Research Interests

My general research interests are in the population and evolutionary biology of amphibians and reptiles. Much of my research has involved the use of DNA sequence and morphological data to address questions pertaining to the evolution and phylogenetic relationships of squamate reptiles (lizards and snakes). Also, a lot of recent research in my lab has also been aimed more at the population level in an attempt to address questions related to lineage diversification (e.g., phylogeography, gene flow, speciation/species delimitation). In addition to the lineage diversification and phylogenetic inference research, increasingly I am pursuing macroevolutionary oriented research that addresses questions related to the tempo and pattern of clade diversification.  Below are some of the specific research projects that I am participating in:

Diversification and Evolution of the Herpetofauna of the Southwest and Mexico:

A major focal area of my research program is the study of the diversification and evolution of the herpetofauna of the southwest U.S. and Mexico.  Much of this research has focused on species- and population-level systematic biology studies of phrynosomatids (Reeder, 1995; Reeder and Wiens, 1996; Wiens and Reeder, 1997; Wiens et al., 1999; Reeder and Montanucci, 2001; Leaché and Reeder, 2002; Wiens et al., 2010; Grummer et al., accepted), but other groups have been studied as well (Richmond and Reeder, 2002; Gergus et al., 2004; Smith et al., 2007; Wood et al., 2008).  Currently, I am particularly interested in further studying the diversification of whiptail lizards of the genus Aspidoscelis (formerly Cnemidophorus; Reeder et al., 2002).  Whiptails are a conspicuous component of the herpetofauna of western North America and have been of great interest to evolutionary biologists because of:  1) the large number of parthenogenetic or unisexual (all-female) “species”, and 2) persistent taxonomic uncertainty in many widespread, morphologically diverse bisexual species.
  • Origin and evolution of unisexual lineages of whiptails.—Within the Aspidoscelis sexlineata group, ~1/3 of the whiptail diversity is composed of unisexual “species”.  These parthenogenetic lineages are of hybrid origin and possess the haploid genomes of 2-3 different bisexual species.  However, the maternal and/or paternal ancestry of some unisexual lineages is still uncertain.  Phylogenetic analysis of mtDNA sequences has allowed the resolution of the maternal ancestry of unisexual lineages where previous low-resolution mtDNA restriction fragment studies failed.  Also, the use of rapidly evolving nuclear gene sequences is providing a finer scale resolution of the paternal ancestry (as well as providing nuclear confirmation of maternal ancestry). These molecular approaches are further elucidating the origins of these clonal lineages and allowing a re-evaluation of what constitutes a “species”.
  • Lineage diversification and species limits within whiptails.—Another significant facet of my whiptail research is addressing population and systematic biology questions within the Aspidoscelis sexlineata and A. tigris species groups.  These groups contain some of North America’s most perplexing herpetological species complexes, namely the A. burti/costata complex and A. “tigris” (1 vs. several species).  Extensive mtDNA data sets have been generated to investigate past and present evolutionary processes that have been responsible for diversification within these widespread species complexes.  Phylogenetic and coalescent-based methods (with multiple independent loci) are being utilized to address questions related to the phylogenetics and delimitation of species limits within these important squamate lineages of the desert Southwest.

Baja California:  A fragmented peninsula.—The biological diversity of both plants and animals of the Baja California peninsula (the second longest in the world!) has intrigued evolutionary biologists for decades.  This interest is largely due to the peninsula's geographic and geologic histories, with the peninsula's vicariant origin from the west coast of mainland Mexico being more complex then earlier studies suggested.  A previously proposed hypothesis of the peninsula formerly representing an archipelago of islands appears to be supported by a large number of studies spanning diverse biota.  But, much remains to be understood.  It still is not clear how effective the historic archipelago was at limiting gene flow and promoting diversification of the biota.  Of the various taxa studied, reptiles have provided the most consistent genetic evidence for the position of each “paleo”-island's historic shoreline.  Yet, we are still discovering new fragments where proposed peninsular seaways split once continuous ancestral populations.  My lab (in collaboration with Dr. Brad Hollingsworth of the San Diego Natural History Museum) is taking a molecular population and systematic biology approach to study diversification in several lizard groups to further evaluate contact zones between genetically differentiated lineages (i.e., lineages formally separated by hypothesized peninsular seaways). Using both mtDNA and multi-locus nuclear DNA data and modern coalescent-based approaches, we are addressing the timing of these past historical events, determining the extent of gene flow occurring across contact zones, and assessing what these evolutionary patterns tell us about the patterns and processes of lineage diversification in Baja California.


Higher-level squamate phylogeny:

A major area of my research involves inferring the phylogenetic relationships among squamate reptiles (lizards and snakes), in particular resolving the origin of snakes and the phylogenetic placements of other major limbless groups (e.g., dibamids, amphisbaenians).  Squamates are the second largest group of terrestrial vertebrates after birds and contain 96% of all living non-avian reptile species.  Squamates are the subject of many phylogeny-based research programs in ecology and evolution, yet, until relatively recently, the phylogenetic relationships among many major squamate clades was still uncertain and/or controversial.  Early molecular systematic research by myself (e.g., Lee et al., 2004) and others suggested previous hypotheses of squamate relationships based on morphology were likely incorrect. However, it was also clear that the types of molecular data being collected at the time (e.g., mitochondrial DNA [mtDNA]; nuclear genes c-myc and c-mos) were insufficient to adequately resolve these deep phylogenetic relationships.  Whereas in the past several years modern molecular phylogenetic studies have been providing new insights on the higher-level relationships among major squamate clades, the relationships among some major squamate clades are still uncertain (e.g., interrelationships among anguimorphs, snakes and iguanians; higher level relationships within Scincidae). The consensus in the systematic community was that resolving squamate phylogeny would require a large number of slowly evolving nuclear protein-coding genes.  Given this, I was involved with putting together a collaborative team of other systematic biologists interested in squamate phylogeny (i.e., J. Wiens, Stony Brook University; J. Sites, Brigham Young University; M. Kearny, National Science Foundation; O. Rieppel, Field Museum of Natural History; J. Gauthier, Yale University) and we successfully secured a collaborative NSF grant from the Assembling the Tree of Life program.

