Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human‐driven faunal declines.     

Historical biogeography of the New Zealand freshwater crayfishes (Parastacidae,Paranephrops spp.): Restoration of a refugial survivor?

Abstract

New Zealand's two species of freshwater parastacid crayfishes have allopatric distributions, with one species in the North Island and northwestern South Island and the other in the eastern and southern South Island and Stewart Island. This gives the appearance of a vicariance event driven by uplift of the Southern Alps beginning in the Pliocene, and of former land connections across both Cook Strait and Foveaux Strait. However, separation of the two species may date from before the Southern Alps were formed. A diverse series of historical geological events is invoked to explain details of the distributions of these two species. Absence of Paranephrops from intermontane valleys of eastern flanks of the Southern Alps is notably different from patterns seen in freshwater fish species.     

A geographic mosaic of evolutionary lineages within the insular endemic newt Euproctus montanus

Islands are hotspots of biodiversity, with a disproportionately high fraction of endemic lineages, often of ancient origin. Nevertheless, intra‐island phylogeographies are surprisingly scarce, leading to a scanty knowledge about the microevolutionary processes induced on island populations by Plio‐Pleistocene climatic oscillations, and the manner in which these processes contributed to shape their current genetic diversity. We investigated the phylogeography, historical demography and species distribution models of the Corsican endemic newt Euproctus montanus (north‐western Mediterranean). As for many island endemics, the continuous distribution of E. montanus throughout its range has hitherto been considered as evidence for a single large population, a belief that also guided the species' categorization for conservation purposes. Instead, we found a geographic mosaic of ancient evolutionary lineages, with five main clades of likely Pliocene origin (2.6–5.8 My), all but one restricted to northern Corsica. Moreover, the copresence between main lineages in the same population was limited to a single case. As also suggested by growing literature on intra‐island phylogeographic variation, it seems that the extensive use of simplifying assumption on the population structure and historical demography of island populations—both in theoretical and applicative studies—should be carefully reconsidered, a claim that is well exemplified by the case presented here.     

Phylogenetic relationships,song and distribution of the endangered Rufous‐headed Robin Larvivora ruficeps

The Rufous‐headed Robin Larvivora ruficeps is one of the world's rarest and least known birds. We summarize the known records since it was first described in 1905 from Shaanxi Province, central China. All subsequent Chinese records are from seven adjacent localities in nearby Sichuan Province. We studied its phylogenetic position for the first time using mitochondrial and nuclear markers for all species of Larvivora and a broad selection of other species in the family Muscicapidae. Our results confirmed that L. ruficeps is appropriately placed in the genus Larvivora, and suggested that it is sister to the Rufous‐tailed Robin Larvivora sibilans, with these two forming a sister clade to a clade comprising both the Japanese Robin Larvivora akahige and Ryukyu Robin Larvivora komadori. Siberian Blue Robin Larvivora cyane and Indian Blue Robin Larvivora brunnea form the sister clade to the other Larvivora species. In contrast, song analyses indicated that the song of L. ruficeps is most similar to that of L. komadori, whereas the song of L. sibilans is relatively more similar to that of L. akahige, and songs of L. cyane and L. brunnea closely resemble each other. We used ecological niche modelling to estimate the suitable habitats of L. ruficeps based on the records from breeding grounds, suggesting that north and central Sichuan, south Gansu, south Shaanxi and south‐east Tibet are likely to contain the most suitable habitats for this species.     

Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.     

Limited contemporary gene flow and high self‐replenishment drives peripheral isolation in an endemic coral reef fish

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long‐term persistence of these species following local extinction. This study explored population connectivity in the ecologically‐specialized endemic three‐striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self‐replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self‐replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self‐replenishment (95%), and low contemporary abundance.     

Global distribution,diversity hot spots and niche transitions of an astaxanthin‐producing eukaryotic microbe

Microbes establish very diverse but still poorly understood associations with other microscopic or macroscopic organisms that do not follow the more conventional modes of competition or mutualism. Phaffia rhodozyma, an orange‐coloured yeast that produces the biotechnologically relevant carotenoid astaxanthin, exhibits a Holarctic association with birch trees in temperate forests that contrasts with the more recent finding of a South American population associated with Nothofagus (southern beech) and with stromata of its biotrophic fungal parasite Cyttaria spp. We investigated whether the association of Phaffia with Nothofagus–Cyttaria could be expanded to Australasia, the other region of the world where Nothofagus are endemic, studied the genetic structure of populations representing the known worldwide distribution of Phaffia and analysed the evolution of the association with tree hosts. The phylogenetic analysis revealed that Phaffia diversity in Australasia is much higher than in other regions of the globe and that two endemic and markedly divergent lineages seem to represent new species. The observed genetic diversity correlates with host tree genera rather than with geography, which suggests that adaptation to the different niches is driving population structure in this yeast. The high genetic diversity and endemism in Australasia indicate that the genus evolved in this region and that the association with Nothofagus is the ancestral tree association. Estimates of the divergence times of Phaffia lineages point to splits that are much more recent than the break‐up of Gondwana, supporting that long‐distance dispersal rather than vicariance is responsible for observed distribution of P. rhodozyma.     

