Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus

Parallel morphological evolution and habitat-dependent sexual dimorphism in cave- vs. surface populations of the Asellus aquaticus (Crustacea: Isopoda: Asellidae) species complex

Studying parallel evolution (repeated, independent evolution of similar phenotypes in similar environments) is a powerful tool to understand environment-dependent selective forces. Surface-dwelling species that repeatedly and independently colonized caves provide unique models for such studies. The primarily surface-dwelling Asellus aquaticus species complex is a good candidate to carry out such research, because it colonized several caves in Europe. By comparing 17 functional morphological traits between six cave and nine surface populations of the A. aquaticus species complex, we investigated population divergence in morphology and sexual dimorphism. We found habitat-dependent population divergence in 10 out of 17 traits, likely reflecting habitat-driven changes in selection acting on sensory systems, feeding, grooming, and antipredator mechanisms. Sexual dimorphism was present in 15 traits, explained by sexual selection acting on male traits important in male-male agonistic behavior or mate guarding and fecundity selection acting on female traits affecting offspring number and nursing. In eight traits, the degree of sexual dimorphism was habitat dependent. We conclude that cave-related morphological changes are highly trait- and function-specific and that the strength of sexual/fecundity selection strongly differs between cave and surface habitats. The considerable population variation within habitat type warrants further studies to reveal cave-specific adaptations besides the parallel patterns.

Temperature effects on metabolic scaling of a keystone freshwater crustacean depend on fish-predation regime

According to the metabolic theory of ecology, metabolic rate, an important indicator of the pace of life, varies with body mass and temperature as a result of internal physical constraints. However, various ecological factors may also affect metabolic rate and its scaling with body mass. Although reports of such effects on metabolic scaling usually focus on single factors, the possibility of significant interactive effects between multiple factors requires further study. In this study, we show that the effect of temperature on the ontogenetic scaling of resting metabolic rate of the freshwater amphipod Gammarus minus depends critically on habitat differences in predation regime. Increasing temperature tends to cause decreases in the metabolic scaling exponent (slope) in population samples from springs with fish predators, but increases in population samples from springs without fish. Accordingly, the temperature sensitivity of metabolic rate is not only size-specific, but also its relationship to body size shifts dramatically in response to fish predators. We hypothesize that the dampened effect of temperature on the metabolic rate of large adults in springs with fish, and of small juveniles in springs without fish are adaptive evolutionary responses to differences in the relative mortality risk of adults and juveniles in springs with versus without fish predators. Our results demonstrate a complex interaction among metabolic rate, body mass, temperature and predation regime. The intraspecific scaling of metabolic rate with body mass and temperature is not merely the result of physical constraints related to internal body design and biochemical kinetics, but rather is ecologically sensitive and evolutionarily malleable.

Phenotypic plasticity as a mechanism of cave colonization and adaptation

A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that many cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus.

The Mexican tetra is a fish that has two forms: a surface-dwelling form, which has eyes and silvery grey appearance, and a cave-dwelling form, which is blind and has lost its pigmentation. Recent studies have shown that the cave-dwelling form evolved rapidly within the last 200,000 years from an ancestor that lived at the surface. The recent evolution of the cave-dwelling form of the tetra poses an interesting evolutionary question: how did the surface-dwelling ancestor of the tetra quickly adapt to the new and challenging environment found in the caves?

‘Phenotypic plasticity’ is a phenomenon through which a single set of genes can produce different observable traits depending on the environment. An example of phenotypic plasticity occurs in response to diet: in animals, poor diets can lead to an increase in the size of the digestive organs and to the animals eating more. To see if surface-dwelling tetras can quickly adapt to cave environments through phenotypic plasticity, Bilandžija et al. have exposed these fish to complete darkness (the major feature of the cave environment) for two years. After spending up to two years in the dark, these fish were compared to normal surface-dwelling and cave-dwelling tetras.

