SG: Will phylogenomics resolve the most difficult parts of the tree of life: an empirical evaluation with the turtle genus Pseudemys

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Species are the most important biological unit of scientific research, conservation and management. As a society, we protect species under the Endangered Species Act, we observe, hunt, and admire species in their native habitats, and we manage national parks for species conservation. As new molecular technologies and tools have become available, researchers can now use the entire genome, including billions of pieces of information, to precisely determine how many species occur in a taxonomic group or geographical region in ways that were inconceivable a few years ago. As these extremely informative data sets become available, those who study species and speciation are currently facing the dilemma of what data to collect and how to analyze those data so that species can be quickly, accurately, and inexpensively identified and delimited across all of life. In this project, the research team will evaluate the three most promising, cutting edge approaches that are currently in use to determine which genomic method is optimal for species identification and delimitation in a group of freshwater turtles from the southeastern United States. This group, although widespread and well studied ecologically, has thwarted accurate species delimitation for decades; it also contains two critically endangered taxa. The work in this project will provide critical guidance for the large group of biologists who seek to identify, delimit, and protect species using genomic data.In this analysis, the turtle genus Pseudemys is used as an empirical example of an extremely difficult group to determine species delimitation and interrelationships. The project uses a comparative genomic approach with extensive rangewide sampling of all nine potential taxa within Pseudemys to evaluate the relative efficacy and power of three genomic approaches: restriction-site associated DNA (RADseq), targeted enrichment where known portions of the genome are sequenced using probes designed from existing genomic resources, and low-coverage, whole genome resequencing. A novel comparative approach is utilized to ask which of these data streams performs optimally based on cost, ease and efficiency of lab work, and empirical performance. In so doing, two fundamental issues in systematics will be addressed. First, what are the prospects for identifying lineages, and for reconstructing species trees for extremely difficult groups using large amounts of genomic data? And second, given the current methods available for generating and analyzing genomic data, what approach is optimal? Overall, the results of this project will provide both general guidelines for analyses of difficult groups and clear resolution of this empirical case study of an important faunal component of the southeastern United States.