Phylogeography of Asparagopsis taxiformis revisited: Combined mtDNA data provide novel insights into population structure in Japan

Six intraspecific lineages (Lineages 1–6) of Asparagopsis taxiformis have been previously established based on mitochondrial cox2‐cox3 intergenic spacer and a partial cox1 sequences. ‘Lineage 2’ (L2) was suggested to be a recent introduction to the Mediterranean Sea, but its source population has not yet been identified. In order to clarify the nature of northwestern Pacific populations, we performed extensive sampling in Japan (60 individuals from 16 locations) and molecular phylogenetic analyses based on mitochondrial sequences. Sixteen additional individuals, collected from eight locations in the Indo‐Pacific, Caribbean, and Mediterranean regions, were also analyzed. Combined sequence analyses revealed that the Japanese populations only consisted of L2. Out of 19 combined haplotypes identified within L2, two are shared between Japan and the Mediterranean Sea and the Hawaiian Islands, and 12 were identified as endemic to Japan. Genetic analyses of population differentiation suggested that Japanese populations are genetically isolated from the Mediterranean and the Hawaiian populations. A genetic disjunction appears to separate two subpopulations within Japan: one between Toi and Kagoshima and the other between Ojikajima Island and Kagoshima in the Kyushu area.     

Sillem's Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Carpodacus,Fringillidae)

Sillem's Mountain Finch Leucosticte sillemi was described in 1992 on the basis of an adult and an immature specimen collected in western Tibet in September 1929, but its taxonomic validity and phylogenetic position have been unclear. Based on phylogenetic analysis of mitochondrial DNA from the holotype, we show that L. sillemi is not a colour morph of Brandt's Mountain Finch Leucosticte brandti but represents a valid, previously overlooked species of rosefinch (Carpodacus) that has secondarily acquired a pale plumage convergent on that of Leucosticte. Sillem's Mountain Finch is one of the least known species of bird and represents the only known species of rosefinch in which males have no reddish plumage coloration. This species and its sister taxon, the Tibetan Rosefinch Carpodacus roborowskii, are likely to be the world's highest‐altitude sister‐species pair of birds.     

Strategic Management of an Invasive Ant‐scale Mutualism Enables Recovery of a Threatened Tropical Tree Species

Mutualisms between invasive ants and honeydew‐producing insects can have widespread negative effects on natural ecosystems. This is becoming an increasingly serious problem worldwide, causing certain ecosystems to change radically. Management of these abundant and influential mutualistic species is essential if the host ecosystem is to recover to its former non‐invaded status. This negative effect is particularly prevalent on some tropical islands, including Cousine Island, Seychelles. On this island, the invasive ant Pheidole megacephala has caused serious indirect damage to the threatened native Pisonia grandis trees via a mutualism with an invasive scale insect, Pulvinaria urbicola. We aimed to suppress the ant, thereby decoupling the mutualism and enabling recovery of the Pisonia trees. We treated all areas where ant pressure was high with a selective formicidal bait, which was deployed in custom‐made bait stations designed to avoid risk of treatment to endemic fauna. In the treated area, ant foraging activity was reduced by 93 percent and was followed by a 100 percent reduction in scale insect density. Abundance of endemic herbivorous insects and herbivorous activity increased significantly, however, after the decline in mutualistic species densities. Despite the native herbivore increase, there was considerable overall improvement in Pisonia shoot condition and an observed increase in foliage density. Our results demonstrate the benefit of strategic management of highly mutualistic alien species to the native Pisonia trees. It also supports the idea that area‐wide suppression is a feasible alternative to eradication for achieving positive conservation management at the level of the forest ecosystem.     