Results revealed that surface-dwelling tetras raised in the dark exhibited traits associated with cave-dwelling tetras. These traits included changes in the activity of many genes involved in diverse processes, resistance to starvation, metabolism, and levels of hormones and molecules involved in neural signaling, which could lead to changes in behavior. However, the fish also exhibited traits, including an increase in the cells responsible for pigmentation, that would have no obvious benefit in the darkness. Even though the changes observed require no genetic mutations, they can help or hinder the fish’s survival once they occur, possibly determining subsequent evolution. Thus, a trait beneficial for surviving in the dark that appears simply through phenotypic plasticity may eventually be selected for and genetic mutations that encode it more reliably may appear too.

These results shed light on how species may quickly adapt to new environments without accumulating genetic mutations, which can take hundreds of thousands of years. They also may help to explain how colonizer species succeed in challenging environments. The principles described by Bilandžija et al. can be applied to different organisms adapting to new environments, and may help understand the role of phenotypic plasticity in evolution.

Effects of Fish Predators on the Mass-Related Energetics of a Keystone Freshwater Crustacean

Little is known about how predators or their cues affect the acquisition and allocation of energy throughout the ontogeny of prey organisms. To address this question, we have been comparing the ontogenetic body-mass scaling of various traits related to energy intake and use between populations of a keystone amphipod crustacean inhabiting freshwater springs, with versus without fish predators. In this progress report, we analyze new and previously reported data to develop a synthetic picture of how the presence/absence of fish predators affects the scaling of food assimilation, fat content, metabolism, growth and reproduction in populations of Gammarus minus located in central Pennsylvania (USA). Our analysis reveals two major clusters of ‘symmorphic allometry’ (parallel scaling relationships) for traits related to somatic versus reproductive investment. In the presence of fish predators, the scaling exponents for somatic traits tend to decrease, whereas those for reproductive traits tend to increase. This divergence of scaling exponents reflects an intensified trade-off between somatic and reproductive investments resulting from low adult survival in the face of size-selective predation. Our results indicate the value of an integrated view of the ontogenetic size-specific energetics of organisms and its response to both top-down (predation) and bottom-up (resource supply) effects.

Ecophysiological and life-history adaptations of Gammarus balcanicus (Schäferna, 1922) in a sinking-cave stream from Western Carpathians (Romania)

Freshwater gammarids are known to colonise occasionally sinking-cave streams, providing contrasting morphological, life-history and ecophysiological adaptations compared to their surface conspecifics. In this study, a subterranean and a surface population of the species Gammarus balcanicus was surveyed for one year in a sinking-cave stream from the Western Carpathians (Romania). The results showed that the cave-dwelling population comprised individuals that were significantly larger compared to their surface conspecifics, had larger body-size at sexual maturity and that the females produced fewer, but larger eggs, compared to the population situated outside the cave. The trophic position and the omnivory were significantly higher for the cave-dwelling compared to surface population and the elemental imbalance for C:P molar ratios lower, but similar for C:N. However, the subterranean population did not present troglomorphic characters or longer lifespan as known for other cave-surface paired crustaceans. This, together with the rather extensive hydrological connection of the habitats, suggests active gene-flow between populations and similar response to seasonality for body-size distributions, indicating that the observed ecophysiological and life-history differences are rather the consequence of phenotypic plasticity than the result of genetic adaptation.

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species

Background

The ancient Lake Baikal is characterized by an outstanding diversity of endemic faunas with more than 350 amphipod species and subspecies. We determined the genetic diversity within the endemic littoral amphipod species Eulimnogammarus verrucosus, E. cyaneus and E. vittatus and investigated whether within those species genetically separate populations occur across Lake Baikal. Gammarus lacustris from water bodies in the Baikal area was examined for comparison.

