Applied Conservation Genetics and the Need for Quality Control and Reporting of Genetic Data Used in Fisheries and Wildlife Management

Morin, Phillip A.; Martien, Karen K.; Archer, Frederick I.; Cipriano, Frank; Steel, Debbie; Jackson, Jennifer A.; Taylor, Barbara L.

doi:10.1093/jhered/esp107

Cited by 82 publications

(79 citation statements)

References 43 publications

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“…Sample sizes (after removal of duplicates) were: Transient, 126; Resident, 245; Offshore, six; Antarctic A, eight; Antarctic B, 15; Antarctic , 42. To test for genotyping errors, we compared replicated genotypes across all loci for replicated samples, and found a per-allele error rate of 0.2%, which is in the low range for published studies (Morin et al 2010). Population differentiation was calculated using G ST and Hedrick's G9 ST to control for the effect of heterozygosity, using the program SMOGD (Crawford 2010).…”

Section: Microsatellitesmentioning

confidence: 99%

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

Morin¹,

Archer²,

Foote³

et al. 2010

Genome Res.

360

429

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Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric “ecotypes” with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from ∼150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.

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Section: Microsatellitesmentioning

confidence: 99%

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

Morin¹,

Archer²,

Foote³

et al. 2010

Genome Res.

360

429

View full text Add to dashboard Cite

show abstract

“…Rigorous error-checking procedures were carried out by each respective research group, enabling the integration of these data sets for the subsequent analysis (Morin et al 2010). All 3009 sequences were aligned in Geneious Pro 4.6.5 (Biomatters) using MUSCLE 3.6 (Edgar 2004) with a maximum of 10 iterations.…”

Section: Sample Collection and Dna Sequencingmentioning

confidence: 99%

First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Rosenbaum¹,

Kershaw²,

Mendez³

et al. 2017

Endang. Species. Res.

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The description of genetic population structure over a species' geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across the species' range in the Southern Hemisphere and Arabian Sea. We combine new and existing data from the mitochondrial (mt)DNA control region that resulted in a 311 bp consensus sequence of the mtDNA control region for 3009 individuals sampled across 14 breeding stocks and subpopulations currently recognized by the International Whaling Commission. We assess genetic diversity and test for genetic differentiation and also estimate the magnitude and directionality of historic matrilineal gene flow between putative populations. Our results indicate that maternally directed site fidelity drives significant genetic population structure between breeding stocks within ocean basins. However, patterns of connectivity differ across the circumpolar range, possibly as a result of differences in the extent of longitudinal movements on feeding areas. The number of population comparisons observed to be significantly differentiated were found to diminish at the subpopulation scale when nucleotide differences were examined, indicating that more complex processes underlie genetic structure at this scale. It is crucial that these complexities and uncertainties are afforded greater consideration in management and regulatory efforts.

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“…Extensive methodological and analytical development has been invested in establishing protocols to maximize success rates and minimize error rates when using these low-quality DNA sources for genetic monitoring (Beja-Pereira et al, 2009;Broquet & Petit, 2004;Miquel et al, 2006;Morin et al, 2010;Smith & Wang, 2014;Taberlet, Griffin, et al, 1996;Taberlet & Luikart, 1999;Wang, 2016). Genetic monitoring is set to become more important in the future, largely because many vertebrate species have undergone rapid, anthropogenic population declines (Li et al, 2016) that are unlikely to abate without intensive management efforts.…”

Section: Introductionmentioning

confidence: 99%

Genetic and genomic monitoring with minimally invasive sampling methods

Carroll

Bruford

DeWoody

et al. 2017

Preprint

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Emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.3209v1 | CC BY 4.0 Open Access |

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Applied Conservation Genetics and the Need for Quality Control and Reporting of Genetic Data Used in Fisheries and Wildlife Management

Cited by 82 publications

References 43 publications

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Genetic and genomic monitoring with minimally invasive sampling methods

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