Explore the vast range of titles available.

Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.

Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

The taxonomy of wolves ( Canis sp. complex) is under increasing scrutiny due to molecular evidence revealing the existence of multiple cryptic lineages. Among these, the Himalayan wolf ( Canis cf. lupus chanco ), native to the Tibetan Plateau and the Himalayas, represents one of the most ancient lineages in Eurasia. Its morphological distinction from grey wolf populations remains poorly understood. In this study, we evaluated the morphological differentiation of the Himalayan wolf by analyzing specimens from museum collections using linear and 2D geometric morphometrics. Our comparative analysis included skulls from various wolf populations across Eurasia, grouped according to known genetic lineages. Although linear measurements failed to reveal clear diagnostic features, geometric morphometric analysis indicated that Himalayan wolves possess a shorter muzzle and wider zygomatic arch than other populations. These traits may reflect adaptations to their environment and prey preferences. However, the overlap with other wolf populations was significant, and cross-validation analyses showed low reclassification rates, indicative of morphological conservatism within Canidae. Moreover, several museum specimens previously labeled as Himalayan wolves were misidentified, complicating the taxonomic assessment. Our findings provide support for the subtle morphological distinctiveness of the Himalayan wolf, though further integrative studies incorporating genomic and 3D modeling approaches are required to clarify the taxonomic status of this group.

Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross‐bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population (“Javan Pied Starling”) is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.

The grey partridge (Perdix perdix Linnaeus, 1758), is a polytypic species with seven recognized subspecies, including P. p. italica (Hartert, 1917), which is endemic to Italy. Until World War II, the species was widespread across Europe but severely declined due to anthropogenic causes, jeopardizing the Italian subspecies gene pool. Genetic characterization and haplotype identification were performed by analyzing the 5′-end of the mitochondrial control region (CR). A total of 15 haplotypes were detected, seven of which were present in the population before 1915. Among them, three haplotypes were never detected again in the individuals collected after 1915. Interestingly, eight of the 15 haplotypes detected in Italian museum samples belonged exclusively to individuals collected after 1915. The obtained data highlight a high presence of specimens originating from other European populations and, despite all the conservation efforts, suggest an uncertain situation of the subspecies in Italy. This research was strongly backed up by extensive bibliographic research on historical documents, allowing the identification of hundreds of restocking events all over Italy. This is an integral part of this research and has laid the foundations for identifying and circumscribing historical periods in which introductions from the rest of Europe had different pressures, aiming to define a baseline.

