Rob Ogden

Rob Ogden
The University of Edinburgh | UoE · Royal (Dick) School of Veterinary Studies

PhD

About

100
Publications
35,706
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Introduction
Rob Ogden works at the Royal (Dick) School of Veterinary Studies, The University of Edinburgh, where he is Director of Conservation Science. Rob specialises in applied conservation genetics and wildlife DNA forensics. He's currently working on the conservation genetic management of eagles, squirrels, antelope and rays, using a range of whole genome sequence data and SNP panels.

Publications

Publications (100)
Preprint
In an age of habitat loss and overexploitation, small populations, both captive and wild, are increasingly facing the effects of isolation and inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how the type and intensity of intervention shape the genomic landscape of in...
Article
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Genetic diversity is one of the three main levels of biodiversity recognised in the Convention on Biological Diversity (CBD). Fundamental for species adaptation to environmental change, genetic diversity is nonetheless under‐reported within global and national indicators. When it is reported, the focus is often narrow and confined to domesticated o...
Article
Full-text available
The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the...
Article
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A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9
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Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been d...
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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...
Article
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We believe the 20 species extinction metric is a retrograde proposal, which does not adequately consider the lessons learnt from the 2020 Aichi Biodiversity Targets. Whilst having a single simple overarching target is appealing, we believe a positively-framed target will garner support, rather than one that aims to, at best, limit negative impacts....
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The highly valuable timber species Dalbergia cochinchinensis is severely threatened due to habitat loss and illegal logging throughout its distribution in mainland Southeast Asia and is listed on CITES Appendix II. This study proposes a strategy for conservation and sustainable management of the species based on assessment of genetic structure with...
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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 out...
Technical Report
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As there is no agreed national list of species of socio-economic and/or cultural value for Scotland, a set of criteria for selecting species has been developed. These include: • Species prioritised for conservation value • Species identified as being culturally important • Species providing important ecosystem services • Game species • Species coll...
Technical Report
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Aichi Target 13 (T13) focuses on the conservation of genetic diversity. • Major challenges in implementing T13 are that the type of genetic diversity to conserve is not clearly defined, and that key issues in genetic conservation vary across different sectors (e.g., forestry vs agriculture vs other species of socio-economic importance). • In Scotla...
Article
The reintroduction of the scimitar-horned oryx to Chad is a multi-disciplinary endeavour, planned and implemented over the past decade, utilizing a wide range of conservation science applications to maximise the chances of long-term population sustainability. The principle of incorporating genetic diversity information into founder selection for sp...
Preprint
Full-text available
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 planning. Recent developments in sequencing technologies have the potential to improv...
Preprint
Conservation efforts are often informed by measures of genetic structure within or between isolated populations. We have established a simulation approach to investigate how isolated or captive populations can display misleading (i.e recently acquired) genetic structure as a result of genetic drift. We utilized a combination of softwares to generat...
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Full-text available
Despite the critical need for non-invasive tools to improve monitoring of wildlife populations, especially for endangered and elusive species, faecal genetic sampling has not been adopted as regular practice, largely because of the associated technical challenges and cost. Substantial work needs to be undertaken to refine sample collection and prep...
Data
Distribution of elephant DNA concentration in 496 fecal samples collected using a swab. DNA concentrations ranged between 0 and 28.0 ng/μl. Samples were preserved into a lysis buffer and elution volume was 75 μl for all samples. (TIFF)
Data
Coefficients of random effects for the 9 sampling locations in the two-part model. The model included (A) the best binomial generalized linear mixed model for the effects of storage time and faeces quality on elephant DNA extraction success, and (B) the best truncated negative binomial generalized linear mixed model for the effects of storage time...
Data
A modified protocol for DNA extraction from faecal samples collected using a swab. Faeces were scrubbed using a buccal swab (Isohelix, Cell projects) and preserved into storage buffer (500 μl of LS buffer and 25 μl of proteinase K, Stabilizing kit, Isohelix, Cell Projects). The protocol is derived from the QIAamp Fast Stool Mini kit (51604) protoco...
Data
Sampling and laboratory data. (CSV)
Data
Genotyping success at 4 SNP loci at four dilutions (1:5, 1:10, 1:20 and 1:40). The pilot study included 88 faecal DNA extracts DNA extracts classified into four categories based on target DNA concentration. (TIFF)
Data
Observed and predicted probability to extract elephant DNA from faeces per week of storage for different faecal qualities. The four categories of faecal quality were: (A) very fresh (collected within 1 hour after defecation), (B) fresh (collected within 24 hours after defecation), (C) reduced surface (less than 24 hours old but partly destroyed by...
Data
Effects of storage time and faecal quality on elephant DNA concentration. (A) Mean elephant DNA concentration (± SD) and (B) predicted elephant DNA concentration per week of storage for four categories of faecal quality. (C) Summary of the best truncated negative binomial generalized linear mixed model using 396 faecal DNA extracts. Faecal quality...
Preprint
Full-text available
Practical biodiversity conservation relies on delineation of meaningful units, particularly with respect to global conventions and regulatory frameworks. Species delimitation methods have been revolutionised with the advent of next-generation sequencing approaches, allowing diversity within species radiations to be assessed with genome-wide data. M...
