B. bombina and B. variegata are ecologically distinct taxa that nevertheless hybridise in nature wherever their distribution ranges adjoin. These data were collected to test the hypothesis that B. variegata tadpoles are more susceptible to predation than those of B. bombina. The former develop in ephemeral aquatic sites that can be predator-free, whereas the latter are found in predator-rich semi-permanent ponds. Tadpoles of both taxa were raised under under uniform laboratory conditions and their relative...
Data from: When a clonal genome finds its way back to a sexual species: evidence from ongoing but rare introgression in the hybridogenetic water frog complexPeter Mikulíček, Matej Kautman, Boris Demovič & Karel Janko
Besides several exceptions, asexual metazoans are usually viewed as ephemeral sinks for genomes, which become ‘frozen’ in clonal lineages after their emergence from ancestral sexual species. Here, we investigated whether and at what rate the asexuals are able to introgress their genomes back into the parental sexual population, thus more or less importantly affecting the gene pools of sexual species. We focused on hybridogenetic hybrids of western Palaearctic water frogs (Pelophylax esculentus), which originate through...
Genetic diversity, differentiation and historical origin of the isolated population of rooksCorvus frugilegusin IberiaPablo Salinas, Francisco Morinha, Ivan Literak, Javier García, Borja Milá & Guillermo Blanco
Current bird populations in southern temperate latitudes often represent relicts of glacial refugia from which northern populations expanded as the climate became suitable following the last glacial maximum, 18 000 years before present. Alternatively, these southern populations could be the result of the fragmentation of large distributions and other processes not related to glaciations, like recent recolonization from northern populations and human impact in historical times. Here, we investigate the origin of a small, isolated...
Data from: A revision of African helmeted terrapins (Testudines: Pelomedusidae: Pelomedusa), with descriptions of six new speciesAlice Petzold, Mario Vargas-Ramírez, Christian Kehlmaier, Melita Vamberger, William R. Branch, Louis Du Preez, Margaretha D. Hofmeyr, Leon Meyer, Alfred Schleicher, Pavel Široký & Uwe Fritz
Using nearly range-wide sampling, we analyze up to 1848 bp of mitochondrial DNA of 183 helmeted terrapins and identify a minimum of 12 deeply divergent species-level clades. Uncorrected p distances of these clades equal or clearly exceed those between the currently recognized species of Pelusios, the genus most closely related to Pelomedusa. We correlate genetic discontinuities of Pelomedusa with data on morphology and endoparasites and describe six new Pelomedusa species. Moreover, we restrict the name...
Data from: Natural and anthropogenic influences on the population structure of white-tailed eagles in the Carpathian Basin and Central EuropeEdina Nemesházi, Szilvia Kövér, Frank E. Zachos, Zoltán Horváth, Gábor Tihanyi, Attila Mórocz, Tibor Mikuska, István Hám, Ivan Literák, Suvi Ponnikas, Tadeusz Mizera & Krisztián Szabó
European populations of the white-tailed eagle (Haliaeetus albicilla) suffered a drastic decline during the 20th century. In many countries, only a few dozen breeding pairs survived or the species disappeared completely. By today, the populations have recovered, naturally or through restocking (e.g. in Scotland or the Czech Republic). In the Carpathian Basin, which is now a stronghold in southern Europe for the species in the southern part of the distribution range with more than 500...
Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assembliesJean Elbers, Sara Lado, Mark Rogers, José Melo-Ferreira, Jukka Corander, Petr Horin, Pamela Burger & Adiya Yadamsuren
Background Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, genetic diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic...
Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, René Meißner, Katerina Guschanski, Jaelle C. Braeley, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Botriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze & Pamela Burger
We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict, and illegal trafficking, there are only approximately...
Data from: Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecologyAndres Gomez, Klara Petrzelkova, Carl J. Yeoman, Klara Vlckova, Jakub Mrázek, Ingrid Koppova, Franck Carbonero, Alexander Ulanov, David Modry, Angelique Todd, Manolito Torralba, Karen Nelson, H. Rex Gaskins, Brenda Wilson, Rebecca M. Stumpf, Bryan A. White, Steven R. Leigh & Karen E. Nelson
The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro-ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga-Sangha Protected Areas, Central African Republic. Results show that...
Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populationsAlan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Seecharan, Minna Vehkala, Niko Välimäki, Michael B. Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schauffler, Lothar H. Wieler, Zong Zhiyong, Samuel K. Sheppard, James O. McInerney, Jukka Corander & Tristan Sreecharan
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could...
Data from: Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedaryJean P. Elbers, Mark F. Rogers, Polina L. Perelman, Anastasia A. Proskuryakova, Natalia A. Serdyukova, Warren E. Johnson, Petr Horin, Jukka Corander, David Murphy & Pamela A. Burger
Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome...
There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah’s phylogeography using a large-scale mtDNA data...
University of Veterinary and Pharmaceutical Sciences11
University of Veterinary Medicine Vienna3
University of Oslo3
Institute of Animal Physiology and Genetics2
Wildlife Conservation Society2
University of Oulu2
University of Porto2
South African National Biodiversity Institute1
West China Hospital of Sichuan University1
Universidad Iberoamericana León1