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Browsing by Author "Koepfli, Klaus-Peter"

Browsing by Author "Koepfli, Klaus-Peter"

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  • Applying genomics to metapopulation management in North American insurance populations of southern sable antelope (Hippotragus niger niger) and addra gazelle (Nanger dama ruficollis) 
    Gooley, Rebecca M.; Dicks, Kara L.; Ferrie, Gina M.; Lacy, Robert C.; Ballou, Jonathan D.; Callicrate, Taylor; Senn, Helen; Koepfli, Klaus-Peter; Edwards, Cody W.; Pukazhenthi, Budhan S. (2022)
    Insurance populations can provide a short-term safeguard for at-risk species. The goal for all insurance populations should be to maintain a high welfare, genetically diverse, self-sustaining population that is available ...
  • Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter 
    Beichman, Annabel C.; Koepfli, Klaus-Peter; Li, Gang; Murphy, William; Dobrynin, Pasha; Kilver, Sergei; Tinker, M. T.; Murray, Michael J.; Johnson, Jeremy; Lindblad-Toh, Kerstin; Karlsson, Elinor K.; Lohmueller, Kirk E.; Wayne, Robert K. (2019)
    Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely ...
  • Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours 
    Kukekova, Anna V.; Johnson, Jennifer L.; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Rando, Halie M.; Kharlamova, Anastasiya V.; Herbeck, Yury; Serdyukova, Natalya A.; Xiong, Zijun; Beklemischeva, Violetta; Koepfli, Klaus-Peter; Gulevich, Rimma G.; Vladimirova, Anastasiya V.; Hekman, Jessica P.; Perelman, Polina L.; Graphodatsky, Aleksander S.; O'Brien, Stephen J.; Wang, Xu; Clark, Andrew G.; Acland, Gregory M.; Trut, Lyudmila N.; Zhang, Guojie (2018)
    In the version of this Article originally published, there were some errors in the affiliations: Stephen J. O'Brien's affiliations were incorrectly listed as 8,9; they should have been 7,9. Affiliation 3 was incorrectly ...
  • Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (<I>Hippotragus leucophaeus</I>) 
    Hempel, Elisabeth; Bibi, Faysal; Faith, J. T.; Koepfli, Klaus-Peter; Klittich, Achim M.; Duchêne, David,A.; Brink, James S.; Kalthoff, Daniela C.; Dalén, Love; Hofreiter, Michael; Westbury, Michael V. (2022)
    The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that ...
  • Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations 
    Wildt, David; Miller, Philip; Koepfli, Klaus-Peter; Pukazhenthi, Budhan; Palfrey, Katy; Livingston, Gavin; Beetem, Dan; Shurter, Stephen; Gregory, Jimmy; Takács, Michael; Snodgrass, Kelley (2019)
    Human-induced changes to environments are causing species declines. Beyond preserving habitat (in situ), insurance (ex situ) populations are essential to prevent species extinctions. The Conservation Centers for Species ...
  • Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates 
    Damas, Joana; Hughes, Graham M.; Keough, Kathleen C.; Painter, Corrie A.; Persky, Nicole S.; Corbo, Marco; Hiller, Michael; Koepfli, Klaus-Peter; Pfenning, Andreas R.; Zhao, Huabin; Genereux, Diane P.; Swofford, Ross; Pollard, Katherine S.; Ryder, Oliver A.; Nweeia, Martin T.; Lindblad-Toh, Kerstin; Teeling, Emma C.; Karlsson, Elinor K.; Lewin, Harris A. (2020)
    Abstract The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand ...
  • Characteristics of the complete mitochondrial genome of the monotypic genus <I>Arctictis</I> (Family: Viverridae) and its phylogenetic implications 
    Mitra, Siuli; Kunteepuram, Vaishnavi; Koepfli, Klaus-Peter; Mehra, Neha; Tabasum, Wajeeda; Sreenivas, Ara; Gaur, Ajay (2019)
    The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, ...
  • Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild 
    Humble, Emily; Dobrynin, Pavel; Senn, Helen; Chuven, Justin; Scott, Alan F.; Mohr, David W.; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Lieberman Aiden, Erez; Al Dhaheri, Shaikha Salem; Wildt, David; Oliaji, Shireen; Tamazian, Gaik; Pukazhenthi, Budhan; Ogden, Rob; Koepfli, Klaus-Peter (2020)
    Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a ...
  • Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal 
    Yakupova, Aliya; Tomarovsky, Andrey; Totikov, Azamat; Beklemisheva, Violetta; Logacheva, Maria; Perelman, Polina L.; Komissarov, Aleksey; Dobrynin, Pavel; Krasheninnikova, Ksenia; Tamazian, Gaik; Serdyukova, Natalia A.; Rayko, Mike; Bulyonkova, Tatiana; Cherkasov, Nikolay; Pylev, Vladimir; Peterfeld, Vladimir; Penin, Aleksey; Balanovska, Elena; Lapidus, Alla; DNA, Zoo Consortium; OBrien, Stephen J.; Graphodatsky, Alexander; Koepfli, Klaus-Peter; Kliver, Sergei (2023)
    Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers ...
  • Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity 
    Houck, Marlys L.; Koepfli, Klaus-Peter; Hains, Taylor; Khan, Ruqayya; Charter, Suellen J.; Fronczek, Julie A.; Misuraca, Ann C.; Kliver, Sergei; Perelman, Polina L.; Beklemisheva, Violetta; Graphodatsky, Alexander; Luo, Shu-Jin; O’Brien, Stephen J.; Lim, Norman T. -L; Chin, Jason S. C.; Guerra, Vanessa; Tamazian, Gaik; Omer, Arina; Weisz, David; Kaemmerer, Kenneth; Sturgeon, Ginger; Gaspard, Joseph; Hahn, Alicia; McDonough, Mark; Garcia-Treviño, Isabel; Gentry, Jordan; Coke, Rob L.; Janecka, Jan E.; Harrigan, Ryan J.; Tinsman, Jen; Smith, Thomas B.; Aiden, Erez Lieberman; Dudchenko, Olga (2023)
  • Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (<I>Mustela nigripes</I>) 
    Kliver, Sergei; Houck, Marlys L.; Perelman, Polina L.; Totikov, Azamat; Tomarovsky, Andrei; Dudchenko, Olga; Omer, Arina D.; Colaric, Zane; Weisz, David; Aiden, Erez Lieberman; Chan, Saki; Hastie, Alex; Komissarov, Aleksey; Ryder, Oliver A.; Graphodatsky, Alexander; Johnson, Warren E.; Maldonado, Jesús E.; Pukazhenthi, Budhan S.; Marinari, Paul E.; Wildt, David E.; Koepfli, Klaus-Peter (2023)
    The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation ...
  • Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology 
    Totikov, Azamat; Tomarovsky, Andrey; Prokopov, Dmitry; Yakupova, Aliya; Bulyonkova, Tatiana; Derezanin, Lorena; Rasskazov, Dmitry; Wolfsberger, Walter W.; Koepfli, Klaus-Peter; Oleksyk, Taras K.; Kliver, Sergei (2021)
    Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, ...
  • Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences 
    Tamazian, Gaik; Dobrynin, Pavel; Krasheninnikova, Ksenia; Komissarov, Aleksey; Koepfli, Klaus-Peter; O'Brien, Stephen J. (2016)
    BackgroundAs the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, ...
