Dataset Information

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads.

ABSTRACT: Background:A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes and local adaptation and can aid in the development of breeding management plans. This information is important for fields such as conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets. Findings:Here, we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost (<$3000), thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold and contig N50 of 21 Mb and 83 Kb, respectively, and completely reconstructed 95% of a set of conserved mammalian genes. Additionally, we estimate the heterozygosity and demographic history of African wild dogs, revealing that although they have historically low effective population sizes, heterozygosity remains high. Conclusions:We show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes from Illumina short-read data of intermediate coverage (?25x-50x). Interestingly, the wild dog shows higher heterozygosity than other species of conservation concern, possibly due to its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog and help conservationists to better understand the ecology and adaptability of those species in a changing environment.

SUBMITTER: Armstrong EE

PROVIDER: S-EPMC6350039 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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Publications

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads.

Armstrong Ellie E EE Taylor Ryan W RW Prost Stefan S Blinston Peter P van der Meer Esther E Madzikanda Hillary H Mufute Olivia O Mandisodza-Chikerema Roseline R Stuelpnagel John J Sillero-Zubiri Claudio C Petrov Dmitri D

GigaScience 20190201 2

<h4>Background</h4>A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes and local adaptation and can aid in the development of breeding management plans. This information is important for fields such as conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, ...[more]

PMID: 30346553

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Project description:Human-carnivore conflict can threaten human life and livelihoods, leading to retaliation that negatively affects carnivore conservation. The endangered African wild dog Lycaon pictus is prone to human-carnivore conflict. Therefore, it is imperative to understand which landscape features are associated with African wild dog occurrence since selection or avoidance of these features could predict the levels of conflict. We investigated resource selection in the African wild dog in relation to four anthropogenic landscape features (livestock density, agriculture, roads and human land use) within the landscape that may pose a mortality risk, as well as one natural feature (nature reserves). We compared spatio-temporal space use patterns of four African wild dog packs in north-eastern South Africa. Data were collected from one collared individual per pack. These packs constituted approximately 10% of the total remaining African wild dog population in South Africa. Two packs occurred outside of the Kruger National Park and had access to multiple areas with farmland and other anthropogenic features, whereas the remaining two packs mainly occurred within the boundaries of the Kruger National Park but made occasional forays outside of park boundaries. Utilising Resource Selection Functions and GIS analyses, we found that agricultural landscape features, roads and nature reserves were important predictors of African wild dog occurrence for all four packs. In addition to potential conflict with farmers, high odds of occurrence on roads with fast-moving traffic and road mortality was highlighted as a concern for three of the packs. While farms and areas that house livestock were readily available, pack presence occurred in areas with few farms and low livestock densities, pointing to avoidance of areas where human-carnivore conflict and resulting mortality could occur. Our study highlights potential threats to the persistence of the African wild dog, which can be used to inform future conservation efforts of the species.

Project description:BackgroundThe African wild dog (Lycaon pictus), an endangered canid native to southern and eastern Africa, is distinct among canids in being described as entirely tetradactyl and in its nomadic lifestyle and use of exhaustive predation to capture its prey instead of speed, strength, or stealth. These behavioral and morphological traits suggest a potentially unique set of adaptations.MethodsHere, we dissected the forelimbs of an adult male L. pictus specimen and performed detailed descriptions and quantitative analyses of the musculoskeletal anatomy.ResultsStatistical comparisons of muscle masses and volumes revealed that L. pictus has relatively smaller wrist rotators (mm. pronator teres, pronator quadratus, supinator) than any other included carnivoran taxon, suggesting adaptive pressures for antebrachial stability over rotatory movement in the carpus of L. pictus. While a complete digit I is absent in L. pictus, a vestigial first metacarpal was discovered, resulting in changes to insertions of mm. extensor digiti I et II, abductor (et opponens) digiti I and flexor digiti I brevis. Mm. anconeus, brachialis and flexor carpi ulnaris caput ulnare all have more extensive origins in L. pictus than other canids suggesting an emphasis on posture and elbow stability. M. triceps brachii caput laterale has a larger origin in L. pictus and m. triceps brachii caput longum has an additional accessory head. Electromyographic studies have shown this muscle is active during the stance phase of trotting and galloping and is important for storing elastic energy during locomotion. We interpret these differences in size and attachments of muscles in L. pictus as adaptations for long distance running in this highly cursorial species, likely important for exhaustive predation. Absence of a full digit I in L. pictus may increase speed and stride length; however, the retention of a vestigial digit permits the attachment of reduced pollical muscles which may provide additional stability and proprioception to the carpus.

