Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D‐loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 334–349.     

Contemporary genetic structure reflects historical drainage isolation in an Australian snapping turtle,Elseya albagula

Effective spatial classification of freshwater biodiversity remains a worldwide conservation challenge. The isolating nature of catchment boundaries over evolutionary timescales makes them potentially important in defining natural units for biodiversity management. We sought to clarify biogeographical relationships amongst drainages within Australia's biodiverse mid‐eastern coastal region (Fitzroy, Burnett, and Mary Catchments) where freshwater communities face considerable urban pressure, using a locally endemic riverine specialist, the white‐throated snapping turtle, Elseya albagula. Mitochondrial and nuclear microsatellite data sets were employed to investigate past and present influences on population connectivity and to identify units for management. Populations within catchments were largely well connected genetically. However, the Fitzroy Catchment contained a distinct genetic lineage, deeply divergent from a second lineage present across the Burnett and Mary Catchments. The two lineages can be considered evolutionarily significant units that reflect historical isolation of the Fitzroy and recent coalescence of the Burnett‐Mary Catchments during lowered Pleistocene sea levels. Congruence with geological evidence and patterns reported for fish and macroinvertebrates supports a shared biogeographical history of a diverse regional biota. This work highlights the need for better spatial classification of freshwater biodiversity at local as well as regional scales, including recognition of potentially cryptic diversity amongst individual river drainages. © 2013 The Linnean Society of London     

Patterns of freshwater biodiversity in Europe: lessons from the spring snail genus Bythinella

Aim We analyse patterns of biodiversity in the spring snail genus Bythinella, a group of highly isolated and stenotopic freshwater species. We aim to test: (1) whether there are European areas of increased diversity (i.e. ‘hotspots’), (2) whether the potential hotspots inferred show qualitative differences in biodiversity characteristics such as endemicity, distinctiveness of taxa, age of lineages or degree of fragmentation, and (3) whether these hotspots match the Pleistocene refugia of Bythinella spp. Location Europe, Asia Minor. Methods The analyses are based on genetic data from 717 Bythinella specimens sampled at 194 sites. We used haplotypes as operational units in all analyses. To test hypothesis 1, mean pairwise genetic distances between Bythinella populations within each 1° × 1° geographical grid cell sampled in Europe were calculated. Within individual mountain ranges, grid cells with high diversity were grouped with neighbouring ones and hotspots were identified based on pre‐defined criteria. Then, to test hypothesis 2, different biodiversity indices of these regions were calculated and compared. Finally, to test hypothesis 3, the spatial distribution of the identified hotspots was compared with the known Pleistocene refugia of Bythinella spp. Results Five areas showed increased levels of genetic diversity: the Massif Central/Pyrenees, the western and eastern Alps, and the western and eastern Carpathians. These regions showed qualitative differences in biodiversity, with the eastern Carpathians holding the highest number of (endemic) haplotypes, the oldest and most distinct lineages and the highest degree of fragmentation. Only three of the five detected hotspots matched previously identified Pleistocene refugia for Bythinella spp. Main conclusions The genetic diversity of Bythinella spp. is not randomly distributed throughout Europe. Some of the hotspots we identify coincide with those found in other freshwater taxa; others have not previously been reported. Thus, spring organisms may reflect a unique evolutionary history that is distinct from lentic and lotic taxa. Our findings may be useful for conservation purposes even though the species‐level taxonomy of the genus is still under discussion.     

Australian parasitic Ogyris butterflies: east–west divergence of highly‐specialized relicts

