ALBERT

Description: 〈p〉Mountains contribute disproportionately to the terrestrial biodiversity of Earth, especially in the tropics, where they host hotspots of extraordinary and puzzling richness. With about 25% of all land area, mountain regions are home to more than 85% of the world’s species of amphibians, birds, and mammals, many entirely restricted to mountains. Biodiversity varies markedly among these regions. Together with the extreme species richness of some tropical mountains, this variation has proven challenging to explain under traditional climatic hypotheses. However, the complex climatic characteristics of rugged mountain regions differ fundamentally from those of lowland regions, likely playing a key role in generating and maintaining diversity. With ongoing global changes in climate and land use, the role of mountains as refugia for biodiversity may well come under threat.〈/p〉

Description: 〈p〉Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth’s biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology—notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.〈/p〉

Description: Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, Ben G -- Lessard, Jean-Philippe -- Borregaard, Michael K -- Fritz, Susanne A -- Araujo, Miguel B -- Dimitrov, Dimitar -- Fabre, Pierre-Henri -- Graham, Catherine H -- Graves, Gary R -- Jonsson, Knud A -- Nogues-Bravo, David -- Wang, Zhiheng -- Whittaker, Robert J -- Fjeldsa, Jon -- Rahbek, Carsten -- New York, N.Y. -- Science. 2013 Jan 4;339(6115):74-8. doi: 10.1126/science.1228282. Epub 2012 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen O, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23258408" target="_blank"〉PubMed〈/a〉

