Jef R. Jaeger

MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS

Abstract We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of ∼270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an “introgression conveyor” model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.

Cryptic Neogene vicariance and Quaternary dispersal of the red-spotted toad ( Bufo punctatus ): insights on the evolution of North American warm desert biotas

We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid‐dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species’ range. Parsimony‐based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene–Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert–Colorado Plateau) and Western (Mojave–Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene–early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post‐Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.

Pleistocene Impacts on the Phylogeography of the Desert Pocket Mouse (Chaetodipus penicillatus)

Abstract The desert pocket mouse (Chaetodipus penicillatus) comprises 6 nominate subspecies that occupy warm, sandy desert-scrub habitats across the Mojave and Sonoran deserts. The most thorough morphological assessment within the species noted variable levels of distinctiveness, leading to uncertainty regarding the geographic distributions of subspecies. Subsequent genetic assessments using chromosomal, allozymic, and mitochondrial DNA (mtDNA) sequence data detected a general east–west divergence centered on the Colorado River, but few locations were included in these assessments. We investigated phylogeographic structure in C. penicillatus by sequencing regions of mtDNA for 220 individuals from 51 locations representing all continental subspecies. We identify 2 major monophyletic mtDNA lineages (clades) roughly centered in the Mojave and Sonoran deserts. These clades broadly overlap along the Lower Colorado River valley and adjacent desert regions across most of the range of C. p. penicillatus. Outside this zone of mtDNA clade overlap, Sonoran clade haplotypes occur in populations from across the range of C. p. pricei and extend to the northwestern edge of the Sonoran Desert within the southern range of C. p. angustirostris. Northern clade haplotypes occur in populations within the ranges of C. p. sobrinus and C. p. stephensi and in populations from the western Mojave Desert in the northern range of C. p. angustirostris. Based on rough estimates for rates of sequence evolution, divergence among the major clades appears to have occurred during the Pleistocene, but well before the latest glacial maximum. The secondary contact among the major clades appears to have some longevity, with little evidence of recent, postglacial range expansion. We develop ecological niche models (EMNs) for the major lineages of C. penicillatus, and project these models onto reconstructions of climatic conditions during the latest glacial maximum (LGM; 18,000–21,000 years ago). The ENMs for each clade indicate differences in predicted current geographic distributions as well as distributions during the LGM. Models for the LGM indicate broad retention of potential habitat within the area of contact among the major clades. Furthermore, the ENM for the Mojave clade in particular indicates retention of suitable habitat during the LGM in small isolated patches within northern areas, consistent with the haplotype network that supports the perspective that some populations from the Mojave clade were isolated within northern refugia during the last glacial period.

Desert tortoise (Gopherus agassizii) survival at two Eastern Mojave Desert sites: Death by short-term drought?

Abstract Survival of adult Desert Tortoises (Gopherus agassizii) appears related to site-specific variation in precipitation and productivity of annual plants. We studied adult tortoise survival rates at two closely situated, but physiographically different, sites in the eastern Mojave Desert over a nine-year period (spring 1992 to spring 2001). Survival rates were initially derived from population surveys conducted over a three-year period and by radio-telemetry monitoring over a seven-year period beginning in 1994. After a period of initial stability, survival rates on the two sites diverged over the study period, and seven-year survival rates estimated from radio-telemetry monitoring were 0.900 and 0.269, respectively. A die-off in 1996 on the latter site appears to have been triggered by a period of drought, which began in the summer of 1995, coupled with a failure of annual vegetation production in 1996. Depressed survival rates on this site were associated with drought conditions during three of four years. Although the decline had the appearance of an epizootic, there were no clinical signs of disease. Relatively short-term drought, combined with little or no annual biomass, appears to have caused severe reductions in tortoise survival. If periods of drought-induced low survival are common over relatively small areas, then source-sink population dynamics may be an important factor determining tortoise population densities.

ELUCIDATION OF CRYPTIC DIVERSITY IN A WIDESPREAD NEARCTIC TREEFROG REVEALS EPISODES OF MITOCHONDRIAL GENE CAPTURE AS FROGS DIVERSIFIED ACROSS A DYNAMIC LANDSCAPE

We investigate the evolutionary history of the wide‐ranging Nearctic treefrog Hyla arenicolor through the integration of extensive range‐wide sampling, phylogenetic analyses of multilocus genetic data, and divergence dating. Previous phylogeographic studies of this frog documented a potential signature of introgressive hybridization from an ecologically and morphologically divergent sister species. Based on our Bayesian phylogenetic analyses of mitochondrial DNA, we inferred strong phylogeographic structure in H. arenicolor as indicated by seven well‐supported clades, five of which correspond to well‐defined biogeographic regions. Clades from the Balsas Basin and southwestern Central Mexican Plateau in Mexico, and the Grand Canyon of Arizona, group with the morphologically, behaviorally, and ecologically divergent mountain treefrogs in the H. eximia group, rendering H. arenicolor as paraphyletic. The phylogenetic position of at least two of these three H. arenicolor clades within the H. eximia group, however, is most likely the result of several episodes of introgressive hybridization and subsequent mitochondrial gene capture separated in time and space, as supported by evidence from the nuclear genes. Hyla arenicolor from the Balsas Basin appear to be deeply divergent from other H. arenicolor and represent a distinctly different species. Results suggests that introgressive hybridization events, both ancient and contemporary, coupled with late Neogene vicariance and Pleistocene climate‐driven range shifts, have all played a role in the historical diversification of H. arenicolor.

