A Research Strategy to Examine the Taxonomy of the Red Wolf (2020) / Chapter Skim
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3 Collecting Genomic Data from Historical and Ancient Canids
3 Collecting Genomic Data from Historical and Ancient Canids
Pages 41-56
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From page 41... ...
a continuous lineage with ancient wolves in the eastern United States? SAMPLE SELECTION To assess whether ancient wolves in all or parts of the eastern United States are a distinct lineage that is also ancestral to historical red wolves, it is essential that sampling for genetic analyses include individuals from a broad geographic range and across different time points.
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From page 42... ...
hybridization between coyotes and gray wolves. Useful samples for addressing questions regarding red wolf population history exist in museum and archaeological collections.
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From page 43... ...
Finding 3-1: To collect a data set maximally useful for discerning the taxonomic status of the red wolf, it will be necessary to include canid samples of broad geographic and temporal provenance and to prioritize individual samples that can yield high-quality morphological and genomic data. PARTIAL VERSUS WHOLE-GENOME DATA COLLECTION To assess the relationships among North American canid lineages, identify significant populations, and examine patterns of hybridization among lineages over time with sufficient statistical power, data from whole-genome sequence rather than just a subset of genes or sites is essential.
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From page 44... ...
Application of SNP arrays to the present challenges could obscure evidence critical for assessing genetic continuity across historical and contemporary canid populations, including populations of the red wolf. Existing data from RAD-seq and SNP arrays are not applicable to the present questions, and care must be taken to avoid destructive use of precious samples to collect data of these types.
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From page 45... ...
ANCIENT DNA ANALYSES Ancient DNA recovery can be challenging, particularly from samples that originated from warm, humid environments such as found in the southeastern United States; thus, the use of current methods that optimize DNA extraction, minimize contamination, and apply next-generation sequencing (NGS) technology is paramount (Figure 3-1)
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DNA LIBRARY CONSTRUCTION, TARGETED CAPTURE, AND SEQUENCING For next-generation sequencing analyses of ancient DNA, most researchers first construct a DNA li brary from the DNA extract, and then this library is used for shotgun sequencing or targeted DNA capture prior to sequencing. The libraries are made by end-repairing the DNA and annealing a set of adapters (compatible with the sequencing technology used)
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From page 47... ...
DATA FILTERING Ancient DNA data provide access to different snapshots of time, which is particularly important for inferring evolutionary processes in such taxa as the red wolf that have been heavily affected by human anthropogenic activity. Prior to the development of new NGS-based methods, ancient DNA analyses were PCR-based and focused on small fragments of mitochondrial DNA.
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From page 48... ...
Are a Distinct Lineage from Those of Gray Wolves and Coyotes To address the distinctiveness of the ancient red wolf, gray wolf, and coyote lineages, it is essential to first define what is meant by a "distinct lineage." One reasonable approach would be to ask whether the ancient red wolf gene pool can -- or cannot -- be adequately modeled as a mixture of the modern gray wolf gene pool and the modern coyote gene pool. Though focused on the problem of inferring population structure, the popular program STRUCTURE can sometimes give the misleading impression that one species is a simple mixture of the gene pools of two other species.
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From page 49... ...
Are a Continuous Lineage to Ancient Wolves in the Eastern United States Evidence of the genetic continuity of "historical" 19th century red wolf specimens with ancient samples would imply that the red wolves still existed as a distinct lineage before the coyote expansion to the eastern United States. To assess this possibility, it will be useful to first estimate the allele frequency spectrum -- that is, to identify genetic variants and calculate their frequencies -- in ancient canid specimens from the eastern United States for which genomic data can be collected using the methods outlined above.
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consensus report on the red wolf, genetic research that includes ancient and historical red wolves has been based solely on mitochondrial DNA data obtained using older PCR-based methods and has found that the red wolf haplotypes cluster with the coyote clade
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From page 51... ...
This study suggests that there was a rapid expansion of wolves out of Beringia about 25,000 years ago with a population bottleneck occurring between 15,000 and 40,000 years ago and that North American wolves predating the last glacial maximum were either replaced by or similar to the Beringian wolves. CONCLUSIONS AND RECOMMENDATIONS To understand and define red wolf populations today and from the late 20th century, it is necessary to have genomic data from red wolves that lived prior to the eastward expansion of coyotes and to compare these data with genomic data from other canids along the proposed range boundaries and from further afield.
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2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.
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1993. Individual DNA identification from ancient human remains.
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From page 54... ...
2019. Evaluating the taxonomic status of the Mexican gray wolf and the red wolf.
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From page 55... ...
2003. Mitochondrial DNA extracted from eastern North American wolves killed in the 1800s is not of gray wolf origin.
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