HYBRIDIZATION AND CRYPTIC SPECIES IN DICAMPTODON (CAUDATA: DICAMPTODONTIDAE)

Shrinking sizes of trout and salamanders are unexplained by climate warming alone

Decreases in body sizes of animals related to recent climate warming can affect population persistence and stability. However, direct observations of average sizes over time and their interrelationships with underlying density-dependent and density-independent processes remain poorly understood owing to the lack of appropriate long-term datasets. We measured body size of two species common to headwater streams in coastal and Cascades ecoregions of the Pacific Northwest of North America over multiple decades, comparing old-growth and managed forests. We found consistent decreases in median length of Coastal Cutthroat Trout Oncorhynchus clarkii clarkii, but a coexisting species, the Coastal Giant Salamander Dicamptodon tenebrosus, appears to be more resilient to size changes over time. Based on observed trends, adult trout have decreased in length by 6-13% over the last 30 years. Length decreased more in larger compared to smaller animals, suggesting that these effects reflect changes in growth trajectories. Results from a model-selection approach that included hydroclimatic and biological information as covariates in one of our study ecoregions demonstrated that stream temperature alone did not explain observed length reductions. Rather, a combination of density-dependent (animal abundances) and local density-independent factors (temperature, habitat, and streamflow) explained observed patterns of size. Continued decreases in size could lead to trophic cascades, biodiversity loss, or in extreme cases, species extirpation. However, the intricate links between density-independent and density-dependent factors in controlling population-level processes in streams need further attention.

POSTGLACIAL RANGE FLUCTUATION, GENETIC SUBDIVISION AND SPECIATION IN THE WESTERN NORTH AMERICAN SPOTTED FROG COMPLEX, RANA PRETIOSA

The western North American complex of spotted frogs (Rana pretiosa) exhibits isolation-by-distance, genetic subdivision, and speciation in association with its extensive northward range shift in postglacial times. The southern relict populations of R. pretiosa species B existing at high altitudes or in desert springs have been subjected to restricted gene flow, high inbreeding, and bottlenecks to produce significant between-population genetic diversity. The more recently established northern populations, however, show genetic uniformity and isolation-by-distance, as estimated using Slatkin's (1993) statistic M̂. Middle latitude populations have higher heterozygosities than populations at either extreme. Fixed differences in allozyme variation separate 21 populations of species B from five populations of R. pretiosa species A found in southwest Washington State and the Cascades Mountains of Oregon. Morphological variation of 20 metric characters among 38 samples, examined using multiple discriminant function analysis, could partially resolve partitioning among populations but specimens from the vicinity of the type series of R. p. pretiosa could not be assigned to either species A or species B. Speciation in these frogs may not be correlated with morphological evolution since comparatively neutral allozyme changes may be established more rapidly than changes in morphology.

An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the Arboreal Salamander (Aneides lugubris)

BACKGROUND

Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris.

RESULTS

We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate.

CONCLUSIONS

Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.

Predator-driven nutrient recycling in California stream ecosystems

Nutrient recycling by consumers in streams can influence ecosystem nutrient availability and the assemblage and growth of photoautotrophs. Stream fishes can play a large role in nutrient recycling, but contributions by other vertebrates to overall recycling rates remain poorly studied. In tributaries of the Pacific Northwest, coastal giant salamanders (Dicamptodon tenebrosus) occur at high densities alongside steelhead trout (Oncorhynchus mykiss) and are top aquatic predators. We surveyed the density and body size distributions of D. tenebrosus and O. mykiss in a California tributary stream, combined with a field study to determine mass-specific excretion rates of ammonium (N) and total dissolved phosphorus (P) for D. tenebrosus. We estimated O. mykiss excretion rates (N, P) by bioenergetics using field-collected data on the nutrient composition of O. mykiss diets from the same system. Despite lower abundance, D. tenebrosus biomass was 2.5 times higher than O. mykiss. Mass-specific excretion summed over 170 m of stream revealed that O. mykiss recycle 1.7 times more N, and 1.2 times more P than D. tenebrosus, and had a higher N:P ratio (8.7) than that of D. tenebrosus (6.0), or the two species combined (7.5). Through simulated trade-offs in biomass, we estimate that shifts from salamander biomass toward fish biomass have the potential to ease nutrient limitation in forested tributary streams. These results suggest that natural and anthropogenic heterogeneity in the relative abundance of these vertebrates and variation in the uptake rates across river networks can affect broad-scale patterns of nutrient limitation.

