

ABSTRACT Interactions between wolves (Canis lupus) and coyotes (C. latrans) can have significant impacts on their distribution and abundance. We compared diets of recently translocated Mexican wolves (C. l. baileyi) with diets of resident coyotes in Arizona and New Mexico, USA. We systematically collected scats during 2000 and 2001. Coyote diet was composed mostly of mammalian species, followed by vegetation and insects. Elk (Cervus elaphus) was the most common item in coyote scats. Mexican wolf diet had a higher proportion of large mammals and fewer small mammals than coyote diet; however, elk was also the most common food item in Mexican wolf scats. Our results suggest that Mexican wolf diet was more similar to coyote diet than previously reported, but coyotes had more seasonal variation. Considering results in other areas, we expect that Mexican wolves will have a negative impact on coyotes through direct mortality and possibly competition. Reintroduction of Mexican wolves may have great impacts on communities by changing relationships among other predators and their prey.     

DOGSET: pre-designed primer sets for fine-scale mapping and DNA sequence interrogation in the dog

DOGSET is an online resource that provides access to primer sequences that have been computationally mined from the reference genome using heuristic algorithms. The electronic repository includes PCR primers corresponding to 32 135 markers for genetic mapping and 334 657 sequence-tagged gene elements for targeted re-sequencing and mutation discovery. A customized report that tailors primer design to wet bench protocols can be exported for a region of interest by specifying genome coordinates in a graphical user interface.     

Genetic nature of eastern wolves: Past, present and future

Eastern North American wolves have long been recognized as morphologically distinct from both coyotes and gray wolves. This has led to questions regarding their origins and taxonomic status. Eastern wolves are mainly viewed as: (1) a smaller subspecies of gray wolf (Canis lupus lycaon), potentially the result of historical hybridization between gray wolves (C. lupus) and red wolves (C. rufus), (2) a hybrid, the result of gray wolf (C. lupus) and coyote (C. latrans) interbreeding, or (3) a distinct species, C. lycaon, closely related to the red wolf (C. rufus). Although debate persists, recent molecular studies suggest that the eastern wolf is not a gray wolf subspecies, nor the result of gray wolf/coyote hybridization. Eastern wolves were more likely a distinct species, C. lycaon, prior to the eastward spread of coyotes in the late 1800s. However, contemporary interbreeding exits between C. lycaon to both C. lupus and C. latrans over much of its present range complicating its present taxonomic characterization. While hybridization may be reducing the taxonomic distinctiveness of C. lycaon, it should not necessarily be viewed as negative influence. Hybridization may be enhancing the adaptive potential of eastern wolves, allowing them to more effectively exploit available resources in rapidly changing environments.     

Changes in desert avifauna associated with the functional extinction of a terrestrial top predator

We investigated how long‐term suppression of populations of a top predator, the dingo Canis dingo, affected composition of sympatric avifauna in Australian deserts, by surveying bird assemblages across ~80 000 km² of arid dune‐fields on either side of the Dingo Barrier Fence (DBF; a 5614 km‐long fence separating ecosystems in which dingoes are abundant from ecosystems in which dingoes are functionally extinct). Using fourth‐corner modelling, incorporating species’ traits, we identified apparent declines of sedentary birds that nest in low vegetation and small birds that feed primarily on grass seed, and increases in scavenging birds associated with the functional extinction of dingoes. Occupancy differed between sites inside and outside the DBF in 13 bird species. We hypothesise that these differences in bird assemblages across the DBF result, in part, from increases in kangaroos Macropus spp. and red foxes Vulpes vulpes in arid landscapes where dingoes have been removed. Our study provides evidence that the functional extinction of a large terrestrial predator has had pervasive ecosystem effects, including shifts in composition of avian assemblages.