259 research outputs found
Molecular Biogeography: Towards an Integrated Framework for Conserving Pan-African Biodiversity
BACKGROUND: Biogeographic models partition ecologically similar species assemblages into discrete ecoregions. However, the history, relationship and interactions between these regions and their assemblages have rarely been explored. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop a taxon-based approach that explicitly utilises molecular information to compare ecoregion history and status, which we exemplify using a continentally distributed mammalian species: the African bushbuck (Tragelaphus scriptus). We reveal unprecedented levels of genetic diversity and structure in this species and show that ecoregion biogeographic history better explains the distribution of molecular variation than phenotypic similarity or geography. We extend these data to explore ecoregion connectivity, identify core habitats and infer ecological affinities from them. CONCLUSIONS/SIGNIFICANCE: This analysis defines 28 key biogeographic regions for sub-Saharan Africa, and provides a valuable framework for the incorporation of genetic and biogeographic information into a more widely applicable model for the conservation of continental biodiversity
Colonization of the Scottish islands via long-distance Neolithic transport of red deer (Cervus elaphus)
Red deer (Cervus elaphus) have played a key role in human societies throughout history, with important cultural significance and as a source of food and materials. This relationship can be traced back to the earliest human cultures and continues to the present day. Humans are thought to be responsible for the movement of a considerable number of deer throughout history, although the majority of these movements are poorly described or understood. Studying such translocations allows us to better understand ancient humanâwildlife interactions, and in the case of island colonizations, informs us about ancient human maritime practices. This study uses DNA sequences to characterise red deer genetic diversity across the Scottish islands (Inner and Outer Hebrides and Orkney) and mainland using ancient deer samples, and attempts to infer historical colonization events. We show that deer from the Outer Hebrides and Orkney are unlikely to have originated from mainland Scotland, implying that humans introduced red deer from a greater distance. Our results are also inconsistent with an origin from Ireland or Norway, suggesting long-distance maritime travel by Neolithic people to the outer Scottish Isles from an unknown source. Common haplotypes and low genetic differentiation between the Outer Hebrides and Orkney imply common ancestry and/or gene flow across these islands. Close genetic proximity between the Inner Hebrides and Ireland, however, corroborates previous studies identifying mainland Britain as a source for red deer introductions into Ireland. This study provides important information on the processes that led to the current distribution of the largest surviving indigenous land mammal in the British Isles
High performance computation of landscape genomic models integrating local indices of spatial association
Since its introduction, landscape genomics has developed quickly with the
increasing availability of both molecular and topo-climatic data. The current
challenges of the field mainly involve processing large numbers of models and
disentangling selection from demography. Several methods address the latter,
either by estimating a neutral model from population structure or by inferring
simultaneously environmental and demographic effects. Here we present
Samada, an integrated approach to study signatures of local adaptation,
providing rapid processing of whole genome data and enabling assessment of
spatial association using molecular markers. Specifically, candidate loci to
adaptation are identified by automatically assessing genome-environment
associations. In complement, measuring the Local Indicators of Spatial
Association (LISA) for these candidate loci allows to detect whether similar
genotypes tend to gather in space, which constitutes a useful indication of the
possible kinship relationship between individuals. In this paper, we also
analyze SNP data from Ugandan cattle to detect signatures of local adaptation
with Samada, BayEnv, LFMM and an outlier method (FDIST approach in
Arlequin) and compare their results. Samada is an open source software
for Windows, Linux and MacOS X available at \url{http://lasig.epfl.ch/sambada}Comment: 1 figure in text, 1 figure in supplementary material The structure of
the article was modified and some explanations were updated. The methods and
results presented are the same as in the previous versio
A Qualitative Assessment of Guinea-Bissauâs Hunting History and Culture - and Their Implications for Primate Conservation
Illegal hunting and trade threaten the high biodiversity of Guinea-Bissau (GB) in West Africa,
particularly for nonhuman primates (NHP). Primate carcasses are sold at bushmeat markets and at restaurants
and the primate pet trade is active. Traditional medicine practitioners also use NHP body-parts further
promoting the commerce of NHP skins. A better understanding of hunting and related trade activities,
including the profile of hunters and their motivations, would improve NHP conservation in GB. However,
information on commercial hunting is incomplete due to a general unwillingness to describe illegal activities
by the local communities. Here, we investigated aspects of hunting practice and related commercial activities
targeting NHP in GB by collecting qualitative ethnographic information using semi-structured interviews.
