A Research Strategy to Examine the Taxonomy of the Red Wolf (2020) / Chapter Skim
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4 Genomic Analyses of Extant Canids
4 Genomic Analyses of Extant Canids
Pages 57-70
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From page 57... ...
. This chapter draws upon the knowledge about complex speciation clines in other organisms to describe possible ways to analyze how extant red wolf populations and GCC populations might be related to each other and to historical red wolves described in Chapter 3 as well as to the wild populations of coyotes and gray wolves that may have hybridized (i.e., interbred)
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From page 58... ...
. Specifically, to answer questions about lineage continuity among the extant red wolves, the GCC populations, and the historical red wolf populations in the southeastern United States, whole-genome sequence data provide several advantages over reduced representation sequencing approaches (RAD-seq; see Box 3-1)
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From page 59... ...
While all of these data types can provide useful information, whole-genome sequence data constitute the least biased data type that can provide maximum genomic representation and strong inferential power to address questions related to the taxonomic identity and continuity among extant and historical canid populations. SAMPLING Samples Required to Address the Genetic Continuity of the Extant Captive and Managed Populations, the Gulf Coast Canid Populations, and the Historical Red Wolf Populations in the Southeastern United States The acquisition and analysis of ancient and historical samples of canids throughout North America (as presented in Chapter 3)
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From page 60... ...
should be expected. Besides collecting data from putative red wolf populations, there is a need for obtaining representative whole-genome sequence data from extant populations of gray wolves and coyotes that can serve as reference data for assessing levels of admixture in the captive and managed red wolf and GCC populations, which is important in determining the extent of red wolf ancestry in each population.
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From page 61... ...
. A more extensive sampling of the target extant canid populations (i.e., the captive and managed red wolf populations as well as the GCC populations)
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From page 62... ...
Presented here are some analytical approaches that could use wholegenome data to resolve whether there is continuity between the extant red wolf populations, the GCC populations, and the historical red wolves (i.e., those that lived in the southeastern United States before the anthropogenically driven expansion of coyotes)
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From page 63... ...
tested by selection counting sites with ABBA • Can underestimate gene flow and BABA patterns into the hybrid lineage if user accidentally chooses an outgroup that exchanged gene flow with one of the other lineages continued
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From page 64... ...
or arbitrarily large length of nonrecombining "blocks" admixture times sample sizes to use • Can use RAD-seq or whole-genome • New method; not extensively tested sequencing data yet Local Ancestry HMM • Can distinguish between ancient • New method; not extensively tested (Hidden Markov Model) and recent hybridization as well as yet Infer extent and time since haplotypes present in a common hybridization based on ancestor the ancestry and size of • Jointly estimates which regions of haplotypes in the genome the genome are introgressed and what of individuals and admixed time the hybridization occurred populations • Must use whole-genome sequence data wolf populations appears to be a subsample of the diversity of the GCC populations, without even allowing for genetic drift or mutation in the short time that has elapsed since the ancestors of the captive and managed red wolf populations were putatively part of the GCC populations.
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From page 65... ...
Finding 4-3: The allele frequency spectrum of variation of the reference historical red wolf populations and the statistical test of Schraiber can be used to analyze whole-genome data from the extant red wolf populations and the GCC populations to determine whether these populations represent a continuous line of descent from the historical population. Similarly, this analytical approach could be used to determine whether extant red wolves represent a subset of the GCC populations.
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From page 66... ...
If coyotes never interbred with either wolf species in the time since red wolf and gray wolves diverged from each other, population genetic theory would predict that there should be equal counts of these two types of discordant SNPs, known as ABBA and BABA sites. However, if there was gene flow from coyotes to red wolves but not gray wolves, this gene flow would have had the potential to create extra ABBA sites.
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From page 67... ...
However, if a similar total amount of coyote ancestry entered the red wolf gene pool via low levels of introgression over a longer period of time, it is more likely that weak selection against hybrid individuals has maintained a stable coyote/red wolf speciation cline and purged coyote ancestry away from the most functionally distinctive regions of the red wolf genome. In this scenario, the remaining red wolf ancestry would be more likely to be enriched for a distinctive genetic profile that encodes this species' distinctive traits.
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From page 68... ...
CONCLUSIONS AND RECOMMENDATIONS Conclusion 4-1: To trace the genetic history of extant red wolf populations (captive and managed) and the Gulf Coast canid populations, using whole-genome sequencing methods on modern fresh tissue samples will provide the most informative data with which to assess both genetic continuity between populations over space and time and historical admixture with other North American canids.
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From page 69... ...
2018a. Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast.
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