Molecular systematics of new world gopher, bull, and pinesnakes (Pituophis: Colubridae), a transcontinental species complex

DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age

Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.

Diversity and conservation of terrestrial vertebrates (birds, mammals, and reptiles) of Sierra Cucapá, Mexicali, Baja California, Mexico

Knowledge about the biodiversity of Baja California has been obtained mainly from natural protected areas (NPAs), while some unprotected natural areas have been poorly studied. The Sierra Cucapá in the northeast of the peninsula is one example. The objectives of this study are 1) to integrate existing knowledge of bird, mammal, and reptile diversity in Cucapá from public databases, citizen science platforms, and information generated from fieldwork, 2) to identify the spatial distribution of records in the study area, 3) to compare the composition of vertebrate species of Cucapá with that of NPAs of northern part of the peninsula, and 4) to assess the biological conservation value of Cucapá. We obtained records of 150 species of native vertebrates (102 birds, 34 mammals, and 14 reptiles) of which 10 species of birds, four mammals, and seven reptiles are included in a risk extinction category. The different sources of information contributed in a complementary way to the species inventories. Large areas in western and northern Cucapá lack records. The total difference in species composition between Cucapá and nearby NPAs ranged between 58 and 69% for birds, 61 and 79% for mammals, and 69 and 87% for reptiles. The species richness of Cucapá, its particular species composition, the presence of species in risk extinction categories, and the number and size of unexplored areas indicate that this area represents an opportunity for biological conservation in the northern part of the Peninsula. This work provides compelling data for the protection of Cucapá.

Hatchling survival to breeding age in Northern Pine Snakes (Pituophis melanoleucus) in the New Jersey Pine Barrens: Human effects on recruitment from 1986 to 2017

To conserve threatened/endangered species, we need to understand the factors contributing to reproductive success and recruitment to reproductive stage. Obtaining this information is difficult for snakes because they are secretive, are not easy to locate at the same stage each year, and are sometimes sparsely distributed. We determined nest fate, hatchling growth and survival to age 5 years, and recruitment to breeding age of Northern Pine Snakes (Pituophis melanoleucus) in New Jersey Pine Barrens from 1986 to 2017. Pine Snakes are ‘threatened’ in New Jersey and in other states, and are at risk because of increased human population, habitat loss, predation, and poaching. Age of first-breeding was 4-years, based on snout-vent length of gravid and laying females, and snout-vent length of females followed as hatchlings to 5-years. Mean clutch size (+ 1 SE) was 9.5 + 0.3 (N = 53). The annual percent of nests in which eggs hatched averaged 25% (N = 288 nests), and varied among 5-year periods (5% to 30%/year). Of lab-reared hatchlings released into natal nests (N = 90), 26% (2015) and 32% (2016) reached hibernacula excavated in 2016 and 2017. The sex ratio of hatchlings reaching hibernation sites (N = 181) between 1986 and 2015 was skewed toward females (74/106, 59% females), and varied among 5-year periods (47–75% females). Once hatchlings reached a hibernaculum, there was a sex-related difference in survival. For hatchlings reaching a monitored hibernaculum, survival to 3-years was 35% in females and 40% in males, and to 4-years was 25% in females and 33% in males. Using these data, only 10% of females reached 3 years (first possible breeding age), and 7% survived to 4-years. Methodological problems with determining survival rates during these early critical years are discussed.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.

The endemic insular and peninsular species Chaetodipus spinatus (Mammalia, Heteromyidae) breaks patterns for Baja California

The Baja California peninsula is the second longest, most geographically isolated peninsula on Earth. Its physiography and the presence of many surrounding islands has facilitated studies of the underlying patterns and drivers of genetic structuring for a wide spectrum of organisms. Chaetodipus spinatus is endemic to the region and occurs on 12 associated islands, including 10 in the Gulf of California and two in the Pacific Ocean. This distribution makes it a model species for evaluating natural historical barriers. We test hypotheses associated with the relationship between the range of the species, patterns in other species, and its relationship to Pleistocene-Holocene climatic changes. We analyzed sequence data from mtDNA genes encoding cytochrome b (Cytb) and cytochrome c oxidase subunits I (COI) and III (COIII) in 26 populations including all 12 islands. The matrilineal genealogy, statistical parsimony network and Bayesian skyline plot indicated an origin of C. spinatus in the southern part of the peninsula. Our analyses detected several differences from the common pattern of peninsular animals: no mid-peninsula break exists, Isla Carmen hosts the most divergent population, the population on an ancient southern Midriff island does not differ from peninsular populations, and a mtDNA peninsular discordance occurs near Loreto.

