Forensic assessment of kinship, genomic ancestry, and natural history of an iconic tiger of Harlem, New York City.

In the fall of 2003, a 2-yr-old tiger named Ming, weighing around 300 pounds, was discovered living in an apartment in Harlem, New York. Ming's rescue by NYPD was witnessed, recalled, and venerated by scores of neighbors. The tiger's history and ancestry stimulated considerable media interest, investigative sleuthing, and forensic genomic analyses.

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals.

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species.

An Enhanced Method for the Use of Reptile Skin Sheds as a High-Quality DNA Source for Genome Sequencing.

With the emergence of high-throughput sequencing technology, a number of non-avian reptile species have been sequenced at the genome scale, shedding light on various scientific inquiries related to reptile ecology and evolution. However, the routine requirement of tissue or blood samples for genome sequencing often poses challenges in many elusive reptiles, hence limiting the application of high-throughput sequencing technologies to reptile studies. An alternative reptilian DNA resource suitable for genome sequencing is in urgent need.

Genomic analysis reveals a cryptic pangolin species.

Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population.

Ancient DNA reveals genetic admixture in China during tiger evolution.

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.

Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.

We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males.

Genetic mapping and molecular mechanism behind color variation in the Asian vine snake.

Background: Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.

Results: We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations.

Phylogeography of the endangered "eyed" turtles (genus ) and the discovery of a lineage derived from natural interspecific hybridization.

The herpetofauna of the Indomalayan bioregion of Asia suffers from severe habitat loss, unsustainable harvesting, and lack of research and conservation. Here, we investigated the range-wide phylogeography of the endangered "eyed" turtles (genus , including the Beale's Eyed Turtle and the Four-eyed Turtle ) and discovered a natural interspecific hybrid turtle population in China. Based on phylogeny of the mitochondrial Cytochrome b gene of 101 samples in this study and public data, three major clades and six subclades were identified: (SBE) in eastern-southern China, east in South China (northern east [SQUen] and southern east [SQUes] subclades), and west mainly in Vietnam (northern west [SQUwn], central west [SQUwc], and southern west [SQUws] subclades).

The genetics and evolution of eye color in domestic pigeons (Columba livia).

The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration.

Genomic evidence for the Chinese mountain cat as a wildcat conspecific () and its introgression to domestic cats.

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat () subspecies and whether it has contributed to cat () domestication in East Asia. Here, we sampled lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific , which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat ().

Sorting Out the Genetic Background of the Last Surviving South China Tigers.

The South China tiger (Panthera tigris amoyensis) is endemic to China and also the most critically endangered subspecies of living tigers. It is considered extinct in the wild and only about 150 individuals survive in captivity to date, whose genetic heritage, however, is ambiguous and controversial. Here, we conducted an explicit genetic assessment of 92 studbook-registered South China tigers from 14 captive facilities using a subspecies-diagnostic system in the context of comparison with other voucher specimens to evaluate the genetic ancestry and level of distinctiveness of the last surviving P.

Tigers of the World: Genomics and Conservation.

Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales.

Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World's Tigers.

No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3-6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7].

Effects of the Qinghai-Tibet Railway on the Landscape Genetics of the Endangered Przewalski's Gazelle (Procapra przewalskii).

The Przewalski's gazelle (Procapra przewalskii) is one of the most endangered ungulates in the world, with fewer than 2,000 individuals surviving in nine habitat fragments on the Qinghai-Tibet Plateau and isolated by human settlements and infrastructure. In particular, the Qinghai-Tibet railway, which crosses the largest part of the gazelle's distribution, remains a major concern because of its potential to intensify landscape genetic differentiation. Here, using mtDNA sequencing and microsatellite genotyping to analyze 275 Przewalski's gazelle samples collected throughout the range, we observed low level of genetic diversity (mtDNA π = 0.

The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth.

Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here, we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and 9 nuclear genes.

Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein.

Cephalopods, the group of animals including octopus, squid, and cuttlefish, have remarkable ability to instantly modulate body coloration and patterns so as to blend into surrounding environments [1, 2] or send warning signals to other animals [3]. Reflectin is expressed exclusively in cephalopods, filling the lamellae of intracellular Bragg reflectors that exhibit dynamic iridescence and structural color change [4]. Here, we trace the possible origin of the reflectin gene back to a transposon from the symbiotic bioluminescent bacterium Vibrio fischeri and report the hierarchical structural architecture of reflectin protein.

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification.

Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp).

Whole Genome Sequencing Identifies a Missense Mutation in HES7 Associated with Short Tails in Asian Domestic Cats.

Domestic cats exhibit abundant variations in tail morphology and serve as an excellent model to study the development and evolution of vertebrate tails. Cats with shortened and kinked tails were first recorded in the Malayan archipelago by Charles Darwin in 1868 and remain quite common today in Southeast and East Asia. To elucidate the genetic basis of short tails in Asian cats, we built a pedigree of 13 cats segregating at the trait with a founder from southern China and performed linkage mapping based on whole genome sequencing data from the pedigree.

Pangolin genomes and the evolution of mammalian scales and immunity.

Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins.

The phylogeography of Fagus hayatae (Fagaceae): genetic isolation among populations.

The beech species Fagus hayatae is an important relict tree species in subtropical China, whose biogeographical patterns may reflect floral responses to climate change in this region during the Quaternary. Previous studies have revealed phylogeography for three of the four Fagus species in China, but study on F. hayatae, the most sparsely distributed of these species, is still lacking.

A magnetic protein biocompass.

The notion that animals can detect the Earth's magnetic field was once ridiculed, but is now well established. Yet the biological nature of such magnetosensing phenomenon remains unknown. Here, we report a putative magnetic receptor (Drosophila CG8198, here named MagR) and a multimeric magnetosensing rod-like protein complex, identified by theoretical postulation and genome-wide screening, and validated with cellular, biochemical, structural and biophysical methods.

The development and application of a multiplex short tandem repeat (STR) system for identifying subspecies, individuals and sex in tigers.

Poaching and trans-boundary trafficking of tigers and body parts are threatening the world's last remaining wild tigers. Development of an efficient molecular genetic assay for tracing the origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed a multiplex genotyping system "tigrisPlex" to simultaneously assess 22 short tandem repeat (STR, or microsatellite) loci and a gender-identifying SRY gene, all amplified in 4 reactions using as little as 1 ng of template DNA.