Genetic differentiation of aquatic snails (Gastropoda: Hydrobiidae) from artesian springs in arid Australia

Electrophoretic surveys of 10 species of hydrobiid snails in two indigenous genera (Fonscochlea and Trochidrobia) living in arid-zone artesian ‘mound’ springs are reported. The study is based on 96 populations of hydrobiid snails living in 32 different springs representing 18 spring groups in the Lake Eyre Supergroup, northern South Australia. The species-level taxonomy of these snails, previously based on morphological differences alone, was tested and modified. The snails were examined within five clear-cut morphological groups: the two largest, fully aquatic species (Fonscochlea accepta and F. aquatica) were treated independently, as was the amphibious F. Zfidleri The morphologically similar three smaller aquatic species were investigated as a group. Within this group one new species is described and, on the basis of the genetic evidence, two others (F. variabilis and F. conica) are considered conspecific. The four species of Trochidrobia are investigated together and T. punicea separately in more detail. Sympatry between Trochidrobia smithi and T. punicea is recorded for the first time. The springs are arranged in an essentially linear pattern and genetic differentiation largely follows an isolation by distance model, although there is a significant genetic discontinuity between two nearby spring groups, Beresford/Warburton Springs and Strangways Spring, which is presumably the result of differential historical continuity of spring habitat. The size of the spring influences the degree of genetic difference between springs within spring groups, with small springs attaining greater levels of differentiation than large springs. The findings suggest diat if genetic diversity is to be conserved, current management strategies protecting only single springs within a group are inadequate. Despite the considerable number of indigenous species found in these springs, currendy all remain on pastoral leases and some are threatened by the continuing expansion of water extraction from the Great Artesian Basin.     

Persistence in the desert: ephemeral waterways and small‐scale gene flow in the desert spring amphipod,Wangiannachiltonia guzikae

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Independent colonization and extensive cryptic speciation of freshwater amphipods in the isolated groundwater springs of Australia's Great Artesian Basin

The groundwater-dependent springs of the Great Artesian Basin (GAB) in arid inland Australia represent a unique and threatened ecosystem. These incredibly isolated springs support a diverse array of endemic flora and fauna. One of the common faunal groups in the GAB springs is the freshwater amphipods of the family Chiltoniidae. The morphological conservatism and taxonomic uncertainty associated with these amphipods has ensured their true biodiversity, phylogeographical history and evolutionary affinities have remained unknown. We have used mitochondrial DNA and allozyme data to unravel a complicated history of isolation, extinction and dispersal among spring amphipod populations across the GAB. The results provide evidence for multiple independent colonizations in the GAB springs, particularly within the Lake Eyre group of springs. The inclusion of a group of Western Australian (WA) stygobitic amphipods from populations up to 1500 km away found surprising evidence for a shared evolutionary history between stygobitic and GAB spring amphipods. Approximate dating of the diversity found between major clades suggests the majority of lineages originated in the late Miocene, around the time of the aridification of inland Australia. The large number of independent lineages and the close connection between GAB spring and WA stygobitic amphipods suggest that a significantly rich amphipod fauna existed in the much wetter environment that once existed in inland Australia. The results also provide evidence for a gross underestimation of the species diversity within the springs, with 12 putative species identified, a conclusion with significant implications for the ongoing conservation of the GAB springs.     

Desert spring refugia: museums of diversity or evolutionary cradles?

Refugia play a critical role in preserving species unable to move or adapt to cope with environmental change. The role of refugia as ‘museums of diversity’ means these environments have a high conservation priority. Less well known, however, is the role that isolated and fragmented refugia can play in the generation of new diversity. Here, we examined the diversification and evolutionary history of a community of endemic invertebrates that inhabit Australian desert spring refugia. We compared the phylogenies of seven endemic groups (Haloniscus and Phreatomerus isopods, chiltoniid amphipods, Ngarawa ostracods, Trochidrobia and Fonscochlea snails and Gymnochthebius beetles) from these springs and examine the rates and timing of diversification and reconstructed the phylogeographic history of each taxon. Despite major life‐history differences among these taxa, they demonstrate remarkable similarities in their evolutionary histories. All groups have multiple lineages that extend back to a time before the formation of present‐day deserts, and significant geographic‐based diversification since adapting to a refugial habitat. The results provide further evidence that refugia act as museums of biodiversity, preserving lineages that would have otherwise gone extinct. However, we also observed that isolation in refugia corresponds with significant diversification, leading to a recently evolved, novel endemic fauna, supporting the idea that fragmented refugia provide ideal conditions for the generation of future biodiversity hotspots.     

