Jack W. Sites

PHYLOGENY AND PHYLOGEOGRAPHY OF THE LIOLAEMUS DARWINII COMPLEX (SQUAMATA: LIOLAEMIDAE): EVIDENCE FOR INTROGRESSION AND INCOMPLETE LINEAGE SORTING

Abstract Although mitochondrial DNA markers have several properties that make them suitable for phylogeographic studies, they are not free of difficulties. Phylogeographic inferences within and between closely related species can be mislead by introgression and retention of ancestral polymorphism. Here we combine different phylogenetic, phylogeographic, and population genetic methods to extract the maximum information from the Liolaemus darwinii complex. We estimate the phylogeographic structure ofL. darwinii across most of its distributional range, and we then estimate relationships between L. darwinii and the syntopic species L. laurenti and L. grosseorum. Our results suggest that range expansion of these lineages brought them into secondary contact in areas where they are presently in syntopy. Here we present the first evidence for introgression in lizards from temperate South America (ofL. darwinii mitochondrial DNA into L. laurenti and L. grosseorum), and for incomplete lineage sorting (between L. darwinii and L. laurenti). We show that a combination of methods can provide additional support for inferences derived from any single method and thus provide more robust interpretations and narrow the range of plausible hypotheses about mechanisms and processes of divergence. Additional studies are needed in this group of lizards and in other codis‐tributed groups to determine if Pleistocene climatic changes could be a general factor influencing the evolutionary history of a regional biota.

Lizards as model organisms for linking phylogeographic and speciation studies

Lizards have been model organisms for ecological and evolutionary studies from individual to community levels at multiple spatial and temporal scales. Here we highlight lizards as models for phylogeographic studies, review the published population genetics/phylogeography literature to summarize general patterns and trends and describe some studies that have contributed to conceptual advances. Our review includes 426 references and 452 case studies: this literature reflects a general trend of exponential growth associated with the theoretical and empirical expansions of the discipline. We describe recent lizard studies that have contributed to advances in understanding of several aspects of phylogeography, emphasize some linkages between phylogeography and speciation and suggest ways to expand phylogeographic studies to test alternative pattern‐based modes of speciation. Allopatric speciation patterns can be tested by phylogeographic approaches if these are designed to discriminate among four alternatives based on the role of selection in driving divergence between populations, including: (i) passive divergence by genetic drift; (ii) adaptive divergence by natural selection (niche conservatism or ecological speciation); and (iii) socially‐mediated speciation. Here we propose an expanded approach to compare patterns of variation in phylogeographic data sets that, when coupled with morphological and environmental data, can be used to to discriminate among these alternative speciation patterns.

Lizards from the end of the world: Phylogenetic relationships of the Liolaemus lineomaculatus section (Squamata: Iguania: Liolaemini)

The Liolaemus lineomaculatus section is a geographically widely distributed group of lizards from the Patagonian region of southern South America, and includes 18 described species representing the most southerly distributed Liolaemus taxa (the genus includes 228 species and extends from Tierra del Fuego north to south-central Peru). Despite high species diversity, the phylogenetic relationships of this section are unknown. In the present work we sampled all described species in the L. lineomaculatus section as well as currently undescribed candidate species to reconstruct the first complete phylogenetic hypothesis for the clade. Our data set included four anonymous nuclear loci, three nuclear protein-coding loci, and two mitochondrial genes. We compared results obtained with three different phylogenetic methods for the concatenated data set (Maximum Parsimony, Maximum Likelihood and Bayesian Inference) with a coalescent-based species tree approach (BEST), and recovered congruent, strongly-supported topological arrangements across all methods. We identified four main clades within the L. lineomaculatus section: the lineomaculatus, magellanicus, somuncurae, and kingii+archeforus groups, for which we estimated divergence times. We discuss the taxonomic implications of these results and how the future integration of phylogeographic, niche modeling and morphological approaches will allow testing biogeographical hypotheses in this clade.