Rediscovering Rana onca: Evidence for Phylogenetically Distinct Leopard Frogs from the Border Region of Nevada, Utah, and Arizona

Abstract Remnant populations of leopard frogs within the Virgin River drainage and adjacent portions of the Colorado River (Black Canyon) in northwestern Arizona and southern Nevada either represent the reportedly extinct taxon Rana onca or northern, disjunct Rana yavapaiensis. To determine the evolutionary distinctiveness of these leopard frogs, we evaluated mitochondrial DNA (mtDNA) restriction site variation (RFLP), mtDNA control region sequences, randomly amplified polymorphic DNA (RAPD) markers, and morphological characters. Individuals from the Virgin River drainage and Black Canyon represented a single RFLP haplotype and were identical for nucleotides along a portion of control region sequence. Evaluations of RAPD data demonstrated high levels of similarity among individuals and populations from this region. Leopard frogs from the Virgin River drainage and Black Canyon differed from R. yavapaiensis from west-central Arizona and northern Mexico in maximum parsimony and distance analyses of RFLP and control region sequence data and in maximum-likelihood analysis of the sequence data. Multidimensional scaling of RAPD data provided a similar and congruent indication of this separation. Analysis of principal component scores demonstrated significant morphological differentiation between leopard frog specimens from the Virgin River drainage and R. yavapaiensis. Parallel patterns of divergence observed in the mtDNA, RAPD, and morphological analyses indicate that leopard frogs from the Virgin River drainage and adjacent portions of the Colorado River are phylogenetically distinct. These leopard frogs should be recognized as a lineage separate from southern populations of R. yavapaiensis and classified as the species R. onca.

POPULATION STATUS AND DISTRIBUTION OF A DECIMATED AMPHIBIAN, THE RELICT LEOPARD FROG (RANA ONCA)

Abstract The relict leopard frog (Rana onca) was once thought to be extinct, but has recently been shown to comprise a valid taxon with extant populations. We delineate the minimum historical range of the species based on records from 24 localities, report the extinction of 2 of 7 populations extant in the 1990s, and estimate total population size. The 5 remaining populations occurred in 2 areas: near the Overton Arm of Lake Mead and in Black Canyon along the Colorado River below Lake Mead, Nevada. These 2 areas are only 3.6 and 5.1 km long, respectively. The 5 extant populations inhabited spring systems with largely unaltered hydrology and no introduced American bullfrogs (Rana catesbeiana) or game fishes. In a mark-recapture study conducted in the Overton Arm area, the estimated number of adult frogs averaged 36 over 555 m of stream habitat, and estimated annual survivorship of adults averaged 0.27. A single mark-recapture estimate for the size of the largest population within Black Canyon, at a site approximately 450 m in length, was 637 adult frogs. An estimate for the total number of frogs at all sites, based on mark-recapture data, visual encounter surveys, and extent of habitat, was approximately 1,100 adults (range 693–1,833). The 2 recent population extinctions occurred concomitantly with encroachment of emergent vegetation into pools. We speculate that this occurred as a result of natural processes in one case, and anthropogenic processes in the other.

A multilocus perspective on the speciation history of a North American aridland toad (Anaxyrus punctatus).

Interpretations of phylogeographic patterns can change when analyses shift from single gene-tree to multilocus coalescent analyses. Using multilocus coalescent approaches, a species tree and divergence times can be estimated from a set of gene trees while accounting for gene-tree stochasticity. We utilized the conceptual strengths of a multilocus coalescent approach coupled with complete range-wide sampling to examine the speciation history of a broadly distributed, North American warm-desert toad, Anaxyrus punctatus. Phylogenetic analyses provided strong support for three major lineages within A. punctatus. Each lineage broadly corresponded to one of three desert regions. Early speciation in A. punctatus appeared linked to late Miocene-Pliocene development of the Baja California peninsula. This event was likely followed by a Pleistocene divergence associated with the separation of the Chihuahuan and Sonoran Deserts. Our multilocus coalescent-based reconstruction provides an informative contrast to previous single gene-tree estimates of the evolutionary history of A. punctatus.

Wernerius inyoensis, an elusive new scorpion from the Inyo Mountains of California (Scorpiones, Vaejovidae)

Abstract A new scorpion species is described from the Inyo Mountains of California (USA). The presence of a strong subaculear spine, along with other characters, places the new species within Wernerius, an incredibly rare genus that until now consisted of only two species. Wernerius inyoensis sp. n. can be most easily distinguished from the other members of the genus by smaller adult size, femur and pedipalp dimensions, and differences in hemispermatophore morphology. Previous studies have suggested that the elusive nature of this genus may be attributed to low densities and sporadic surface activity. Herein, we provide another hypothesis, that Wernerius are primarily subterranean. Mitochondrial sequence data are provided for the holotype.

Isolation and characterization of microsatellite markers in the lowland leopard frog (Rana yavapaiensis) and the relict leopard frog (R. onca), two declining frogs of the North American desert southwest

We characterized 15 microsatellite loci for the lowland leopard frog (Rana yavapaiensis) and the relict leopard frog (R. onca) for future studies of population genetic structure and relatedness. Analysis of 20 individuals from single populations of each species showed that all markers were polymorphic in at least one species. Observed and expected heterozygosities ranged from 0 to 0.94 and from 0.11 to 0.85, respectively, and there were three to 11 alleles per locus. No loci were in linkage disequilibrium, but six loci deviated significantly from Hardy–Weinberg equilibrium, and the presence of a null allele was detected in two of these loci.