Genetic analysis of hybridization and introgression between wild mongoose and brown lemurs

Background  

Hybrid zones generally represent areas of secondary contact after speciation. The nature of the interaction between genes of individuals in a hybrid zone is of interest in the study of evolutionary processes. In this study, data from nuclear microsatellites and mitochondrial DNA sequences were used to genetically characterize hybridization between wild mongoose lemurs (Eulemur mongoz) and brown lemurs (E. fulvus) at Anjamena in west Madagascar.     

Patterns of habitat and invertebrate diet overlap between tiger salamanders and ducks in prairie potholes

During the breeding season, migratory waterfowl are attracted to wetlands characterized by high macroinvertebrate availability. Many of these prairie potholes are fishless and this apparent void is filled, at least partially, by tiger salamanders. Based on gut contents from 98 tiger salamanders and published diet data from over 1500 ducks, we show that there is general overlap in diet between both larval and adult tiger salamanders and 10 duck species. Furthermore, when the ducks were split into foraging guilds and compared with tiger salamanders, prey type overlap was 1.7 times higher and prey size was 1.8 times higher with dabbling ducks than diving ducks. Field surveys show that tiger salamander density is more highly correlated with diving duck density across potholes than dabbling duck density. Tiger salamanders have higher diet overlap with dabbling ducks than diving ducks whereas tiger salamanders have higher spatial overlap with diving ducks than dabbling ducks suggesting that these consumers coarsely partition diet and habitat resources. It has been reported that tiger salamanders have specialized diets that are associated with foraging preferences for benthic habitats. This view is too narrow: in southwestern Manitoba, Canada, tiger salamanders are more general consumers with diets more like dabbling ducks that forage mostly in planktonic and littoral habitats. Our results suggest that dabbling and diving ducks are, to different extents, liable to the effects of indirect interactions, specifically competition for common prey, with tiger salamanders.     

Concentrations of lactic acid in neotenic and transformed tiger salamanders (Ambystoma tigrinum) before and after activity

Summary Concentrations of lactic acid in bodies of inactive neotenic tiger salamanders were similar to those recorded for inactive transformed animals. Transformed salamanders swimming against a water current for 5 min accumulated significantly more lactate in their body fluids than did neotenic salamanders, but subsequently metabolized the lactate at higher rates than characterized neotenic animals. Total body lactate in both morphs decreased rapidly in the first 1–1/2 h after activity, and within 6 h had returned to the level (common to both morphs) observed prior to activity. Whereas neotenic animals apparently swim with greater efficiency than transformed salamanders (4.26 mole ATP/gvs. 6.06 mole ATP/g expended by neotenic and transformed animals, respectively, during 5 min of continuous swimming), the transformed animals exhibit a metabolic adaptation to aquatic existence enabling them rapidly to recover from a lactacid debt.     

Two behavioural traits promote fine-scale species segregation and moderate hybridisation in a recovering sympatric fur seal population

Background  

In systems where two or more species experience secondary contact, behavioural factors that regulate interspecific gene flow may be important for maintaining species boundaries and reducing the incidence of hybridisation. At subantarctic Macquarie Island, two species of fur seal breed in close proximity to one another, hybridise at very high levels (up to 21% of hybrid pups are born annually), yet retain discrete gene pools. Using spatial and genetic information collected for pups and adults over twelve years, we assessed two behavioural traits - inter-annual site fidelity and differences in habitat use between the species - as possible contributors to the maintenance of this species segregation. Further, we explored the breakdown of these traits in pure-species individuals and hybrids.     

Experimental morphology of the feeding mechanism in salamanders

The subarcualis rectus I muscle (SAR) in the feeding mechanism of four tiger salamanders (Ambystoma tigrinum) was removed early in ontogeny and these individuals were allowed to complete metamorphosis. This procedure resulted in postmetamorphic tiger salamanders which differed from control individuals in the size (and thus force generating capacity) of the SAR muscle. The experimental manipulation of muscle ontogeny allowed a test of previous hypotheses of SAR function in postmetamorphic individuals. Multivariate analysis of variance for kinematic variables measured from high-speed video records of feeding revealed that experimentally modified tiger salamanders did not protract the hyobranchial apparatus or project the tongue from the mouth during feeding. Removal of the SAR muscle resulted in significantly reduced hyobranchial elevation in the buccal cavity and reduced maximum tongue projection distance.     

Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks

Background  

Estimates of divergence dates between species improve our understanding of processes ranging from nucleotide substitution to speciation. Such estimates are frequently based on molecular genetic differences between species; therefore, they rely on accurate estimates of the number of such differences (i.e. substitutions per site, measured as branch length on phylogenies). We used simulations to determine the effects of dataset size, branch length heterogeneity, branch depth, and analytical framework on branch length estimation across a range of branch lengths. We then reanalyzed an empirical dataset for plethodontid salamanders to determine how inaccurate branch length estimation can affect estimates of divergence dates.     

Molecular characterization of major histocompatibility complex class II alleles in wild tiger salamanders (Ambystoma tigrinum)

Major histocompatibility complex (MHC) class II genes are usually among the most polymorphic in vertebrate genomes because of their critical role (antigen presentation) in immune response. Prior to this study, the MHC was poorly characterized in tiger salamanders (Ambystoma tigrinum), but the congeneric axolotl (Ambystoma mexicanum) is thought to have an unusual MHC. Most notably, axolotl class II genes lack allelic variation and possess a splice variant without a full peptide binding region (PBR). The axolotl is considered immunodeficient, but it is unclear how or to what extent MHC genetics and immunodeficiency are interrelated. To study the evolution of MHC genes in urodele amphibians, we describe for the first time an expressed polymorphic class II gene in wild tiger salamanders. We sequenced the PBR of a class II gene from wild A. tigrinum (n=33) and identified nine distinct alleles. Observed heterozygosity was 73%, and there were a total of 46 polymorphic sites, most of which correspond to amino acid positions that bind peptides. Patterns of nucleotide substitutions exhibit the signature of diversifying selection, but no recombination was detected. Not surprisingly, transspecies evolution of tiger salamander and axolotl class II alleles was apparent. We have no direct data on the immunodeficiency of tiger salamanders, but the levels of polymorphism in our study population should suffice to bind a variety of foreign peptides (unlike axolotls). Our tiger salamander data suggest that the monomorphism and immunodeficiencies associated with axolotl class II genes is a relict of their unique historical demography, not their phylogenetic legacy. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Background  

We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of C _α traces for short proteins (up to 200 amino acids).     

Shifty salamanders: transient trophic polymorphism and cannibalism within natural populations of larval ambystomatid salamanders

Introduction

Many species of ambystomatid salamanders are dependent upon highly variable temporary wetlands for larval development. High larval densities may prompt the expression of a distinct head morphology that may facilitate cannibalism. However, few studies have characterized structural cannibalism within natural populations of larval salamanders. In this study we used two species of larval salamanders, long-toed (Ambystoma macrodactylum) and ringed salamanders (A. annulatum). Head morphometrics and stable isotopic values of carbon (δ¹³C) and nitrogen (δ¹⁵N) were used to identify the presence or absence of structural cannibalism. Weather conditions were also analyzed as a potential factor associated with the expression of cannibalistic morphology.

Results

Populations of salamander larvae did not consistently exhibit cannibalistic morphologies throughout collection periods. Larval long-toed salamanders exhibited trophic polymorphisms when relatively lower precipitation amounts were observed. Larval ringed salamanders were observed to be cannibalistic but did not exhibit polymorphisms in this study.

Conclusions

Structural cannibalism may be transient in both species; however in long-toed salamanders this morphology is necessary for cannibalism. Ringed salamanders can be cannibalistic without morphological adaptations; however the cannibal morph may prolong the viable time period for cannibalism. Additionally, weather conditions may alter pond hydroperiod, subsequently influencing head morphology and cannibalism.

