A single nucleotide polymorphism assay for the identification of unisexual Ambystoma salamanders

Unisexual (all female) salamanders in the genus Ambystoma are animals of variable ploidy (2N‐5N) that reproduce via a unique system of ‘leaky’ gynogenesis. As a result, these salamanders have a diverse array of nuclear genome combinations from up to five sexual species: the blue‐spotted (A. laterale), Jefferson (A. jeffersonianum), smallmouth (A. texanum), tiger (A. tigrinum) and streamside (A. barbouri) salamanders. Identifying the genome complement, or biotype, is a critical first step in addressing a broad range of ecological and evolutionary questions about these salamanders. Previous work relied upon genome‐related differences in allele size distributions for specific microsatellite loci, but overlap in these distributions among different genomes makes definitive identification and ploidy determination in unisexuals difficult or impossible. Here, we develop the first single nucleotide polymorphism assay for the identification of unisexual biotypes, based on species‐specific nucleotide polymorphisms in noncoding DNA loci. Tests with simulated and natural unisexual DNA samples show that this method can accurately identify genome complement and estimate ploidy, making this a valuable tool for assessing the genome composition of unisexual samples.     

GYNOGENETIC REPRODUCTION IN HYBRID MOLE SALAMANDERS (GENUS AMBYSTOMA)

Ambystoma platineum, a unisexual clonal triploid taxon of mole salamander, originated by hybridization between the Mendelian species A. jeffersonianum and A. laterale. Studies of lampbrush chromosomes indicated that A. platineum reproduces gynogenetically, that is, sperm from a sexual host species is required to activate egg development but makes no genetic contribution to the developing embryo. Nevertheless, electrophoretic diversity in populations of some hybrid Ambystoma suggested continual in situ recreation of unisexual hybrids and bidirectional gene exchange between the parental species and the hybrids. A. platineum usually lives with, and is sexually dependent on, one of its parental species, A. jeffersonianum. In central Indiana, however, A. platineum populations have shifted their host dependency to A. texanum. Such A. texanum-dependent populations of A. platineum provide an almost ideal system for studying reproductive mode in A. platineum, because both replacement of a jeffersonianum or laterale genome of A. platineum by a texanum genome, and movement of genes from A. platineum to the host species, A. texanum, would be readily detected by electrophoretic markers. Our samples of A. texanum provided no evidence for the transfer of jeffersonianum or laterale genes into A. texanum. Similarly, among 32 A. platineum sampled from six localities in east-central Illinois and central Indiana, we find no texanum alleles, and thus no evidence for genome replacement. The one diploid hybrid individual contained only a jeffersonianum and a laterale genome; because of the absence of either parental species from these populations, this hybrid could only have come from a diploid ovum produced by A. platineum. Both morphometric and electrophoretic results for the two tetraploid individuals indicate that they resulted from fertilization of triploid oocytes of A. platineum by sperm of A. texanum. Because genome replacement in A. texanum-dependent populations of A. platineum is irreversible, the persistence of A. platineum in A. texanum-dependent populations demonstrates conclusively that the major mode of reproduction in A. platineum populations is clonal: A. platineum produces mainly triploid eggs that develop gynogenetically.     

Genome‐specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species

Quantifying introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what drives the longevity of putatively asexual groups. Here, we capitalize on three recent innovations—ultraconserved element (UCE) sequencing, bioinformatic techniques for identifying genome‐specific variation in polyploids, and model‐based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all‐female salamanders and two ancestral sexual species. Our analyses support a scenario in which the genomes sampled in unisexual salamanders last shared a common ancestor with genomes in their parental species ～3.4 million years ago, followed by a period of divergence between homologous genomes. Recently, secondary introgression has occurred at different times with each sexual species during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage is the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have undergone long periods of divergence without introgression. Unlike other sperm‐dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could explain why these salamanders are among the oldest described unisexual animals.     

