Tempo and mode of species diversification in Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae)

Phylogeny and biogeography of the wingless orthopteran family Rhaphidophoridae

Cave crickets (Rhaphidophoridae) are insects of an ancient and wingless lineage within Orthoptera that are distributed worldwide except in Antarctica, and each subfamily has a high level of endemicity. Here, we show the comprehensive phylogeny of cave crickets using multi-gene datasets from mitochondrial and nuclear loci, including all extant subfamilies for the first time. We reveal phylogenetic relationships between subfamilies, including the sister relationship between Anoplophilinae and Gammarotettiginae, based on which we suggest new synapomorphies. Through biogeographic analyses based on divergence time estimations and ancestral range reconstruction, we propose novel hypotheses regarding the biogeographic history of cave crickets. We suggest that Gammarotettiginae in California originated from the Asian lineage when Asia and the Americas were connected by the Bering land bridge, and the opening of the western interior seaway affected the division of Ceuthophilinae from Tropidischiinae in North America. We estimate that Rhaphidophoridae originated at 138 Mya throughout Pangea. We further hypothesize that the loss of wings in Rhaphidophoridae could be the result of their adaptation to low temperatures in the Mesozoic era.

Geological events and climate change drive diversification and speciation of mute cicadas in eastern continental Asia

The poor mobility of nymphs living underground, usually for many years and the weak flying ability of adults make cicadas unique for evolutionary biology and bio-geographical study. Cicadas of the genus Karenia are unusual in Cicadidae in lacking the timbals that produce sound. Population differentiation, genetic structure, dispersal and evolutionary history of the eastern Asian mute cicada Karenia caelatata were investigated based on morphological, acoustic and molecular data. The results reveal a high level of genetic differentiation in this species. Six independent clades with nearly unique sets of haplotypes corresponding to geographically isolated populations are recognized. Genetic and geographic distances are significantly correlated among lineages. The phenotypic differentiation is generally consistent with the high levels of genetic divergence across populations. Results of ecological niche modeling suggest that the potential distribution range of this mountain-habitat specialist during the Last Glacial Maximum was broader than its current range, indicating this species had benefited from the climate change during the early Pleistocene in southern China. Geological events such as orogeny in Southwest China and Pleistocene climate oscillations have driven the differentiation and divergence of this species, and basins, plains and rivers function as natural "barriers" to block the gene flow. Besides significant genetic divergence being found among clades, the populations occurring in the Wuyi Mountains and the Hengduan Mountains are significantly different in the calling song structure from other populations. This may have resulted from significant population differentiation and subsequent adaptation of related populations. We conclude that ecological differences in habitats, coupled with geographical isolation, have driven population divergence and allopatric speciation. This study provides a plausible example of incipient speciation in Cicadidae and improves understanding of population differentiation, acoustic signal diversification and phylogeographic relationships of this unusual cicada species. It informs future studies on population differentiation, speciation and phylogeography of other mountain-habitat insects in the East Asian continent.

A subterranean adaptive radiation of amphipods in Europe

Adaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genus Niphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.

Global Diversification of Anelosimus Spiders Driven by Long-Distance Overwater Dispersal and Neogene Climate Oscillations

Vicariance and dispersal events, combined with intricate global climatic history, have left an imprint on the spatiotemporal distribution and diversity of many organisms. Anelosimus cobweb spiders (Theridiidae), are organisms ranging in behavior from solitary to highly social, with a cosmopolitan distribution in temperate to tropical areas. Their evolutionary history and the discontinuous distribution of species richness suggest that 1) long-distance overwater dispersal and 2) climate change during the Neogene (23-2.6 Ma), may be major factors in explaining their distribution and diversification. Here, we test these hypotheses, and explicitly test if global Miocene/Pliocene climatic cooling in the last 8 Ma affected Anelosimus radiation in parallel in South America and Madagascar. To do so, we investigate the phylogeny and spatiotemporal biogeography of Anelosimus through a culmination of a 20-year comprehensive global sampling at the species level (69 species, including 84% of the known 75 species worldwide, represented by 268 individuals) using nucleotide data from seven loci (5.5 kb). Our results strongly support the monophyly of Anelosimus with an Oligocene ($\sim $30 Ma) South American origin. Major clades on other continents originate via multiple, long-distance dispersal events, of solitary or subsocial-but not social-lineages, from the Americas. These intercontinental dispersals were to Africa, Madagascar (twice), and SE Asia/Australasia. The early diversification of Anelosimus spiders coincides with a sudden thermal increase in the late Oligocene ($\sim $27-25 Ma), though no causal connection can be made. Our results, however, strongly support the hypothesis that global Neogene climatic cooling in the last 8 Ma drove Anelosimus radiation in parallel in South America and Madagascar, offering a rare empirical evidence for diversification of a socially diverse group driven by an interplay between long-distance dispersal and global Neogene climatic changes. [Cobweb spiders; diversification; global biogeography; long-distance dispersal; molecular phylogenetics; neogene climate changes; sociality; vicariance.].