Results

Genetic diversities within a species were determined based on fragments of cytochrome c oxidase I (COI) and for E. verrucosus additionally of 18S rDNA. Highly location-specific haplogroups of E. verrucosus and E. vittatus were found at the southern and western shores of Baikal that are separated by the Angara River outflow; E. verrucosus from the eastern shore formed a further, clearly distinct haplotype cluster possibly confined by the Selenga River and Angarskiy Sor deltas. The genetic diversities within these haplogroups were lower than between the different haplogroups. Intraspecific genetic diversities within E. verrucosus and E. vittatus with 13 and 10%, respectively, were similar to interspecies differences indicating the occurrence of cryptic, morphologically highly similar species; for E. verrucosus this was confirmed with 18S rDNA. The haplotypes of E. cyaneus and G. lacustris specimens were with intraspecific genetic distances of 3 and 2%, respectively, more homogeneous indicating no or only recent disruption of gene flow of E. cyaneus across Baikal and recent colonization of water bodies around Baikal by G. lacustris.

Conclusions

Our finding of separation of subgroups of Baikal endemic amphipods to different degrees points to a species-specific ability of dispersal across areas with adverse conditions and to potential geographical dispersal barriers in Lake Baikal.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1470-8) contains supplementary material, which is available to authorized users.

Morphology and life history divergence in cave and surface populations of Gammarus lacustris (L.)

Cave animals provide a unique opportunity to study contrasts in phenotype and life history in strikingly different environments when compared to surface populations, potentially related to natural selection. As such, we compared a permanent cave-living Gammarus lacustris (L.) population with two lake-resident surface populations analyzing morphology (eye- and antennal characters) and life-history (size at maturity, fecundity and egg-size). A part of the cytochrome c oxidase subunit I gene in the mitochondrion (COI) was analyzed to contrast genetic relationship of populations and was compared to sequences in GenBank to assess phylogeography and colonization scenarios. In the cave, a longer life cycle was implied, while surface populations seemed to have a shorter life cycle. Egg size, and size at maturity for both sexes, were larger in the cave than in surface populations, while fecundity was lower in the cave than in surface populations. The cave population had longer first- and second antennae with more articles, longer first- and second peduncles, and fewer ommatidia than surface populations. The cold low-productive cave environment may facilitate different phenotypic and life-history traits than in the warmer and more productive surface lake environments. The trait divergences among cave and surface populations resembles other cave-surface organism comparisons and may support a hypothesis of selection on sensory traits. The cave and Lake Ulvenvann populations grouped together with a sequence from Slovenia (comprising one genetic cluster), while Lake Lille Lauarvann grouped with a sequence from Ukraine (comprising another cluster), which are already recognized phylogenetic clusters. One evolutionary scenario is that the cave and surface populations were colonized postglacially around 9 000–10 000 years ago. We evaluate that an alternative scenario is that the cave was colonized during an interstadial during the last glaciation or earlier during the warm period before onset of the last glaciation.

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole.

Melanization in response to wounding is ancestral in arthropods and conserved in albino cave species

Many species adapted to aphotic subterranean habitats have lost all body pigmentation. Yet, melanization is an important component of wound healing in arthropods. We amputated appendages in a variety of cave-adapted and surface-dwelling arthropods. A dark clot formed at the site of injury in most species tested, including even albino cave-adapted species. The dark coloration of the clots was due to melanin deposition. The speed of wound melanization was uncorrelated with a difference in metabolic rate between surface and cave populations of an amphipod. The chelicerate Limulus polyphemus, all isopod crustaceans tested, and the cave shrimp Troglocaris anophthalmus did not melanize wounds. The loss of wound melanization in T. anophthalmus was an apomorphy associated with adaptation to subterranean habitats, but in isopods it appeared to be a symplesiomorphy unrelated to colonization of subterranean habitats. We conclude that wound melanization i) is an important part of innate immunity because it was present in all major arthropod lineages, ii) is retained in most albino cave species, and iii) has been lost several times during arthropod evolution, indicating melanization is not an indispensable component of wound healing in arthropods.

