10 Works

Data from: Phylogeography and population history of Leopardus guigna, the smallest American felid

Constanza Napolitano, Warren E. Johnson, Jim Sanderson, Stephen J. O'Brien, Rus Hoelzel, Rachel Freer, Nigel Dunstone, Kermit Ritland, Carol E. Ritland, Elie Poulin & A. Rus Hoelzel
The guigna (Leopardus guigna) is the smallest and most-restricted New World cat species, inhabiting only around 160,000 km2 of temperate rain forests in southern South America and is currently threatened by habitat loss, fragmentation and human persecution. We investigated phylogeographic patterns of genetic diversity, demographic history and barriers to gene flow with 116 individuals sampled across the species geographic range by analyzing 1,798 base pairs of the mtDNA (496 bp HVSI region, 720 bp NADH-5...

Pontocaspian habitat polygon shapefiles from: Decline of unique Pontocaspian biodiversity in the Black Sea Basin: a review

Aleksandre Gogaladze, Mikhail Son, Matteo Lattuada, Vitaliy Anistratenko, Vitaly Syomin, Ana Bianca Pavel, Oana Popa, Luis Popa, Jan-Johan Ter Poorten, Jacobus Biesmeijer, Niels Raes, Thomas Wilke, Arthur Francis Sands, Teodora Trichkova, Zdravko Hubenov, Maxim Vinarski, Olga Anistratenko, Tatiana Alexenko & Frank Wesselingh
The unique aquatic Pontocaspian (PC) biota of the Black Sea Basin (BSB) is in decline. The lack of detailed knowledge on the status and trends of species, populations and communities hampers a thorough risk assessment and precludes effective conservation. This paper reviews PC biodiversity trends in the BSB ( Bulgaria, Romania, Moldova, Ukraine and Russia) using endemic molluscs as a model group. We aim to assess changes in PC habitats, community structure and species distribution...

Data from: Effects of a trophic cascade on a multi-level facilitation cascade

Eugeniy Yakovis & Anna Artemieva
1. The role of cascades in natural communities has been extensively studied, but interactions between trophic and facilitation cascades are unexplored. In the White Sea (65° N) shallow subtidal bivalve primary facilitators provide hard substrate for secondary facilitator barnacles, that in turn provide substrate for conspecifics, ascidians, red algae, and multiple associated organisms, composing a multi-level facilitation cascade. Previous research revealed that predation by the whelk (Boreotrophon clathratus) accounts for ~7% of adult barnacle mortality....

Data from: Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas

Hanna M. Laakkonen, Dmitry L. Lajus, Petr Strelkov & Risto Väinölä
Background: The relationships between North Atlantic and North Pacific faunas through times have been controlled by the variation of hydrographic circumstances in the intervening Arctic Ocean and Bering Strait. We address the history of trans-Arctic connections in a clade of amphi-boreal pelagic fishes using genealogical information from mitochondrial DNA sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C. harengus) have basically vicarious distributions in the two oceans since pre-Pleistocene times. However, remote populations...

Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability

Nicholas J. Marra, Michael J. Stanhope, Nathaniel K. Jue, Minghui Wang, Qi Sun, Paulina P. Bitar, Vincent P. Richards, Aleksey Komissarov, Mike Rayko, Sergey Kliver, Bryce J. Stanhope, Chuck Winkler, Stephen J. O'Brien, Agostinho Antunes, Salvador J. Jorgensen & Mahmood S. Shivji
The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding...

Data from: 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...

Data from: Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds

Andrey Yurchenko, Nikolay Yudin, Ruslan Aitnazarov, Alexandra Plysnina, Vladimir Brukhin, Vladimir Soloshenko, Bulat Lhasaranov, Ruslan Popov, Ivan Paronyan, Kirill Plemyashov & Denis M. Larkin
One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred...

Data from: Time-keeping programme can explain seasonal dynamics of leukocyte profile in a migrant bird

Irina Demina, Arseny Tsvey, Olga Babushkina & Julia Bojarinova
It has been proposed that immune functioning in wild animals is shaped by the trade-off between a probability of encountering pathogens and an availability of resources for maintaining immune system in active state. Due to resources’ seasonality one can expect that immune functioning, e.g., absolute and relative counts of white blood cells, WBC (leukocyte profile) also follows an annual cycle. However, dynamics of the seasonal changes of leukocyte profile are controversial and specific inquiries so...

Draft de novo genome assembly of the elusive jaguarundi, Puma yagouaroundi

Gaik Tamazian, Pavel Dobrynin, Anna Zhuk, Daria Zhernakova, Polina Perelman, Natalia Serdyukova, Alexander Graphodatsky, Aleksey Komissarov, Sergei Kliver, Nikolay Cherkasov, Alan Scott, David Mohr, Klaus-Peter Koepfli, Stephen O'Brien & Ksenia Krasheninnikova
The Puma lineage within the family Felidae consists of three species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of two species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome...

Data from: Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista

Fabien Burki, Maia Kaplan, Denis V. Tikhonekov, Vasily Zlatogursky, Bui Quang Minh, Liudmila V. Radaykina, Alexey Smirnov, Alexander P. Mylnikov, Patrick J. Keeling & Denis V. Tikhonenkov
Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of...

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