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The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field....
Article
The loss of biological diversity within species has the potential to significantly reduce resilience in the face of environmental change. Conservation of genetic variation needs to consider all available sources of diversity within a species, and approaches are required to integrate population management across traditionally separate wild and capti...
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As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins—which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level a...
Data
Details of samples included in this study. The table contains information about samples included in this study along with the corresponding haplotypes inferred from sequence variation across a mitochondrial cytochrome b fragment. (PDF)
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In a recent paper in Current Biology, Fennessy and colleagues [1] conclude that there are four species of giraffe and that their numbers are declining in Africa. Giraffes (Giraffa camelopardalis) are presently classified as one species, with nine subspecies, which are considered ‘Vulnerable’ on the IUCN Red List [2]. The present consensus of one sp...
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Zoo conservation breeding programs manage the retention of population genetic diversity through analysis of pedigree records. The range of demographic and genetic indices determined through pedigree analysis programs allows the conservation of diversity to be monitored relative to the particular founder population for a species. Such approaches are...
Article
Domestication and commercial production of the grasscutter, Thryonomys swinderianus, a large rodent, represents an important opportunity to secure sustainable animal protein for local communities in West Africa. To support production, DNA markers are required for population diversity assessment, pedigree analysis and marker-assisted selection. This...
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Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred...
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Androgen receptor genes (AR) have been found to have associations with reproductive development, behavioral traits, and disorders in humans. However, the influence of similar genetic effects on the behavior of other animals is scarce. We examined the loci AR glutamine repeat (ARQ) in 44 Grevy's zebras, 23 plains zebras, and three mountain zebras, a...
Article
Ninety-five microsatellite loci were isolated from the output of two Next Generation Sequencing projects: a genomic Illumina RADSeq and a transcriptomic Roche 454 cDNA sequencing of the Adriatic sturgeon (Acipenser naccarii). From a total of 7697 loci identified, 72 were characterized and 57 were polymorphic in the tetraploid A. naccarii, providing...
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Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy's zebra E. grevyi and the mountain zebra E. zebra. The Grevy's zebra and the mountain zebra are endangered, and hybridization between the Grevy's zebra and the plains zebra has been documented, leading to a requirement for conservatio...
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Conservation management of species distributed across fragmented habitats requires consideration of population genetic structure and relative levels of genetic diversity throughout the relevant geographic range. The Golden Eagle Aquila chrysaetos is monitored within Scotland to ensure its survival in the face of land-use pressure, persecution and f...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice, and we discuss how scaling-up to genome-wide inference can benefit traditional conservation genetic approaches and provide qualitatively novel insights. Yet, the generation of genomic data and subseque...
Article
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and in...
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Full-text available
The Tudor warship the Mary Rose sank in the Solent waters between Portsmouth and the Isle of Wight on the 19th of July 1545, whilst engaging a French invasion fleet. The ship was rediscovered in 1971 and between 1979 and 1982 the entire contents of the ship were excavated resulting in the recovery of over 25,000 objects, including the skeleton of a...
Technical Report
The Scottish Wildcat (Felis silvestris) is in urgent need of action to save remaining populations in the wild. Following habitat loss and persecution through the nineteenth century, the Wildcat is now restricted in the UK to the Scottish Highlands north of the Central Belt of Scotland. Recently, hybridisation of remaining Wildcats with feral and do...
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BREED specifications for pure-bred/pedigree dogs are laid down by the organisations that register and judge dogs, such as the Kennel Club of the UK (KCUK) and the Kennel Union of South Africa (KUSA), as well as the umbrella body the Federation Cynologique Internationale (FCI). Reproductive isolation between breeds results because animals can only b...
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The pygmy hippo is an Endangered mammal endemic to West Africa, of which only 2,000-3,000 are left in the wild. Until now genetic resources to conduct monitoring of wild populations and to facilitate captive breeding have been lacking. In this study we used restriction-site associated DNA sequencing of five pygmy hippo samples to generate 1,619 hig...
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Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last r...
Article
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Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conductin...
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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 homogeneit...
Article
Full-text available
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 starte...
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High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) in...
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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 i...
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Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better und...
Article
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...
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In this study, we used restriction site-associated DNA (RAD) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the Eurasian beaver (Castor fibre) to Scotland. In the absence of a reference genome for beaver, we built contigs and discovered SNPs w...
Article
Full-text available
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 starte...
Article
Full-text available
Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to Britis...
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The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphis...
Article
High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus),...