Phylogeny,Diversity, Distribution,and Host Specificity of Haemoproteus spp. (Apicomplexa: Haemosporida: Haemoproteidae) of Palaearctic Tortoises

A complex wide‐range study on the haemoproteid parasites of chelonians was carried out for the first time. Altogether, 811 samples from four tortoise species from an extensive area between western Morocco and eastern Afghanistan and between Romania and southern Syria were studied by a combination of microscopic and molecular‐genetic methods. Altogether 160 Haemoproteus‐positive samples were gathered in the area between central Anatolia and eastern Afghanistan. According to variability in the cytochrome b gene, two monophyletic evolutionary lineages were distinguished; by means of microscopic analysis it was revealed that they corresponded to two previously described species—Haemoproteus anatolicum and Haemoproteus caucasica. Their distribution areas overlap only in a narrow strip along the Zagros Mts. range in Iran. This fact suggests the involvement of two different vector species with separated distribution. Nevertheless, no vectors were confirmed. According to phylogenetic analyses, H. caucasica represented a sister group to H. anatolicum, and both of them were most closely related to H. pacayae and H. peltocephali, described from South American river turtles. Four unique haplotypes were revealed in the population of H. caucasica, compared with seven haplotypes in H. anatolicum. Furthermore, H. caucasica was detected in two tortoise species, Testudo graeca and Testudo horsfieldii, providing evidence that Haemoproteus is not strictly host‐specific to the tortoise host species.     

Application of multigene phylogenetics and site‐stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)

Previous molecular assessments of the red algal order Rhodymeniales have confirmed its monophyly and distinguished the six currently recognized families (viz. Champiaceae, Faucheaceae, Fryeellaceae, Hymenocladiaceae, Lomentariaceae, and Rhodymeniaceae); however, relationships among most of these families have remained unresolved possibly as a result of substitution saturation at deeper phylogenetic nodes. The objective of the current study was to improve rhodymenialean systematics by increasing taxonomic representation and using a more robust multigene dataset of mitochondrial (COB, COI/COI‐5P), nuclear (LSU, EF2) and plastid markers (psbA, rbcL). Additionally, we aimed to prevent phylogenetic inference problems associated with substitution saturation (particularly at the interfamilial nodes) by removing fast‐evolving sites and analyzing a series of progressively more conservative alignments. The Rhodymeniales was resolved as two major lineages: (i) the Fryeellaceae as sister to the Faucheaceae and Lomentariaceae; and (ii) the Rhodymeniaceae allied to the Champiaceae and Hymenocladiaceae. Support at the interfamilial nodes was highest when 20% of variable sites were removed. Inclusion of Binghamiopsis, Chamaebotrys, and Minium, which were absent in previous phylogenetic investigations, established their phylogenetic affinities while assessment of two genera consistently polyphyletic in phylogenetic analyses, Erythrymenia and Lomentaria, resulted in the proposition of the novel genera Perbella and Fushitsunagia. The taxonomic position of Drouetia was reinvestigated with re‐examination of holotype material of D. coalescens to clarify tetrasporangial development in this genus. In addition, we added three novel Australian species to Drouetia as a result of ongoing DNA barcoding assessments—D. aggregata sp. nov., D. scutellata sp. nov., and D. viridescens sp. nov.     

Narrow water barriers prevent multiple colonizations and limit gene flow among California Channel Island wild buckwheats (Eriogonum: Polygonaceae)

The relative roles of chance colonization and subsequent gene flow in the development of insular endemic biotas have been extensively studied in remote oceanic archipelagos, but are less well characterized on nearshore island systems. The current study investigated patterns of colonization and divergence between and within two wild buckwheat species (Polygonaceae), Eriogonum arborescens and E. giganteum, endemic to the California Channel Islands to determine whether geographical isolation is driving diversification. Using plastid and nuclear sequence data and microsatellite allele frequencies, we determined that gene flow in these Eriogonum spp. is restricted by isolation. The data suggest that successful colonization of and gene flow among the islands are infrequent. Colonization appears to have followed a stepping‐stone model that is consistent with a north‐to‐south pattern across the islands. This colonization pattern coupled with relatively little post‐colonization inter‐island gene flow, particularly among southern islands, has generated a pattern of more divergent lineages on the isolated southern islands. These results run counter to the general expectation that all islands close to a continental source should receive a high level of gene flow. Finally, management recommendations focused on protecting the lineages from loss of private alleles and the erosion of the remaining genetic diversity are offered.     

