17 Works

Data from: Is population structure in the European white stork determined by flyway permeability rather than translocation history?

Jill M. Shephard, Rob Ogden, Piotr Tryjanowski, Ola Olsson & Peter Galbusera
European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country-specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to...

Data from: Signatures of diversifying selection in European pig breeds

Samantha Wilkinson, Zen H. Lu, Hendrik-Jan Megens, Alan L. Archibald, Chris Haley, Ian J. Jackson, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Rob Ogden & Pamela Wiener
Porcine_60K_Data_Wilkinsonetal2013.tarMapping and variant calling data on SSC5:98000000-99000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_98000000-99000000.tarMapping and variant calling data on SSC5:3100000-34000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_3100000-34000000.tarMapping and variant calling data on SSC11:53500000-55500000SSC11_53500000-55500000.tar

Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

Rob Ogden, Karim Gharbi, Nikolai Mugue, Jann Martinsohn, Helen Senn, John Davey, Mohammad Pourkazemi, Ross McEwing, Cathlene Eland, Michele Vidotto, Alexander Sergeev, Leonardo Congiu & J. W. Davey
Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a...

Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild

Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F. Scott, David W. Mohr, Olga Dudchenko, Arina D. Omer, Zane Colaric, Erez Lieberman Aiden, Shaikha Salem Al Dhaheri, David Wildt, Shireen Oliaji, Gaik Tamazian, Budhan Pukazhenthi, Rob Ogden & Klaus‐Peter Koepfli
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 critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar‐horned oryx (Oryx dammah) is a North African antelope that has...

Data from: Disruptive viability selection on a black plumage trait associated with dominance

Paul Acker, Arnaud Grégoire, Margaux Rat, Claire N. Spottiswoode, René E. Van Dijk, Matthieu Paquet, Jennifer C. Kaden, Roger Pradel, Ben J. Hatchwell, Rita Covas & Claire Doutrelant
Traits used in communication, such as colour signals, are expected to have positive consequences for reproductive success, but their associations with survival are little understood. Previous studies have mainly investigated linear relationships between signals and survival, but both hump-shaped and U-shaped relationships can also be predicted, depending on the main costs involved in trait expression. Furthermore, few studies have taken the plasticity of signals into account in viability selection analyses. The relationship between signal expression...

Data from: Parallel evolution and adaptation to environmental factors in a marine flatfish: implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Fernanda Dotti Do Prado, Manuel Vera, Miguel Hermida, Carmen Bouza, Belén G. Pardo, Román Vilas, Andrés Blanco, Carlos Fernández, Francesco Maroso, Gregory E. Maes, Cemal Turan, Filip A.M. Volckaert, John B. Taggart, Adrian Carr, Rob Ogden, Einar E. Nielsen, The Aquatrace Consortium, Paulino Martínez & Filip A. M. Volckaert
Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in Southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range...

The distribution of plant consumption traits across habitat types and the patterns of fruit availability suggest a mechanism of coexistence of two sympatric frugivorous mammals

Luc Roscelin Dongmo Tédonzong, Jacob Willie, Nikki Tagg, Martin N. Tchamba, Tsi Evaristus Angwafo, Ada Myriane Patipe Keuko, Jacques Keumo Kuenbou, Charles-Albert Petre & Luc Lens
Understanding the mechanisms governing the coexistence of organisms is an important question in ecology, and providing potential solutions contributes to conservation science. In this study, we evaluated the contribution of several mechanisms to the coexistence of two sympatric frugivores, using western lowland gorillas (Gorilla gorilla gorilla) and central chimpanzees (Pan troglodytes troglodytes) in a tropical rainforest of southeast Cameroon as a model system. We collected great ape fecal samples to determine and classify fruit species...

Data from: Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria)

Anna P. Muir, Roman Biek, Rob Thomas & Barbara K. Mable
Both environmental- and genetic-influences can result in phenotypic variation. Quantifying the relative contributions of local adaptation and phenotypic plasticity to phenotypes is key to understanding the effect of environmental variation on populations. Identifying the selective pressures that drive divergence is an important, but often lacking, next step. High gene flow between high- and low-altitude common frog (Rana temporaria) breeding sites has previously been demonstrated in Scotland. The aim of this study was to assess whether...

Data from: A genomic island linked to ecotype divergence in Atlantic cod

Jakob Hemmer-Hansen, Einar E. Nielsen, Nina O. Therkildsen, Martin I. Taylor, Rob Ogden, Audrey J. Geffen, Dorte Bekkevold, Sarah Helyar, Christophe Pampoulie, Torild Johansen & Gary R. Carvalho
The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome-wide or localized in “genomic mosaics” during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate...

