Diversification and biogeographical history of Neotropical plethodontid salamanders

The Neotropical bolitoglossine salamanders represent an impressive adaptive radiation, comprising roughly 40% of global salamander species diversity. Despite decades of morphological studies and molecular work, a robust multilocus phylogenetic hypothesis based on DNA sequence data is lacking for the group. We estimated species trees based on multilocus nuclear and mitochondrial data for all major lineages within the bolitoglossines, and used our new phylogenetic hypothesis to test traditional biogeographical scenarios and hypotheses of morphological evolution in the group. In contrast to previous phylogenies, our results place all Central American endemic genera in a single clade and suggest that Central America played a critical role in the early biogeographical history of the group. The large, predominantly Mexican genus Pseudoeurycea is paraphyletic, and analyses of the nuclear data place two lineages of Pseudoeurycea as the sister group of Bolitoglossa. Our phylogeny reveals extensive homoplasy in morphological characters, which may be the result of truncation or alteration of a shared developmental trajectory. We used our phylogenetic results to revise the taxonomy of the genus Pseudoeurycea. © 2015 The Linnean Society of London     

Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.     

An evolutionary correlate of genome size change in plethodontid salamanders

Variation in the amount of nuclear DNA, the C-value, does not correlate with differences in morphological complexity. There are two classes of explanations for this observation, which is known as the ''C-value paradox''. The quantity of DNA may serve a ''nucleotypic'' function that is positively selected. Alternatively, large genomes may consist of junk DNA, which increases until it negatively affects fitness. Attempts to resolve the C-value paradox focus on the link between genome size and fitness. This link is usually sought in life history traits, particularly developmental rates. I examined the relationship among two life history traits, egg size and embryonic developmental time and genome size, in 15 species of plethodontid salamanders. Surprisingly, there is no correlation between egg size and developmental time, a relationship included in models of life history evolution. However, genome size is positively correlated with embryonic developmental time, a result that is robust with respect to many sources of variation in the data. Without information on the targets of natural selection it is not possible with these data to distinguish between nucleotypic and junk DNA explanations for the C-value paradox.     

Linking movement behaviour to dispersal and divergence in plethodontid salamanders

To better understand the evolutionary and ecological effects of dispersal, there is growing emphasis on the need to integrate direct data on movement behaviour into landscape-scale analyses. However, little is known about the general link between movement behaviour and large-scale patterns of dispersal and gene flow. Likewise, although recent studies suggest that nonrandom, directionally biased movement and dispersal can promote evolutionary divergence, the generality of this mechanism is unknown. We test the hypothesis that directionally biased movement and dispersal by plethodontid salamanders interact with the topography of headwater areas to affect genetic and phenotypic divergence. Movements by Gyrinophilus porphyriticus and Eurycea bislineata show contrasting directional biases: upstream bias in G. porphyriticus and downstream bias in E. bislineata. Consistent with predictions of how these biases interact with slope to affect dispersal and gene flow, genetic distance increased with slope in G. porphyriticus and decreased with slope in E. bislineata over a standardized distance of 1 km along six headwater streams. In both species, phenotypic divergence in relative trunk length was positively related to genetic divergence. These results indicate that landscape-scale patterns of dispersal and gene flow are closely related to movement behaviour in G. porphyriticus and E. bislineata, and underscore the value of information on movement behaviour for predicting and interpreting patterns of dispersal and gene flow in complex landscapes. This study also provides new evidence that directionally biased movement and dispersal can be important sources of intra- and interspecific variation in population divergence, and highlights the value of explicit, a priori predictions in landscape genetic studies.     

Localization of 5S RNA genes on chromosomes of plethodontid salamanders

Ribosomal 5S RNA, labelled with 125 I, was annealled to denatured spermatocyte chromosomes of salamanders from 11 different genera of the family Plethodontidae. The salamanders studied have genomes with 1, 2 or 3 gene clusters. Eleven sites are located interstitially on short chromosome arms; 3 are found interstitially on long arms; 5 sites are at centromeric regions and one is telomeric. — Salamanders from five genera of Neotropical plethodontids carry a 5S gene cluster on the short arm of a large asymmetric chromosome, presumably a linkage group that has remained stable since the divergence of these genera in Tertiary time. In Lineatriton lineola this short arm is heterochromatic during pachytene and it shows a high incidence of chiasma failure at the first meiotic metaphase, contrasting with the situation found in two other species. The localization and number of 5S gene sites is consistent with the proposed phylogeny of these Neotropical genera by Wake and Lynch (1976).     

