Filipek: The Role of Reticulate Evolution in the Diversification of the Snake Tribe Thamnophiini

Grants and Contracts Details


Objectives: More and more evidence from molecular systematic research is demonstrating that continued use of traditional phylogenetic methods could be leading to incorrect conclusions on the evolutionary history of life [1]. Traditional phylogenetic methods represent evolutionary diversification in a strict bifurcating pattern, which could be highly misleading and produce erroneous results for taxonomic systems that have undergone significantly high levels of horizontal gene flow between branches. I will acquire tissue samples from all 60 currently recognized Thamnophiine species from museum collections, other researchers, and personal field collecting. Museum resources for this group are plentiful; samples for ~50 species have been identified so far and will soon be requested through museum tissue loans. Phylogeographic studies, wide distributions, numerous subspecies, and extensive morphological variation within Thamnophiini suggests a high potential for cryptic and undescribed species. Missing taxa can lead to inaccurate and/or unresolved trees during phylogenetic analyses [7]. To address this potential issue, I will acquire representative samples from throughout the distribution of all Thamnophiine species to cover as much potential genetic variation as possible. Localities can be guided by previously published phylogeographic studies when available, and for the remaining species the localities will be chosen based on common phylogeographic patterns of the region. Also, samples will be obtained from localities where species are sympatric since these areas have a higher potential of reticulation. The number of samples per species will depend on distribution size, number of subspecies, known hybrid zones, and number of known intraspecific lineages. I anticipate sequencing at least 100 samples covering Thamnophiine diversity, and as many as 175 depending on the availability of funding and tissue resources. Genomic DNA will be extracted from tissue samples using a DNeasy Blood & Tissue Kit (Qiagen) and a target capture approach will be used to produce a large genomic dataset using the recently developed Squamate Conserved Loci (SqCL) probe set [8]. This probe set was designed specifically for the order Squamata (lizards and snakes) and consists of loci derived from anchored hybrid enrichment, ultraconserved elements, and traditionally used nuclear markers. Thousands of high coverage loci have been recovered using this probe set, and these loci are more appropriate for reconstructing well-resolved gene trees due to their larger size [8]. I will submit DNA extractions for sequencing using the SqCL probe set and use an established pipeline [8] to process the sequence data for use in downstream analyses. Phylogenetic network construction will be performed using SNaQ [9], a maximum pseudolikelihood method in the PhyloNetworks package [2]. This method helps reduce computational time by using a quartet approach, which samples subsets of four taxa instead of calculating likelihoods for all taxa simultaneously and makes this approach better suited for large genomic datasets [9]. These analyses will provide an estimate of the species tree history for this group, but more importantly they will provide estimates of the abundance, topological location, and directionality of potential reticulation events within a phylogenetic network. Importantly, for any branch in the tree, this will allow for the quantification of the amount of a reticulate evolutionary history contributed by other species or branches in the tree. Input for SNaQ includes a traditional bifurcating species tree as a starting tree and a table of concordance factors for each quartet which allows the analyses to account for gene tree estimation uncertainty. The starting species tree will be created using ASTRAL II [10] and concordance factors will be produced using the TICR pipeline [11], which will perform gene tree estimation for each individual locus in MrBayes [12] and using the MrBayes output will generate concordance factors for each quartet set of taxa using BUCKy [13]. Ancestral area reconstruction will be performed using BioGeoBEARS [14], which estimates historical biogeography of ancestral species within a phylogenetic tree using varying models of dispersal, vicariance, sympatry, founder events, and extinction. Since the geographic distributions of two species must have at least partial overlap for interspecific gene flow to occur, if deep reticulation is observed using the above discussed network methods, then the ancestral distributions of reticulating species must have at least partially overlapping or adjacent distributions. Locality input for BioGeoBEARS will be approximated to regions for ancestral area reconstruction using InfoMap Bioregions [15], which takes locality data of species and creates major biogeographic regions using network theory. Using measures of reticulate evolution, I will test for associations between shallow reticulate evolution and two different factors (geographic range overlap and ecological niche overlap) that could likely control the degree to which species come into contact and exchange genetic material. Because these measures may be phylogenetically correlated, I will use age-overlap correlation tests in ENMTools [16], which allows examination of patterns in geographic ranges and ecological niches while accounting for phylogenetic history. Localities for geographic ranges will be acquired from online databases for both the range overlap analyses and the ecological niche analyses. The ecological niche models will be produced using Maxent [17]. I will also use the measures of reticulate evolution from SNaQ to test for associations between levels of reticulate evolution and diversification rates among clades in BAMM [18], which allows the tracking of evolutionary rate change across clades through time. I will use the primary species tree provided by SNaQ in both ENMTools and BAMM analyses, and I will explore ways to incorporate nonbifurcating trees into analyses to further test associations with reticulation. Significance: The proposed research will use recently developed phylogenetic network methods, made specifically to handle large datasets, to provide much needed insight into the role of reticulate evolution in speciation and diversification, an understudied phenomenon with strong phylogenetic ramifications. In addition, this work could provide some of the first insights on the factors contributing to reticulate evolution among diverging lineages. This study will also provide a phylogenetic framework that will allow me to further explore the factors contributing to the sharing of genetic information among diverging species. In addition to this larger-scale perspective, I also aim to delve further into finer-scale population level factors that either mitigate or contribute to reproductive exchange. Results from this larger-scale work will help me identify good systems for further fine-scale comparisons. This research also represents a new system and direction of study in my lab and is providing me opportunities for collaborations with new colleagues, including evolutionary biologists at the American Museum of Natural History. Schedule: Samples are expected to be acquired by Spring 2019, with data generation to be completed
Effective start/end date1/1/1912/31/19


  • Society of Systematic Biologists: $2,000.00


Explore the research topics touched on by this project. These labels are generated based on the underlying awards/grants. Together they form a unique fingerprint.