     

The effects of conspecifics on burrow selection in juvenile spotted salamanders (<Emphasis Type="Italic">Ambystoma maculatum)</Emphasis>

Spotted salamanders (Ambystoma maculatum) are pond-breeding amphibians that disperse into terrestrial habitat from natal wetlands after undergoing metamorphosis, relying on small-mammal burrows and coarse woody debris for refugia. The effect of conspecifics on burrow use in juvenile salamanders is poorly understood. Determining how the presence of conspecifics influences the settlement decisions of juvenile salamanders can increase our understanding of amphibian dispersal and our ability to predict population dynamics. We conducted behavioral laboratory trials using 58 recently metamorphosed salamanders to examine how salamanders selected burrows in the presence of conspecifics. Salamanders were more likely to settle in a burrow that was occupied by a conspecific versus an unoccupied burrow. Our results indicate that juvenile salamanders may show conspecific attraction and/or trailing behavior during the dispersal phase.     

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks

Background  

One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate prediction methods will serve as a basis for these and other purposes.     

Time and time again: unisexual salamanders (genus <Emphasis Type="Italic">Ambystoma</Emphasis>) are the oldest unisexual vertebrates

Background  

The age of unisexual salamanders of the genus Ambystoma is contentious. Recent and ancient evolutionary histories of unisexual Ambystoma were proposed by a few separate studies that constructed phylogenies using mitochondrial DNA markers (cytochrome b gene vs. non-coding region). In contrast to other studies showing that unisexual Ambystoma represent the most ancient unisexual vertebrates, a recent study by Robertson et al. suggests that this lineage has a very recent origin of less than 25,000 years ago.     

Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

Aim

Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction‐site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.

Location

Baja California and Southern California.

Methods

We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).

Results

Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern‐most portion of the range of C. ruber was not suitable habitat during the LGM.

Main conclusions

We provide the first explicitly model‐based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa.     

Thyroid hormone responsive QTL and the evolution of paedomorphic salamanders

The transformation of ancestral phenotypes into novel traits is poorly understood for many examples of evolutionary novelty. Ancestrally, salamanders have a biphasic life cycle with an aquatic larval stage, a brief and pronounced metamorphosis, followed by a terrestrial adult stage. Repeatedly during evolution, metamorphic timing has been delayed to exploit growth-permissive environments, resulting in paedomorphic salamanders that retain larval traits as adults. We used thyroid hormone (TH) to rescue metamorphic phenotypes in paedomorphic salamanders and then identified quantitative trait loci (QTL) for life history traits that are associated with amphibian life cycle evolution: metamorphic timing and adult body size. We demonstrate that paedomorphic tiger salamanders (Ambystoma tigrinum complex) carry alleles at three moderate effect QTL (met1–3) that vary in responsiveness to TH and additively affect metamorphic timing. Salamanders that delay metamorphosis attain significantly larger body sizes as adults and met2 explains a significant portion of this variation. Thus, substitution of alleles at TH-responsive loci suggests an adaptive pleiotropic basis for two key life-history traits in amphibians: body size and metamorphic timing. Our study demonstrates a likely pathway for the evolution of novel paedomorphic species from metamorphic ancestors via selection of TH-response alleles that delay metamorphic timing and increase adult body size.     

Genetic evidence of tiger population structure and migration within an isolated and fragmented landscape in Northwest India

Background

Majority of the tiger habitat in Indian subcontinent lies within high human density landscapes and is highly sensitive to surrounding pressures. These forests are unable to sustain healthy tiger populations within a tiger-hostile matrix, despite considerable conservation efforts. Ranthambore Tiger Reserve (RTR) in Northwest India is one such isolated forest which is rapidly losing its links with other tiger territories in the Central Indian landscape. Non-invasive genetic sampling for individual identification is a potent technique to understand the relationships between threatened tiger populations in degraded habitats. This study is an attempt to establish tiger movement across a fragmented landscape between RTR and its neighboring forests, Kuno-Palpur Wildlife Sanctuary (KPWLS) and Madhav National Park (MNP) based on non-invasively obtained genetic data.

Methods

Data from twelve microsatellite loci was used to define population structure and also to identify first generation migrants and admixed individuals in the above forests.