Faecal pellets as burrow markers: intra- and interspecific odour recognition by western plethodontid salamanders

Chemical communication is widespread among plethodontid salamanders (Caudata: Plethodontidae), but little information exists on the role of odours in interspecific competition in general and among species in western North America in particular. The present study examined the potential of faecal odours for intra- and interspecific communication among sympatric plethodontids in two-choice tests in the laboratory. In experiment 1, Plethodon vehiculum and Aneides ferrus from Vancouver Island, B.C., Canada, were presented with two burrows marked with (1) a faecal pellet of male P. vehiculum versus a control clay pellet, and (2) a faecal pellet of male A. ferreus versus a control pellet. In experiment 2, responses of P. vehiculum, P. dunni and P. vandykei from Washington, U.S.A., were tested towards faecal pellets of conspecific males and females, and towards pellets of congeneric males. Both P. vehiculum and P. dunni distinguished odours of conspecific males and females, based on their behavioural responses towards faecal and control pellets. Only P. dunni, however, avoided burrows marked with faeces of conspecific individuals. In contrast, neither A. ferreus nor P. vandykei appeared to distinguish faecal odours of conspecific salamanders from control pellets. In tests with odours of heterospecific individuals, P. dunni and P. vehiculum distinguished odours of each other, and P. vandykei distinguished odours of P. vehiculum. The data from these two experiments suggest that P. dunni use faecal pellets as territorial markers both in intraspecific communication and in interspecific encounters with P. vehiculum.     

The arrangement of chromosomes in nuclei of sperm from plethodontid salamanders

Plethodontid salamanders have n = 13 or 14 large metacentric or sub-metacentric chromosomes. Sperm nuclei from Plethodon cinereus measure 72×1 m. The nucleoprotein of spermatids is at first finely granular. In elongate spermatids it clumps into larger granules, which then fuse to form the compact nucleoprotein of the mature sperm. The nuclei of mature sperm are negatively birefringent with respect to their length. — ³H RNA complementary to high-density satellite DNA of centromeric heterochromatin in P. cinereus has been hybridized in-situ to spermatids and sperm, and its site of binding to these cells has been examined by autoradiography. Labelling of round spermatid nuclei is localized in a single patch. Elongate spermatid nuclei are labelled only over the rear quarter of the nucleus. Label over the nuclei of mature sperm is localized in a region extending 10–20 m forwards from the rear of the nucleus. — In P. cinereus the ribosomal genes are located near the centromere on the short arm of chromosome 7. ³H ribosomal RNA hybridizes to a single patch in round spermatid nuclei. Elongate spermatid nuclei show label over a short segment of the rear half of the nucleus. In spermatids nearing maturity the labelled region is never more than 20 m long. — These results indicate that in P. cinereus each chromosome is arranged in a U formation with its centromere at the base of the sperm nucleus, and its arms extended forwards along the length of the nucleus. — Among plethodontids, increase in C value and corresponding increase in chromosome size is accompanied by increase in the length rather than the width of the sperm nucleus. — ³H ribosomal RNA hybridizes to a short segment in spermatid and sperm nuclei from Xenopus and Triturus. In these animals, the position of the labelled segment varies from sperm to sperm.     

Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders

The transition from aquatic to terrestrial eggs is a key evolutionary change that has allowed vertebrates to successfully colonize and exploit the land. Although most amphibians retain the primitive biphasic life cycle (eggs deposited in water that hatch into free-living aquatic larvae), direct development of terrestrial eggs has evolved repeatedly and may have been critical to the evolutionary success of several amphibian groups. We provide the first conclusive evidence for evolutionary reversal of direct development in vertebrates. The family Plethodontidae (lungless salamanders) contains the majority of salamander species, including major radiations of direct developers. We reconstruct the higher level phylogenetic relationships of plethodontid salamanders using molecular and morphological data and use this phylogeny to examine the evolution of direct development. We show that the predominantly biphasic desmognathines, previously considered the sister group of other plethodontids, are nested inside a group of direct-developing species (Plethodontini) and have re-evolved the aquatic larval stage. Rather than being an evolutionary dead end, the reversal from direct developing to biphasic life history may have helped communities in eastern North America to achieve the highest local diversity of salamander species in the world.     