PHYLOGENETIC RELATIONSHIPS OF LIZARDS OF THE LIOLAEMUS PETROPHILUS GROUP (SQUAMATA, LIOLAEMIDAE), WITH DESCRIPTION OF TWO NEW SPECIES FROM WESTERN ARGENTINA

We describe two new species of lizards of the genus Liolaemus from western Argentina. Both species belong to the petrophilus group and are easily distinguished from other members by a combination of chromatic and squamation characters. We used sequences of the mitochondrial cyt–b, 12S, and ND4 and the nuclear C–mos genes to infer the phylogeny of described species of the group. We found evidence for a monophyletic petrophilus group within the L. elongatus–kriegi complex. The petrophilus group includes Liolaemus petrophilus and two strongly supported clades, one containing the species distributed in the north, which includes one of the new species, L. talampaya; the second clade includes the species distributed in the south, including the new species, L. gununakuna.

DELIMITING SPECIES: COMPARING METHODS FOR MENDELIAN CHARACTERS USING LIZARDS OF THE SCELOPORUS GRAMMICUS (SQUAMATA: PHRYNOSOMATIDAE) COMPLEX

Abstract Species form the fundamental units of analysis in many areas of biology and, therefore, rigorous delimitation of this unit is important to a broad array of researchers. Recently, many new empirical methods have been proposed to delimit species in nature, and a large literature exists on the theoretical merit and superiority of each method. However, few empirical studies actually compare the results of these methods applied in the same study system. We used a large allozyme and chromosome dataset to apply a number of genetic‐distance, character‐based, and tree‐based methods to a well‐studied, data‐rich system: the Sceloporus grammicus lizard complex of central Mexico. We hypothesized species boundaries under a general lineage or evolutionary species conceptual framework in an a priori fashion using mapped restriction‐site data (mitochondrial DNA and nuclear rDNA), allozymes, and morphology. We then compared the ability of different methods to recover the “hypothesized evolutionary species” (HES). Hightons genetic‐distance method and a tree‐based method consistently recovered all four HES, although sometimes with weak support. With two exceptions, other methods recovered the same HES, but additional groups were weakly delimited and nested within the HES. Given the apparent recent divergence of some of the chromosome races and distinct populations in this complex, these are encouraging results. We emphasize the value of specifying testable criteria as clearly as possible and testing these with methods that make use of different properties of a single dataset.

Amphibian phylogeography in the Antipodes: Refugia and postglacial colonization explain mitochondrial haplotype distribution in the Patagonian frog Eupsophus calcaratus (Cycloramphidae)

Climatic oscillations, heterogeneity in elevation, topographical position, and isolation time in southwestern Patagonia have been important in promoting diversification of the biota. Geological studies have shown that this region had wide ice-free areas during periods of the last glacial maximum and provided forested refugia for the biota during Pleistocene glaciations. In this study, we sampled the endemic frog Eupsophus calcaratus from 20 localities, covering most of its distribution and including glaciated and non-glaciated regions. We collected DNA sequences for three mitochondrial regions (D-loop, cyt b, 16S), and describe patterns of variation consistent with a history of both the displacement to glacial refugia and recent recolonization to extensively glaciated regions. The inferred demographic history and divergence times of the lineages of E. calcaratus suggest that the Pleistocene had profound effects on the genetic patterns within this taxon in which some populations were able to survive in refugia within colder regions followed by demographic increases but without evidence of significant range expansion. The mtDNA gene tree recovers six major haploclades of E. calcaratus, which we consider diagnostic of species lineages. These results contribute to our understanding of how geological events, predominately glacial oscillations, have influenced current population structure of a broad-ranging, ectothermic vertebrate in the Valdivian Forest region of southern South America.

Molecular phylogeny, biogeography and insights into the origin of parthenogenesis in the Neotropical genus Leposoma (Squamata: Gymnophthalmidae): Ancient links between the Atlantic Forest and Amazonia

Leposoma is a conspicuous component of leaf litter herpetofauna of South and Central American rainforests. The 15 bisexual and one parthenogenetic species are allocated to the parietale and scincoides groups based on morphology. Phylogenetic analyses of 1830 bp (mtDNA+nuclear) were performed on 63 specimens of four species from Amazonian and Panamanian rainforests, and six species and one undescribed form from the Atlantic Forest. Different methods of tree reconstruction were explored, with Anotosaura vanzolinia and Colobosauroides cearensis as outgroups. The monophyly of the parietale and scincoides groups is strongly supported. Contrary to previous hypotheses suggesting a recent contact between Atlantic and Amazon forests, our estimates point to an initial split in Miocene. The position of Leposoma baturitensis, endemic to relictual forests in the semiarid Caatingas northeastern Brazil, and its divergence from the remaining species of the Atlantic Forest, suggests an ancient isolation with no indication of a secondary contact with forests of the eastern coast. Our data do not permit unambiguous assignment of parental species of the unisexual Leposoma percarinatum or the mechanism involved in the origin of parthenogenesis, but revealed two highly divergent diploid and triploid lineages within L. percarinatum, indicating that the unisexuals represent a species complex.