Project description:African wild dogs (Lycaon pictus) are endangered and their population continues to decline throughout their range. Given their conservation status, more research focused on their population dynamics, population growth and age specific mortality is needed and this requires reliable estimates of age and age of mortality. Various age determination methods from teeth and skull measurements have been applied in numerous studies and it is fundamental to test the validity of these methods and their applicability to different species. In this study we assessed the accuracy of estimating chronological age and age class of African wild dogs, from dental age measured by (i) counting cementum annuli (ii) pulp cavity/tooth width ratio, (iii) tooth wear (measured by tooth crown height) (iv) tooth wear (measured by tooth crown width/crown height ratio) (v) tooth weight and (vi) skull measurements (length, width and height). A sample of 29 African wild dog skulls, from opportunistically located carcasses was analysed. Linear and ordinal regression analysis was done to investigate the performance of each of the six age determination methods in predicting wild dog chronological age and age class. Counting cementum annuli was the most accurate method for estimating chronological age of wild dogs with a 79% predictive capacity, while pulp cavity/tooth width ratio was also a reliable method with a 68% predictive capacity. Counting cementum annuli and pulp cavity/tooth width ratio were again the most accurate methods for separating wild dogs into three age classes (6-24 months; 25-60 months and > 60 months), with a McFadden's Pseudo-R2 of 0.705 and 0.412 respectively. The use of the cementum annuli method is recommended when estimating age of wild dogs since it is the most reliable method. However, its use is limited as it requires tooth extraction and shipping, is time consuming and expensive, and is not applicable to living individuals. Pulp cavity/tooth width ratio is a moderately reliable method for estimating both chronological age and age class. This method gives a balance between accuracy, cost and practicability, therefore it is recommended when precise age estimations are not paramount.

Project description:Large carnivores have experienced widespread extirpation and species are now threatened globally. The ecological impact of the loss of large carnivores has been prominent in Gorongosa National Park, Mozambique, after most were extirpated during the 1977-92 civil war. To remedy this, reintroductions are now being implemented in Gorongosa, initiating with endangered African wild dogs (Lycaon pictus), hereafter 'wild dogs'. We describe the first transboundary translocation and reintroduction of founding packs of wild dogs to Gorongosa over a 28-month study period and evaluate the success of the reintroduction based on five key indicator categories. We also assess how wild dog space use and diet influenced their success. We found that pre-release, artificial pack formation in holding enclosures aided group cohesion and alpha pair establishment. Post-release, we also observed natural pack formations as a result of multiple dispersal events. Founder and naturally formed packs produced pups in two of the three breeding seasons and packs successfully recruited pups. Survival rate for all wild dogs was 73% and all mortality events were from natural causes. Consequently, the population grew significantly over the study period. All indicators of success were fully achieved and this study documents the first successful reintroduction of wild dogs into a large, unfenced landscape in Mozambique and only the second on the continent. Potential mechanisms underlying these early successes were the avoidance of habitats intensively used by lions, dietary partitioning with lion, avoidance of human settlements, and Gorongosa's management strategy. We predict further population expansion in Gorongosa given that 68% of the park is still unused by wild dogs. This expansion could be stimulated by continued reintroductions over the short- to medium-term. Recovery of wild dogs in Gorongosa could aid in the re-establishment of a larger, connected population across the greater Gorongosa-Marromeu landscape.

Dataset Information

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads.

Publications

Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads.

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