The genetic differentiation of a cricket (Velarifictorus micado) with two modes of life cycle in East Asia after the middle Pleistocene and the invasion origin of the United States of America

The cricket Velarifictorus micado is widely distributed in East Asia and colonized the United States of America (the USA) in 1959. It has two life cycles: egg and nymph diapause. We aimed to investigate the biogeographic boundary between them and determine when and why V. micado diverged. Mitochondrial fragments including COI and CytB were used for haplotype network, demographic analysis, and divergence time estimation in individuals of East Asia. We selected several samples from the USA to find out the colonization origin. The haplotype network indicated there were three lineages based on COI, NE lineage (the egg diapause and mainly distributed in the northern regions), SE lineage (the egg diapause and mainly distributed in the southern regions), and SN lineage (the nymph diapause and mainly distributed in the southern regions). The molecular chronograms indicated that the first divergence of V. micado into two main lineages, NE and southern lineages (SE and SN), was essentially bounded by the Yangtze River. It occurred around ~0.79 Ma (95% HPD: 1.13-0.46 Ma) in the Middle Pleistocene Transition. This was followed by the divergence of the southern lineage into two sublineages, SE and SN lineage, occurred around ~0.50 Ma (95% HPD: 0.71-0.25 Ma), corresponding to the time of development of glaciers in various parts of the Qinghai-Tibet Plateau (QTP) (0.73-0.46 Ma). SE lineage might originate from southwestern China based on the comparison between the haplotype network based on COI and CytB. Our study suggested that divergences of lineages have twice co-occurred with tendency of cooling climatic in Asia after the Mid-Pleistocene, and the life-history strategy may play an important role in lineage diversification. Additionally, our results indicated that the USA populations were revealed at least twice separate Asian invasions. These both belonged to the egg diapause, which might provide a new perspective for invasion control.

Biogeographical patterns and processes in the genus group Scotussae (Acrididae: Melanoplinae): an integrative approach

A biogeographical study of the genus group Scotussae, a clade of grasshoppers endemic to the subtropical temperate region of the La Plata Basin, South America, was performed within a phylogenetic context to test whether wing reduction reflects evolutionary and ecological processes within the clade. We used an integrative biogeographical approach to determine the role of geohistorical events, geography, ecology and phylogenetic niche conservatism on the distribution and diversification processes of the group. We performed a total evidence phylogenetic analysis and tested the phylogenetic signal of ecological niche traits (niche optimum and niche breadth). We also assessed the degree to which phylogenetic distance is correlated with geographical and ecological niche traits and we used BioGeoBEARS to estimate ancestral ranges. The results provided evidence for phylogenetic niche conservatism as well as a significant association between phylogeny and both geographical and, more strongly, ecological traits. Two main clades were clearly associated with wing development, and evidence points to the evolutionary and ecological processes within these two groups being different. The Brachypterous clade shows evidence that allopatric speciation was the main source of diversification, while for the Macropterous clade sympatric speciation seems more likely.

Subterranean life: Behavior, metabolic, and some other adaptations of Astyanax cavefish

The ability of fishes to adapt to any aquatic environment seems limitless. It is enthralling how new species keep appearing at the deep sea or in subterranean environments. There are close to 230 known species of cavefishes, still today the best-known cavefish is Astyanax mexicanus, a Characid that has become a model organism, and has been studied and scrutinized since 1936. There are two morphotypes for A. mexicanus, a surface fish and a cavefish. The surface fish lives in central and northeastern Mexico and south of the United States, while the cavefish is endemic to the "Sierra del Abra-Tanchipa region" in northeast Mexico. The extensive genetic and genomic analysis depicts a complex origin for Astyanax cavefish, with multiple cave invasions and persistent gene flow among cave populations. The surface founder population prevails in the same region where the caves are. In this review, we focus on both morphotype's main morphological and physiological differences, but mainly in recent discoveries about behavioral and metabolic adaptations for subterranean life. These traits may not be as obvious as the troglomorphic characteristics, but are key to understand how Astyanax cavefish thrives in this environment of perpetual darkness.

Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area

The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.

Phylogeography of the cicada Platypleura hilpa in subtropical and tropical East Asia based on mitochondrial and nuclear genes and microsatellite markers

Climate change and geographical events play key roles in driving population genetic structure of organisms, but different scenarios were suggested for species occurring in tropical and subtropical areas. We investigated the population genetic structure, diversity and demographic history of the cicada Platypleura hilpa which occurs in coastal areas of southern China and northeastern Indo-Burma, and analysed the potential impact of climate change and geological events on its evolutionary history. Our data imply that P. hilpa comprises five main lineages with nearly unique sets of haplotypes and distinct geographic distributions. A major split of the lineages occurred in the Pleistocene. Geographic distance and geomorphic barriers serve as the primary factors shaping the genetic population structure, and several climatic factors are associated with the divergence. The potential range during the Last Glacial Maximum has apparently increased in south China and the exposed South China Sea Shelf. The Pleistocene sea-level fluctuations had profound effects on the regional genetic structure. The Beibu Gulf represents a more important geographic barrier than the Qiongzhou Strait in blocking gene flow among populations. These results contribute to a better understanding of the pressure climatic change and geographical events impose on insects in coastal areas of East Asia.

Insights into the molecular phylogeny of Rhaphidophoridae, an ancient, worldwide lineage of Orthoptera

We investigated the molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the family Rhaphidophoridae (Orthoptera, Ensifera). We used taxa representative of most of the regions embraced by the family, considering samples of Macropathinae from Gondwana land (i.e., Tasmania, Australia, New Zealand, South Africa, and South America); Aemodogryllinae and Rhaphidophorinae from Southern-eastern Asia (i.e., India, Bhutan, China, Philippines and the Sulawesi islands); Dolichopodainae and Troglophilinae from the Mediterranean region and Ceuthophilinae from North America. Based on previous papers, we carried out an analysis of both mitochondrial and nuclear DNA sequences considering the ribosomal RNA units 12S, 16S, 18S, and 28S. To reconstruct phylogeny, we use cladistics, Maximum Likelihood (ML), and Bayesian analyses. All phylogenetic analyses showed the same highly supported topology generally congruent with the classical systematic arrangement at the level of each sub-family but strongly disagree with previous affinity hypotheses between sub-families based on morphological characters. Our results reveal a close affinity between Asiatic and Gondwanian taxa from one hand and between North American and Mediterranean ones from the other hand. Dating estimates indicated that Rhaphidophoridae originated in the Cretaceous period during the Mesozoic era with the ancestral area located both in the northern and southern hemisphere. A possible biogeographic scenario, reconstructed using S-DEC with RASP software, suggested that the current distribution of Rhaphidophoridae might be explained by a combination of both dispersal and vicariance events occurred especially in the ancestral populations. The radiation of Rhaphidophoridae started within the Pangaea, where the ancestor of Rhaphidophoridae occurred throughout an ancestral area including Australia, North America, and the Mediterranean region. The opening of the Atlantic Ocean promoted the divergence of North American and Mediterranean lineages while the differentiation of the southern lineages, spread from Australia, appears to be related to the fragmentation of Gondwana land.

A revised phylogeny of macropathine cave crickets (Orthoptera: Rhaphidophoridae) uncovers a paraphyletic Australian fauna

Australian cave crickets are members of the subfamily Macropathinae (Orthoptera: Rhaphidophoridae). The subfamily is thought to have originated prior to the tectonic separation of the supercontinent Gondwana based on distributions of extant lineages and molecular phylogenetic evidence, although the Australian fauna have been underrepresented in previous studies. The current study augments existing multigene data (using 12S, 16S, and 28S rRNA genes) to investigate the placement of the Australian representatives within the Macropathinae and to assess divergence dates of select clades. Results suggest that the endemic Tasmanian genus Parvotettix is the sister lineage to the remaining members of the subfamily, an outcome that presents a paraphyletic Australian fauna in contrast to previous studies. All other Australian taxa represented in this study (Micropathus and Novotettix) emerged as a sister group to the New Zealand and South American macropathine lineages. Estimation of phylogenetic divergence ages among the aforementioned clades were calibrated using two methods, in absence of suitable fossil records: (i) tectonic events depicting the fragmentation of Gondwanan landmasses that invoke vicariant scenarios of present day geographic distributions; and (ii) molecular evolutionary rates. Geological calibrations place the median age of the most recent common ancestor of extant macropathines at ∼125 to ∼165 Ma, whereas analyses derived from molecular substitution rates suggest a considerably younger origin of ∼32 Ma. This phylogenetic study represents the most rigorous taxonomic sampling of the Australian cave cricket fauna to date and stresses the influence of lineage representation on biogeographic inference.