Data from: Using genetic variation to infer associations with climate in the common frog, Rana temporaria

Anna P. Muir, Rob Thomas, Roman Biek & Barbara K. Mable
Recent and historical species' associations with climate can be inferred using molecular markers. This knowledge of population and species-level responses to climatic variables can then be used to predict the potential consequences of ongoing climate change. The aim of this study was to predict responses of Rana temporaria to environmental change in Scotland by inferring historical and contemporary patterns of gene flow in relation to current variation in local thermal conditions. We first inferred colonization...

Data from: Dunnock social status correlates with sperm speed, but fast sperm does not always equal high fitness

Carlos E. Lara, Helen R. Taylor, Benedikt Holtmann, Eduardo S. A. Santos, Sheri L. Johnson, Neil J. Gemmell & Shinichi Nakagawa
Sperm competition theory predicts that males should modulate sperm investment according to their social status. Sperm speed, one proxy of sperm quality, also influences the outcome of sperm competition because fast sperm cells may fertilize eggs before slow sperm cells. We evaluated whether the social status of males predicted their sperm speed in a wild population of dunnocks (Prunella modularis). In addition to the traditional analysis of the average speed of sperm cells per sample,...

Data from: Distinguishing the victim from the threat: SNP‐based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration

Helen V. Senn, Muhammad Ghazali, Jennifer Kaden, David Barcaly, Ben Harrower, Ruairidh D. Campbell, David W. MacDonald, Andrew C. Kitchener & David Barclay
The degree of introgressive hybridisation between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here we use a 35-SNP-marker test, designed to assess hybridisation between wildcat and domestic cat populations in Scotland, to assess a database of 265 wild-living and captive cat samples, and test the assumptions of the test using 3097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic...

On the use of genome-wide data to model and date the time of anthropogenic hybridisation: an example from the Scottish wildcat

Jo Howard-McCombe, Daniel Ward, Andrew Kitchener, Dan Lawson, Helen Senn & Mark Beaumont
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. We develop a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6,546 loci, we show...

Data from: Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species

Johanna L. Baily, Guillaume Méric, Sion Bayliss, Geoffrey Foster, Simon E. Moss, Eleanor Watson, Ben Pascoe, Jane Mikhail, Robert J. Goldstone, Romain Pizzi, David G. E. Smith, Kim Willoughby, Alisa J. Hall, Mark P. Dagleish, Samuel K. Sheppard & Ailsa J. Hall
Environmental pollution often accompanies the expansion and urbanization of human populations where sewage and wastewaters commonly have an impact on the marine environments. Here, we explored the potential for faecal bacterial pathogens, of anthropic origin, to spread to marine wildlife in coastal areas. The common zoonotic bacterium Campylobacter was isolated from grey seals (Halichoerus grypus), an important sentinel species for environmental pollution, and compared to isolates from wild birds, agricultural sources and clinical samples to...

Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Ilaria Milano, Massimiliano Babbucci, Alessia Cariani, Miroslava Atanassova, Dorte Bekkevold, Gary R. Carvalho, Montserrat Espiñeira, Fabio Fiorentino, Germana Garofalo, Audrey J. Geffen, Einar E. Nielsen, Rob Ogden, Tomaso Patarnello, Marco Stagioni, Fausto Tinti & Luca Bargelloni
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed...

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Emily Humble, Jane Hosegood, Rob Ogden, Mark De Bruyn, Simon Creer, Guy Stevens, Mohammed Abudaya, Kim Bassos-Hull, Ramon Bonfil, Daniel Fernando, Andrew Foote, Helen Hipperson, Rima Jabado, Jenny Kaden, Muhammad Moazzam, Lauren Peel, Stephen Pollett, Alessandro Ponzo, Marloes Poortvliet, Jehad Salah, Helen Senn, Joshua Stewart, Sabine Wintner & Gary Carvalho
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal...

Genetic diversity of the Nubian ibex in Oman as revealed by mitochondrial DNA

Mataab Al-Ghafri, Patrick White, Robert Briers, Kara Dicks, Alex Ball, Muhammad Ghazali, Steve Ross, Taimur Al-Said, Haitham Al-Amri, Mudhafar Al-Umairi, Hani Al Saadi, Ali Aka’ak, Ahmed Hardan, Nasser Zabanoot, Mark Craig & Helen Senn
The Nubian ibex (Capra nubiana) is patchily distributed across parts of Africa and Arabia. In Oman, it is one of the few free-ranging wild mammals found in the central and southern regions. Its population is declining due to habitat degradation, human expansion, poaching, and fragmentation. Here we investigated the population’s genetic diversity using mitochondrial DNA (D-loop 186bp and cytochrome b 487bp). We found that the Nubian ibex in the southern region of Oman was more...

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