The Evolutionary Dynamics Of The Lion Panthera Leo Revealed By Host And Viral Population Genomics, 2016 National Cancer Institute at Frederick; Universidade do Porto
The Evolutionary Dynamics Of The Lion Panthera Leo Revealed By Host And Viral Population Genomics, Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Graham Hemson, Laurence G. Frank, Philip Stander, Ludwig Siefert, Margaret Driciru, Paul J. Funston, Kathy A. Alexander, Katherine C. Prager, Gus Mills, David E. Wildt, Mitch E. Bush, Stephen J. O'Brien, Warren E. Johnson
The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIVPle), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse ...
The Tiger Genome And Comparative Analysis With Lion And Snow Leopard Genomes, 2016 Genome Research Foundation - Republic of Korea
The Tiger Genome And Comparative Analysis With Lion And Snow Leopard Genomes, Yun Sung Cho, Li Hu, Haolong Hou, Hang Lee, Jiaohui Xu, Soowhan Kwon, Sukhun Oh, Hak-Min Kim, Sungwoong Jho, Sangsoo Kim, Young-Ah Shin, Byung Chul Kim, Hyunmin Kim, Chang-Uk Kim, Shu-Jin Luo, Warren E. Johnson, Klaus-Peter Koepfli, A. Schmidt-Kunzel, Jason A. Turner, L. Marker, Cindy K. Harper, Susan M. Miller, Wilhelm Jacobs, Laura D. Bertola, Tae Hyung Kim, Sunghoon Lee, Qian Zhou, Hyun-Ju Jung, Xiao Xu, Priyvrat Gadhvi, Pengwei Xu, Yingqi Xiong, Yadan Luo, Shengkai Pan, Caiyun Gou, Xiuhui Chu, Jilin Zhang, Sanyang Liu, Jing He, Ying Chen, Linfeng Yang, Yulan Yang, Jiaju He, Sha Liu, Junyi Wang, Chul Hong Kim, Hwanjong Kwak, Jong-Soo Kim, Seungwoo Hwang, Junsu Ko, Chang-Bae Kim, Sangtae Kim, Damdin Bayarlkhagva, Woon Kee Paek, Seong-Jin Kim, Stephen J. O'Brien, Jun Wang, Jong Bhak
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 signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR ...
The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, 2016 Genome Research Foundation - Republic of Korea
The First Whole Genome And Transcriptome Of The Cinereous Vulture Reveals Adaptation In The Gastric And Immune Defense Systems And Possible Convergent Evolution Between The Old And New World Vultures, Oksung Chung, Seondeok Jin, Yun Sung Cho, Jeongheui Lim, Hyunho Kim, Sungwoong Jho, Hak-Min Kim, Jehoon Jun, Hyejin Lee, Alvin Chon, Junsu Ko, Jeremy Edwards, Jessica A. Weber, Kyudong Han, Stephen J. O'Brien, Andrea Manica, Jong Bhak, Woon Kee Paek
Background: The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with constant exposure to pathogens, making this species an interesting target for discovering functionally selected genetic variants. Furthermore, the presence of two independently evolved vulture groups, Old World and New World vultures, provides a natural experiment in which to investigate convergent evolution due to obligate scavenging.
Results: We sequenced the genome of a cinereous vulture, and mapped it to the bald eagle reference genome ...
The Dynamic Proliferation Of Cansines Mirrors The Complex Evolution Of Feliforms, 2016 American University
The Dynamic Proliferation Of Cansines Mirrors The Complex Evolution Of Feliforms, Kathryn B. Walters-Conte, Diana L. E. Johnson, Warren E. Johnson, Stephen J. O'Brien, Jill Pecon-Slattery
Background: Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the ...
The Adaptive Evolution Of The Mammalian Mitochondrial Genome, 2016 Universidade do Porto - Portugal; University of Copenhagen - Denmark
The Adaptive Evolution Of The Mammalian Mitochondrial Genome, Rute R. Da Fonseca, Warren E. Johnson, Stephen J. O'Brien, Maria J. Ramos, Agostinho Antunes
The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.
Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation ...
Subspecific Status Of The Korean Tiger Inferred By Ancient Dna Analysis, 2016 Seoul National University - South Korea; National Cancer Institute at Frederick
Subspecific Status Of The Korean Tiger Inferred By Ancient Dna Analysis, Mu-Yeong Lee, Jee Yun Hyun, Seo-Jin Lee, Junghwa An, Eunok Lee, Mi-Sook Min, Junpei Kimura, Shin-Ichirio Kawada, Nozomi Kurihara, Shu-Jin Luo, Stephen J. O'Brien, Warren E. Johnson, Hang Lee
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 been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far ...
Recurrent Evolution Of Melanism In South American Felids, 2016 PUCRS - Brazil
Recurrent Evolution Of Melanism In South American Felids, Alexsandra Schneider, Corneliu Henegar, Kenneth Day, Devin Absher, Constanza Napolitano, Leandro Silveira, Victor A. David, Stephen J. O'Brien, Marilyn Menotti-Raymond, Gregory S. Barsh, Eduardo Eizirik
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes of melanism in three closely related South American species: the pampas cat (Leopardus colocolo), the kodkod (Leopardus guigna), and Geoffroy’s cat (Leopardus geoffroyi). To ...