Coalescent-based hypothesis testing supports multiple Pleistocene refugia in the Pacific Northwest for the Pacific giant salamander (Dicamptodon tenebrosus)

Phylogeographic patterns of many taxa are explained by Pleistocene glaciation. The temperate rainforests within the Pacific Northwest of North America provide an excellent example of this phenomenon, and competing phylogenetic hypotheses exist regarding the number of Pleistocene refugia influencing genetic variation of endemic organisms. One such endemic is the Pacific giant salamander, Dicamptodon tenebrosus. In this study, we estimate this species' phylogeny and use a coalescent modeling approach to test five hypotheses concerning the number, location and divergence times of purported Pleistocene refugia. Single refugium hypotheses include: a northern refugium in the Columbia River Valley and a southern refugium in the Klamath-Siskiyou Mountains. Dual refugia hypotheses include these same refugia but separated at varying times: last glacial maximum (20,000 years ago), mid-Pleistocene (800,000 years ago) and early Pleistocene (1.7 million years ago). Phylogenetic analyses and inferences from nested clade analysis reveal distinct northern and southern lineages expanding from the Columbia River Valley and the Klamath-Siskiyou Mountains, respectively. Results of coalescent simulations reject both single refugium hypotheses and the hypothesis of dual refugia with a separation date in the late Pleistocene but not hypotheses predicting dual refugia with separation in early or mid-Pleistocene. Estimates of time since divergence between northern and southern lineages also indicate separation since early to mid-Pleistocene. Tests for expanding populations using mismatch distributions and 'g' distributions reveal demographic growth in the northern and southern lineages. The combination of these results provides strong evidence that this species was restricted into, and subsequently expanded from, at least two Pleistocene refugia in the Pacific Northwest.

Can common species provide valuable information for conservation?

To demonstrate the importance of genetic data for multispecies conservation approaches, we examined the distribution of genetic variation across the range of the mountain whitefish (Prosopium williamsoni) at microsatellite and allozyme loci. The mountain whitefish is a common species that is particularly well suited for accurately revealing historical patterns of genetic structure and differs markedly from previously studied species in habitat requirements and life history characteristics. As such, comparing the population genetic structure of other native fishes to similar data from mountain whitefish could inform management and conservation strategies. Genetic variation for mountain whitefish was hierarchically distributed for both allozymes and microsatellites. We found evidence for a total of five major genetically differentiated assemblages and we observed subdivision among populations within assemblages that generally corresponded to major river basins. We observed little genetic differentiation within major river basins. Geographic patterns of genetic differentiation for mountain whitefish were concordant with other native species in several circumstances, providing information for the designation of conservation units that reflect concordant genetic differentiation of multiple species. Differences in genetic patterns between mountain whitefish and other native fishes reflect either differences in evolutionary histories of the species considered or differences in aspects of their ecology and life history. In addition, mountain whitefish populations appear to exchange genes over a much larger geographic scale than co-occurring salmonids and are likely to be affected differently by disturbances such as habitat fragmentation.

Phylogeography of two European newt species--discordance between mtDNA and morphology

The newts Triturus vulgaris and Triturus montandoni are sister species that exhibit contrasting levels of intraspecific morphological variation. Triturus vulgaris has a broad Eurasiatic distribution encompassing both formerly glaciated and unglaciated areas and shows substantial morphological differentiation in the southern part of its range, while T. montandoni, confined to the Carpathians, is morphologically uniform. We analysed sequence variation of two mtDNA fragments of the total length of c. 1850 bp in 285 individuals of both species collected from 103 localities. Phylogenetic analysis of 200 unique haplotypes defined 12 major clades, their age estimated at c. 4.5-1.0 million years (Myr). Most of the older clades were found in the southern part of the range, and also in central Europe, mainly in Romania. The distribution of mtDNA clades points to the existence of several glacial refugia, located in the Caucasus region, Anatolia, the Balkan Peninsula, Italy, and more to the north in central Europe. The concordance between mtDNA based phylogeny and the distribution of T. vulgaris subspecies was weak. Triturus montandoni haplotypes did not form a monophyletic group. Instead they were found in six clades, in five of them mixed with T. vulgaris haplotypes, most likely as a result of past or ongoing hybridization and multiple introgression of mtDNA from T. vulgaris to T. montandoni. Patterns of sequence variation within clades suggested long-term demographic stability in the southern groups, moderate and relatively old demographic growth in the populations inhabiting central Europe, and high growth in some of the groups that colonized northern parts of Europe after the last glacial maximum.

Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa

Allozymes and mitochondrial DNA sequences were used to examine the phylogeographical history of the rough-skinned newt, Taricha granulosa, in western North America. Nineteen populations were analysed for allozyme variation at 45 loci, and 23 populations were analysed for cytochrome b sequence variation. Both data sets agree that populations in the southern part of the range are characterized by isolation by distance, whereas northern populations fit the expectations of a recent range expansion. However, the northern limit of isolation by distance (and the southern limit of range expansion) is located in Oregon State by the mtDNA data, and in Washington State by the allozyme data. Nevertheless, both data sets are consistent with the known Pleistocene history of western North America, with phylogenetically basal populations in central and northern California, and a recent range expansion in the north following the retreat of the Cordilleran ice sheet 10,000 years ago. Additionally, a population in Idaho, previously considered introduced from central California based on morphometric analyses, possesses a distinct mtDNA haplotype, suggesting it could be native. The relevance of these results for Pacific Northwest biogeography is discussed.

Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group

Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensisby collecting genetic data (669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence (estimated using MDIV) is 3.75 x 106 years, and the 95%credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. WithinP. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate (g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima's Dand mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the significance of the population growth-rate parameter.

Ontogeny Discombobulates Phylogeny: Paedomorphosis and Higher-Level Salamander Relationships

Evolutionary developmental biology ("evo-devo") has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of higher-level salamander relationships based on combined molecular and morphological data. Many authors have suggested that paedomorphosis may be problematic in studies of salamander phylogeny, but this hypothesis has never been tested with a rigorous phylogenetic analysis. We find that the misleading effects of paedomorphosis on phylogenetic analysis go beyond the sharing of homoplastic larval traits by paedomorphic adults, and the problem therefore is not solved by simply excluding suspected paedomorphic characters. Instead, two additional factors are critically important in causing paedomorphic species to be phylogenetically "misplaced": (1) the absence of clade-specific synapomorphies that develop during metamorphosis in nonpaedomorphic taxa and allow their "correct" placement and (2) parallel adaptive changes associated with the aquatic habitat of the larval stage. Our results suggest that the effects of paedomorphosis on phylogenetic analyses may be complex, difficult to detect, and can lead to results that are both wrong and statistically well supported by parsimony and Bayesian analyses.

Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.

Genetic structure in a montane ranid frog: restricted gene flow and nuclear-mitochondrial discordance

There is substantial debate over the criteria that should be used to group populations of a species into distinct units for conservation (e.g. evolutionarily significant units, management units, distinct population segments). However, in practice molecular genetic differentiation is often the only or main criterion used to identify such units. Most genetic studies attempting to define conservation units in animals use a single molecular marker, most often mitochondrial, and use samples from a limited number of populations throughout the species' range. Although there are many benefits to using mtDNA, certain features can cause it to show patterns of differentiation among populations that do not reflect the history of differentiation at the nuclear genome where loci controlling traits of adaptive significance presumably occur. Here we illustrate an example of such mitochondrial-nuclear discordance in a ranid frog, and show how using mtDNA or nuclear loci alone could have led to very different conservation recommendations. We also found very high genetic differentiation among populations on a local scale, and discuss the conservation implications of our results.

Structure and evolution of supernumerary chromosomes in the Pacific giant salamander, Dicamptodon tenebrosus

We examined the genetic make-up and plausible origins of the supernumerary (B) chromosomes of the Pacific giant salamander, Dicamptodon tenebrosus, from the Pacific Northwest of North America. These salamanders have variable numbers of B chromosomes, from 0 to 10 per individual. Salamanders from the most southerly and northerly regions of the species' range have lower average numbers of B chromosomes than salamanders in the middle of the range. To assess how the supernumerary chromosomes originated in D. tenebrosus, B chromosome DNA was isolated by microdissection and amplified by degenerate oligonucleotide-primed PCR. The B chromosome DNA hybridized similarly to genomic DNA from individuals of D. tenebrosus and the related species D. copei and D. ensatus, thus demonstrating that the supernumerary chromosomes were derived from the normal chromosome complement. Unique hybridization bands in both D. copei and D. tenebrosus suggest that the shared sequences have evolved independently.

Spatial models for hybrid zones

We introduce a spatially explicit model of natural hybrid zones that allows us to consider how patterns of allele frequencies and linkage disequilibria change over time. We examine the influence of hybrid zone origins on patterns of variation at two loci, a locus under selection in a two-patch environment, and a linked neutral locus. We consider several possible starting conditions that represent explicit realizations of two alternative scenarios for hybrid zone origins: primary intergradation and secondary contact. Our results indicate that in some circumstances, differences in hybrid zone origins will result in substantially different patterns of variation that may persist for thousands of generations. Our conclusions are generally similar to those previously derived from partial differential equations, but there are also some important differences.