  • A collective statement in support of saving pangolins 
    Choo, Siew Woh; Chong, Ju Lian; Gaubert, Philippe; Hughes, Alice Catherine; O'Brien, Stephen; Chaber, Anne-Lise; Antunes, Agostinho; Platto, Sara; Sun, Nick Ching-Min; Yu, Li; Koepfli, Klaus-Peter; Suwal, Tulshi Laxmi; Thakur, Mukesh; Ntie, Stephan; Panjang, Elisa; Kumaran, Jayaraj Vijaya; Mahmood, Tariq; Heighton, Sean P.; Dorji, Dago; Gonedele, Bi Sery; Nelson, Bryan Raveen; Djagoun, Chabi A. M. S.; Loh, Ing Hoe; Kaspal, Prativa; Pauklin, Siim; Michelena, Toby; Zhu, Hongxiang; Lipovich, Leonard; Tian, Xuechen; Deng, Siwei; Mason, Christopher E.; Hu, Jingyang; White, Robert; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Tze King; Wong, Kum Thong; Paterson, Steve; Chen, Ming; Zhang, Yixin; Othman, Rofina Yasmin; Brown, Larry C.; Shen, Bairong; Shui, Guanghou; Ang, Mia Yang; Zhao, Yunqi; Li, Yongming; Zhang, Bo; Chong, Cheng Tung; Meng, Yu; Wong, Aloysius; Su, Jianzhong; Omar, Hasmahzaiti; Shen, Hua; Tan, Choo Hock; Xu, Hongyu; Paterson, Ian C.; Wang, Minyan; Chan, Chee-Kai; Zhang, Siyuan; Dutta, Avirup; Tee, Tay Sun; Juvigny-Khenafou, Noel P. D.; Mutha, Naresh V. R.; Aziz, Muhamad Afiq (2022)
  • Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance 
    Pumpitakkul, Vichayanee; Chetruengchai, Wanna; Srichomthong, Chalurmpon; Phokaew, Chureerat; Pootakham, Wirulda; Sonthirod, Chutima; Nawae, Wanapinun; Tongsima, Sissades; Wangkumhang, Pongsakorn; Wilantho, Alisa; Utara, Yongchai; Thongpakdee, Ampika; Sanannu, Saowaphang; Maikaew, Umaporn; Khuntawee, Suphattharaphonnaphan; Changpetch, Wirongrong; Phromwat, Phairot; Raschasin, Kacharin; Sarnkhaeveerakul, Phunyaphat; Supapannachart, Pannawat; Buthasane, Wannapol; Pukazhenthi, Budhan S.; Koepfli, Klaus-Peter; Suriyaphol, Prapat; Tangphatsornruang, Sithichoke; Suriyaphol, Gunnaporn; Shotelersuk, Vorasuk (2023)
    Eld’s deer, a conserved wildlife species of Thailand, is facing inbreeding depression, particularly in the captive Siamese Eld’s deer (SED) subspecies. In this study, we constructed genomes of a male SED and a male Burmese ...
  • Comparative genomics provides new insights into the remarkable adaptations of the African wild dog (<I>Lycaon pictus</I>) 
    Chavez, Daniel E.; Gronau, Ilan; Flains, Taylor; Kliver, Sergei; Koepfli, Klaus-Peter; Wayne, Robert K. (2019)
    Within the Canidae, the African wild dog (Lycaon pictus) is the most specialized with regards to cursorial adaptations (specialized for running), having only four digits on their forefeet. In addition, this species is one ...
  • Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids 
    Chavez, Daniel E.; Gronau, Ilan; Hains, Taylor; Dikow, Rebecca B.; Frandsen, Paul B.; Figueiró, Henrique V.; Garcez, Fabrício S.; Tchaicka, Ligia; de Paula, Rogério C.; Rodrigues, Flávio H. G.; Jorge, Rodrigo S. P.; Lima, Edson S.; Songsasen, Nucharin; Johnson, Warren E.; Eizirik, Eduardo; Koepfli, Klaus-Peter; Wayne, Robert K. (2022)
    The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, ...
  • Comparison of genomic diversity and structure of sable antelope (<I>Hippotragus niger</I>) in zoos, conservation centers, and private ranches in North America 
    Gooley, Rebecca M.; Tamazian, Gaik; Castaneda-Rico, Susette; Murphy, Katherine R.; Dobrynin, Pavel; Ferrie, Gina M.; Haefele, Holly; Maldonado, Jesus E.; Wildt, David E.; Pukazhenthi, Budhan S.; Edwards, Cody W.; Koepfli, Klaus-Peter (2020)
    As we enter the sixth mass extinction, many species that are no longer self-sustaining in their natural habitat will require ex situ management. Zoos have finite resources for ex situ management, and there is a need for ...
  • The complete mitochondrial genome and phylogenetic characterization of two putative subspecies of golden jackal (Canis aureus cruesemanni and Canis aureus moreotica) 
    Sosale, Medhini S.; Songsasen, Nucharin; Ibis, Osman; Edwards, Cody W.; Figueiró, Henrique V.; Koepfli, Klaus-Peter (2023)
  • Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx 
    Humble, Emily; Stoffel, Martin A.; Dicks, Kara; Ball, Alex D.; Gooley, Rebecca M.; Chuven, Justin; Pusey, Ricardo; Remeithi, Mohammed Al; Koepfli, Klaus-Peter; Pukazhenthi, Budhan S.; Senn, Helen; Ogden, Rob (2023)
    In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring ...

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