The transcriptomes of cave and surface populations of Gammarus minus (Crustacea: Amphipoda) provide evidence for positive selection on cave downregulated transcripts

Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is an excellent model for investigating evolutionary adaptation to the subterranean environment. RNA-Seq was conducted on one pair of morphologically distinct sister populations inhabiting surface and cave habitats to identify genes that were differentially expressed in the two populations, as well as to compare levels and patterns of genetic variation within and between populations. Of the 104,630 transcripts identified in the transcriptome assembly, 57% had higher average levels of expression in the cave population. After Benjamini-Hochberg correction for multiple tests, 1517 and 551 transcripts were significantly upregulated or downregulated, respectively, in the cave population, indicating an almost three-fold enrichment of cave-upregulated genes. The average level of nucleotide diversity across all transcripts was significantly lower in the cave population. Within the cave population, where the average nucleotide diversity of cave-downregulated transcripts was 75% that of the cave-upregulated transcripts, a highly significant difference, whereas within the spring population the nucleotide diversities of cave-downregulated and cave-upregulated transcripts was virtually identical. Three lines of evidence suggest that the reduced variation in cave downregulated transcripts is due to positive selection in the cave population: 1) the average neutrality index of cave-downregulated genes was < 1, consistent with positive selection, and significantly less than that of cave-upregulated genes; 2) Tajima’s D was positively correlated with the cave:surface expression ratio, and 3) cave-downregulated transcripts were significantly more likely to be highly diverged from their surface homologs than cave-upregulated transcripts. Five transcripts had fixed premature termination codons in the cave population. The expression patterns and sequence variation in one such transcript, encoding the DNA repair protein photolyase, were examined in more detail and provide the first evidence for the relaxation of functional constraint in this light-dependent protein in a subterranean population.

The Evolution of Epigean and Stygobitic Species of Koonunga Sayce, 1907 (Syncarida: Anaspidacea) in Southern Australia, with the Description of Three New Species

Three new species of Koonunga were discovered in surface and subterranean waters in southern Australia, and were defined using mtDNA analyses and morphology. The new species are: Koonunga hornei Leijs & King; K. tatiaraensis Leijs & King and K. allambiensis Leijs & King. Molecular clock analyses indicate that the divergence times of the species are older than the landscape that they currently inhabit. Different scenarios explaining this apparent discrepancy are discussed in the context of the palaeography of the area. A freshwater epigean origin for Koonunga is considered the most likely hypothesis, whereby some lineages made the transition to the subterranean environment within the last few million years influenced by significant climatic cooling/drying. We discuss the possibility that one stygobitic lineage secondarily regained some of its body pigmentation as adaptation to increased photic conditions after cave collapse and forming of cenotes during the last glacial maximum.

Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda)

Background

Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is a premier candidate for studying the evolution of troglomorphic traits such as pigmentation loss, elongated appendages, and reduced eyes. In G. minus, multiple pairs of genetically related, physically proximate cave and surface populations exist which exhibit a high degree of intraspecific morphological divergence. The morphology, ecology, and genetic structure of these sister populations are well characterized, yet the genetic basis of their morphological divergence remains unknown.

Results

We used degenerate PCR primers designed to amplify opsin genes within the subphylum Crustacea and discovered two distinct opsin paralogs (average inter-paralog protein divergence ≈ 20%) in the genome of three independently derived pairs of G. minus cave and surface populations. Both opsin paralogs were found to be related to other crustacean middle wavelength sensitive opsins. Low levels of nucleotide sequence variation (< 1% within populations) were detected in both opsin genes, regardless of habitat, and dN/dS ratios did not indicate a relaxation of functional constraint in the cave populations with reduced or absent eyes. Maximum likelihood analyses using codon-based models also did not detect a relaxation of functional constraint in the cave lineages. We quantified expression level of both opsin genes and found that the expression of both paralogs was significantly reduced in all three cave populations relative to their sister surface populations.