Hybridization poses a major challenge for species conservation because it threatens both genetic integrity and adaptive potential. Yet, hybridization can occasionally offer unprecedented opportunity for species recovery if the genome of an extinct taxon is present among living hybrids such that selective breeding could recapture it. We explored the design elements for establishing a captive-breeding program for Galapagos tortoises (Chelonoidis spp.) built around individuals with admixed ancestry involving an extinct species. The target individuals were hybrids between the extinct species from Floreana Island, C. niger, and an extant species, C. becki, which were recently found in the endemic range of C. becki, from Wolf Volcano on Isabela Island. We combined genotypic data from 35 tortoises with high ancestry from C. niger with forward-in-time simulations to explore captive breeding strategies that maximized overall genetic diversity and ancestry from C. niger while accommodating resource constraints, species biology, and the urgency to return tortoises to Floreana Island for facilitating ecosystem restoration. Overall genetic diversity was maximized when in the simulation tortoises were organized in relatively small breeding groups. Substantial amounts of the C. niger genome were captured despite limited resources available for selectively breeding tortoises in captivity. Genetic diversity was maximized when captive-bred offspring were released to the wild rather than being used as additional breeders. Our results provide genetic-based and practical guidance on the inclusion of hybrids with genomic representation from extinct taxa into species restoration programs and informs the ongoing debate on the value of hybrids in biodiversity conservation. La hibridación representa un obstáculo importante para la conservación de especies ya que amenaza tanto a la integridad genética como al potencial adaptativo. Aun así, la hibridación ocasionalmente puede ofrecer una oportunidad sin precedentes para la recuperación de una especie si el genoma de un taxón extinto está presente entre los híbridos vivientes de tal manera que la reproducción selectiva pudiera recuperarlo. Exploramos los elementos de diseño para el establecimiento de un programa de reproducción en cautiverio de la tortuga de las Galápagos (Chelonoidis spp.) construido en torno a los individuos con linajes mixtos que incluyeran una especie extinta. Los individuos fueron los híbridos de la especie extinta en la Isla Floreana, C. niger, y la especie viviente C. becki, encontrados recientemente en la distribución geográfica endémica de la segunda especie en el Volcán Wolf (Isla Isabela). Combinamos los datos genotípicos de 35 tortugas con un linaje cargado de C. niger usando simulaciones futuras de la descendencia generada por el programa para explorar las estrategias de reproducción en cautiverio que maximizaran en general la diversidad genética y el linaje de C. niger a la vez que se ajustaba a las restricciones de recursos, la biología de la especie y la urgencia por regresar las tortugas a la Isla Floreana para facilitar la restauración del ecosistema. En general, la diversidad genética se maximizó cuando en la simulación las tortugas estuvieron organizadas en grupos de reproducción relativamente pequeños y cuando cantidades sustanciales del genoma de C. niger fueron capturados con base en los recursos disponibles para reproducir selectivamente a las tortugas en cautiverio. La diversidad genética se vio especialmente maximizada cuando las crías reproducidas en cautiverio fueron liberadas en lugar de ser utilizadas como reproductoras adicionales. Nuestros resultados proporcionanuna guía práctica y basada en la genética para la inclusión de híbridos con representación genómica de un taxón extinto en los programas de restauración de especies. Cuando incorporamos a los híbridos con diversidad genética que previamente se creía perdida en los programas con el propósito de la reintroducción de especies, nuestro estudio informa al debate continuo sobre el valor de los híbridos para la conservación de la biodiversidad. 杂交对物种保护提出了重大挑战，因为它威胁着物种的遗传完整性和适应性潜力。然而，如果一个已灭 绝类群的基因组存在于现存的杂交种中，那么杂交也可以为物种恢复提供前所未有的机遇，通过选择性育种重 新获得灭绝物种的基因组。本研究探讨了如何利用含有已灭绝物种基因组的混合血统个体，为加拉帕戈斯陆龟 (Chelonoidis spp：) 建立圏养繁殖计划。我们的目标个体是弗洛里安娜岛灭绝物神C. niger与近期在其分布范围 内伊莎贝拉岛沃尔夫火山发现的现存物种C. becki的杂交后代。我们将35只含有较高比例C. niger血统的乌 龟的基因型数据与对该计划获得后代的前进式模拟相结合，在满足总体遗传多祥性和C. niger血统最大化，且考 虑资源限制、物种生物学特性和弗洛里安娜岛急需重引人乌龟来促进生态系统恢复的情况下，分析了可能的圏 养繁殖策略。在模拟实验中, 建立相对较小的乌龟繁殖群时的总体ゝ遗传多祥性最高，且根据已有资源对圏养乌龟 进行选择性育种可以捕获大量的C niger基因组。若将圏养繁殖的后代释放到野外而不是继续用于繁殖，则遗 传多样性会特別高。我们的研究结果为将携带已灭绝类群的代表性基因组的杂交种纳人物种恢复计划提供了基 于遗传学的实践指导。我们的研究还表明，可以在物种重引人项目中纳人携带了被认为已经丟失的遗传多祥性 的杂交种，这也为目前杂交种在生物多祥性保护中的价值的争论提供了信息。