Large Intercontinental Differentiation of Moina Micrura (Crustacea: Anomopoda): One Less Cosmopolitan Cladoceran?

Moina micrura Kurz, 1874 (Crustacea: Anomopoda), commonly regarded as a cosmopolitan cladoceran species, can be found almost all over the world except for arctic and cold-temperate regions. M. micrura has been recorded from virtually all types of limnetic habitats, including temperate permanent ponds, lakes, ephemeral desert pools, and tropical brackish fishponds. Its high morphological and ecological variability has so far been considered a result of intraspecific diversity. We tested the hypothesis that genetically isolated groups exist within M. micrura with crossing experiment and DNA sequence analysis. We compared two clones originating from populations from Central Europe (area of the type locality) and Australia. As there was extremely low production of hybrid eggs, the results of the crossing experiment strongly suggest the existence of reproductive isolation. The sequence divergence of mitochondrial gene for 12S rRNA (7.9%) was comparable to intraspecific differences within Daphnia pulex group. The sequence divergence of the clones of Moina macrocopa from Europe and Central Africa was much lower (1.4%). Our results suggest that at least two sibling species exist within M. micrura complex, which is in agreement with other data questioning the cosmopolitanism of various cladoceran species.     

Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus)

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North‐West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Biogeographical patterns of endemic diversity and its conservation in Australia's artesian desert springs

Aim

Springs in the Australian arid zone are distinct from other waterways because they house a large number of endemic species. We aimed to assess spatial patterns in endemic diversity at a basin‐wide scale and whether environmental features can help to explain them. In doing so, we take the opportunity to summarize the current state of conservation in the system.

Location

Great Artesian Basin (GAB), arid and semiarid regions of eastern Australia

Methods

We combine data regarding the location of springs with published GIS layers regarding environmental characteristics and a literature review of all species and subspecies documented in the published literature to be endemic to GAB springs.

Results

We found evidence of 96 species and subspecies of fishes, molluscs, crustaceans and plants endemic to these springs. The majority of endemic species are invertebrates with geographical distributions limited to a single spring complex (<61 km²). Endemic taxa are concentrated in 75 of the 326 spring complexes. Spring complexes with a large number of springs, high connectivity via drainage basins and low rainfall were more likely to contain endemic taxa, but environmental models were poor predictors of diversity. Only 24% spring complexes with high conservation value are within conservation reserves, and the majority of endemic species are unassessed under the IUCN and Australian conservation legislation, particularly the invertebrates.

Main conclusions

Diversity in this system is underestimated given the current rate of species discovery and prevailing data deficiency for many taxa. Historical processes and species‐specific environmental requirements may be more important for explaining why diversity is concentrated in particular complexes. Almost a decade after this system was listed as endangered, most complexes of high conservation value remain outside of conservation reserves, and the endangered species status of many taxa, and particularly the invertebrates, remain unassessed.

     

Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66–1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.     