Dobzhansky-Muller model of hybrid dysfunction supported by poor burst-speed performance in hybrid tiger salamanders

Speciation may result from 'complementary' genetic differences that cause dysfunction when brought together in hybrids despite having no deleterious effects within pure species genomes. The theory of complementary genes, independently proposed by Dobzhansky and Muller, yields specific predictions about the genetics of hybrid fitness. Here, I show how alternative models of hybrid dysfunction can be compared using a simple multivariate analysis of hybrid indices calculated from molecular markers. I use the approach to fit models of hybrid dysfunction to swimming performance in hybrid tiger salamander larvae. Poor burst-speed performance is a dysfunction suggesting low vigour and could translate directly into low survival. My analyses show that the Dobzhansky-Muller model fits these data better than heterozygote disadvantage. The approach demonstrated here can be applied to a broad array of nonmodel species, potentially leading to important generalizations about the genetics of hybrid dysfunction.     

The origin and evolution of a unisexual hybrid: Poecilia formosa

Clonal reproduction in vertebrates can always be traced back to hybridization events as all known unisexual vertebrates are hybrids between recognized species or genetically defined races. Interestingly, clonal vertebrates often also rely on interspecific matings for their reproduction because gynogenesis (sperm-dependent parthenogenesis) and hybridogenesis are common modes of propagation. While in most cases these hybridization events leave no hereditary traces in the offspring, occasionally the genome exclusion mechanism fails and either small parts of male genetic material remain inside the oocyte in the form of microchromosomes, or fusion of the sperm nucleus with the oocyte nucleus leads to polyploid individuals. In this review, we highlight the important role of hybridization for the origin and evolution of a unisexual hybrid: the Amazon molly, Poecilia formosa.     

Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.     

Frozen F1's amidst a masterpiece of nature: new insights into the rare hybrid origin of gynogenesis in the Amazon molly (Poecilia formosa)

All‐female ‘species’ of fish have been shown to be great models in ecological and evolutionary studies because of the insights they can provide into the origin and evolution of asexuality, the ecology of hybrids, associations between genotype and environment, and the maintenance of sex. Gynogenetic organisms that evolved from sexual ancestors, and combine the disadvantageous traits from sexuality and asexuality, have long baffled evolutionary biologists trying to understand their origin and persistence with their sympatric sexual counterparts. In this issue, a new study using an integrated molecular phylogenetic and classical genetic approach has uncovered compelling evidence regarding the obscure asexual origin of the Amazon molly, Poecilia formosa. By performing an extensive phylogeographic analysis, Stöck et al. (2010) provide evidence that the Amazon molly arose only once within its history, with monophyly being strongly supported by mitochondrial DNA and microsatellite analyses. This result, combined with an elaborate failed attempt to resynthesize the lineage, suggests that vertebrate gynogens such as the Amazon molly are not rare because they are at a disadvantage to their sexual counterparts, but because the genomic conditions under which they arise are rare. Organisms that apparently combine the disadvantages of both sexuality and asexuality remain difficult to understand from both an ecological and an evolutionary perspective, and Stöck et al. (2010) highlight several outstanding important questions. Nonetheless, given that we now have a better knowledge of the origin and history of this unique ‘species’, this should allow researchers to better understand how these frozen F1’s can persist amidst the masterpiece of nature.     

Introgression of mitochondrial DNA among lineages in a hybridogenetic ant

We report a remarkable pattern of incongruence between nuclear and mitochondrial variations in a social insect, the desert ant Cataglyphis hispanica. This species reproduces by social hybridogenesis. In all populations, two distinct genetic lineages coexist; non-reproductive workers develop from hybrid crosses between the lineages, whereas reproductive offspring (males and new queens) are typically produced asexually by parthenogenesis. Genetic analyses based on nuclear markers revealed that the two lineages remain highly differentiated despite constant hybridization for worker production. Here, we show that, in contrast with nuclear DNA, mitochondrial DNA (mtDNA) does not recover the two lineages as monophyletic. Rather, mitochondrial haplotypes cluster according to their geographical origin. We argue that this cytonuclear incongruence stems from introgression of mtDNA among lineages, and review the mechanisms likely to explain this pattern under social hybridogenesis.     