Conclusions

The concordantly lowered expression level of both opsin genes in cave populations of G. minus compared to sister surface populations, combined with evidence for persistent purifying selection in the cave populations, is consistent with an unspecified pleiotropic function of opsin proteins. Our results indicate that phototransduction proteins such as opsins may have retained their function in cave-adapted organisms because they may play a pleiotropic role in other important processes that are unrelated to vision.

Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

The genetic mechanisms underlying regressive evolution-the degeneration or loss of a derived trait--are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appears to have retained functional amino acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 Mya. Although several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.

Parallel reduction in expression of the eye development gene hedgehog in separately derived cave populations of the amphipod Gammarus minus

Caves provide excellent settings to examine evolutionary questions. Subterranean environments are characterized by similar and consistent conditions. Cave-adapted species often share characteristics such as diminished pigmentation, elongated limbs and reduced or absent eyes. Relatively little is known about the evolution and development of troglomorphic traits in invertebrates. In this study, we compare expression of the eye development genes hedgehog, pax6, sine oculis and dachshund in individuals from multiple independently derived cave populations of the amphipod Gammarus minus. hedgehog expression was significantly reduced in cave populations, compared to genetically related surface populations. Interestingly, no differences were found in pax6, sine oculis or dachshund expression. Because hedgehog-related genes are also involved in eye reduced in Astyanax mexicanus, these genes may be consistent targets of evolution during cave adaptation. These results provide support for the hypothesis of genomic 'hotspots' of evolution and allow comparison of adaptive mechanisms among diverse animals in subterranean environments.

Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae)

A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study.

Evidence of hidden biodiversity, ongoing speciation and diverse patterns of genetic structure in giant Antarctic amphipods

Recent molecular research on Antarctic benthic organisms has challenged traditional taxonomic classifications, suggesting that our current perceptions of Antarctic biodiversity and species distributions must be thoroughly revised. Furthermore, genetic differentiation at the intraspecific level remains poorly understood, particularly in eastern Antarctica. We addressed these issues using DNA sequence data for two sibling amphipod species that could be collected on a circum-Antarctic scale: Eusirus perdentatus and Eusirus giganteus. Haplotype networks and Bayesian phylogenies based on mitochondrial (COI, CytB) and nuclear (ITS2) DNA provided strong evidence of multiple cryptic species of Eusirus, with several occurring in sympatry and at least one likely to have a true circum-Antarctic distribution. Within species, gene flow was often highly restricted, consistent with a brooding life history and in some cases suggestive of current or future allopatric speciation. Patterns of genetic structure were not always predictable: one cryptic species showed preliminary evidence of high genetic differentiation across ∼150 km in eastern Antarctica (F(ST) > 0.47, P < 0.01), yet another was remarkably homogenous across ∼5000 km (F(ST) = 0.00, P = 1.00). Genetic diversity also varied among cryptic species, independent of sample size (π = 0.00-0.99). These results indicate several hidden levels of genetic complexity in these Antarctic amphipods that are neither apparent from previous taxonomic or ecological studies nor predictable from their life history. Such genetic diversity and structure may reflect different modes of survival for Antarctic benthic organisms during historic glacial cycles, and/or subsequent re-establishment of populations on the shelf, and highlight our misunderstanding of Antarctic marine species diversity.

Transmission mode affects the population genetic structure of Daphnia parasites

Parasite life cycle variation can shape parasite evolution, by predisposing them towards different population genetic structures. We compared the population genetic structure of two co-occurring parasite species of Daphnia, to collect evidence for their expected transmission modes. The ichthyosporean Caullerya mesnili has a direct life cycle, whereas the microsporidian Berwaldia schaefernai is hypothesized to require passage through a secondary host. The parasites were collected from three geographically isolated Daphnia populations. The nucleotide variation in the internal transcribed spacer (ITS) region was assessed at the within-individual, within-population and among-population levels, using amova. We detected significant partitioning at all levels, except for a lack of among-population variation in Berwaldia. This was confirmed by neighbour-joining and principal component analyses; Caullerya populations were distinct from each other, while there was much overlap among parasite isolates representing different populations of Berwaldia. This all implies a higher amount of gene flow for Berwaldia, consistent with the hypothesized transmission mode.