Divergence and hybridization in the desert plant Reaumuria soongarica

Speciation is widely accepted to be a complex and continuous process. Due to complicated evolutionary histories, desert plants are ideal model systems to understand the process of speciation along a continuum. Here, we elucidate the evolutionary history of Reaumuria soongarica (Pall.) Maxim., a typical desert plant that is wildly distributed across arid central Asia. Based on variation patterns present at nine nuclear loci in 325 individuals (representing 41 populations), we examined the demographic history, patterns of gene flow, and degree of ecological differentiation among wild R. soongarica. Our findings indicate that genetic divergence between the ancient western and eastern lineages of R. soongarica occurred approximately 0.714 Mya, probably due to the Kunlun–Yellow River tectonic movement and the Naynayxungla glaciation. Later, multiple hybridization events between the western and eastern lineages that took place between 0.287 and 0.543 Mya, and which might have been triggered by the asynchronous historical expansion of the western and eastern deserts, contributed to the formation of a hybrid northern lineage. Moreover, despite continuing gene flow into this population from its progenitors, the northern lineage maintained its genetic boundary by ecological differentiation. The northern lineage could be an incipient species, and provides an opportunity to study the continuous process of speciation. This study suggests that two opposite evolutionary forces, divergence and hybridization, coexisting in the continuous speciation of the desert plant R. soongarica in a short time. Moreover, we provide evidence that this continuous speciation process is affected by geological events, climatic change, and ecological differentiation.     

Diversification across the Palaearctic desert belt throughout the Pleistocene: phylogeographic history of the Houbara–Macqueen's bustard complex (Otididae: Chlamydotis) as revealed by mitochondrial DNA

Studies on the influence of Pleistocene climatic fluctuations and associated habitat changes on arid‐adapted bird species living in the Holarctic region are comparatively rare. In contrast to temperate species, the populations of arid‐adapted avian species might be characterized by low genetic differentiation because periods of population isolation were associated with the short interglacial periods, while population expansion events might have occurred during the longer glacial periods when steppe‐like vegetation might have been prevalent. In this study, we tested this hypothesis in a widespread arid‐adapted taxon of the Palaearctic desert belt, the Houbara–Macqueen's bustard complex. The later includes the Houbara bustard Chlamydotis undulata, comprising the North African subspecies Chlamydotis u. undulata and Chlamydotis u. fuertaventurae from the Canary Islands, and the Asian Macqueen's bustard Chlamydotis macqueenii. A long fragment (1042 bp) of the Cyt‐b gene was investigated in 39 representatives of the two species to assess phylogenetic and phylogeographic patterns, and demographic history and to compute divergence time estimates using a Bayesian relaxed molecular clock approach based on different coalescent priors. While the two species are genetically distinct, we found little intraspecific genetic differentiation. The divergence time of the two species falls within a period of extreme aridity at around 0.9 million years ago, which most likely resulted in an east–west vicariance along the Arabo‐Saharan deserts. Differentiation within Houbara and Macqueen's bustard occurred later during the Middle to Upper Pleistocene, and as we have predicted, periods of range expansion were associated to the last glacial period at least in the Macqueen's bustard.     

Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichtys minckleyi

Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The ‘desert cichlid’ Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco‐morphotypes coexist in small spring‐fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco‐morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco‐morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.     

Defining spatial and temporal patterns of phylogeographic structure in Madagascar's iguanid lizards (genus Oplurus)

Understanding the remarkably high species diversity and levels of endemism found among Madagascar’s flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Quaternary climate fluctuations spurred diversification. While spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA sequence data to test whether divergence times among Malagasy iguanid lizards of the subfamily Oplurinae are compatible with a hypotheses of Pliocene–Pleistocene diversification. We estimate the oplurine species tree and associated divergence times under a relaxed‐clock model. In addition, we examine the phylogeographic structure and population divergence times within two sister species of Oplurus primarily distributed in the north‐west and south‐west of Madagascar (Oplurus cuvieri and Oplurus cyclurus, respectively). We find that divergence events among oplurine lineages occurred in the Oligocene and Miocene and are thus far older and incompatible with the hypothesis that recent climate fluctuations are related to current species diversity. However, the timing of intraspecific divergences and spatial patterns of population genetic structure within O. cuvieri and O. cyclurus suggest a role for both intrinsic barriers and recent climate fluctuations at population‐level divergences. Integrating information across spatial and temporal scales allows us to identify and better understand the mechanisms generating patterns diversity.     