Interaction of an insecticide with larval density in pond-breeding salamanders (Ambystoma)

1. Amphibian populations residing in or near agricultural areas are often susceptible to pesticide contamination. Recent evidence suggests that the effects of pesticides on amphibians often exceed those estimated in laboratory toxicity tests because other environmental factors (e.g. predators, resource abundance) can influence pesticide toxicity. 2. To examine the effects of an insecticide (carbaryl) on two species of Ambystoma salamanders experiencing the natural stress of competition, we manipulated chemical concentration (control, 3.5 and 7.0 mg L^?1) and larval density (low and high). We determined the effect of treatments on snout‐vent length (SVL), growth rate, lipid reserves, time to metamorphosis, per cent survival and per cent metamorphosis. 3. Carbaryl negatively affected all response variables of Ambystoma maculatum significantly, and significantly reduced survival and metamorphosis of A. opacum. Increased density significantly influenced SVL, lipid reserves, growth rate and metamorphosis of A. maculatum. 4. The effects of carbaryl and increased density on per cent metamorphosis were nearly additive, but were generally less than additive on other variables. 5. The negative effects of chemical contamination on salamanders were likely because of pesticide‐induced reductions of food resources, as zooplankton abundance decreased by as much as 97% following carbaryl application. 6. Our study demonstrates the importance of the interactive effects that chemical contamination and natural environmental factors have on salamanders.     

Condition-dependent mate choice and a reproductive disadvantage for MHC-divergent male tiger salamanders

Major histocompatibility complex (MHC) alleles likely have adaptive value because of overdominance, in which case MHC heterozygous individuals have increased fitness relative to homozygotes. Because of this potential benefit, the evolution of sexual reproduction between MHC-divergent individuals (i.e. negative assortative mating, NAM) may be favoured. However, the strongest evidence for MHC-based NAM comes from inbred animals, and context-dependent mating preferences have rarely been evaluated although they often occur in nature. We assessed the extent MHC-based mating preferences among wild tiger salamanders ( Ambystoma tigrinum ) using multiple molecular approaches. We genotyped 102 adults and 864 larvae from 36 breeding trials at both microsatellite and MHC loci. Parentage analysis revealed that reproductive success among males was positively associated with increased tail length and that with respect to the focal female, MHC-similar males sired a significantly higher number of offspring than more dissimilar males. This trend was consistent, even under context-dependent scenarios that favour traditional MHC-based NAM. These results suggest that the most MHC-divergent males may be at a reproductive disadvantage in pairwise breeding trials. Our data add to a growing body of evidence that suggests where it exists, MHC-based choice is probably dynamic and mediated by many factors that vary in the wild, notably signals from other indicator traits and by the quality and quantity of potential mates.     

Isolation of microsatellite loci in spotted salamanders (Ambystoma maculatum)

To assess the level and spatial pattern of genetic diversity in the spotted salamander, Ambystoma maculatum, we characterized hypervariable molecular markers by screening genomic libraries enriched for microsatellite motifs. We designed primers that reliably amplify twelve polymorphic loci and checked for variability in individuals from populations in the vicinity of Ithaca, New York. Loci show high variability in the number of alleles and heterozygosities, suggesting they will be useful for determining local population differentiation and mating systems in this pond‐breeding amphibian.     

A test of alternative hypotheses for kin recognition in cannibalistic tiger salamanders

The function of kin recognition is controversial. We investigatedthe adaptive significance of kin discrimination in cannibalistictiger salamander larvae, Ambystoma tigrinum. Previous laboratoryexperiments show that cannibals preferentially consume lessrelated individuals. We hypothesized that this example of kinrecognition (1) is a laboratory artifact, (2) is a by-productof sibship-specific variation in escape responses, because cannibalsfrom families with rapid responses may be more likely to cannibalize slowlyescaping non-kin, (3) is an epiphenomenon of species recognition,(4) functions in disease avoidance, because kin may be moreinfectious than non-kin, or (5) is favored by kin selection.We evaluated these five hypotheses by using laboratory and fieldexperiments to test specific predictions made by each hypothesis.We rejected hypotheses 1-4 above because (1) kin recognitionwas expressed in the wild, (2) escape responses did not reliablypredict whether a cannibal would ingest kin or non-kin, (3)kin recognition was not most pronounced in populations wheretiger salamanders co-occur with other species of salamanders,and (4) non-kin prey were more likely than kin to transmit pathogensto cannibals. However, we established that the necessary conditionfor kin selection, Hamilton's rule, was met. Thus, our resultsimplicate kin selection as the overriding reason that cannibalistictiger salamanders discriminate kin.     

Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae)

Although most vertebrates reproduce sexually, a small number of fishes, amphibians and reptiles are known in which reproduction is asexual, i.e. without meiotic recombination. In fishes, these so-called unisexual lineages usually comprise only females and utilize co-occurring males of a related sexual species to reproduce via gynogenesis or hybridogenesis. Here, we examine patterns of microsatellite and mitochondrial DNA (mtDNA) variation in a widespread group of freshwater fishes (carp gudgeons; Hypseleotris spp.) to investigate a long-standing proposal that this group includes unisexual forms. We show that the mtDNA genome of most carp gudgeons in tributaries of the Goulburn River belongs to one of two deeply divided clades (～10% cyt b divergence) and that nuclear variation divides the same individuals into four distinct groups. Group 1 exhibits the genotypic proportions of a random mating population and has a 1:1 sex ratio. Two other groups are extremely sex-biased (98% male, 96% female), exhibit excess heterozygosity at most loci and share at least one allele per locus with group 1. We propose that these two groups represent 'unisexual' hybridogenetic lineages and that both utilize co-occurring group 1 as sexual host. Interestingly, the fourth distinct group appears to represent hybrid offspring of the two putative hybridogenetic lineages. The propagation of clonal haploid genomes by both males and females and the ability of these clones to unite and form sexually mature diploid hybrid offspring may represent a novel mechanism that contributes to the dynamics of coexistence between hybridogenetic lineages and their sexual hosts.     

Water‐borne and plasma corticosterone are not correlated in spotted salamanders

Water‐borne hormone measurement is a noninvasive method suitable for amphibians of all sizes that are otherwise difficult to sample. For this method, containment‐water is assayed for hormones released by the animal. Originally developed in fish, the method has expanded to amphibians, but requires additional species‐specific validations. We wanted to determine physiological relevance of water‐borne corticosterone in spotted salamanders (Ambystoma maculatum) by comparing concentrations to those taken using established corticosterone sampling methods, such as plasma. Using a mixture of field and laboratory studies, we compared water‐borne corticosterone levels to other traditional methods of sampling corticosterone for spotted salamander larvae, metamorphs, and adults. Despite multiple attempts, and detecting differences between age groups, we found no correlations between water‐borne and plasma corticosterone levels in any age group. Water‐borne sampling measures a rate of release; whereas plasma is the concentration circulating in the blood. The unique units of measurement may inherently prevent correlations between the two. These two methods may also require different interpretations of the data and the physiological meaning. We also note caveats with the method, including how to account for differences in body size and life history stages. Collectively, our results illustrate the importance of careful validation of water‐borne hormone levels in each species in order to understand its physiological significance.     

Candidate gene analysis of metamorphic timing in ambystomatid salamanders

Although much is known about the ecological significance of metamorphosis and metamorphic timing, few studies have examined the underlying genetic architecture of these traits, and no study has attempted to associate phenotypic variation to molecular variation in specific genes. Here we report on a candidate gene approach (CGA) to test specific loci for a statistical contribution to variation in metamorphic timing. Three segregating populations (SP1, SP2 and SP3) were constructed utilizing three species of paedomorphic Mexican ambystomatid salamander, including the axolotl, Ambystoma mexicanum. We used these replicated species to test the hypothesis that inheritance of alternate genotypes at two thyroid hormone receptor loci (TRalpha, TRbeta) affects metamorphic timing in ambystomatid salamanders. A significant TRalpha*SP effect indicated that variation in metamorphic timing may be influenced by TRalpha genotype, however, the effect was not a simple one, as both the magnitude and direction of the phenotypic effect depended upon the genetic background. These are the first data to implicate a specific gene in contributing to variation in metamorphic timing. In general, candidate gene approaches can be extended to any number of loci and to any organism where simple genetic crosses can be performed to create segregating populations. The approach is thus of particular value in ecological studies where target genes have been identified but the study organism is not one of the few well-characterized model systems that dominate genetic research.     

