Genome scale assessment of a species translocation program

Dresser, Cassie; Ogle, R. Michael; Fitzpatrick, Benjamin M.

doi:10.1007/s10592-017-0970-6

Cited by 20 publications

(14 citation statements)

References 45 publications

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“…Cardador et al (2018) specifically stated that their "SDMs should also help the optimal design of potential reintroduction or population reinforcement programmes that are projected for the species," implicitly endorsing reintroduction or population reinforcement for the species. Reinforcement and reintroduction are still controversial subjects in conservation genetics (Amato et al 2009, Dresser et al 2017 and, for the Blue-throated Macaw in particular, are a highly debatable management action that could pose an additional threat to the recovery of the species (Herzog et al 2018).…”

Section: Conservation Implications and Research Prioritiesmentioning

confidence: 99%

First systematic sampling approach to estimating the global population size of the Critically Endangered Blue-throated MacawAra glaucogularis

Herzog

Maillard

Boorsma

et al. 2020

Bird Conservation International

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Summary Reliable population size estimates are imperative for effective conservation and management of globally threatened birds like the ‘Critically Endangered’ Blue-throated Macaw Ara glaucogularis. Endemic to one of South America’s largest grassland floodplains, the Llanos de Moxos in northern Bolivia, the species’ global population size is uncertain. The region’s inaccessibility renders the application of traditional methods for obtaining bird population estimates impracticable or cost prohibitive. We developed a simultaneous, multilocality, double-sampling approach combined with quantitative habitat availability analyses to obtain the first rigorous population size estimate for the Blue-throated Macaw. We established 11 survey areas across its three subpopulations that were visited twice by one team in each subpopulation over a 23-day period in the 2015 dry season and obtained additional count data from two roost sites. We classified suitable habitat (palm forest islands) using Landsat 8 images and CLASlite forest monitoring software. We extrapolated the number of macaws detected (conservative estimate of the total number of macaws [CETN], highest single count [HSC]) per 100 ha of suitable habitat in each survey area to the entire area of suitable habitat in all subpopulations combined, corrected for the species’ range occupancy of 34.3%. The total number of Blue-throated Macaws detected by survey (CETN) and roost site counts was 137. Across all survey areas, the number of macaws per 100 ha of suitable habitat was 4.7 for the first and 4.4 for the second period for CETN and 3.2 and 3.4, respectively, for HSC data. Corresponding global population estimates were 426–455 (CETN) and 312–329 (HSC) individuals. Other recent research and anecdotal data support these estimates. Although it would be premature to propose downlisting the species to ‘Endangered’, our findings indicate that it has a larger population and slightly larger range than previously thought, and that the positive effects of conservation actions are now becoming apparent.

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Section: Conservation Implications and Research Prioritiesmentioning

confidence: 99%

First systematic sampling approach to estimating the global population size of the Critically Endangered Blue-throated MacawAra glaucogularis

Herzog

Maillard

Boorsma

et al. 2020

Bird Conservation International

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“…The adaptation to different environments is an example of a future research topic leading to important biological discoveries among this subfamily. Furthermore, the availability of the roan antelope’s reference genome and the additional genomic resources included in this work may prove highly valuable on management and conservation decisions ( Dresser et al 2017 ; Supple and Shapiro 2018 ; Brandies et al 2019 ). Improvements to the roan’s draft genome can be accomplished by proximity ligation sequencing (Hi-C) to generate chromosome-length scaffolds ( Dudchenko et al 2018 ).…”

Section: Resultsmentioning

confidence: 99%

“…Over parts of its range, roan antelope has become established as an economically-important game species, leading to intensive captive breeding of animals. To this end, appropriately planned and executed translocations of wild animals are becoming an important management tool ( Jansen van Vuuren et al 2017 ), whereas the availability of reference genomes and high-resolution genomic resources add significantly to the management and conservation toolbox ( Allendorf et al 2010 ; Shafer et al 2015 ; Dresser et al 2017 ; Brandies et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

De novowhole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope

Gonçalves

Siegismund

Vuuren

et al. 2021

G3 Genes|Genomes|Genetics

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Roan antelope (Hippotragus equinus) is the second largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Although listed as Least Concern across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the de novo assembly and annotation of the whole genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.

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“…Although outcomes have been less widely monitored and reported than desirable (Burke ), case studies demonstrating growth and survival of head‐starts (Vander Haegen et al , Masin et al , Michell and Michell , Tuberville et al , Quinn et al ), recruitment of reproductive adults (Vander Haegen et al , Masin et al , Shaver and Caillouet ), and shifts in size distribution (Peñaloza et al ) similar to what we report for Blanding's turtles are accumulating. Future refinements to the use of head‐starting will benefit from studies of phenotypic effects of head‐starting (Geist et al ), disease status of head‐starts (Smith ), behavior following release (Hazard et al ), and genetic consequences of head‐starting (Dresser et al , Jensen et al ). A larger, more challenging goal will be to determine whether head‐starting can be used as a conservation tactic carried out over a modest time frame (e.g., while threat mitigation is implemented, Vander Haegen et al ) or is a necessary long‐term strategy to ensure persistence of a conservation‐reliant species (Scott et al ).…”

Section: Management Implicationsmentioning

confidence: 99%

Benefits of Head‐starting for Blanding's Turtle Size Distributions and Recruitment

et al. 2020

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Head‐starting is a widely used turtle conservation measure but its effectiveness is incompletely known. We evaluated the success of 2 long‐term Blanding's turtle (Emydoidea blandingii) head‐starting programs in northeastern Illinois, USA, focusing on the effect that head‐starting has on turtle population body‐size distributions and whether head‐started turtles are successfully recruited as reproductive adults. From 1994 to 2017, we collected and incubated eggs from wild females and reared hatchlings for release back into 2 source populations in DuPage and Lake counties, Illinois. Releases occurred annually for 21‐ and 11‐year spans (~1,400 and 800 releases, respectively). We found that head‐starting resulted in significant shifts in Blanding's turtle population body‐size distributions. Prior to intervention, size distributions were strongly skewed toward large adults at both sites, a pattern sometimes interpreted as arising from elevated egg and hatchling mortality and a lack of juvenile recruitment. Currently, population body‐size distributions include a wide range of juvenile and adult size turtles. Importantly, head‐starts have begun reproducing in the 21‐year program and are approaching adult size in the 11‐year program. Blanding's turtle head‐starting shows promise for increasing recruitment in existing populations while threat mitigation is implemented. © 2020 The Wildlife Society.

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Genome scale assessment of a species translocation program

Cited by 20 publications

References 45 publications

First systematic sampling approach to estimating the global population size of the Critically Endangered Blue-throated MacawAra glaucogularis

First systematic sampling approach to estimating the global population size of the Critically Endangered Blue-throated MacawAra glaucogularis

De novowhole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope

Benefits of Head‐starting for Blanding's Turtle Size Distributions and Recruitment

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