Habitat selection in two species of aquatic hyphomycetes

Two species of aquatic hyphomycetes,Tetracladium marchalianum andTricladium splendens, were isolated from decaying leaves in a stream.T. marchalianum was abundant on alder leaves but absent on beech leaves, which were dominated byT. splendens. It was hypothesized that differences in some chemical key factors in the leaves would account for differences in the distribution of the 2 species. In the experiment designed to test the hypothesis, combinations of sterilized leaves and isolated fungi were used. Differences in growth of FDA active mycelium were related to differences in leaf weight loss;T. splendens decomposed beech leaves andT. marchalianum decomposed alder leaves. Extracellular protease activity corresponded with these trends but there was no detectable protein loss in the leaves. Both fungi showed a nitrogen demand, and hydrolysis of leaf proteins was complemented with absorption of free amino acids and ammonium. High concentrations of free amino acids modified the pattern for habitat selection so thatT. splendens grew substantially on alder leaves andT. marchalianum colonized beech leaves. No protease activity was, however, found fromT. marchalianum on beech leaves, and it is concluded that a more general metabolic inhibition prevents extensive growth of this species on beech leaves. The low natural abundance ofT. splendens on alder leaves, where it may grow well, may be a consequence of a specific protease inhibition and competition from other species.     

Intraguild predation among larval plethodontid salamanders: a field experiment in artificial stream pools

Intraguild predation can be important in determining community structure and dynamics. Artificial stream pools were used to test for the impacts of intraguild predation among three species of larval plethodontid salamanders. Intraguild predators (large Gyrinophilus porphyriticus and Pseudotriton ruber) significantly decreased the survival of small Pseudotriton ruber. There was a trend toward reduced growth of Pseudotriton and Eurycea cirrigera in the presence of intraguild predators. The presence of large Gyrinophilus significantly reduced the growth rate of large Pseudotriton, both in the absence and presence of intraguild prey. The presence of intraguild prey did not significantly increase the growth rates of the intraguild predators. Intraguild predation is likely to be an important force shaping the evolution and ecology of these salamanders.     

Habitat selection by Drosophila melanogaster larvae

Drosophila melanogaster larvae are used to examine habitat choice behavior and its effect on a component of preadult fitness (pupal survivorship). We established strains of flies by collecting pupae from two microhabitats from an orchard. Strain differences in pupation site choice (on versus off fruit) persisted in a field-like laboratory assay without artificial selection. To produce heterogeneous environments, air temperature and soil water content were varied in these assays. A habitat suitability difference measure was used to determine for each environment, which microhabitat (on or off fruit) resulted in greater pupal survivorship. We found 1) that habitat choice behavior had both plastic and heritable components, 2) that strain-by-environment interactions influenced habitat choice behavior and pupal survivorship and, 3) a significant positive correlation between habitat suitability and larval habitat choice behavior.     

A centromeric satellite DNA in the European plethodontid salamanders (Amphibia, Urodela).

A highly repeated satellite DNA (Hy500) located in the centromeric heterochromatin of the European plethodontid salamander Speleomantes (formerly Hydromantes) was studied. The Hy500 family represents about 1% of the Speleomantes supramontis genome and has a major repeating unit of about 500 base pairs, which may have evolved from the progressive amplification of shorter sequences. This centromeric satellite is conserved in all the Speleomantes species, which nevertheless show distinct patterns of chromosomal distribution, which are of relevance as to their phylogenetic relationships.     

Cytogenetics of the European plethodontid salamanders of the genus Hydromantes (Amphibia,Urodela)

A karyological analysis was carried out on different European species of the genus Hydromantes (Plethodontidae). All the species examined share the same chromosome number (2n=28) and, with the exception represented by pair XIV, morphologically similar karyotypes. While the karyotypes display a similar distribution — mainly centromeric and pericentric — of C-heterochromatin, quantitative variations in pericentric heterochromatin are observed among species. In the continental species Hydromantes italicus and ambrosii as well as in the eastern Sardinian species imperialis, flavus and specie nova, pair XIV consists of heteromorphic sex chromosomes of the XX/XY type. It is proposed that the differentiation of the Y might have taken place through the occurrence of a structural rearrangement, such as a pericentric inversion, starting from a hypothetical, homomorphic pair XIV. A sex-related heteromorphism is not found in the western Sardinian species H. genei. A further karyological differentiation among these species concerns the position of the nucleolus organizing region (NOR), which is located on chromosome XII (H. italicus and ambrosii) or on chromosome X, close to the centromere (H. genei, H. imperialis and H. specie nova), or in an intercalary position (H. flavus). The location and the number of the 5 S DNA sites have been conserved during species divergence. On the basis of these karyological data, as well as of results obtained through a preliminary restriction enzyme analysis of the ribosomal and genomic DNAs, the phyletic relationships among the European Hydromantes species are discussed.     