Two unisexual artificial polyploid clones constructed by genome addition of common carp (Cyprinus carp) and crucian carp (Carassius auratus)

The application of hybrid vigor and crossbreeding is conventional and proved effective. Nevertheless, the phenotype of the progeny of hybrids, which carry hybrid vigor and produce their offspring through bisexual reproduction, will segregate inevitably and their hybrid vigor will de-crease in subsequent generations. The more serious consequence might result in destroying com-pletely those endemic populations when hybrids are released into open water bodies, because hy-brids will cross with the…     

Group size structure affects patterns of aggression in larval salamanders

The potential importance of intrapopulation phenotypic variabilityto population-level ecology has been demonstrated in both theoreticaland field studies. One way to connect individuals to the dynamicsof populations they compose is to study behavioral response(an individual-level characteristic) to variability in conspecificphenotypes (a population-level characteristic). We examinedeffects of variation in size of individuals on patterns of aggressionin larval tiger salamanders (Ambystoma tigrinum nebulosum) byobserving aggressive behavior in groups of three larvae in alaboratory experment. We assessed effects of variability insize of conspecifics independently of mean larval size and larvaldensity Overall levels of aggression were generally higher ingroups in which all individuals were similprly sized than ingroups of variably sized individuals. Medium-sized individualsexhibited significantly higher levels of aggression and wereattacked significantly more often when in groups consistingonly of similarly sized larvae as compared to groups composedof larvae representing a wider range of body sizes. Activitylevels of larvae were also generally lower when all individualswere the same size, resulting in a negative correlation betweenactivity and levels of iggressititi. These results suggest thatgioups of similarly sized individuals experience a more aggressivesocial environment than groups of variably sized individuals,and they suggest a promising avenue of research for connectingindividual behavioral and physiological responses to size structure(phenotypic variability) with population dynamics.     

Biomass export of salamanders and anurans from ponds is affected differentially by changes in canopy cover

1. Previous research shows that canopy‐associated shifts from an algal to a detritus‐based food web can affect anuran tadpoles negatively. This may not be true of salamander larvae, however, because they are predators. 2. To investigate the influence of canopy cover on the survival and growth of salamanders, and on the subsequent export of biomass from ponds, we conducted a mesocosm experiment examining effects of shading (high or low) and litter (leaves or grass) on Ambystoma maculatum (a forest specialist) and A. texanum (a habitat generalist). Additionally, we reanalysed data from Williams, Rittenhouse & Semlitsch (2008) to examine the effects of shading and litter on biomass export of three anurans: Rana sphenocephala, Pseudacris crucifer and Hyla versicolor. 3. In contrast to previous studies, we found that salamanders performed better in mesocosms with the characteristics of closed canopy ponds (high shade and leaf litter), which resulted in a greater export of biomass. Salamanders grew larger under closed canopy conditions, probably because of differences in prey abundance among treatments. Anurans responded differently to canopy cover than caudates. The biomass export of R. sphenocephala and P. crucifer was reduced under closed canopy conditions (although differently affected by litter and shading), while the biomass of H. versicolor was not affected. 4. This and other studies suggest that changes in canopy cover may induce a shift in the amphibians emerging from ponds, from primarily anurans in open canopy ponds to primarily salamanders in closed canopy ponds. Additional multispecies studies will determine whether these trends hold true for more diverse amphibian assemblages. Further investigation into the effects of canopy cover on salamanders will be important for understanding aquatic–terrestrial linkages.     

Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape

Understanding the impacts of landscape-level processes on the population biology of amphibians is critical, especially for species inhabiting anthropogenically modified landscapes. Many pond-breeding amphibians are presumed to exist as metapopulations, but few studies demonstrate the extent and consequences of this metapopulation structure. Gene flow measures may facilitate the construction of more realistic models of population structure than direct measures of migration. This is especially true for species that are cryptic, such as many amphibians. We used eight polymorphic microsatellite loci to determine the genetic population structure of spotted salamanders ( Ambystoma maculatum ) breeding at 17 ponds in northeastern Ohio, a landscape fragmented by roads, agriculture, urban areas and the Cuyahoga River. Using a variety of analyses (Bayesian clustering, F -statistics, AMOVA) we generated a model of salamander population genetic structure. Our data revealed patterns of genetic connectivity that were not predicted by geographical distances between ponds (no isolation by distance). We also tested for a relationship between population structure and several indices of landscape resistance, but found no effect of potential barriers to dispersal on genetic connectivity. Strong overall connectivity among ponds, despite the hostile habitat matrix, may be facilitated by a network of riparian corridors associated with the Cuyahoga River; however, high gene flow in this system may indicate a general ability to disperse and colonize beyond particular corridors.