Description: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390078/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Guojie -- Li, Cai -- Li, Qiye -- Li, Bo -- Larkin, Denis M -- Lee, Chul -- Storz, Jay F -- Antunes, Agostinho -- Greenwold, Matthew J -- Meredith, Robert W -- Odeen, Anders -- Cui, Jie -- Zhou, Qi -- Xu, Luohao -- Pan, Hailin -- Wang, Zongji -- Jin, Lijun -- Zhang, Pei -- Hu, Haofu -- Yang, Wei -- Hu, Jiang -- Xiao, Jin -- Yang, Zhikai -- Liu, Yang -- Xie, Qiaolin -- Yu, Hao -- Lian, Jinmin -- Wen, Ping -- Zhang, Fang -- Li, Hui -- Zeng, Yongli -- Xiong, Zijun -- Liu, Shiping -- Zhou, Long -- Huang, Zhiyong -- An, Na -- Wang, Jie -- Zheng, Qiumei -- Xiong, Yingqi -- Wang, Guangbiao -- Wang, Bo -- Wang, Jingjing -- Fan, Yu -- da Fonseca, Rute R -- Alfaro-Nunez, Alonzo -- Schubert, Mikkel -- Orlando, Ludovic -- Mourier, Tobias -- Howard, Jason T -- Ganapathy, Ganeshkumar -- Pfenning, Andreas -- Whitney, Osceola -- Rivas, Miriam V -- Hara, Erina -- Smith, Julia -- Farre, Marta -- Narayan, Jitendra -- Slavov, Gancho -- Romanov, Michael N -- Borges, Rui -- Machado, Joao Paulo -- Khan, Imran -- Springer, Mark S -- Gatesy, John -- Hoffmann, Federico G -- Opazo, Juan C -- Hastad, Olle -- Sawyer, Roger H -- Kim, Heebal -- Kim, Kyu-Won -- Kim, Hyeon Jeong -- Cho, Seoae -- Li, Ning -- Huang, Yinhua -- Bruford, Michael W -- Zhan, Xiangjiang -- Dixon, Andrew -- Bertelsen, Mads F -- Derryberry, Elizabeth -- Warren, Wesley -- Wilson, Richard K -- Li, Shengbin -- Ray, David A -- Green, Richard E -- O'Brien, Stephen J -- Griffin, Darren -- Johnson, Warren E -- Haussler, David -- Ryder, Oliver A -- Willerslev, Eske -- Graves, Gary R -- Alstrom, Per -- Fjeldsa, Jon -- Mindell, David P -- Edwards, Scott V -- Braun, Edward L -- Rahbek, Carsten -- Burt, David W -- Houde, Peter -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Avian Genome Consortium -- Jarvis, Erich D -- Gilbert, M Thomas P -- Wang, Jun -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R01 HL087216/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1311-20. doi: 10.1126/science.1251385. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. ; Royal Veterinary College, University of London, London, UK. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal. ; Department of Biological Sciences, University of South Carolina, Columbia, SC, USA. ; Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA. ; Department of Animal Ecology, Uppsala University, Norbyvagen 18D, S-752 36 Uppsala, Sweden. ; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia. Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore 169857, Singapore. ; Department of Integrative Biology University of California, Berkeley, CA 94720, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. College of Life Sciences, Wuhan University, Wuhan 430072, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. BGI Education Center,University of Chinese Academy of Sciences,Shenzhen, 518083, China. ; Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. ; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK. ; School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. ; Centro de Investigacion en Ciencias del Mar y Limnologia (CIMAR)/Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR), Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal. Instituto de Ciencias Biomedicas Abel Salazar (ICBAS), Universidade do Porto, Portugal. ; Department of Biology, University of California Riverside, Riverside, CA 92521, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile. ; Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Post Office Box 7011, S-750 07, Uppsala, Sweden. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea. ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Republic of Korea. ; Cho and Kim Genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. College of Animal Science and Technology, China Agricultural University, Beijing 100094, China. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, UK. Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA. Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA. ; The Genome Institute at Washington University, St. Louis, MO 63108, USA. ; College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China. ; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. ; Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia. Nova Southeastern University Oceanographic Center 8000 N Ocean Drive, Dania, FL 33004, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA. ; Genetics Division, San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, CA 92027, USA. ; Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Post Office Box 37012, Washington, DC 20013-7012, USA. Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China. Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-750 07 Uppsala, Sweden. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Center for Macroecology, Evolution and Climate, the Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Imperial College London, Grand Challenges in Ecosystems and the Environment Initiative, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK. ; Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The Roslin Institute Building, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Department of Biology, New Mexico State University, Box 30001 MSC 3AF, Las Cruces, NM 88003, USA. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. ; Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia, 6102, Australia. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn. ; China National GeneBank, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Medicine, University of Hong Kong, Hong Kong. zhanggj@genomics.cn jarvis@neuro.duke.edu mtpgilbert@gmail.com wangj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504712" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rocha, L A -- Aleixo, A -- Allen, G -- Almeda, F -- Baldwin, C C -- Barclay, M V L -- Bates, J M -- Bauer, A M -- Benzoni, F -- Berns, C M -- Berumen, M L -- Blackburn, D C -- Blum, S -- Bolanos, F -- Bowie, R C K -- Britz, R -- Brown, R M -- Cadena, C D -- Carpenter, K -- Ceriaco, L M -- Chakrabarty, P -- Chaves, G -- Choat, J H -- Clements, K D -- Collette, B B -- Collins, A -- Coyne, J -- Cracraft, J -- Daniel, T -- de Carvalho, M R -- de Queiroz, K -- Di Dario, F -- Drewes, R -- Dumbacher, J P -- Engilis, A Jr -- Erdmann, M V -- Eschmeyer, W -- Feldman, C R -- Fisher, B L -- Fjeldsa, J -- Fritsch, P W -- Fuchs, J -- Getahun, A -- Gill, A -- Gomon, M -- Gosliner, T -- Graves, G R -- Griswold, C E -- Guralnick, R -- Hartel, K -- Helgen, K M -- Ho, H -- Iskandar, D T -- Iwamoto, T -- Jaafar, Z -- James, H F -- Johnson, D -- Kavanaugh, D -- Knowlton, N -- Lacey, E -- Larson, H K -- Last, P -- Leis, J M -- Lessios, H -- Liebherr, J -- Lowman, M -- Mahler, D L -- Mamonekene, V -- Matsuura, K -- Mayer, G C -- Mays, H Jr -- McCosker, J -- McDiarmid, R W -- McGuire, J -- Miller, M J -- Mooi, R -- Mooi, R D -- Moritz, C -- Myers, P -- Nachman, M W -- Nussbaum, R A -- Foighil, D O -- Parenti, L R -- Parham, J F -- Paul, E -- Paulay, G -- Perez-Eman, J -- Perez-Matus, A -- Poe, S -- Pogonoski, J -- Rabosky, D L -- Randall, J E -- Reimer, J D -- Robertson, D R -- Rodel, M-O -- Rodrigues, M T -- Roopnarine, P -- Ruber, L -- Ryan, M J -- Sheldon, F -- Shinohara, G -- Short, A -- Simison, W B -- Smith-Vaniz, W F -- Springer, V G -- Stiassny, M -- Tello, J G -- Thompson, C W -- Trnski, T -- Tucker, P -- Valqui, T -- Vecchione, M -- Verheyen, E -- Wainwright, P C -- Wheeler, T A -- White, W T -- Will, K -- Williams, J T -- Williams, G -- Wilson, E O -- Winker, K -- Winterbottom, R -- Witt, C C -- New York, N.Y. -- Science. 2014 May 23;344(6186):814-5. doi: 10.1126/science.344.6186.814.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Academy of Sciences, San Francisco, CA 94118, USA. LRocha@calacademy.org. ; Museu Paraense Emilio Goeldi, Belem, PA, 66040-170, Brazil. ; Western Australian Museum, Perth, WA, 6986, Australia. ; California Academy of Sciences, San Francisco, CA 94118, USA. ; Smithsonian Institution, Washington, DC 20560, USA. ; Natural History Museum, London, SW7 5BD, UK. ; Field Museum of Natural History, Chicago, IL 60605, USA. ; Villanova University, Villanova, PA 19085, USA. ; University of Milano-Bicocca, Milan, 20126, Italy. ; Utica College, Utica, NY 13502, USA. ; King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia. ; Universidad de Costa Rica, San Jose, 11501-2060, Costa Rica. ; University of California, Berkeley, CA 94720-3161, USA. ; University of Kansas, Lawrence, KS 66045, USA. ; Universidad de los Andes, Bogota, 4976, Colombia. ; Old Dominion University, Norfolk, VA 23529, USA. ; Museu Nacional de Historia Natural e da Ciencia, Lisbon, 7005-638, Portugal. ; Louisiana State University, Baton Rouge, LA 70803, USA. ; James Cook University, Townsville, 4811, Australia. ; University of Auckland, Auckland, 1142, New Zealand. ; NOAA Systematics Laboratory, Washington, DC 20013, USA. ; University of Chicago, Chicago, IL 60637, USA. ; American Museum of Natural History, New York, NY 10024, USA. ; Universidade de Sao Paulo, Sao Paulo, SP, 05508-090, Brazil. ; Universidade Federal do Rio de Janeiro, Macae, RJ, 27965-045, Brazil. ; University of California, Davis, CA 95616, USA. ; Conservation International, Denpasar, Bali, 80235, Indonesia. ; University of Nevada, Reno, NV 89557-0314, USA. ; Natural History Museum of Denmark, Copenhagen, DK-2100, Denmark. ; Museum National d'Histoire Naturelle, Paris, 75005, France. ; Addis Ababa University, Addis Ababa, 1176, Ethiopia. ; University of Sydney, Sydney, NSW, 2006, Australia. ; Museum Victoria, Melbourne, 3001, VIC, Australia. ; University of Colorado, Boulder, CO 80309-0334, USA. ; Harvard University, Cambridge, MA 02138, USA. ; Smithsonian Institution, Washington, DC 20560, USA. National University of Singapore, 117543, Singapore. ; Museum and Art Gallery of the Northern Territory, Darwin, 0820, NT, Australia. ; CSIRO Marine & Atmospheric Research, Hobart, TAS, 7000, Australia. ; Australian Museum, Sydney, NSW, 2010, Australia. ; Smithsonian Tropical Research Institute, Balboa, 0843-03092, Panama. ; Cornell University, Ithaca, NY 14853, USA. ; Universite Marien Ngouabi, Brazzaville, B.P. 69, Republic of Congo. ; National Museum of Nature and Science, Tsukuba, 305-0005, Japan. ; University of Wisconsin-Parkside, Kenosha, WI 53141-2000, USA. ; Cincinnati Museum Center, Cincinnati, OH 45203, USA. ; The Manitoba Museum, Winnipeg, MB, R3B 0N2, Canada. ; Australian National University, Canberra, ACT, 0200, Australia. ; University of Michigan, Ann Arbor, MI 48109-1079, USA. ; California State University, Fullerton, CA 92831, USA. ; The Ornithological Council, Chevy Chase, MD 20815, USA. ; University of Florida, Gainesville, fl32611, USA. ; Universidad Central de Venezuela, Caracas, 1041, Venezuela. ; Pontif cia Universidad Catolica de Chile, Santiago 6513677, Chile. ; University of New Mexico, Albuquerque, NM 87131-0001, USA. ; Bernice P. Bishop Museum, Honolulu, HI 96817, USA. ; University of the Ryukyus, Nishihara, 903-0213, Japan. ; Museum fur Naturkunde, Berlin, 10115, Germany. ; Naturhistorisches Museum der Burgergemeinde Bern, Bern, CH-3005, Switzerland. ; American Museum of Natural History, New York, NY 10024, USA. Long Island University, Brooklyn, NY 11201-8423, USA. ; Auckland Museum, Auckland, 1142, New Zealand. ; Centro de Ornitologia y Biodiversidad, Lima, 33, Peru. ; Royal Belgian Institute of Natural Sciences, Brussels, 1000, Belgium. ; McGill University, Montreal, QC, H9X 3V9, Canada. ; University of Alaska Museum, Fairbanks, AK 99775, USA. ; Royal Ontario Museum, Toronto, ON, M5S 2C6, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24855245" target="_blank"〉PubMed〈/a〉