Landscape-level influences of terrestrial snake occupancy within the southeastern United States

Habitat loss and degradation are thought to be the primary drivers of species extirpations, but for many species we have little information regarding specific habitats that influence occupancy. Snakes are of conservation concern throughout North America, but effective management and conservation are hindered by a lack of basic natural history information and the small number of large-scale studies designed to assess general population trends. To address this information gap, we compiled detection/nondetection data for 13 large terrestrial species from 449 traps located across the southeastern United States, and we characterized the land cover surrounding each trap at multiple spatial scales (250-, 500-, and 1000-m buffers). We used occupancy modeling, while accounting for heterogeneity in detection probability, to identify habitat variables that were influential in determining the presence of a particular species. We evaluated 12 competing models for each species, representing various hypotheses pertaining to important habitat features for terrestrial snakes. Overall, considerable interspecific variation existed in important habitat variables and relevant spatial scales. For example, kingsnakes (Lampropeltis getula) were negatively associated with evergreen forests, whereas Louisiana pinesnake (Pituophis ruthveni) occupancy increased with increasing coverage of this forest type. Some species were positively associated with grassland and scrub/shrub (e.g., Slowinski's cornsnake, Elaphe slowinskii) whereas others, (e.g., copperhead, Agkistrodon contortrix, and eastern diamond-backed rattlesnake, Crotalus adamanteus) were positively associated with forested habitats. Although the species that we studied may persist in varied landscapes other than those we identified as important, our data were collected in relatively undeveloped areas. Thus, our findings may be relevant when generating conservation plans or restoration goals. Maintaining or restoring landscapes that are most consistent with the ancestral habitat preferences of terrestrial snake assemblages will require a diverse habitat matrix over large spatial scales.

Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis

Many species inhabiting the Peninsular Desert of Baja California demonstrate a phylogeographic break at the mid-peninsula, and previous researchers have attributed this shared pattern to a single vicariant event, a mid-peninsular seaway. However, previous studies have not explicitly considered the inherent stochasticity associated with the gene-tree coalescence for species preceding the time of the putative mid-peninsular divergence. We use a Bayesian analysis of a hierarchical model to test for simultaneous vicariance across co-distributed sister lineages sharing a genealogical break at the mid-peninsula. This Bayesian method is advantageous over traditional phylogenetic interpretations of biogeography because it considers the genetic variance associated with the coalescent and mutational processes, as well as the among-lineage demographic differences that affect gene-tree coalescent patterns. Mitochondrial DNA data from six small mammals and six squamate reptiles do not support the perception of a shared vicariant history among lineages exhibiting a north-south divergence at the mid-peninsula, and instead support two events differentially structuring genetic diversity in this region.

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.

Budding speciation and neotropical origin of the Azorean endemic liverwort, Leptoscyphus azoricus

The origin of plant species endemism in Macaronesia, one of the 25 world biodiversity hotspots, has traditionally been either interpreted as a result of the dramatic reduction of a broader tertiary distribution range during the Ice Age or neoendemism. This hypothesis is tested here in the context of a species-level phylogeny employing chloroplast trnL-trnF and atpB-rbcL sequences in the leafy liverwort genus Leptoscyphus (Lophocoleaceae). The data suggest that the Azorean endemic Leptoscyphus azoricus originated from parental populations of the Neotropical Leptoscyphus porphyrius by long-distance dispersal across the Atlantic and subsequent isolation. Possible reasons for the differences in the origin of endemism in angiosperms, wherein by far most endemic species have their close relatives on the European and North African continents, are discussed.

Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula

Comparative phylogenetic and phylogeographic analyses have revealed a pervasive midpeninsular divergence in the mitochondrial genealogies of numerous vertebrate taxa distributed on the Baja California Peninsula. In this study, we extend the investigation of regional vicariance in Baja California to an arthropod taxon by examining patterns of phylogenetic and morphological divergence in the spider genus Homalonychus (Araneae, Homalonychidae). We analyzed data from two mtDNA genes (16S rRNA and NADH dehydrogenase subunit (1) and a nuclear gene (28S rRNA) using maximum parsimony and Bayesian phylogenetic analyses, and also conducted geometric morphometric analyses employing landmark data on male and female genitalia. Genes and morphology both reveal a deep split across the Colorado River and Gulf of California, separating Homalonychus selenopoides on the east side of river from its congener Homalonychus theologus on the west side of the river, including the Baja California Peninsula. Along the north-south axis of the Baja Peninsula, an apparently more recent midpeninsular phylogenetic break is evident within H. theologus in the mitochondrial genome and in female genitalia. However, there is no measurable divergence between northern and southern populations in either nuclear DNA or male genitalia. We suggest that this discordance between datasets reflects either a difference in rates of evolution between male versus female systems, or that male-based nuclear gene flow is obscuring a phylogenetic split that is fixed in the female-based systems. Our findings provide additional support for a midpeninsular Baja divergence event, although the timing and geological evidence for such an event remain elusive.

Deep genealogical history without population differentiation: discordance between mtDNA and allozyme divergence in the zebra-tailed lizard (Callisaurus draconoides)

The peninsula of Baja California has a complex geological history that has strongly affected the regional biota. Genealogical histories of many species have revealed congruent patterns, which suggest that the peninsula was temporarily submerged at two locations. We sequenced a total of 1953 base pairs (bp) of the mitochondrial genome for 42 specimens of the zebra-tailed lizard (Callisaurus draconoides). The resulting maternal genealogy supports the former existence of a mid-peninsular seaway and a Plio-Quaternary seaway across the Isthmus of La Paz. In addition, a genealogical break is revealed in the vicinity of Loreto. This genealogical break may have resulted from prolonged submergence of the Loreto Basin during Pliocene. The mid-peninsular seaway may have occurred as early as late Miocene, at a time significantly earlier than previously hypothesized. Comparison with other genealogies and geological evidence suggests that current models on the evolution of Baja California's fauna are temporally shallow. The deep genealogical patterns of C. draconoides also disagree with the very limited population differentiation previously reported for allozyme markers, suggesting that maternal history may not be an appropriate approximation for population differentiation.

Testing Species Boundaries in an Ancient Species Complex with Deep Phylogeographic History: GenusXantusia(Squamata: Xantusiidae)

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic range of Xantusia. Maximum likelihood, Bayesian, and nested cladogram analyses were used to estimate relationships among haplotypes and to infer evolutionary processes. We found multiple well-supported independent lineages within Xantusia, for which there is considerable discordance with the currently recognized taxonomy. High levels of sequence divergence (21.3%) suggest that the pattern in Xantusia may predate the vicariant events usually hypothesized for the fauna of the Baja California peninsula, and the existence of deeply divergent clades (18.8%-26.9%) elsewhere in the complex indicates the occurrence of ancient sundering events whose genetic signatures were not erased by the late Wisconsin vegetation changes. We present a revised taxonomic arrangement for this genus consistent with the distinct mtDNA lineages and discuss the phylogeographic history of this genus as a model system for studies of speciation in North American deserts.

The Impact of Species Concept on Biodiversity Studies

Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.

Phylogeny of the Mexican coastal leopard frogs of the Rana berlandieri group based on mtDNA sequences

Phylogenetic relationships among specimens from 25 different locations for the six Mexican coastal leopard frog species of the Rana berlandieri species group were investigated using 797 bp of the mitochondrial 12S rDNA gene. Relationships among the haplotypes obtained were recovered using maximum parsimony and Bayesian analyses. Most of the clades recovered by both tree building methods are strongly supported, but conflicting clades recovered by each analysis are generally poorly supported. Both analyses reject the previously proposed subgroupings of the R. berlandieri species group. Based on the strongly supported relationships, genetic differentiation, and geographic distribution of the haplotypes examined, nine independent lineages appear to comprise the group of study. However, confirmation of the new proposed lineages will require further analyses based on other genetic markers and additional samples that cover their entire geographic distribution. Concordance was noted between Miocene-Pliocene geological and climatic events in Mexico and the relationships recovered among the lineages proposed and their geographic distribution.

Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum)

The high species diversity of aquatic and terrestrial faunas in eastern North America has been attributed to range reductions and allopatric diversification resulting from historical climate change. The role these processes may have played in speciation is still a matter of considerable debate; however, their impacts on intraspecific genetic structure have been well documented. We use mitochondrial DNA sequences to reconstruct an intraspecific phylogeny of the widespread North American spotted salamander, Ambystoma maculatum, and test whether phylogenetic patterns conform to regional biogeographical hypotheses about the origins of diversity in eastern North America. Specifically, we address the number and locations of historical refugia, the extent and patterns of postglacial colonization by divergent lineages, and the origin and affinities of populations in the Interior Highland region. Despite apparent morphological uniformity, genetic discontinuities throughout the range of this species suggest that populations were historically fragmented in at least two refugia in the southern Appalachian Mountains. The ranges of these two highly divergent clades expanded northward, resulting in two widely distributed lineages that are sympatric in regions previously proposed as suture zones for other taxa. The evolutionary history of spotted salamander populations underscores the generality of biogeographical processes in eastern North America: despite differences in population size, glacial refugia, and vagility, similar signatures of differentiation are evident among and within widespread taxa.

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.

Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complex

The painted turtle, Chrysemys picta, is currently recognized as a continentally distributed polytypic species, ranging across North America from southern Canada to extreme northern Mexico. We analyzed variation in the rapidly evolving mitochondrial control region (CR) in 241 turtles from 117 localities across this range to examine whether the painted turtle represents a continentally distributed species based on molecular analysis. We found strong support for the novel hypothesis that C. p. dorsalis is the sister group to all remaining Chrysemys, with the remaining Chrysemys falling into a single, extremely wide-ranging and genetically undifferentiated species. Given our goal of an evolutionarily accurate taxonomy, we propose that two evolutionary lineages be recognized as species within Chrysemys: C. dorsalis (Agassiz 1857) in the southern Mississippi drainage region, and C. picta (Schneider 1783) from the rest of the range of the genus. Neither molecular nor recent morphological analyses argue for the hybrid origin of C. p. marginata as previously proposed. Within C. picta, we find evidence of at least two independent range expansions into previously glaciated regions of North America, one into New England and the other into the upper Midwest. We further find evidence of a massive extinction/recolonization event across the Great Plains/Rocky Mountain region encompassing over half the continental United States. The timing and extent of this colonization is consistent with a recently proposed regional aridification as the Laurentide ice sheets receded approximately 14,000 years ago, and we tentatively propose this paleoclimatological event as a major factor shaping genetic variation in Chrysemys.

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.

Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes

Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.

Mitochondrial DNA-Based phylogeography of North American rubber boas, Charina bottae (Serpentes: Boidae)

We used 783 bp of mitochondrial DNA sequences to study the phylogeography of Charina bottae (rubber boa) in western North America, with an emphasis on populations from California (U.S.A.). Maximum-parsimony and maximum-likelihood methods identified a basal divergence within C. bottae that corresponds to southern and northern segments of its current distribution. These clades coincide with the ranges of the two recognized subspecies, C. b. umbratica in the south and C. b. bottae to the north. A subsequent cladogenetic event in the C. b. bottae clade resulted in two groupings, which we refer to as the Sierra Nevada and the Northwestern subclades, based on the geographic distribution of their constituent populations. The two subclades have completely allopatric distributions, with a genetic break in the vicinity of Lassen Volcanic National Park in northeastern California, an area that was subjected to glaciation during the Pleistocene and that has been volcanically active in the past 100 years. An earlier genetic study documented fixed differences between populations of bottae and umbratica in four of seven allozymes surveyed, and despite noticeable variation and overlap in the characters that define C. b. bottae and C. b. umbratica, the two forms still can be separated in most cases using a suite of morphological traits. All available evidence thus indicates that C. b. umbratica is a genetically cohesive, allopatric taxon that is morphologically diagnosable, and we conclude that it is an independent evolutionary unit that should be recognized as a distinct species, Charina umbratica.