Comparative anatomy and phylogeny of the cloacae of salamanders (Amphibia: Caudata). VI. Ambystomatidae and Dicamptodontidae

Histology of the cloacae of Rhyacotriton olympicus and representative species from the genera Ambystoma and Dicamptodon was examined by light microscopy. Females of Ambystoma possess sperm storage glands, the spermathecae, as well as ventral glands and dorsal glands, both of uncertain function. Females of Ambystoma examined from the subgenus Linguaelapsus differ from those in the subgenus Ambystoma by possessing more extensive ventral gland clusters and a shorter cloacal tube. Females of Dicamptodon possess spermathecae and ventral glands, but differ in cloacal conformation from females of Ambystoma and lack the dorsal glands. Females of R. olympicus possess more extensive epidermal lining in the cloaca than that found in females of Ambystoma and Dicamptodon, and the only glands present are spermathecae, which cluster around a tube in the dorsal roof. Males of Ambystoma, Dicamptodon, and R. olympicus possess five types of cloacal glands (dorsal pelvic glands, lateral pelvic glands, anterior ventral glands, posterior ventral glands, and Kingsbury's glands) that function in spermatophore formation, and vent glands that may produce a courtship pheromone. In Ambystoma and Dicamptodon, vent glands secrete along the medial borders of the cloacal orifice. Males of A. opacum and A. talpoideum differ from males of other species examined from the two genera by possessing more extensive vent glands. Males of R. olympicus possess unique vent glands in which tubules secrete onto the surface of vent lobes lateral to the posterior end of the cloacal orifice, and distal ends of the glands pass anteriorly, superficial to the fascia enclosing the other cloacal glands. The results from analysis of cloacal anatomy support other data indicating that Ambystoma and Dicamptodon are sister groups, and that Rhyacotriton olympicus is not closely related to either of the other two genera and merits placement in a separate family.

The comparative myology of the thigh and crus in the salamanders Ambystoma tigrinum and Dicamptodon tenebrosus

Variation in myology of the hind limb among salamanders has been poorly characterized. Nineteen major hind limb muscles of Ambystoma tigrinum (Ambystomatidae) and Dicamptodon tenebrosus (Dicamptodontidae) were studied to provide baseline descriptive data on hind limb myology in salamanders and to generate hypotheses of hind limb muscle function. Most superficial muscles of the hind limbs span multiple joints, including a unique three-joint muscle, the ischioflexorius, that extends from the pelvic girdle to the plantar fascia. The deeper hind limb muscles spen single joints. No myological diffrences were observed between the hind limbs of A. tigrinum larvae and individuals that had just metamorphosed. Fully adult tiger salamanders that had been housed in terraria for many years had hypertrophied femorofibularis and ischiofemoralis muscles, a condition similar to that reported in Paramesotriton and Taricha, which engage in terrestrial locomotion. In contrast, adults of D. tenebrosus, which are also good walkers, possess a hypertrophied ischioflexorius muscle and a reduced femorofibularis. These regular myological diffences, and those described by previous workers for different salamnder taxa, may be associated with differences in life-history traits, and in the case of A. tigrinum, with patterns of muscle use.

ISOZYMATIC VARIATION IN GUATEMALAN RACES OF MAIZE

Isozymatic data taken from 67 Guatemalan collections of maize were subjected to numerical taxonomic analyses to elucidate systematic relationships among the 19 maize races and subraces described for Guatemala by Wellhausen et al. As with Bolivian and Mexican races, isozymatic variation in Guatemalan maize was strongly associated with altitude. Guatemalan lowland races were in general isozymatically distinct from races of higher elevations. Two middle elevation Guatemalan races proved difficult to place taxonomically. As a group, Guatemalan highland races were isozymatically more diverse than races from lower elevations, and were rather weakly differentiated from Mexican highland races. Notably, variational patterns evident from phenetic analyses of isozyme data were generally congruent with those apparent in phylogenetic analyses. The data reported here, and in earlier studies, suggested that divergent combinations of isozymatic, karyotypic, and morphological features have evolved in local maize races from Mexico, Guatemala, and Bolivia, perhaps as the result of the different selective regimens indigenous cultivators have imposed on different regional phylogenetic lineages.