Description: Kreft and Jetz's critique of our recent update of Wallace's zoogeographical regions disregards the extensive sensitivity analyses we undertook, which demonstrate the robustness of our results to the choice of phylogenetic data and clustering algorithm. Their suggested distinction between "transition zones" and biogeographic regions is worthy of further investigation but is thus far unsubstantiated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, Ben G -- Lessard, Jean-Philippe -- Borregaard, Michael K -- Fritz, Susanne A -- Araujo, Miguel B -- Dimitrov, Dimitar -- Fabre, Pierre-Henri -- Graham, Catherine H -- Graves, Gary R -- Jonsson, Knud A -- Nogues-Bravo, David -- Wang, Zhiheng -- Whittaker, Robert J -- Fjeldsa, Jon -- Rahbek, Carsten -- New York, N.Y. -- Science. 2013 Jul 26;341(6144):343. doi: 10.1126/science.1237541.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen O, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23888024" target="_blank"〉PubMed〈/a〉

Description: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jarvis, Erich D -- Mirarab, Siavash -- Aberer, Andre J -- Li, Bo -- Houde, Peter -- Li, Cai -- Ho, Simon Y W -- Faircloth, Brant C -- Nabholz, Benoit -- Howard, Jason T -- Suh, Alexander -- Weber, Claudia C -- da Fonseca, Rute R -- Li, Jianwen -- Zhang, Fang -- Li, Hui -- Zhou, Long -- Narula, Nitish -- Liu, Liang -- Ganapathy, Ganesh -- Boussau, Bastien -- Bayzid, Md Shamsuzzoha -- Zavidovych, Volodymyr -- Subramanian, Sankar -- Gabaldon, Toni -- Capella-Gutierrez, Salvador -- Huerta-Cepas, Jaime -- Rekepalli, Bhanu -- Munch, Kasper -- Schierup, Mikkel -- Lindow, Bent -- Warren, Wesley C -- Ray, David -- Green, Richard E -- Bruford, Michael W -- Zhan, Xiangjiang -- Dixon, Andrew -- Li, Shengbin -- Li, Ning -- Huang, Yinhua -- Derryberry, Elizabeth P -- Bertelsen, Mads Frost -- Sheldon, Frederick H -- Brumfield, Robb T -- Mello, Claudio V -- Lovell, Peter V -- Wirthlin, Morgan -- Schneider, Maria Paula Cruz -- Prosdocimi, Francisco -- Samaniego, Jose Alfredo -- Vargas Velazquez, Amhed Missael -- Alfaro-Nunez, Alonzo -- Campos, Paula F -- Petersen, Bent -- Sicheritz-Ponten, Thomas -- Pas, An -- Bailey, Tom -- Scofield, Paul -- Bunce, Michael -- Lambert, David M -- Zhou, Qi -- Perelman, Polina -- Driskell, Amy C -- Shapiro, Beth -- Xiong, Zijun -- Zeng, Yongli -- Liu, Shiping -- Li, Zhenyu -- Liu, Binghang -- Wu, Kui -- Xiao, Jin -- Yinqi, Xiong -- Zheng, Qiuemei -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Smeds, Linnea -- Rheindt, Frank E -- Braun, Michael -- Fjeldsa, Jon -- Orlando, Ludovic -- Barker, F Keith -- Jonsson, Knud Andreas -- Johnson, Warren -- Koepfli, Klaus-Peter -- O'Brien, Stephen -- Haussler, David -- Ryder, Oliver A -- Rahbek, Carsten -- Willerslev, Eske -- Graves, Gary R -- Glenn, Travis C -- McCormack, John -- Burt, Dave -- Ellegren, Hans -- Alstrom, Per -- Edwards, Scott V -- Stamatakis, Alexandros -- Mindell, David P -- Cracraft, Joel -- Braun, Edward L -- Warnow, Tandy -- Jun, Wang -- Gilbert, M Thomas P -- Zhang, Guojie -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R24 GM092842/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Universite Montpellier II Montpellier, France. ; Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. ; Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan. ; Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ; Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Universite de Lyon, F-69622 Villeurbanne, France. ; Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Spain. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. ; Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. ; Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark. ; The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ; Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil. ; Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark. ; Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates. ; Dubai Falcon Hospital, Dubai, United Arab Emirates. ; Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand. ; Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. ; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. ; Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia. ; Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biological Sciences, National University of Singapore, Republic of Singapore. ; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA. ; Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA. ; San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA. ; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA. ; Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany. ; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504713" target="_blank"〉PubMed〈/a〉

Description: Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cracraft, Joel -- Houde, Peter -- Ho, Simon Y W -- Mindell, David P -- Fjeldsa, Jon -- Lindow, Bent -- Edwards, Scott V -- Rahbek, Carsten -- Mirarab, Siavash -- Warnow, Tandy -- Gilbert, M Thomas P -- Zhang, Guojie -- Braun, Edward L -- Jarvis, Erich D -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1578.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. ; School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. ; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu. ; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. jlc@amnh.org ebraun68@ufl.edu jarvis@neuro.duke.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404820" target="_blank"〉PubMed〈/a〉