Biogeographic history of subterranean isopods from groundwater calcrete islands in Western Australia

Groundwater calcretes in arid central Western Australia contain a diverse invertebrate groundwater fauna (stygofauna). Surveys have uncovered a diverse oniscidean isopod subterranean fauna above the water table (troglofauna), including species of a recently described genus Paraplatyarthrus. The aim of this study was to investigate the biogeographic history of Paraplatyarthrus and the timing of transitions from surface to subterranean habitats. Phylogenetic relationships among the isopod troglofauna from 11 groundwater calcretes along three palaeodrainage systems were assessed using one mitochondrial gene, cytochrome c oxidase subunit 1 (COI), and two nuclear markers, lysyl‐tRNA synthetase (LysRS) and 18S rRNA (18S) genes. Phylogenetic analyses revealed multiple sister lineage relationships between troglophile and troglobite lineages and evidence for divergent mtDNA lineages within species, providing a range of nodes for dating evolutionary transitions from surface to subterranean habitats. Relaxed molecular clock analyses provided evidence that evolutionary transitions from surface to subterranean environments took place between 13.3 and 1.75 million years ago, coinciding with the onset of aridification of Australia from the late Tertiary. In cases where groundwater calcretes contained multiple species, the taxa were not closely related phylogenetically, suggesting that these calcretes were independently colonised by multiple ancestral species. The study further confirmed the role of late/post‐Miocene aridification as a key driver of the evolution of subterranean invertebrates in the calcrete islands of Western Australia, supporting the climatic relict hypothesis. Troglobites most likely evolved from the troglophile ancestors that were capable of dispersal among, and active colonisation of, calcretes.     

A phylogeographic investigation of the kelp genus Laminaria (Laminariales,Phaeophyceae), with emphasis on the South Atlantic Ocean

The genus Laminaria has a wide distribution range compared with other kelp genera because it is found in both the North and the South Atlantic, on both sides of the North Pacific, as well as in the Mediterranean. Hypotheses behind this biogeographical pattern have been discussed by several authors but have not yet been fully evaluated with time‐calibrated phylogenies. Based on the analysis of four molecular markers (ITS2, rbcL, atp8 and trnWI), our goal was to reassess the Laminaria species diversity in South Africa, assess its relationship with the other species distributed in the South Atlantic and reconstruct the historical biogeography of the genus. Our results confirm the occurrence of a single species, L. pallida, in southern Africa, and its sister relationship with the North Atlantic L. ochroleuca. Both species belonged to a clade containing the other South Atlantic species: L. abyssalis from Brazil, and the Mediterranean L. rodriguezii. Our time‐calibrated phylogenies suggest that Laminaria originated in the northern Pacific around 25 mya, followed by at least two migration events through the Bering Strait after its opening (~5.32 mya). Today, the first is represented by L. solidungula in the Arctic, while the second gave rise to the rest of the Atlantic species. The colonization of the North Atlantic was followed by a gradual colonization southward along the west coast of Europe, into the Mediterranean (~2.07 mya) and two recent, but disconnected, migrations (~1.34 and 0.87 mya) across the equator, giving rise to L. abyssalis in Brazil and L. pallida in southern Africa, respectively.     

Molecular Phylogeny and Evolutionary Relationships between the Ciliate Genera Peniculistoma and Mytilophilus (Peniculistomatidae,Pleuronematida)

Peniculistoma mytili and Mytilophilus pacificae are placed in the pleuronematid scuticociliate family Peniculistomatidae based on morphology and ecological preference for the mantle cavity of mytiloid bivalves. We tested this placement with sequences of the small subunit rRNA (SSUrRNA) and cytochrome c oxidase subunit 1 (cox1) genes. These species are very closely related sister taxa with no distinct genetic difference in the SSUrRNA sequence but about 21% genetic difference for cox1, supporting their placement together but separation as distinct taxa. Using infection frequencies, M. pacificae, like its sister species P. mytili, does not interact with Ancistrum spp., co‐inhabitants of the mantle cavity. On the basis of these ecological similarities, the fossil record of host mussels, and features of morphology and stomatogenesis of these two ciliates, we argue that M. pacificae derived from a Peniculistoma‐like ancestor after divergence of the two host mussels. Our phylogenetic analyses of pleuronematid ciliates includes the SSUrRNA gene sequence of Sulcigera comosa, a Histiobalantium‐like ciliate from Lake Baikal. We conclude: (i) that the pleuronematids are a monophyletic group; (ii) that the genus Pleuronema is paraphyletic; and (iii) that S. comosa is a Histiobalantium species. We transfer S. comosa to Histiobalantium and propose a new combination Histiobalantium comosa n. comb.     