Warmblood fragile foal syndrome (WFFS) is an autosomal recessive disorder caused by a single nucleotide variant in the procollagen-lysine-2-oxoglutarate-5-dioxygenase 1 gene (PLOD1:c.2032G>A, p.Gly678Arg). Homozygosity for the PLOD1 variant causes an Ehler-Danlos-like syndrome, which has to date only been reported in warmblood breeds but the WFFS allele has been also detected in the Thoroughbred. To investigate the breed distribution of the WFFS allele, 4081 horses belonging to 38 different breeds were screened. In total, 4.9% of the horses representing 21 breeds carried the WFFS allele. The affected breeds were mainly warmbloods, with carrier frequency as high as 17% in the Hanoverian and Danish Warmblood. The WFFS allele was not detected in most non-warmblood breeds. Exceptions include WFFS carriers in the Thoroughbred (17/716), Haflinger (2/48), American Sport Pony (1/12), and Knabstrupper (3/46). The origin of the WFFS allele remains unknown. The Arabian breed and specifically the stallion Bairactar Or. Ar. (1813), whose offspring were reported to have a similar phenotype in the 19th century, were hypothesized as the origin. DNA from a museum sample of Bairactar Or. Ar. showed that he did not carry the mutated allele. This result, together with the genotypes of 302 Arabians, all homozygous for the reference allele, does not support an Arabian origin of the WFFS allele. Our extensive survey shows the WFFS allele to be of moderate frequency and concern in warmbloods and also in breeds where it may not be expected.

Red foxes (Vulpes vulpes) are native to boreal and western montane portions of North America but their origins are unknown in many lowland areas of the United States. Red foxes were historically absent from much of the East Coast at the time of European settlement and did not become common until the mid-1800s. Some early naturalists described an apparent southward expansion of native foxes that coincided with anthropogenic habitat changes in the region. Alternatively, red foxes introduced from Europe during Colonial times may have become established in the east and subsequently expanded their range westward. The red fox also was absent historically from most lowland areas of the western United States. Extant populations of red foxes in those areas are considered to have arisen from intentional introductions from the east (and by extension are putatively European), escapes or releases from fur farms, or range expansions by native populations. To test these hypotheses we compared mitochondrial DNA sequences (cytochrome b and D-loop) from 110 individuals from 6 recently established populations to 327 native (primarily historical) individuals from Eurasia, Alaska, Canada, the northeastern United States, and montane areas in the western contiguous United States, and to 38 individuals from fur farms. We found no Eurasian haplotypes in North America, but found native haplotypes in recently established populations in the southeastern United States and in parts of the western United States. Red foxes from the southeastern United States were closely related to native populations in eastern Canada and the northeastern United States, suggesting that they originated from natural range expansions, not from translocation of European lineages, as was widely believed prior to this study. Similarly, recently established populations in the Great Basin and in western Oregon originated primarily from native populations in western montane regions, but also contained a few nonnative North American haplotypes. In contrast, populations in western Washington and southern California contained nonnative, highly admixed stock that clearly resulted from intracontinental translocations. Several common haplotypes in these populations originated in regions where fur-farm stocks originated. Although European red foxes translocated to the eastern United States during Colonial times may have contributed genetically to extant populations in that region, our findings suggest that most of the matrilineal ancestry of eastern red foxes originated in North America.

Background Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples ( N  = 298) obtained after the population recovery in the mid-1990s, were used as a reference. Results Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of N e were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected. Conclusions Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.

Strong anthropogenic impact has caused 28 of the currently recognized 55 species of deer (Cervidae) to be listed on the IUCN Red List. Particular threats to vulnerable species include habitat deterioration and hybridization with alien, introduced species. The scarcity of many species has severely hampered genetic analyses of their populations, including the detection of loci for cross-species amplification. Because deer antlers are shed and re-grown annually, antlers offer the possibility for non-invasive genetic sampling of large individual numbers, and may provide material for reference genotyping from historical samples stored in zoos, museums and trophy collections of rare and extinct species/populations. In this paper, we report cross-species amplification of 19 nuclear microsatellite loci and the amplification of 16S mtDNA for barcoding from nearly a third of all deer species worldwide based on high quality DNA extracted from antler bone up to 40 years old. Phylogenetic analysis based on mtDNA of seventeen species and five subspecies corroborate previously published phylogenetic data, thus confirming the specific resolution of the DNA extraction methodology.