Results

Population structure was consistent with the Central Indian landscape and we could determine significant gene flow between RTR and MNP. We could identify individuals of admixed ancestry in both these forests, as well as first generation migrants from RTR to KPWLS and MNP.

Conclusions

Our results indicate reproductive mixing between animals of RTR and MNP in the recent past and migration of animals even today, despite fragmentation and poaching risk, from RTR towards MNP. Substantial conservation efforts should be made to maintain connectivity between these two subpopulations and also higher protection status should be conferred on Madhav National Park.     

Stimulation of terrestrial-substrate preferences and locomotor activity in newly transformed tiger salamanders (Ambystoma tigrinum) by exogenous or endogenous thyroxine

Recently transformed adult tiger salamanders (Ambystoma tigrinum) that had never resided on land were treated with increasing, alternate-day injections of thyroxine (experiment 1) or single injections of particular dosages of this hormone (experiment 2). In all cases control salamanders received equivalent volumes of saline on a similar schedule. In both experiments, subjects treated with thyroxine displayed significant levels of terrestrial-substrate preference in a moisture-gradient apparatus. Salinetreated controls never emerged from the water. In experiment 2, animals that received single thyroxine treatments also displayed heightened levels of land-directed locomotor activity. In experiment 3, blood plasma was collected from salamanders displaying spontaneous land preference and others displaying water preference. Radioimmunoassay for thyroxine indicated that salamanders that had moved to, and resided upon, a terrestrial substrate some time subsequent to metamorphosis had significantly higher plasma levels of this hormone than did animals preferring to remain submerged. These results indicate (1) that thyroxine stimulates, and possibly maintains, emergence from water and terrestrial preference in newly transformed tiger salamanders and (2) that this hormone stimulates a locomotor activity component associated with the movement of formerly aquatic adults to the terrestrial habitat.     

Philopatry and Dispersal Patterns in Tiger (Panthera tigris)

Background

Tiger populations are dwindling rapidly making it increasingly difficult to study their dispersal and mating behaviour in the wild, more so tiger being a secretive and solitary carnivore.

Methods

We used non-invasively obtained genetic data to establish the presence of 28 tigers, 22 females and 6 males, within the core area of Pench tiger reserve, Madhya Pradesh. This data was evaluated along with spatial autocorrelation and relatedness analyses to understand patterns of dispersal and philopatry in tigers within this well-managed and healthy tiger habitat in India.

Results

We established male-biased dispersal and female philopatry in tigers and reiterated this finding with multiple analyses. Females show positive correlation up to 7 kms (which corresponds to an area of approximately 160 km²) however this correlation is significantly positive only upto 4 kms, or 50 km² (r  = 0.129, p<0.0125). Males do not exhibit any significant correlation in any of the distance classes within the forest (upto 300 km²). We also show evidence of female dispersal upto 26 kms in this landscape.

Conclusions

Animal movements are important for fitness, reproductive success, genetic diversity and gene exchange among populations. In light of the current endangered status of tigers in the world, this study will help us understand tiger behavior and movement. Our findings also have important implications for better management of habitats and interconnecting corridors to save this charismatic species.     

A genetically explicit model of speciation by sensory drive within a continuous population in aquatic environments

Background  

The sensory drive hypothesis predicts that divergent sensory adaptation in different habitats may lead to premating isolation upon secondary contact of populations. Speciation by sensory drive has traditionally been treated as a special case of speciation as a byproduct of adaptation to divergent environments in geographically isolated populations. However, if habitats are heterogeneous, local adaptation in the sensory systems may cause the emergence of reproductively isolated species from a single unstructured population. In polychromatic fishes, visual sensitivity might become adapted to local ambient light regimes and the sensitivity might influence female preferences for male nuptial color. In this paper, we investigate the possibility of speciation by sensory drive as a byproduct of divergent visual adaptation within a single initially unstructured population. We use models based on explicit genetic mechanisms for color vision and nuptial coloration.     

Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone?

Premise

Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology.

Methods

We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression.

Results

Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (F_ST = 0.44). However, the F_ST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation.

Conclusions

Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.