Diversification in tropics and subtropics following the mid-Miocene climate change: A case study of the spider genus Nesticella

Caves may offer suitable refugia for troglophilic invertebrates during periods of unfavourable climatic conditions because of their stable microclimates. As a consequence, allopatric divergence from their epigean counterparts may occur, leading to formation of truly hypogean communities (the Climatic Relict Hypothesis). Unlike the well-studied effects of Pleistocene glaciations, we know little about how ancient climate changes drove the development of cave-dwelling organisms living at both middle and lower latitudes. We investigate the evolutionary history of the troglophilic spider genus Nesticella (Araneae, Nesticidae) in relation to Asian Neogene (23-2.6 Ma) climatic changes. Our analyses discern clear differences in the evolution of the two main clades of Nesticella, which occur in temperate/subtropical and tropical latitudes. Eastern Asian Nesticella gradually evolved greater sedentariness and a strict subterranean lifestyle starting from the middle Miocene Epoch (~15-14 Ma) in conjunction with the progressive deterioration of the climate and vegetational shifts. Caves appear to have acted as refugia because of their internally uniform temperature and humidity, which allowed these spiders to survive increasing external seasonality and habitat loss. In contrast, a uniform accumulation of lineages, long-lasting times for dispersals and the lack of a comparable habitat shifting characterized the tropical lineage. This difference in pattern likely owes to the mild effects of climate change at low latitudes and the consequent lack of strong climatic drivers in tropical environments. Thus, the mid-Miocene climatic shift appears to be the major evolutionary force shaping the ecological differences between Asian troglophilic invertebrates and the driver of the permanent hypogean communities in middle latitudes.

Unraveling the diversification history of grasshoppers belonging to the "Trimerotropis pallidipennis" (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes

The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.

Is radon emission in caves causing deletions in satellite DNA sequences of cave-dwelling crickets?

The most stable isotope of radon, ²²²Rn, represents the major source of natural radioactivity in confined environments such as mines, caves and houses. In this study, we explored the possible radon-related effects on the genome of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae) sampled in caves with different concentrations of radon. We analyzed specimens from ten populations belonging to two genetically closely related species, D. geniculata and D. laetitiae, and explored the possible association between the radioactivity dose and the level of genetic polymorphism in a specific family of satellite DNA (pDo500 satDNA). Radon concentration in the analyzed caves ranged from 221 to 26000 Bq/m³. Specimens coming from caves with the highest radon concentration showed also the highest variability estimates in both species, and the increased sequence heterogeneity at pDo500 satDNA level can be explained as an effect of the mutation pressure induced by radon in cave. We discovered a specific category of nuclear DNA, the highly repetitive satellite DNA, where the effects of the exposure at high levels of radon-related ionizing radiation are detectable, suggesting that the satDNA sequences might be a valuable tool to disclose harmful effects also in other organisms exposed to high levels of radon concentration.

Phylogeography and systematics of the westernmost Italian Dolichopoda species (Orthoptera, Rhaphidophoridae)

The genus Dolichopoda (Orthoptera; Rhaphidopohoridae) is present in Italy with 9 species distributed from northwestern Italy (Piedmont and Liguria) to the southernmost Apennines (Calabria), occurring also in the Tyrrhenian coastal areas and in Sardinia. Three morphologically very close taxa have been described in Piedmont and Liguria, i.e., D. ligustica ligustica, D. ligustica septentrionalis and D. azami azami. To investigate the delimitation of the northwestern species of Dolichopoda, we performed both morphological and molecular analyses. Morphological analysis was carried out by considering diagnostic characters generally used to distinguish different taxa, as the shape of epiphallus in males and the subgenital fig in females. Molecular analysis was performed by sequencing three mitochondrial genes, 12S rRNA, 16S rRNA, partially sequenced and the entire gene of COI. Results from both morphological and molecular analyses highlighted a very homogeneous group of populations, although genetically structured. Three haplogroups geographically distributed could be distinguished and based on these results we suggest a new taxonomic arrangement. All populations, due to the priority of description, should be assigned to D. azami azami Saulcy, 1893 and to preserve the names ligustica and septentrionalis, corresponding to different genetic haplogroups, we assign them to D. azami ligustica stat. n. Baccetti & Capra, 1959 and to D. azami septentrionalis stat. n. Baccetti & Capra, 1959.