Participants were asked about hunted species, techniques and hunting locations, their motivations to hunt
wild NHP, uses of carcasses, and their perceptions on the demographic trajectory of hunted species. Eight
participants in the study listed species hunted in GB, which included a total of seven NHP. Hunting areas
described were spread across southern GB and included locations within the limits of national protected areas
and formalized ecological corridors. Participants mentioned the trade in NHP meat at bushmeat restaurants
as the primary motivation for primate-targeted hunting, with the exception of western chimpanzees, which
are specifically targeted for the exotic pet trade. Several strategies are used in hunting NHP, including traps,
firearms, and hunting dogs. The majority of hunted NHP were perceived as having declined in population
size during recent decades. Episodes when military groups hunted NHP intensively using more sophisticated
weapons and methods in the 1980s were also described. This study highlights how hunting and related
activities are complex and multi-dimensional and illustrates the use of ethnographic methods to improve
knowledge about illegal and concealed practices impacting NHP conservation. Our results suggest an urgent
need to raise awareness of local communities and subsistence hunters living within protected areas about the
environmental and social impacts of hunting.info:eu-repo/semantics/publishedVersio
Advances in farm animal genomic resources
Livestock conservation is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define and manage Farm Animal Genetic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR management in terms of technological continuity, analytical capacity and integrative methodologies. Indeed, high-throughput single-nucleotide polymorphism genotyping is available for all major farm animal species and beyond the technological challenge to deal with these large molecular datasets, their integration with geo-environmental and socio-economic information is key to making sense of the data in practical conditions
Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics
The introduction of Iberian cattle in the Americas after Columbusâ arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD), and Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on crossâpopulation extended haplotype homozygosity (XPâEHH) and population differentiation (FST) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic Ne contraction. NeS analysis provided insights into shortâterm complexity in population change and depicted a decrease/expansion episode at the end of the ABCâinferred expansion, as well as several additional fluctuations in Ne with the attainment of the current small Ne only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (GDNF), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in futureâproofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change
Ecology, conservation, and phylogenetic position of the Madagascar Jacana Actophilornis albinucha
The Madagascar Jacana Actophilornis albinucha (Jacanidae) is an endemic shorebird found in the threatened wetlands of western Madagascar. This species is presumed to exhibit classical polyandry; however, few data are available to support that assumption. More generally, a lack of basic understanding of this species hinders conservation efforts. We conducted the most extensive study of the Madagascar Jacana to date, and report on its: 1) distribution, population size and density; 2) degree of sexual size dimorphism; and 3) phylogenetic position. The surveys were conducted at 54 lakes, between January and October in 2016. Madagascar Jacana were found at 22 lakes, and within these were distributed at a mean density of 3.5 ± 0.74 [SE] individuals per hectare of surveyed habitat. We estimate the global population size to be between 975 and 2 064 individuals, and habitat destruction appears to be the main threat to the species. Females were significantly larger than males, consistent with reports for other Jacanidae species. Using a mitochondrial DNA fragment, we expanded the Jacanidae genetic phylogeny, and confirmed that Madagascar Jacana is the sister species to the African Jacana Actophilornis africanus. Further studies are urgently needed to thoroughly re-assess the threat status and population trend of the Madagascar Jacana
Conservation of adaptive potential and functional diversity
The conservation of adaptive potential to enable populations and species to respond to environmental change is one of the cornerstones of conservation genetics. To date, however, most work has by necessity focused on neutral markers and demographic questions. Now, with the rapid development of genomic technologies, we have new tools with which to address this essential but poorly understood aspect of conservation strategy. This was the motivation for a meeting on this subject held at Durham University in November 2017 that generated papers for this special issue. In this brief introduction we summarise the presentations and discussions that took place over the course of the meeting, and provide some initial conclusions together with ideas about the way forward
'Intentional genetic manipulation' as a conservation threat
Wildlife ranching including the hunting, collection, sales and husbandry of wild animals in captivity, is practised worldwide and is advocated as an approach towards the conservation of wild species. While many authors have explored the biological impacts of intensive wild population management, primarily with respect to disease transmission (especially in ungulates and fish), the evolutionary and demographic effects of wildlife ranching have been examined less intensively. We discuss this issue through the case of intensive wildlife management in southern Africa. The genetic consequences of this global practice, with an emphasis on Africa, were addressed by a motion passed at the 2016 IUCN World Congress- âManagement and regulation of intensive breeding and genetic manipulation of large mammals for commercial purposesâ. Here, we highlight concerns regarding intensive breeding programs used to discover, enhance and propagate unusual physical traits, hereafter referred to as âIntentional Genetic Manipulationâ. We highlight how âIntentional Genetic Manipulationâ potentially threatens the viability of native species and ecosystems, via genetic erosion, inbreeding, hybridisation and unregulated translocation. Finally, we discuss the need for better policies in southern Africa and globally, regarding âIntentional Genetic Manipulationâ, and the identification of key knowledge gaps
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