The primary goal of this award was to collect DNA sequences for a large number of nuclear protein-coding genes from ~160 squamate species (representing all lizard and snake families and subfamilies) to infer phylogenetic relationships within this diverse clade.  Candidate genes were selected using a dynamic comparative genomic approach (see Townsend et al. 2008), which involved screening of the pufferfish genome against the genome databases of other vertebrates (e.g., human, chicken). This procedure resulted in the development of ~50 nuclear markers for inferring higher-level relationships among squamates.  Given the demand for phylogenetically useful nuclear genes for higher-level studies, these results are of great interest to molecular evolutionary biologists of other vertebrate groups since our method of discovering and developing these nuclear loci suggests they will be useful in other vertebrate groups.

Besides inferring higher-level phylogeny, my lab has also been exploring the use of our many newly developed nuclear loci for addressing lower-level phylogenetic questions within various groups of squamates.  Some ongoing projects involve the following groups of taxa: 1) Australian Sphenomorphus group skinks; 2) gerrhonotine (alligator) lizards; 3) cnemidophorine lizards; 4) phrynosomatid lizards (with J. Wiens).

Skink phylogeny and the evolution of limb reduction:

Evolution of body form.—The Scincidae (=skinks) represents the largest lizard family and is a “model system” for studying the evolution of limb reduction and body elongation.  These transitions are generally correlated and have been common phenomena during scincid evolution.  The majority of skinks exhibit “normal” bodies and limbs, but some taxa are snake-like (very elongated and completely limbless).  Within Squamata, the majority of the independent origins of a snake-like body have occurred within Scincidae (see Wiens et al., 2006).  To address higher-level scincid phylogenetics and obtain an initial “big picture” of the evolution of limb loss, an extensive mtDNA data set was amassed (all subfamilies represented, plus 21 of 28 genera of the “Scincinae”).  The results of this study supported the independent derivation of all other subfamilies from the “Scincinae” (Brandley et al, 2005) and gave the first phylogenetic perspective on the broad patterns of limb loss among skinks.  In a similar study on Madagascan “scincines”, we demonstrated that body elongation evolved multiple times (Schmitz et al., 2005).  However, an equally exciting discovery was the apparent significant reduction in the number of presacral vertebrae (=a reversal from moderate body elongation to “normal” body length) in at least two groups, an unprecedented finding that requires further investigation.

Phylogeny of the Sphenomorphus group.The Sphenomorphus group is cosmopolitan and contains most of the diversity of lygosomine skinks. Most of the species diversity is found within Australia. The Australian Sphenomorphus group is a diverse skink clade (Reeder 2003), composed of many taxa (e.g., Anomalopus, Lerista) possessing limbed and limbless species, as well as many species exhibiting various intermediate conditions towards limblessness. Therefore, this is an ideal group for which to study the evolution of limb reduction from a phylogenetic perspective. Many changes in morphology and life history are postulated to be correlated with limb reduction (e.g., body elongation precedes limb reduction, loss of external ear, reproductive mode). While much of my earlier systematic attention has been on the Australian subgroup, I have more recently incorporated more non-Australian species in order to more rigorously test the monophyly of the Australia group and to get a more global perspective on the evolution of this group.  To date, an extensive mtDNA molecular phylogenetic study of this group is essentially complete, with this phylogeny being used to study the patterns of body elongation and limb reduction from an evolutionary perspective. 

In addition to higher-level phylogenetic relationships within the Australian Sphenomorphus group, I am involved with collaborative research (with N. Crawford; Boston University) to infer the phylogenetic relationships and species limits within "Glaphyromorphus" of Australia. Most of the species occur in northern Australia, with a single species ("G". gracilipes) occurring in southwest Australia. This southwestern species is actually more closely related to Hemiergis of southern Australia (Reeder and Reichet, 2011). However, even the northern assemblage does not appear to be monophyletic. Essentially all species are being examined in an attempt to determine the clades within this assemblage and determine which non-"Glaphyromorphus" taxa are their closest relatives. Also, the widespread "G". isolepis is likely a species complex.

Species-level phylogeny of the Scincidae.—The Scincidae includes >1300 species (~16% of all squamates) divided among 126 genera and four subfamilies.  Skinks are found almost worldwide, but diversity is highest in tropical regions of Asia, Africa, and Australia.  Despite some important papers in the recent past, the generic- and species-level phylogeny of skinks remains very poorly resolved.  There have been few modern studies addressing higher-level scincid phylogeny and these have had limited taxon overlap (<50 species total; <25% of genera represented).  These studies generally disagree, but they do corroborate the gross paraphyly of the “Scincinae” with respect to the other subfamilies.  Though little studied phylogenetically, scincids (along with colubrid snakes) represent the most important unexplored frontier in the squamate Tree of Life.  Since studies of their phylogeny are hampered by paraphyletic genera and higher-taxa, scincid relationships can only be thoroughly resolved by extensive sampling of both species and genera.  Given this and the scope of the problem, I have been involved with the assembly of a large collaborative team of experts (J. Wiens, Stony Brook University; R. Brown, University of Kansas; C. Austin, Louisiana State University; Aaron Bauer, Villanova University; Chris Raxworthy, American Museum of Natural History) who previously have worked independently on different aspects of skink systematics and evolution.  Resources are being pooled and efforts coordinated in order to resolve a global skink phylogeny.