Ancient origin of a Western Mediterranean radiation of subterranean beetles

Background

Cave organisms have been used as models for evolution and biogeography, as their reduced above-ground dispersal produces phylogenetic patterns of area distribution that largely match the geological history of mountain ranges and cave habitats. Most current hypotheses assume that subterranean lineages arose recently from surface dwelling, dispersive close relatives, but for terrestrial organisms there is scant phylogenetic evidence to support this view. We study here with molecular methods the evolutionary history of a highly diverse assemblage of subterranean beetles in the tribe Leptodirini (Coleoptera, Leiodidae, Cholevinae) in the mountain systems of the Western Mediterranean.

Results

Ca. 3.5 KB of sequence information from five mitochondrial and two nuclear gene fragments was obtained for 57 species of Leptodirini and eight outgroups. Phylogenetic analysis was robust to changes in alignment and reconstruction method and revealed strongly supported clades, each of them restricted to a major mountain system in the Iberian peninsula. A molecular clock calibration of the tree using the separation of the Sardinian microplate (at 33 MY) established a rate of 2.0% divergence per MY for five mitochondrial genes (4% for cox1 alone) and dated the nodes separating the main subterranean lineages before the Early Oligocene. The colonisation of the Pyrenean chain, by a lineage not closely related to those found elsewhere in the Iberian peninsula, began soon after the subterranean habitat became available in the Early Oligocene, and progressed from the periphery to the centre.

Conclusions

Our results suggest that by the Early-Mid Oligocene the main lineages of Western Mediterranean Leptodirini had developed all modifications to the subterranean life and were already present in the main geographical areas in which they are found today. The origin of the currently recognised genera can be dated to the Late Oligocene-Miocene, and their diversification can thus be traced to Miocene ancestors fully adapted to subterranean life, with no evidence of extinct epigean, less modified lineages. The close correspondence of organismal evolution and geological record confirms them as an important study system for historical biogeography and molecular evolution.

Fine-scale comparative phylogeography of a sympatric sister species triplet of subterranean diving beetles from a single calcrete aquifer in Western Australia

Calcrete aquifers in the arid Yilgarn region of central Western Australia are a biodiversity hotspot for stygofauna. A distinct pattern of interspecific size class variation among subterranean dytiscid beetle species has been observed in 29 of these aquifers where either two or three small, medium and/or large sympatric species are found that are in some cases sister species. We used a 3.5 km(2) grid of bores to sample dytiscids on a fine-scale and employed a comparative phylogeographical and population genetic approach to investigate the origins of a sympatric sister species triplet of diving beetles from a single aquifer. Mitochondrial DNA sequence data from the Cytochrome oxidase c subunit I gene revealed that all three species have high levels of haplotype diversity with ancient (approximately 1 million years ago) intra-specific coalescence of haplotypes, but low levels of nucleotide diversity. Population analyses provide evidence for multiple expansion events within each species. There was spatial heterogeneity in the distribution of genetic variation and abundance both within and among the three taxa. Population analyses revealed significant fine-scale differentiation with isolation by distance for Paroster macrosturtensis and P. mesosturtensis, but not the smallest species P. microsturtensis. Haplotype network analyses provided limited or no evidence for past population fragmentation within the large and small species, but substantial historical divergence was observed in P. mesosturtensis that was not spatially structured. A patchy population structure with contemporaneous and historical isolation by distance in the three species is likely to have been a significant isolating and diversifying force, preventing us from ruling out a potential role for allopatric divergence during speciation of this beetle sister triplet.