Current Research

Phylogeography and diversification of Ouachita Mountain endemic salamanders of the Plethodon ouachitae complex

Salamanders of the Plethodon ouachitae complex are endemic to the Ouachita Mountains of west-central Arkansas and southeast Oklahoma, where they are largely restricted to high-elevation, mesic forest. Because environmental conditions in the intervening valleys are warmer and drier, the salamanders appear to be isolated on "sky islands" where gene flow among populations on different mountains is restricted. Previous work using allozymes (Duncan and Highton 1979) found significant genetic variation among populations on different mountains, and it would not be surprising if the number of distinct taxa within this complex is higher than the three currently recognized species (P. caddoensis, P. fourchensis, and P. ouachitae).

Frank Burbrink (AMNH), Kelly Irwin (AR Game & Fish), and I intensively sampled salamanders in the region and used DNA sequence data to delimit evolutionary lineages and their boundaries. Results showed that P. ouachitae is composed of seven lineages structured across six major mountains, P. fourchensis is composed of four lineages structured across five montane isolates, and P. caddoensis is composed of four divergent lineages structured across five major hydrographic basins. In addition to our phylogeographic work, we examined morphological variation and found that mitochondrial lineages could be discriminated morphologically with a moderate level of accuracy (57-72%). We are currently sequencing multiple independent nuclear loci for this group to better understand species diversity and their evolutionary history. We will use coalescent-based species delimitiation methods to determine if our previously defined lineages warrant recognition as species and then we will formally describe them.

Related publications: Shepard & Burbrink 2008, 2009, 2011; Shepard et al. 2011

Media coverage: Exploring Arkansas (AETN)

 

Species delimitation and speciation in slimy salamanders (Plethodon glutinosus group)

Delimiting species is a prerequisite for studying species diversifications; however, this can be extremely difficult when morphological variation is lacking, hybridization occurs, and gene lineages have not had sufficient time to sort. Plethodontid salamanders are plagued by all of these problems and consequently, true species diversity has been difficult to establish. These same characteristics, however, make the group a model system in which to study the complexities of the speciation process using recently developed analytical and genomic tools.

In collaboration with Ken Kozak (Univ. Minnesota) and Matt Gifford (Univ. Central Arkansas), I am using genomic sequence data from multiple unlinked loci to delimit species in the Plethodon glutinosus group (Slimy Salamanders) of the eastern U.S. and infer their evolutionary history. Currently, ~29 species are recognized; however, whether these taxa represent independent evolutionary lineages and whether additional species diversity remains undescribed have not been assessed using multilocus data in a coalescent framework. We will then integrate these results with GIS-based niche models and physiological-based mechanistic models to determine what role environmental factors play in driving population divergence, promoting speciation, and setting range limits.

During my PhD research in the Ouachita Mountains, Frank Burbrink and I started examining the phylogeography of P. albagula, which ranges throughout the Ozarks and Ouachitas (AR, MO, OK) with disjunct populations along the Edwards Plateau of TX. Our preliminary results showed that P. albagula, as currently delimited, is not monophyletic. Further, other species in the region, P. kiamichi, P. sequoyah, and P. kisatchie, were more broadly distributed than previously thought. As members of the P. glutinosus group, we want to delimit species and their distributions so we are conducting a multilocus phylogeography study of P. albagula. As of Fall 2013, we have samples from over 200 localities and are working on completing our sampling of P. albagula in AR, MO, and OK with the help of Jeff Briggler (MDOC) and Kelly Irwin (AGFC).

Related publications: Spatola et al. 2013

 

Phylogenetic relationships and niche evolution in dusky salamanders (genus Desmognathus)

The extremely large and variable genome sizes found in plethodontids (~15 - 75 Gb) make this clade an excellent system for studying the evolutionary processes and molecular mechanisms that determine genome size, but it also hinders the development of genomic resources for the group. Using methods for identifying de novo repeat elements from next-generation sequence data, I devised a bioinformatic pipeline for developing markers in taxa with giant genomes. I have used this method to develop nuclear markers and build a well-resolved phylogeny for the plethodontid genus Desmognathus, which includes 21 recognized species and spans ~30 million years of evolutionary history. Ken Kozak (Univ. Minnesota), Rachel Mueller (Colorado State Univ.), and I are presently writing a paper on the marker development method, and Ken and I are using the phylogeny of Desmognathus to examine rates of climatic niche and body-size evolution.

 

Phylogeography of the queensnake (Regina septemvittata)

Geographic isolation is the primary mechanism by which populations diverge and new species arise. The queensnake (Regina septemvittata) occurs throughout much of the eastern U.S., but has a disjunct range segment in the Ozark region of Arkansas, >250 miles separated from its eastern range. Previous work using allozymes (Weatherby 1974) found that Ozark populations were genetically distinct and suggested that gene flow with eastern populations was reduced or absent. Derek Filipek (UCA MS student) and I are sequencing a few mitochondrial and nuclear genes for queensnakes to examine genetic divergence among populations and determine if Ozark queensnakes represent a distinct evolutionary lineage.