Molecular phylogeny,systematics, and revision of the type species of Lobomonas,L. francei (Volvocales,Chlorophyta) and closely related taxa

In the present study, three new strains of the rare volvocalean green alga Lobomonas were isolated from field‐collected samples, one from Sardinia (Italy) and two from Argentina, and comparatively studied. The Sardinian and one of the Argentinian strains were identified as Lobomonas francei, the type species of the genus, whereas the second Argentinian strain corresponded to L. panduriformis. Two additional nominal species of Lobomonas from culture collections (L. rostrata and L. sphaerica) were included in the analysis and shown to be morphologically and molecularly identical to the L. francei strains. The presence, number, and shapes of cell wall lobes, the diagnostic criterion of Lobomonas, were shown to be highly variable depending on the chemical composition of the culture medium used. The analyses by SEM gave evidence that the cell wall lobes in Lobomonas originate at the junctions of adjacent cell wall plates by extrusion of gelatinous material. The four L. francei strains had identical nrRNA gene sequences and differed by only one or two substitutions in the ITS1 + ITS2 sequences. In the phylogenetic analyses, L. francei and L. panduriformis were sister taxa; however, another nominal Lobomonas species (L. monstruosa) did not belong to this genus. Lobomonas, together with taxa designated as Vitreochlamys, Tetraspora, and Paulschulzia, formed a monophyletic group that in the combined analyses was sister to the “Chlamydomonas/Volvox‐clade.” Based on these results, Lobomonas was revised, the diagnosis of the type species emended, a lectotype and an epitype designated, and several taxa synonymized with the type species.     

Some like it cold: the glossiphoniid parasites of the Sicilian endemic pond turtle Emys trinacris (Testudines,Emydidae), an example of ‘parasite inertia’?

The freshwater turtles of the genus Emys and some leech species of the family Glossiphoniidae are the only Palaearctic representatives of primarily Nearctic taxa, which jointly colonized Eurasia and the Maghreb during the Miocene. The strict trophic relationships occurring between the glossiphoniid parasite leech Placobdella costata and its host, the emydid Emys orbicularis, make them a prime example of host–parasite cophylogenetic evolution. In the light of the discovery of the Sicilian cryptic endemic species Emys trinacris, which is the sister species to the widespread Palaearctic E. orbicularis, the possible cophylogenetic divergence of the turtle hosts and their leech parasites was investigated. In spite of the deep divergence scored between the two pond turtle species and of their allopatric distribution, their leech parasites proved to be conspecific and indistinguishable based on the implemented molecular marker. This unexpected decoupling might likely be ascribed to the different dispersal abilities of the two taxa and/or to the recent, human‐mediated introduction of the leech parasites in Sicily. If this last scenario is confirmed, the long‐term effects of the introduced leech parasite on the endemic Sicilian pond turtle Emys trinacris should be carefully monitored. In the frame of this study, representatives of the widely spread predatory leech Helobdella stagnalis were observed on E. trinacris. Molecular analyses of their stomach content allowed to rule out the possibility of the existence of a trophic relationships between these two taxa, in contrast to what was previously suspected, and suggest that H. stagnalis specimens were rather attached to the turtles for non‐nutritional reasons.     

Paleobiogeography of an Iberian endemic species,Luciobarbus sclateri (Günther, 1868) (Actinopterygii,Cyprinidae), inferred from mitochondrial and nuclear markers

Since the Cenozoic Era, the southern Iberian Peninsula has undergone a series of complex geological and climatic changes that have shaped the hydrographic configuration of the freshwater network, influencing the present‐day distribution of primary freshwater species and favoring a high level of local endemicity. The cyprinid species Luciobarbus sclateri (Günther, 1968) is an endemic species confined to the southern Iberian Peninsula and characterized by a complex evolutionary history. Previous studies linked the structure of L. sclateri populations to the effects of climate change during glaciations and were not able to explain the genetic discordance found between nuclear and mitochondrial markers. The results of this study show that the structure of L. sclateri populations is a reflection of diversification processes linked to the geological history of the region. Thus, we found three main mitochondrial phylogroups: the first one corresponding to small basins in southern Iberian Peninsula, a second one in eastern Iberian Peninsula, corresponding to Segura population, and a third one including the rest of the basins where the species is distributed. The southern group began diverging in the Pliocene as result of tectonic dynamics characterized by the emersion of the basins around the Strait of Gibraltar. The other two groups began diverging with the formation of the current Iberian hydrographic system during Pleistocene. So, the isolation of the hydrographic basins was the main factor driving intraspecific differentiation, followed by recent secondary contacts, admixture, and re‐isolation of the populations.