11 Works

Data from: Fossilization of melanosomes via sulfurization

Maria E. McNamara, Bart E. Van Dongen, Nick P. Lockyer, Ian D. Bull & Patrick J. Orr
Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur-bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur-rich phaeomelanosomes. Here we...

Data from: EMMLi: a maximum likelihood approach to the analysis of modularity

Anjali Goswami & John Albert Finarelli
Identification of phenotypic modules, semiautonomous sets of highly correlated traits, can be accomplished through exploratory (e.g., cluster analysis) or confirmatory approaches (e.g., RV coefficient analysis). Although statistically more robust, confirmatory approaches are generally unable to compare across different model structures. For example, RV coefficient analysis finds support for both two- and six-module models for the therian mammalian skull. Here, we present a maximum likelihood approach that takes into account model parameterization. We compare model log-likelihoods...

Data from: The program STRUCTURE does not reliably recover the correct population structure when sampling is uneven: sub-sampling and new estimators alleviate the problem

Sébastien J. Puechmaille
Inferences of population structure and more precisely the identification of genetically homogeneous groups of individuals are essential to the fields of ecology, evolutionary biology, and conservation biology. Such population structure inferences are routinely investigated via the program STRUCTURE implementing a Bayesian algorithm to identify groups of individuals at Hardy-Weinberg and linkage equilibrium. While the method is performing relatively well under various population models with even sampling between subpopulations, the robustness of the method to uneven...

Data from: Mammal madness: is the mammal tree of life not yet resolved?

Nicole M. Foley, Mark S. Springer & Emma C. Teeling
Most molecular phylogenetic studies place all placental mammals into four superordinal groups, Laurasiatheria (e.g. dogs, bats, whales), Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g. armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs), and estimate that these clades last shared a common ancestor 90–110 million years ago. This phylogeny has provided a framework for numerous functional and comparative studies. Despite the high level of congruence among most molecular studies, questions still remain regarding the position...

Data from: Population connectivity and phylogeography of the Mediterranean endemic skate Raja polystigma and evidence of its hybridization with the parapatric sibling R. montagui

Alessia Cariani, ED Farrell, P Carbonara, G Garofalo, M Stagioni, F Tinti, F Fiorentino, N Frodella, A Veloná, R Cannas & MC Follesa
The genetic structure and population connectivity of the Mediterranean endemic speckled skate Raja polystigma were investigated in 10 population samples (N = 232) at 7 exon-primed nuclear microsatellites and at 3 mitochondrial DNA sequence markers. The phylogeographic and population genetic analyses revealed that R. polystigma in the western and central Mediterranean represents a near-panmictic population, with a subtle but significant mitochondrial divergence of the Adriatic deme. Nuclear genotypes revealed that 2.5% of the total individuals...

Data from: Functional traits of marine macrophytes predict primary production

Holger Jänes, Jonne Kotta, Merli Pärnoja, Tasman P. Crowe, Fabio Rindi & Helen Orav-Kotta
The relationship between community structure and the functioning of ecosystems is the subject of ongoing debate. Biological or functional trait-based approaches that capture life strategy, morphology and behavioural characteristics have received far less attention than taxonomic diversity in this context, despite their more intuitive link to ecosystem functioning. Macrophyte primary production underpins aquatic food webs, regulates benthic and pelagic ecosystems and is a key aspect of the global carbon cycle. This study spans a range...

Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Maulik R. Upadhyay, Wei Chen, Johannes A. Lenstra, C. R. J. Goderie, David E. MacHugh, Stephen D. E. Park, David A. Magee, Donato Matassino, Ferdinando Ciani, Hendrik-Jan Megens, J. A. M. Van Arendonk, Martien A. M. Groenen, European Cattle Genetic Diversity Consortium & Richard P. M. A. Crooijmans
The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess...

Data from: Yield of temperate forage grassland species is either largely resistant or resilient to experimental summer drought

Daniel Hofer, Matthias Suter, Eamon Haughey, John A. Finn, Nyncke J. Hoekstra, Nina Buchmann & Andreas Lüscher
Due to climate change, an increasing frequency and severity of drought events are expected to impair grassland productivity, particularly of intensively managed temperate grasslands. To assess drought impacts, a common field experiment to manipulate precipitation was set up at three sites (two Swiss and one Irish) using monocultures and mixtures with two and four key forage species. Species differed in their functional traits: a shallow-rooted non-legume (Lolium perenne L.), a deep-rooted non-legume (Cichorium intybus L.),...

Data from: Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design

Veronica Zamora-Gutierrez, Celia Lopez-Gonzalez, M. Cristina MacSwiney Gonzalez, Brock Fenton, Gareth Jones, Elisabeth K. V. Kalko, Sebastien J. Puechmaille, Vassilios Stathopoulos & Kate E. Jones
Monitoring global biodiversity is critical for understanding responses to anthropogenic change, but biodiversity monitoring is often biased away from tropical, megadiverse areas that are experiencing more rapid environmental change. Acoustic surveys are increasingly used to monitor biodiversity change, especially for bats as they are important indicator species and most use sound to detect, localise and classify objects. However, using bat acoustic surveys for monitoring poses several challenges, particularly in megadiverse regions. Many species lack reference...

Data from: Sex change and effective population size: implications for population genetic studies in marine fish

Ilaria Coscia, Julien Chopelet, Robin S. Waples, Bruce Mann & Stefano Mariani
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected...

Data from: Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

Gloria Gonzalez-Fortes, Aurora Grandal-D'Anglade, Ben Kolbe, Daniel Fernandes, Ioana N. Meleg, Ana Garcia-Vazquez, Ana C. Pinto-Llona, Silviu Constantin, Trino J. De Torres, Jose E. Ortiz, Christine Frischauf, Gernot Rabeder, Michael Hofreiter, Axel Barlow & Gloria G. Fortes
Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost...

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