Evidence of hybridization in the Argentinean lizards Liolaemus gracilis and Liolaemus bibronii (IGUANIA: LIOLAEMINI): An integrative approach based on genes and morphology

The lizard genus Liolaemus is endemic to temperate South America and includes more than 225 species. Liolaemus gracilis and L. bibronii are closely related species that have large and overlapping geographic distributions, and the objective of this work is to further investigate the L. bibronii-L. gracilis mtDNA paraphyletic pattern previously detected, using an integrative approach, based on mtDNA, nuclear DNA and morphological characters. We identified eight morphological L. bibronii introgressed with L. gracilis mtDNAs, and the reciprocal for one L. gracilis, from six localities in the region of sympatry overlap. The morphological identity of these introgressed individuals was confirmed by diagnostic nuclear markers, and this represents the first well-documented case of interspecific hybridization in the lizard genus Liolaemus. Of the three most likely hypotheses for these observed patterns, we suggest that asymmetrical mtDNA introgression as a result of recent or ongoing hybridization between L. bibronii and L. gracilis is the most likely. This may be due to size selection by L. gracilis female preference for the larger L. bibroni males in sympatry, but this requires experimental confirmation.

Phylogenetic Relationships of the Endangered Shenandoah Salamander (Plethodon shenandoah) and Other Salamanders of the Plethodon cinereus Group (Caudata: Plethodontidae)

Abstract The Shenandoah Salamander (Plethodon shenandoah), known from isolated talus slopes on three of the highest mountains in Shenandoah National Park, is listed as state-endangered in Virginia and federally endangered under the U.S. Endangered Species Act. A 1999 paper by G. R. Thurow described P. shenandoah-like salamanders from three localities further south in the Blue Ridge Physiographic Province, which, if confirmed, would represent a range extension for P. shenandoah of approximately 90 km from its nearest known locality. Samples collected from two of these three localities were included in a molecular phylogenetic study of the known populations of P. shenandoah, and all other recognized species in the Plethodon cinereus group, using a 792 bp region of the mitochondrial cytochrome-b gene. Phylogenetic estimates were based on Bayesian, maximum likelihood, and maximum parsimony methods and topologies examined for placement of the new P. shenandoah-like samples relative to all others. All topologies recovered all haplotypes of the P. shenandoah-like animals nested within P. cinereus, and a statistical comparison of the best likelihood tree topology with one with an enforced (Thurow + Shenandoah P. shenandoah) clade revealed that the unconstrained tree had a significantly lower –ln L score (P < 0.05, using the Shimodaira-Hasegawa test) than the constraint tree. This result and other anecdotal information give us no solid reason to consider the Thurow report valid. The current recovery program for P. shenandoah should remain focused on populations in Shenandoah National Park.

Feeding Ecology of the Milksnake (Lampropeltis triangulum, Colubridae) in the Western United States

Abstract We examined the diet of the Milksnake (Lampropeltis triangulum) in the western United States and evaluated predictions about ontogenetic shifts, sexual divergence, and geographic variation in diet. Identifiable prey items were found in 139 specimens, and 41 additional prey items were recorded from the literature, for 180 prey items in total from 175 individual snakes. Lampropeltis triangulum is a generalist predator and feeds primarily on lizards and mammals. Skinks made up a large portion of the total diet. Other lizard taxa were also important prey, whereas reptile eggs, snakes, and birds were consumed infrequently. Ontogenetic shifts in diet were documented. The upper size limit of prey increased with increasing snake size, and adult snakes continued to feed on small prey. Prey type also was related to snake size. Juveniles fed more frequently on lizards, but adults fed mainly on mammals. Although males were longer than females, there was no sexual size dimorphism in mass, and there were no differences in diet between sexes. Diet varied geographically, and the proportion of endothermic prey was greater at higher latitudes after accounting for snake size.