Shu-Jin Luo

Shu-Jin Luo
Peking University | PKU · School of Life Sciences

Ph.D.

About

37
Publications
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Introduction

Publications

Publications (37)
Article
Full-text available
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 p...
Article
Full-text available
The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat ( Felis silvestris ) subspecies and whether it has contributed to cat ( F. s. catus ) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes...
Preprint
The avian eye color, generally referred to the color of the iris, results from both pigments and structural coloration. Avian iris colors exhibit striking interspecific and, in some domestic species, intraspecific variations, suggesting unique evolutionary and ecological histories. Here we tackled the genetic basis of the pearl (white) iris color i...
Preprint
Full-text available
The enigmatic Chinese mountain cat, endemic to the Qinghai-Tibet Plateau, has a controversial taxonomic status, whether a true species or conspecific with the wildcat (Felis silvestris ) and whether it may have contributed to the domestication of cats (F. s. catus ) in Asia. Here, we sampled 270 domestic and wild cats across China, sequenced 51 nuc...
Article
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...
Article
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 [...
Article
Full-text available
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 v...
Article
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 reflec...
Article
The tiger (Panthera tigris) is most recognized for its dark stripes against an orange background. Less well known are three other pelage color variants: white, golden and stripeless snow white (Figure 1A).
Article
Full-text available
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 basi...
Article
Full-text available
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 theoreti...
Article
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 origins of confiscated specimens will assist in law enforcement and wildlife forensics for this iconic flagship species. We developed the multiplex genotyping system...
Article
Full-text available
The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples includ...
Article
Full-text available
Asiatic black bears (Ursus thibetanus) are declining throughout much of their range. In China they are partially protected by a nature reserve system and rely heavily on hard mast as a food source prior to winter denning. Bears may compensate for mast shortages by raiding agricultural crops and killing livestock, mainly outside reserves where they...
Article
Domestic yaks (Bos grunniens) exhibit two major coat color variations: a brown vs. wild-type black pigmentation and a white spotting vs. wild-type solid color pattern. The genetic basis for these variations in color and distribution remains largely unknown and may be complicated by a breeding history involving hybridization between yaks and cattle....
Article
Full-text available
The dynamic geological and climatological history of Southeast Asia has spawned a complex array of ecosystems and 12 of the 37 cat species, making it the most felid-rich region in the world. To examine evolutionary histories of these poorly-known faunas, we compared phylogeography of six species (leopard cat Prionailurus bengalensis, fishing cat P....
Article
Full-text available
Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic si...
Article
Full-text available
The white tiger, an elusive Bengal tiger (Panthera tigris tigris) variant with white fur and dark stripes, has fascinated humans for centuries ever since its discovery in the jungles of India [1]. Many white tigers in captivity are inbred in order to maintain this autosomal recessive trait [2-5] and consequently suffer some health problems, leading...
Article
Full-text available
Recent genetic analysis has shown that the extinct Caspian Tiger (P. t. virgata) and the living Amur Tigers (P. t. altaica) of the Russian Far East are actually taxonomically synonymous and that Caspian and Amur groups historically formed a single population, only becoming separated within the last 200 years by human agency. A major conservation im...
Article
Full-text available
The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis), distinct from the Amur tiger of the Russian Far East (P. t. altaica). However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have be...
Article
Full-text available
The rapidly changing field of molecular genetics, particularly advances in genome sequence analyses, has provided new tools to reconstruct what defines a tiger and its origins. The evolutionary history framing the tiger into the exquisite predator has ancestral roots and history are depicted in its phylogeography, the genetic patterns of diversific...
Article
The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstr...
Conference Paper
Full-text available
Pangolins are strange mammals having atypical morphological characteristics in part resulting from a highly specialized diet of ants and termites. Curiously, the Pholidota have as sister group the Carnivora, with which they share a common ancestor around 70 million years ago. Pangolins are found into two distinct geographical regions: Africa and As...
Article
Tigers (Panthera tigris) are disappearing rapidly from the wild, from over 100,000 in the 1900s to as few as 3000. Javan (P.t. sondaica), Bali (P.t. balica), and Caspian (P.t. virgata) subspecies are extinct, whereas the South China tiger (P.t. amoyensis) persists only in zoos. By contrast, captive tigers are flourishing, with 15,000-20,000 individ...
Article
Full-text available
Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymor...
Article
Thirty-four polymorphic dinucleotide microsatellite loci were developed in the Malayan pangolin Manis javanica. Of the 34 markers, 32 and 18 were also amplified, respectively, in the Chinese pangolin (Manis pentadactyla) and the African tree pangolin (Manis tricuspis). Analysis of 24 Malayan, 12 Chinese and 2 African tree pangolins showed high leve...
Article
Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P....
Article
Full-text available
Of eight traditionally classified subspecies of the tiger Panthera tigris three have recently gone extinct and poaching, habitat loss and fragmentation continue to threaten its survival. China historically harbors four of the existing subspecies and thus has high conservation priority, yet their status, both in the wild and captivity, remains highl...
Data
Bayesian Population Structure Analysis of 111 Tigers Data obtained from microsatellite genotype and mitochondrial haplotype data were analyzed using STRUCTURE (Pritchard et al. 2000). Simulations were set at 50,000 burn-in period followed by 106 replicates. Each individual is represented by a thin vertical bar, which is partitioned into K colored s...
Data
Bayesian Clustering Analyses for Tiger Microsatellite and Mitochondrial Data (59 KB DOC).
Data
Phylogenetic Relationships among the Individual Tigers from Composite Microsatellite Genotypes of 30 Loci Branches of the same color represent tiger individuals of the same classically named subspecies. NJ tree constructed based on kinship coefficient (Dkf) with the (1 – kf) option in MICROSAT (Minch et al. 1995). Numbers are individual Pti codes (...
Article
Full-text available
Eight traditional subspecies of tiger (Panthera tigris),of which three recently became extinct, are commonly recognized on the basis of geographic isolation and morphological characteristics. To investigate the species' evolutionary history and to establish objective methods for subspecies recognition, voucher specimens of blood, skin, hair, and/or...