On glacial refugia,genetic diversity,and microevolutionary processes: deep phylogeographical structure in the endemic newt Lissotriton italicus1

We investigated the phylogeographical patterns of Lissotriton italcus, a newt endemic to the Italian peninsula, aiming to determine why hotspots of intraspecific diversity so ‘hot’. We found two main mitochindrial DNA lineages (net sequence divergence of 6.8% at two fragments of total length of 1897 bp): one restricted to part of the Calabrian peninsula (i.e the southernmost portion of the species range) and the other widespread throughout the rest of the species range. Both lineages, which had a parapatric distribution, showed evidence of further subdivisions, with an overall number of eight terminal haplogroups, most of whose times to the most recent common ancestors were estimated at the Late Pleistocene. Analysis of molecular variance suggested that partitioning populations according to the geographical distribution of these haplogroups can explain 97% of the observed genetic variation. These results suggest that L. italicus underwent repeated cycles of allopatric fragmentation throughout the Pleistocene, and that it likely survived the Late Pleistocene paleoenvironmental changes within eight separate refugia. Thus, the current hotspot of intraspecific diversity of L. italicus (within the Calabrian peninsula) has not been moulded by long‐term stability of large populations but rather by multiple events of allopatric fragmentation and divergence. When compared with the patterns recently identified in other species, these results suggest that the occurrence of phases of allopatric divergence (eventually followed by secondary admixture) could be a common, albeit probably underrated feature in the history of formation of hotspots of intraspecific diversity. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 42–55.     

SPECIATION BY POLYPLOIDY IN TREEFROGS: MULTIPLE ORIGINS OF THE TETRAPLOID,HYLA VERSICOLOR

Speciation by polyploidy is rare in animals, yet, in vertebrates, there is a disproportionate concentration of polyploid species in anuran amphibians. Sequences from the cytochrome b gene of the mitochondrial DNA (mtDNA) were used to determine phylogenetic relationships among 37 populations of the diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and Hyla versicolor. The diploid species, H. chrysoscelis, consists of an eastern and a western lineage that have 2.3% sequence divergence between them. The tetraploid species, H. versicolor, had at least three separate, independent origins. Two of the tetraploid lineages are more closely related to one or the other of the diploid lineages (0.18%–1.4% sequence divergence) than they are to each other (1.9%–3.4% sequence divergence). The maternal ancestor of the third tetraploid lineage is unknown. The phylogenetic relationships between the two species and among lineages within each species support the hypothesis of multiple origins of the tetraploid lineages.     

DNA barcoding of Neotropical bats: species identification and discovery within Guyana

Sequence diversity in the cytochrome c oxidase subunit 1 gene has been shown to be an effective tool for species identification and discovery in various groups of animals, but has not been extensively tested in mammals. We address this gap by examining the performance of DNA barcodes in the discrimination of 87 species of bats from Guyana. Eighty‐one of these species showed both low intraspecific variation (mean = 0.60%), and clear sequence divergence from their congeners (mean = 7.80%), while the other six showed deeply divergent intraspecific lineages suggesting that they represent species complexes. Although further work is needed to examine patterns of sequence diversity at a broader geographical scale, the present study validates the effectiveness of barcoding for the identification of regional bat assemblages, even highly diverse tropical faunas.     

Phylogeographic histories of representative herpetofauna of the southwestern U.S.: mitochondrial DNA variation in the desert iguana (Dipsosaurus dorsalis) and the chuckwalla (Sauromalus obesus)

To determine whether genetic variation in representative reptiles of the southwestern U.S. may have been similarly molded by the geologic history of the lower Colorado River, we examined restriction site polymorphisms in the mitochondrial DNA (mtDNA) of desert iguanas (Dipsosaurus dorsalis) and chuckwallas (Sauromalus obesus). Observed phylogeographic structure in these lizards was compared to that reported for the desert tortoise (Xerobates agassizi), whose mtDNA phylogeny demonstrates a striking genetic break at the Colorado River. Both the desert iguana and chuckwalla exhibit extensive mtDNA polymorphism, with respective genotypic diversities G = 0.963 and 0.983, close to the maximum possible value of 1.0. Individual mtDNA clones, as well as clonal assemblages defined by specific levels of genetic divergence, showed pronounced geographic localization. Nonetheless, for each species the distributions of certain clones and most major clonal groupings encompass both sides of the Colorado River valley, and hence are clearly incongruent with the phylogeographic pattern of the desert tortoise. Overall, available molecular evidence provides no indication that the intraspecific phylogenies of the southwestern U.S. herpetofauna have been concordantly shaped by a singular vicariant factor of overriding significance.     