Climate change and shrinking salamanders: alternative mechanisms for changes in plethodontid salamander body size

An increasing number of studies have demonstrated relationships between climate trends and body size change of organisms. In many cases, climate might be expected to influence body size by altering thermoregulation, energetics or food availability. However, observed body size change can result from a variety of ecological processes (e.g. growth, selection, population dynamics) or imperfect observation of biological systems. We used two extensive datasets to evaluate alternative mechanisms for recently reported changes in the observed body size of plethodontid salamanders. We found that mean adult body size of salamanders can be highly sensitive to survey conditions, particularly rainfall. This systematic bias in the detection of larger or smaller individuals could result in a signature of body size change in relation to reported climate trends when it is simply observation error. We also identify considerable variability in body size distributions among years and find that individual growth rates can be strongly influenced by weather. Finally, our study demonstrates that measures of mean adult body size can be highly variable among surveys and that large sample sizes may be required to make reliable inferences. Identifying the effects of climate change is a critical area of research in ecology and conservation. Researchers should be aware that observed changes in certain organisms can result from multiple ecological processes or systematic bias due to nonrandom sampling of populations.     

Habitat selection by loons in southcentral Alaska

Three species of loons nest in the Matanuska-Susitna Valley, an area 80 km north of Anchorage in southcentral Alaska. This is a region of intense change; its human population doubled between 1980–1990 to almost 36000 people. The Alaska Department of Fish and Game through its Loon Watch Program has monitored 150 to 200 lakes since 1984, half of which are used by loons. Common loons (Gavia immer) nested on lakes of at least 12 ha while Pacific loons (G. pacifica) used lakes as small as 4 ha. Red-throated loons (G. stellata) were found on even smaller ponds. On all waters used by reproductive loons, 89% were connected to other water bodies, 62% of the shore was appropriate for nesting and 85% of the area was <15 ft (4.6 m) deep. This littoral zone comprised habitat for three-spined stickleback fish (Gasterosteus aculeatus), the dominant food source for loons, and supported large macrophyte beds that were used by loons as chick-rearing areas. The effect of human presence on summer loon distribution was dependent on the willingness of humans to accommodate to the needs of loons.     

Habitat selection by helminths: a hypothesis

How do liver worms find the liver? Why are heartworms always found in the heart? Attempts to answer these questions have invariably yielded inconclusive results. A major problem has been the use of models or hypotheses derived from studies of free-living organisms. The parasite's environment is distinct from free-living environments in several fundamental ways and these differences will impact on the evolution of parasite behaviours. In this article, Michael Sukhdeo outlines a hypothesis for habitat selection behavior of helminths that is based on the specific environmental conditions within the host.     

Habitat selection by a threatened desert amphibian

Habitat degradation and fragmentation are major drivers of amphibian declines. The loss of environmental features that allow for movement between water sources may be particularly detrimental for amphibians in arid environments. Climate changes will increase the importance of microhabitats to amphibians. Enhancing areas to facilitate movement may be a necessary conservation strategy for many animal species that depend on wetlands, including federally threatened Chiricahua leopard frogs (Lithobates chiricahuensis). Habitat preferences of this frog species are not well understood. We sought to better understand fine‐scale habitat selection, to inform conservation of Chiricahua leopard frogs. We conducted our study on the Ladder Ranch, a privately owned working bison ranch in New Mexico, USA that supports a large proportion of the remaining Chiricahua leopard frogs in the state. We attached radio transmitters to 44 frogs during summer 2014. We located each frog daily for up to 8 weeks (median = 30 days). We assessed fine‐scale habitat selection by comparing characteristics at each frog location and a random location 5 m away using conditional logistic regression. Frogs preferred features that likely reduce desiccation, even after accounting for the presence of water. Frogs selected areas with more low‐lying cover, especially aquatic vegetation and woody debris, a tree overstory, and a mud substrate. We recommend managing potential movement corridors for Chiricahua leopard frogs by ensuring the presence of muddy creek bottoms, woody debris, riparian overstory, low‐lying ground cover, and pools. Microclimates created by these features seem especially valuable given warming temperatures and modified precipitation regimes, resulting in decreased surface water, soil moisture, and vegetation cover. Retaining or creating preferred habitat features and microclimates in areas between water sources may increase connectivity among isolated populations of Chiricahua leopard frogs and could improve persistence and recovery of other water‐obligate species in arid landscapes.