Not all butterflies are innocuous plant‐feeders. A small number of taxa in the family Lycaenidae have graduated from mutualistic partnerships with ants to predatory or parasitic associations. These highly‐specialized life histories, involving butterfly larvae living inside ant colonies, are often associated with rarity and vulnerability to extinction. In the present study, we examined the evolutionary relationships of a poorly‐known group of seven taxa herein referred to as the idmo‐group within the Australian lycaenid genus Ogyris. The idmo‐group has a relictual distribution across southern Australia and includes taxa with highly‐specialized phytophagous and myrmecophagous life histories. A phylogeny based on mitochondrial DNA (cytochrome oxidase I and cytochrome b] and the nuclear DNA locus elongation factor 1α (EF1α), generally agrees with current taxonomy and supports the recent elevation of endangered taxon Ogyris halmaturia to full species status. The transition to myrmecophagy was dated to the mid‐Miocene (approximately 16 Mya), when southern Australia experienced a humid climate and extensive mesic biome. The arid Nullarbor Plain, a major biogeographical feature of central southern Australia, divides the remnants of this mesic biome into south‐eastern and south‐western isolates. Late‐Miocene to Pliocene divergence estimates for polytypic Ogyris species across the Nullarbor were older than estimates made for similarly distributed birds, butterflies, mammals, and reptiles, which mostly date to the Pleistocene. The concept of highly‐specialized life histories as evolutionary dead‐end strategies is well exemplified by the idmo‐group. Data compiled on the known extant subpopulations for idmo‐group taxa show that all of these extraordinary butterflies are scarce and several face imminent threat of extinction. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 473–484.     

Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius)

Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.     

Renewed sampling of inland aquatic habitats in southern Africa yields two novel freshwater crab species (Decapoda: Potamonautidae: Potamonautes)

A recent survey of the freshwater streams of the Mecula and Yao mountains in the Niassa province of Mozambique resulted in the discovery of a new freshwater crab species. This species is genetically and morphologically distinct from described species from Mozambique or its neighbouring countries, and is described as P otamonautes bellarussus sp. nov. In addition, a new semi‐terrestrial burrowing freshwater crab P otamonautes flavusjo sp. nov. from the Highveld of the Mpumalanga province in South Africa is described based on unique genetic and morphological characters. The phylogenetic affinities of the two new species in relation to the described eastern and southern African Potamonautes species is determined and the biogeographic implications are discussed. © 2014 The Linnean Society of London     

Process‐Based Species Action Plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups

Many endemic plant species belong to taxonomically complex groups. These endemics have often arisen as a consequence of recent and rapid evolutionary divergence facilitated by processes such as hybridization, polyploidy and/or breeding system transitions. The rapid and dynamic nature of divergence in taxonomically complex groups leads to problems in the implementation of traditional species‐based approaches for the conservation of the biodiversity that they contain. Firstly, the taxa of interest can be difficult to define and identify, leading to practical difficulties in implementing conservation measures. Secondly, a species‐based approach often fails to capture the complexity of diversity present in the taxonomically complex group. To accommodate these challenges, we have developed a Process‐Based Species Action Plan approach. This is designed to conserve the processes leading to the generation of biodiversity, rather than focusing on the preservation of individual named taxa. We illustrate the approach using a group of endemic tree species (Sorbus) on the Scottish island of Arran that have originated via a combination of multiple recent hybridization events and apomixis. The plan focuses on the optimization of habitat management to ensure the reproduction and regeneration of Sorbus in the zone in which these evolutionary processes operate, and to facilitate hybridization that will ensure the continued generation of diversity in this group. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 194–203.     

Disjunct,highly divergent genetic lineages within two rare Eremophila (Scrophulariaceae: Myoporeae) species in a biodiversity hotspot: implications for taxonomy and conservation

Effective conservation management should target appropriate conservation units, but evolutionarily and genetically divergent lineages within nominal taxa are often unrecognized. The south‐western Australian biodiversity hotspot may harbour many cryptic taxa, as it contains many plant species with naturally fragmented population distributions. Using microsatellite markers, we tested the hypothesis that disjunct population groups in the rare species Eremophila microtheca and E. rostrata (Scrophulariaceae: Myoporeae) are highly genetically divergent and represent separate evolutionarily significant units (ESUs). Chromosome counts indicated that all individuals assessed were diploid (2n = 36). Genetic differentiation among disjunct population groups was highly significant (P < 0.001) for both E. microtheca (F_ST = 0.301–0.383; D_est = 0.756–0.774) and E. rostrata (F_ST = 0.325–0.346; D_est = 0.628–0.660), and was similar to their differentiation from allied species. These results, including high incidences of private alleles, suggest historical divergence among cryptic taxa within E. microtheca and E. rostrata. Population groups in E. rostrata have recently been taxonomically recognized as two subspecies. Our study suggests that E. microtheca should also be reassessed as two taxa or considered as two ESUs, and the southern occurrence should be listed as Critically Endangered. We suggest a precautionary approach for flora in this and similar landscapes, whereby historically wide geographical disjunctions are assumed to indicate separate units for conservation. © 2014 State of Western Australia. Botanical Journal of the Linnean Society © 2014 The Linnean Society of London, 2015, 177 , 96–111.     