Fine scale patterns of migration and gene flow in the endangered mound spring snail, <Emphasis Type="Italic">Fonscochlea accepta</Emphasis> (Mollusca:Hydrobiidae) in arid Australia

Naturally patchy ecosystems are models for other systems currently undergoing anthropogenic habitat fragmentation. Understanding patterns of gene flow in these model systems can help us manage species and ecosystems threatened by human impacts. The mound springs of central Australia represent such a natural model ecosystem, supporting a unique aquatic fauna distributed within an inhospitable arid landscape. Moreover, these springs are being impacted by over extraction of groundwater, providing a unique opportunity to look at dispersal in a patchy habitat that is changing. The present study represents the first fine scale analysis of gene flow under different scenarios of habitat connectivity for the endangered mound spring snail, Fonscochlea accepta. Within a single spring group pairwise estimates of F _ST between springs were very low (ave 0.015) with no association found between genetic distance and a series of geographical distance matrices based on the degree of habitat connectivity among the springs: results implying unstructured dispersal and limited population isolation. However, results from Bayesian assignment tests showed that on average approximately 97% of snails were assigned to their spring of origin. In a preliminary analysis at broader geographic scales (among spring groups) the results from F _ST estimates, Mantel correlation analyses and assignment tests all suggest much stronger and geographically correlated population structuring. While varying results from F-statistics and Bayesian analyses stem from the different information they utilise, together they provide data on contemporary and historical estimates of gene flow and the influence of landscape dynamics on the spatial genetic patterning of the springs.     

Evolutionary divergence in freshwater insects with contrasting dispersal capacity across a sea of desert

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Genetic divergence of mitochondrial DNA in white char <Emphasis Type="Italic">Salvelinus albus</Emphasis> and northern Dolly Varden char <Emphasis Type="Italic">Salvelinus malma malma</Emphasis>

Comparative analysis of mitochondrial DNA variation was performed in white char Salvelinus albus Glubokovsky and in its putative ancestor species, northern Dolly Varden char Salvelinus malma malma Walbaum. Highly statistically significant differentiation of S. albus and S. m. malma in the areas of sympatric (Kamchatka River basin) and allopatric (Kronotskoe Lake and Kronotskaya River) residence was demonstrated. The mtDNA divergence between S. albus and S. m. malma did not exceed the range of intraspecific variation in the populations of northern Dolly Varden char. At the same time, clusterization pattern of the Salvelinus chars provides hypothesis on the common origin of two allopatric populations of white char. Genealogical analysis of haplotypes indicates that S. albus and S. m. malma currently demonstrate incomplete divergence of mitochondrial lineages. The low nucleotide divergence estimates between S. albus and S. m. malma reflect the short time period since the beginning of the divergence of ancestral lineages. These estimates are determined by ancestral polymorphism and haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.     

Molecular phylogeny of the Canary Island lacertids (Gallotia): mitochondrial DNA restriction fragment divergence in relation to sequence divergence and geological time

Restriction fragment length polymorphisms of 6 base pair recognising endonucleases are used to reconstruct the phylogeny of the endemic Canary Island lacertid, Gallotia. The division into conventional species is upheld by this molecular analysis and the western Canary Island lizard (G. galloti) and eastern Canary Island lizard (G. atlantica) are hypothesized to be sister species. A more comprehensive study of the intraspecific relationships of G. galloti, based on nineteen restriction enzymes, indicates that there are distinct southern and northern lineages within this species. The phylogenetic analysis does not uphold the conventional subspecies, but suggests an alternative arrangement with one northern (La Palma, Tenerife) and one southern (Gomera, Hierro) subspecies. The inferred timing of molecular divergence of populations of G. galloti, based on RFLP analysis, is compatible with the geological timing for island origin and fossil data. Mantel tests show that mitochondrial RFLP divergence is correlated with mitrochondrial 12s rRNA and cytochrome oxidase I sequence divergence and highly correlated with mitochondrial cytochrome b sequence divergence.