Reconstructing The Genomic Architecture Of Mammalian Ancestors Using Multispecies Comparative Maps, 2016 National Cancer Institute at Frederick
Reconstructing The Genomic Architecture Of Mammalian Ancestors Using Multispecies Comparative Maps, William J. Murphy, Guillaume Bourque, Glenn Tesler, Pavel Pevzner, Stephen J. O'Brien
Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are ...
Primate Tnf Promoters Reveal Markers Of Phylogeny And Evolution Of Innate Immunity, 2016 Harvard Medical School
Primate Tnf Promoters Reveal Markers Of Phylogeny And Evolution Of Innate Immunity, Andres Baena, Alan R. Mootnick, James V. Falvo, Alla V. Tsytsykova, Filipa Ligeiro, Ousmane M. Diop, Claudia Brieva, Pascal Gagneux, Stephen J. O'Brien, Oliver A. Ryder, Anne E. Goldfeld
Background. Tumor necrosis factor (TNF) is a critical cytokine in the immune response whose transcriptional activation is controlled by a proximal promoter region that is highly conserved in mammals and, in particular, primates. Specific single nucleotide polymorphisms (SNPs) upstream of the proximal human TNF promoter have been identified, which are markers of human ancestry.
Methodology/Principal findings. Using a comparative genomics approach we show that certain fixed genetic differences in the TNF promoter serve as markers of primate speciation. We also demonstrate that distinct alleles of most human TNF promoter SNPs are identical to fixed nucleotides in primate TNF promoters ...
Phylogeography And Genetic Ancestry Of Tigers (Panthera Tigris), 2016 National Cancer Institute at Frederick; University of Minnesota - St. Paul
Phylogeography And Genetic Ancestry Of Tigers (Panthera Tigris), Shu-Jin Luo, Jae-Heup Kim, Warren E. Johnson, Joelle Van Der Walt, Janice S. Martenson, Naoya Yuhki, Dale Miquelle, Olga Uphyrkina, John M. Goodrich, Howard Quigley, R. Tilson, Gerald Brady, Paolo Martelli, Vellayan Subramaniam, Charles Mcdougal, Sun Hean, Shi-Qiang Huang, Wenshi Pan, Ullas K. Karanth, Melvin Sunquist, James L. D. Smith, Stephen J. O'Brien
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 skin biopsies from 134 tigers with verified geographic origins or heritage across the whole distribution range were examined for three molecular markers: (1) 4.0 kb of mitochondrial DNA (mtDNA) sequence; (2) allele variation in the nuclear major histocompatibility complex class II DRB gene; and (3) composite nuclear microsatellite genotypes based on 30 ...
Mitochondrial Genomes Reveal An Explosive Radiation Of Extinct And Extant Bears Near The Miocene-Pliocene Boundary, 2016 Max Planck Institute for Evolutionary Anthropology - Leipzig, Germany
Mitochondrial Genomes Reveal An Explosive Radiation Of Extinct And Extant Bears Near The Miocene-Pliocene Boundary, Johannes Krause, Tina Unger, Aline Nocon, Anna-Sapfo Malaspinas, Sergios-Orestis Kolokotronis, Mathias Stiller, Leopoldo Soibelzon, Helen Spriggs, Paul H. Dear, Adrian W. Briggs, Sarah C. E. Bray, Stephen J. O'Brien, Gernot Rabeder, Paul Matheus, Alan Cooper, Montgomery Slatkin, Svante Paabo, Michael Hofreiter
Background: Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods.
Results: We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus ...
Mitochondrial Phylogeography Illuminates The Origin Of The Extinct Caspian Tiger And Its Relationship To The Amur Tiger, 2016 University of Oxford; National Cancer Institute at Frederick
Mitochondrial Phylogeography Illuminates The Origin Of The Extinct Caspian Tiger And Its Relationship To The Amur Tiger, Carlos A. Driscoll, Nobuyuki Yamaguchi, Gila Kahila Bar-Gal, Alfred L. Roca, Shu-Jin Luo, David W. Macdonald, Stephen J. O'Brien
The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary ...
Mammalian Keratin Associated Proteins (Krtaps) Subgenomes: Disentangling Hair Diversity And Adaptation To Terrestrial And Aquatic Environments, 2016 Universidade do Porto - Portugal
Mammalian Keratin Associated Proteins (Krtaps) Subgenomes: Disentangling Hair Diversity And Adaptation To Terrestrial And Aquatic Environments, Imran Khan, Emanuel Maldonado, Vitor Vasconcelos, Stephen J. O'Brien, Warren E. Johnson, Agostinho Antunes
Background Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation.
Results We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high ...