Discrimination of two natural biocontrol agents in the Mediterranean region based on mitochondrial DNA sequencing data

Macrolophus pygmaeus and M. melanotoma (Hemiptera: Miridae) are biological control agents used in greenhouse crops, the former preferring plants of the Solanaceae family and the latter the aster Dittrichia viscosa. The discrimination of these species is of high significance for effective biological pest control, but identification based on morphological characters of the host plant is not always reliable. In this study, sequencing analysis of mitochondrial gene segments 12S rDNA and COI has been combined with crossing experiments and morphological observations to develop new markers for Macrolophus spp. discrimination and to provide new data on their genetic variability. This is the first comprehensive research in Greece on M. pygmaeus and M. melanotoma genetic variability based on sequencing data from 12S rDNA and COI gene segments. The relationship of this variability to host plant preference must be investigated in an agricultural ecosystem.

Molecular systematics of the genus Troglophilus (Rhaphidophoridae, Orthoptera) in Turkey: mitochondrial 16S rDNA evidences

This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus.Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.

Fluvial basin history in the northeastern Mediterranean region underlies dispersal and speciation patterns in the genus Dugesia (Platyhelminthes, Tricladida, Dugesiidae)

In this study we analyzed the phylogenetic relationships of eastern Mediterranean freshwater planarians of the genus Dugesia, estimated divergence times for the various clades, and correlated their phylogeographic patterns with geological and paleoclimatic events, in order to discover which evolutionary processes have shaped the present-day distribution of these animals. Specimens were collected from freshwater courses and lakes in continental and insular Greece. Genetic divergences and phylogenetic relationships were inferred by using the mitochondrial gene subunit I of cytochrome oxidase (COI) and the nuclear ribosomal internal transcribed spacer-1 (ITS-1) from 74 newly collected individuals from Greece. Divergence time estimates were obtained under a Bayesian framework, using the COI sequences. Two alternative geological dates for the isolation of Crete from the mainland were tested as calibration points. A clear phylogeographic pattern was present for Dugesia lineages in the Eastern Mediterranean. Morphological data, combined with information on genetic divergences, revealed that eight out of the nine known species were represented in the samples, while additional new, and still undescribed species were detected. Divergence time analyses suggested that Dugesia species became isolated in Crete after the first geological isolation of the island, and that their present distribution in the Eastern Mediterranean has been shaped mainly by vicariant events but also by dispersal. During the Messinian salinity crisis these freshwater planarians apparently were not able to cross the sea barrier between Crete and the mainland, while they probably did disperse between islands in the Aegean Sea. Their dependence on freshwater to survive suggests the presence of contiguous freshwater bodies in those regions. Our results also suggest a major extinction of freshwater planarians on the Peloponnese at the end of the Pliocene, while about 2Mya ago, when the current Mediterranean climate was established, these Peloponnese populations probably began to disperse again. At the end of the Pliocene or during the Pleistocene, mainland populations of Dugesia colonized the western coast, including the Ionian Islands, which were then part of the continent.

Phylogeography of Sardinian cave salamanders (genus Hydromantes) is mainly determined by geomorphology

Detecting the factors that determine the interruption of gene flow between populations is key to understanding how speciation occurs. In this context, caves are an excellent system for studying processes of colonization, differentiation and speciation, since they represent discrete geographical units often with known geological histories. Here, we asked whether discontinuous calcareous areas and cave systems represent major barriers to gene flow within and among the five species of Sardinian cave salamanders (genus Hydromantes) and whether intraspecific genetic structure parallels geographic distance within and among caves. We generated mitochondrial cytochrome b gene sequences from 184 individuals representing 48 populations, and used a Bayesian phylogeographic approach to infer possible areas of cladogenesis for these species and reconstruct historical and current dispersal routes among distinct populations. Our results show deep genetic divergence within and among all Sardinian cave salamander species, which can mostly be attributed to the effects of mountains and discontinuities in major calcareous areas and cave systems acting as barriers to gene flow. While these salamander species can also occur outside caves, our results indicate that there is a very poor dispersal of these species between separate cave systems.