Molecular phylogeny of the Western Palaearctic Cordulegaster taxa (Odonata: Anisoptera: Cordulegastridae)

Although Odonata are a key component of many freshwater ecosystems, their taxonomy and evolutionary history is still far from being well resolved. In the present study, we report the first molecular phylogeny for the Western Palaearctic Cordulegaster genus (Odonata: Anisoptera: Cordulegastridae). We sequenced fragments of both mitochondrial and nuclear genes [cytochrome c oxidase I (COI) and Internal Transcribed Spacer‐1 (ITS‐1)] from eight species and 13 subspecies, from western, southern and central Europe, Turkey, and Morocco. Our data support the existence of two major groups corresponding to the traditional boltonii‐ and bidentata‐groups. Both groups are monophyletic based on COI sequences and the distinctiveness of Cordulegaster princeps, Cordulegaster trinacriae, Cordulegaster picta and Cordulegaster heros relative to Cordulegaster boltonii, and Cordulegaster helladica and Cordulegaster insignis relative to Cordulegaster bidentata, is confirmed. All species are also monophyletic for ITS‐1, with the exception of Cordulegaster helladica buchholzi, which shares the haplotype with C. insignis. Although moderate levels of genetic diversity were found within C. boltonii, there was no clear separation among the four subspecies, with the exception of the populations of Cordulegaster boltonii algirica from North Africa. Similarly, no genetic differentiation was found between the two subspecies of C. bidentata, Cordulegaster bidentata bidentata and Cordulegaster bidenta sicilica. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 49–57.     

Phylogeography and genetic structure of the threatened Canarian Juniperus cedrus (Cupressaceae)

We used plastid sequences (trnL, trnL‐trnF, petN‐psbM and trnT‐trnL) to infer the phylogenetic relationships and inter‐island connections of the Canarian Juniperus cedrus, and AFLP fingerprints to assess its genetic diversity patterns. Maximum Likelihood, Maximum Parsimony and Bayesian methods suggest independent colonization events for the three Macaronesian junipers and support the monophyly of J. cedrus. Plastid sequences reveal a low genetic diversity (three haplotypes) and do not provide sufficient information to resolve its temporal and geographical origin. AFLPs indicate a greater isolation in J. cedrus than in other Macaronesian trees with similar distributions and dispersal syndromes. Gran Canaria harbours the least genetically diverse population, which justifies immediate conservation actions. This island and Tenerife also show independent genetic structure, meaning that genetic exchange from other islands should be avoided in eventual reinforcements. Populations from La Palma and La Gomera show the highest genetic diversity levels and number of polymorphic AFLPs, probably because a lower incidence of felling has allowed a less dramatic influence of genetic bottlenecks. We suggest that management efforts should prioritize populations from these islands to preserve the evolutionary potential of the species, but we also stress the importance of knowledge of the evolutionary history, genetic structure and ecological interactions in conservation strategies. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 376–394.     

Bioclimatic evaluation of geographical range in Fragaria (Rosaceae): consequences of variation in breeding system,ploidy and species age

The evaluation of the intrinsic and extrinsic forces that determine geographical range sizes and niche breadth is key to the understanding of species distributions and for informing the conservation of biodiversity. Fragaria (Rosaceae) contains the economically important cultivated strawberry (Fragaria × ananassa subsp. ananassa) and numerous wild species. Using georeferenced species records and global bioclimatic data, we describe the bioclimatic niches for 21 Fragaria spp. and investigate the relationship between their niches and geographical range size, breeding system, ploidy and time since divergence. We found no evidence of phylogenetic signal for bioclimatic niches. There was also no relationship between ploidy and geographical or bioclimatic range area, but geographical range area was significantly greater for species that were capable of self‐fertilization. In addition, we found a significant decelerating relationship between species age and geographical range area. Overall, our results suggest that Fragaria spp., although similar in morphology and life history, show high levels of divergence in bioclimatic niches and significant over‐dispersion along some bioclimatic gradients, suggesting evolutionary lability in physiology and climate tolerance. As a consequence, wild species will remain a valuable resource for cultivated strawberry sustainability, especially under changing future climate. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 99–114.     