Light Whole Genome Sequence For Snp Discovery Across Domestic Cat Breeds, 2016 National Institutes of Health at Bethesda
Light Whole Genome Sequence For Snp Discovery Across Domestic Cat Breeds, James C. Mullikin, Nancy F. Hansen, Lei Shen, Heather Ebling, William F. Donahue, Wei Tao, David J. Saranga, Adrianne Brand, Marc J. Rubenfield, Alice C. Young, Pedro Cruz, Carlos Driscoll, Victor David, Samer W. K. Al-Murrani, Mary F. Locniskar, Mitchell S. Abrahamsen, Stephen J. O'Brien, Douglas R. Smith, Jeffrey A. Brockman
The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.
To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly ...
Genomic Legacy Of The African Cheetah, Acinonyx Jubatus, 2016 St. Petersburg State University - Russia
Genomic Legacy Of The African Cheetah, Acinonyx Jubatus, Pavel Dobrynin, Shiping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergey Kliver, A. Schmidt-Kunzel, Klaus-Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel Garcia-Perez, Marc De Manuel, Ricardo Godinez, Aleksey Komissarov, Alexey Makunin, Vladimir Brukhin, Weilin Qiu, Long Zhou, Fang Li, Jian Yi, Carlos A. Driscoll, Agostinho Antunes, T. K. Oleksyk, Eduardo Eizirik, Polina Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomas Marques-Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O'Brien
Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.
Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ...
Genomic Microsatellites As Evolutionary Chronometers: A Test In Wild Cats, 2016 National Cancer Institute at Frederick
Genomic Microsatellites As Evolutionary Chronometers: A Test In Wild Cats, Carlos A. Driscoll, Marilyn Menotti-Raymond, George Nelson, David Goldstein, Stephen J. O'Brien
Nuclear microsatellite loci (2- to 5-bp tandem repeats) would seem to be ideal markers for population genetic monitoring because of their abundant polymorphism, wide dispersal in vertebrate genomes, near selective neutrality, and ease of assessment; however, questions about their mode of generation, mutation rates and ascertainment bias have limited interpretation considerably. We have assessed the patterns of genomic diversity for ninety feline microsatellite loci among previously characterized populations of cheetahs, lions and pumas in recapitulating demographic history. The results imply that the microsatellite diversity measures (heterozygosity, allele reconstitution and microsatellite allele variance) offer proportionate indicators, albeit with large variance, of ...
Gene Loss, Adaptive Evolution And The Co-Evolution Of Plumage Coloration Genes With Opsins In Birds, 2016 Universidade do Porto - Portugal
Gene Loss, Adaptive Evolution And The Co-Evolution Of Plumage Coloration Genes With Opsins In Birds, Rui Borges, Imran Khan, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes
Background: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems.
Results: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were ...
Clouded Leopard Phylogeny Revisited: Support For Species Recognition And Population Division Between Borneo And Sumatra, 2016 University of Wurzburg - Germany
Clouded Leopard Phylogeny Revisited: Support For Species Recognition And Population Division Between Borneo And Sumatra, Andreas Wilting, Valerie A. Buckley-Beason, Heike Feldhaar, Jurgen Gadau, Stephen J. O'Brien, K. Eduard Linsenmair
The clouded leopard (Neofelis nebulosa) is one of the least known cat species and depletion of their forested habitats puts it under heavy pressure. Recently reclassification of Bornean clouded leopards (N. nebulosa diardi) to species level (N.diardi) was suggested based on molecular and morphological evidence. Since the genetic results were based solely on three Bornean samples we re-evaluated this partition using additional samples of Bornean clouded leopards (N = 7) and we were also able to include specimens from Sumatra (N = 3), which were lacking in previous analysis.
We found strong support for the distinction between N. nebulosa ...
Comparative Genome Organization Of Human, Murine, And Feline Mhc Class Ii Region, 2016 National Cancer Institute at Frederick
Comparative Genome Organization Of Human, Murine, And Feline Mhc Class Ii Region, Naoya Yuhki, Thomas W. Beck, Robert M. Stephens, Yoko Nishigaki, Kymberly Newmann, Stephen J. O'Brien
To study comparative molecular dynamics in the genesis of the major histocompatibility complex (MHC), we determined a complete nucleotide sequence spanning 758,291 bp of the domestic cat (Felis catus) extended and classical class II region. The feline class II MHC includes 44 genes (31 predicted to be expressed) which display DNA sequence homology and ordered gene synteny with human HLA and mouse H2, in extended class II and centromere proximal regions (DM to DO) of the classical class II region. However, remarkable genomic alterations including gene gain and loss plus size differentials of 250 kb are evident in comparisons ...
Bone-Associated Gene Evolution And The Origin Of Flight In Birds, 2016 Universidade do Porto - Portugal
Bone-Associated Gene Evolution And The Origin Of Flight In Birds, Joao P. Machado, Warren E. Johnson, M. Thomas P. Gilbert, Guojie Zhang, Erich D. Jarvis, Stephen J. O'Brien, Agostinho Antunes
Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure.
We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost ...