Speciation in cave salamanders. Speciation in subterranean organisms is generally thought to follow one of two main models: the climate-relict model which invokes allopatric speciation and the adaptive-shift model where parapatric speciation occurs in the face of gene flow. However, speciation in the face of gene flow is generally thought to be difficult because gene flow constrains differentiation, thereby preventing the evolution of reproductive isolation. In collaboration with Dr. Ben Fitzpatrick, we are investigating divergence with gene flow between the cave-dwelling Gyrinophilus salamanders and their close relative, the Spring Salamander (G. porphyriticus). We have shown previously using coalescent-based analyses under an "isolation with migration" model that divergence of cave species from their surface relative has occurred with gene flow (Niemiller et al. 2008, 2009). We are now applying next-generation sequencing technologies to this system to examine the dynamics of gene flow and divergence in these salamanders in greater detail across multiple cave populations where both surface and cave species co-occur and morphologically-intermediate individuals exist. We are also investigating what factors promote differentiation despite gene flow and rapid adaptation to subterranean habitats.
Southern Cavefish (Typhlichthys subterraneus), Madison Co., AL
Cryptic diversity in subterranean organisms. A major challenge facing the conservation and management of biodiversity is that a signifiant portion of biodiversity remains to be discovered and described. This problem is manifested in subterranean organisms where species delimitation is often hampered by morphological convergence, lack of morphological differentiation, and lack of data on reproductive isolation between groups. Consequently, our understanding of species boundaries is poor for several groups of organisms, compromising our ability to study and conserve these taxa. In collaboration with Drs. Ben Fitzpatrick and Tom Near, we have taken an integrated approach to species delimitation using multilocus data and newly developed methodologies to infer species boundaries in a morphological invariable cavefish species (Typhlichthys subterraneus) and evaluate these new methods empirically (Niemiller et al. in press). In addition to examining subtle morphological variation in this species complex with the prospect of describing several new species (in collaboration with Drs. Jon Armbruster, Geo Graening, and Dante Fenolio), I am also applying these new approaches in an integrative framework in other subterranean taxa to examine temporal and biogeographic patterns of diversification.
Big Mouth Cave Salamander (Gyrinophilus palleucus necturoides)
Systematics, phylogeography, and population genetics of the plethodontid salamander genus Gyrinophilus. The genus Gyrinophilus consists of four spring/cave-associated species ranging throughout the Appalachian Highlands and portions of the Interior Low Plateau. Two species, the Tennessee Cave Salamander (G. palleucus) and (G. gulolineatus), are paedomorphic stygobites inhabiting subterranean streams of eastern and middle Tennessee, northern Alabama, and northwest Georgia. The West Virginia Spring Salamander (G. subterraneus) is known only from a cave in Greenbrier Co., West Virginia, while the Spring Salamander (G. porphyriticus) is found from the Appalachian Highlands in New England southwestward to Alabama and Mississippi. Recent genetic work suggests that the two stygobitic forms are sister species derived from a porphyriticus-like ancestor that inhabited southern sections of the Cumberland Plateau (Niemiller et al. 2008, 2009). Additionally, Gyrinophilus appears to be a relatively young group dating back to the mid-Pliocene. My current research focuses on understanding the intra- as well as interspecific phylogeography of members of the genus and determining the validity of described species and subspecies. Using phylogenetic and population genetics methods, my goals are to examine the effects of Pleistocene glaciation on the evolution of troglomorphic characters within the genus and to examine the extent, if any, of gene flow between subterranean and between subterranean and epigean populations of Gyrinophilus.
Red Salamander (Pseudotriton ruber) with eggs in a subterranean rimstone pool
Distribution and life history of cave-associated organisms. The Appalachian Highlands, Ozark Highlands, and Interior Plateau support more stygobitic and troglobitic diversity than all other karst regions in the continental United States. Among vertebrates at least six species of fishes and four species of amphibians are considered obligate cave-dwellers, and comprehensive inventories have been conducted for several of these species (e.g., Miller & Niemiller 2008; Graening et al. 2010; Niemiller et al. 2010); however, few studies have focused on inventorying and studying the non-obligate cave-associated organisms within the eastern United States. Regrettably, caves and other subterranean haunts largely have been overlooked by biologists as suitable habitat for inhabitation and reproduction by species not considered permanent residents of the hypogean realm. In collaboration with Drs. Brian Miller, Geo Graening, Dante Fenolio, and others, our research aims to better understand the biology of these species by examining their subterranean distribution, and ecology (Niemiller et al. 2006; Niemiller & Miller 2007; Miller et al. 2008; Niemiller & Miller 2009; Niemiller et al. 2009).
Matt with an Ocoee River Bullfrog
Distribution and life history of the herpetofauna of Tennessee. Tennessee is home to a diverse assemblage of salamanders, frogs, snakes, lizards, and turtles. Although diverse, surprisingly little is known about the ecology and life history of most of the herpetofaunal species in state. In collaboration with Drs. R. Graham Reynolds and Brian Miller, we have studied aspects of the life history of several herpetofaunal species and herpetofaunal community assemblages throughout the state. This work has culminated in the book "The Amphibians of Tennessee" published by UT Press in 2011. We are currently working on the companion volume "The Reptiles of Tennessee," which we hope will be published in the next couple of years.
UNDER CONSTRUCTION