Phylogeography of the Petunia integrifolia complex in southern Brazil

In this study, we evaluated the genetic diversity of the Petunia integrifolia species group using a phylogeographical approach, and attempted to understand better its diversification and taxonomy. Plants from five morphological groups were collected, covering a large part of the geographical distribution of most of the species. Two major clades were found in the phylogenetic tree, and an additional lineage, corresponding to P. inflata, was found in the haplotype network obtained for plastid markers. All three lineages are clearly delimited geographically, but, with the exception of P. inflata, the morphological groups were not genetically distinct. Our results suggest that a population expansion after a size reduction resulted in the establishment of two distinct and allopatric groups c. 0.5 Mya, one group occurring in a geologically ancient area, and the other occurring in areas that were under the influence of a series of marine transgressions/regressions at the end of the Pleistocene. These two clades are evolutionarily significant units with significantly different allele frequencies in their nuclear genome and reciprocal monophyly in maternal, uniparentally inherited markers. All our results suggest that the morphology‐based taxonomy in this group does not reflect its evolutionary history, and revision of its species limits should incorporate the distribution of the genetic diversity. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 199–213.     

Molecular phylogenetics and morphological variation reveal recent speciation in freshwater mussels of the genera Arcidens and Arkansia (Bivalvia: Unionidae)

Intra‐ and interspecific morphological variation due to both phenotypic plasticity and evolutionary convergence hinder the work of taxonomists and lead to over‐ and underestimates of species richness. Nevertheless, most species on Earth are recognized solely based on morphological characters. We used molecular phylogenetic and morphometric techniques to examine two freshwater mussel species. One is common and widespread, while the other is imperiled and endemic to the Interior Highlands of the USA. Phylogenetic and molecular clock analyses revealed that divergence of Arcidens confragosus and Arkansia wheeleri is small and relatively recent. Divergence in these and other taxa is probably due to isolation of streams in the Interior Highlands. Morphometric analyses showed distinct shell shapes using traditional morphometrics, but not through geometric morphometrics. Outlined shell shapes are indistinguishable; geometric morphometrics could not capture a three‐dimensional component. Our analyses support the validity of these two species as congeners, with the nomen Arcidens (Simpson 1900) having priority. Because shell morphologies are both heritable and environmentally determined, our study emphasizes the importance of considering both molecular and morphometric analyses for identification of freshwater molluscs of conservation concern. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 535–545.     

Freshwater biodiversity: importance, threats, status and conservation challenges

Freshwater biodiversity is the over‐riding conservation priority during the International Decade for Action ‐‘Water for Life’ ‐ 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8 % of the Earth's surface, yet this tiny fraction of global water supports at least 100 000 species out of approximately 1.8 million ‐ almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the ‘Water for Life’ decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as ‘receivers’ of land‐use effluents, and the problems posed by endemism and thus non‐substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and ‐ in the case of migrating aquatic fauna ‐ downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade‐offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long‐term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management ‐ one that has been appropriately termed ‘reconciliation ecology’.     

Resilience to extreme temperature events: acclimation capacity and body condition of a polymorphic fish in response to thermal stress

Considerable attention has been given to the potential impacts of global climate change on biodiversity. In the present study, we combine understudied themes by examining the ability of a freshwater fish (polymorphic for heat‐sensitivity) to respond to short‐term thermal stress mimicking an extreme temperature event. We simultaneously measured the effect of thermal stress on the body condition of heat‐sensitive and heat‐tolerant forms to evaluate an existing hypothesis regarding the underlying mechanism by which temperature affects the maintenance of genetic variation in this species. Surprisingly, the heat‐sensitive allelic variant increased in body condition equally as much as a heat‐tolerant variant under acute heat stress. More importantly, the heat‐sensitive variant exhibited a significant response to thermal stress, with an upward shift of greater than 2 °C in critical thermal maximum. Our findings suggest a complexity to the relationship between thermal stress and male body condition that may depend on an interaction with other factors such as resource level. Although the evolutionary fate of species with respect to climate change is typically evaluated in terms long‐term adaptive response, short‐term selection events could drastically reduce fitness and reduce evolutionary potential. Our results suggest that heat‐sensitive species may have considerably greater resilience to the short‐term, extreme perturbations to the environment that are expected under climate change. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 504–510.     

Improved genetic markers for monitoring recruitment dynamics in the endangered Mary River cod (Maccullochella mariensis)

The Mary River cod (Maccullochella mariensis) is a large predatory freshwater fish identified as a potential flagship for freshwater ecosystem conservation in Australia. The species is endemic to the Mary River catchment in eastern Australia, and is listed as Endangered. Previous conservation genetic assessment of Mary River cod was based on a small set of microsatellite loci developed for congeneric Maccullochella species. Here we develop a novel set of 15 microsatellite loci specific to M. mariensis, and demonstrate that these markers exhibit higher variability than those used previously. Mean number of alleles per locus was 4 and mean expected heterozygosity was 0.57. We genotyped 35 Mary River cod larvae belonging to a single cohort using the 15 novel loci and eight previously used loci, and found 10 full‐sib family groups along with clear genetic differentiation between individuals collected from the two sub‐catchments – Tinana Creek and Mary River. Microsatellites presented here will be useful for cost‐effective monitoring of genetic diversity and recruitment dynamics in this endangered fish species.     

Emerging threats and persistent conservation challenges for freshwater biodiversity

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e‐commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem‐level changes through bottom‐up and top‐down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation‐oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.     

Cryptic diversity in coastal Australasia: a morphological and mitonuclear genetic analysis of habitat‐forming sibling species

Cryptic diversity represents a major challenge to the accurate assessment of biodiversity, but the combined use of genetic and morphological analyses has proven to be a powerful approach to detect it. This is especially important for groups for which genetic information is not yet available. Here, we studied the highly conspicuous habitat‐forming Pyura stolonifera species complex (Tunicata), which, as has recently been revealed, shows surprising levels of cryptic diversity, but whose systematics and biogeographical patterns in Australasia nonetheless remain poorly understood. We first present detailed taxonomic information of all the species associated with the P. stolonifera species complex. We then proceed to describe the results of an exhaustive survey that included south‐east Australia, Tasmania, and New Zealand. Subsequently, we present morphological and mitonuclear genetic analysis of two unresolved lineages that comprise the species Pyura praeputialis and a species that is formally described here ( Pyura doppelgangera sp. nov. ). Although the ranges of these two species overlap on mainland Australia, we found no sites at which both species live in sympatry, and there was no morphological or genetic evidence of hybridization. Taken together, the present study illustrates the usefulness of a combined morphogenetic approach in unravelling overlooked marine diversity in a relatively well‐studied region. © 2013 The Linnean Society of London     

Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested the hypothesis that the width of the continental shelf affected historical gene flow in P. butleri because a broad continental shelf provides a greater opportunity for rivers to coalesce during historical episodes of low sea levels as opposed to a narrow continental shelf that should restrict the potential for gene flow among adjacent rivers. Hence, we predicted greater amounts of historical gene flow among neighbouring river basins in the region of western Mexico where the continental shelf is wider, whereas, in the region where the continental shelf is narrower, we expected to detect limited levels of historical gene flow. We analyzed mitochondrial DNA sequence data (cytochrome b) taken from 264 individuals of P. butleri collected from 34 locations distributed across four different ecoregions in western Mexico. To examine patterns of phylogenetic diversification and historical gene flow in P. butleri, we employed several analytical approaches, including traditional tree‐based phylogenetic analyses (likelihood and parsimony), haplotype network reconstruction, analyses of molecular variance, and spatial analysis of molecular variance. We found genetic breaks coinciding with two out of three different ecoregion boundaries, suggesting limited historical gene flow. In addition to different species compositions between these adjacent ecoregions, geological features such as the Trans‐Mexican Volcanic Belt and the mountainous topography in south‐western Mexico, likely contributed to these observed genetic breaks. By contrast, no genetic break was evident between two other ecoregions, a result that partially rejects our first hypothesis. Several results were consistent with our second hypothesis. Changes in the width of the continental shelf in western Mexico are associated with the observed patterns of historical gene flow. Our results indicate that the interactions among multiple geological and biological factors affect the spatial patterns of genetic diversity of widespread freshwater species. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 399–416.