A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.     

Cryptic speciation in the Merodon luteomaculatus complex (Diptera: Syrphidae) from the eastern Mediterranean

The Merodon aureus group is characterized by high endemism and the presence of morphologically cryptic species. Within one of its subgroups, M. bessarabicus, seven species and four more species complexes have been described to date. One of these complexes, the M. luteomaculatus, comprises new taxa that are the subject of the present study. Its members have allopatric ranges restricted to the Balkan Peninsula and Aegean islands. This complex exhibits morphological variability that could not be characterized using a traditional morphological approach. Thus, we used integrative taxonomy with independent character sets (molecular, geometric morphometric, distributional) to delimit species boundaries. Data on three molecular markers (COI, 28S rRNA, and ISSR) and geometric morphometry of the wing and male genitalia, together with distributional data, enabled recognition of six cryptic species within the complex: M. andriotes sp. n., M. euri sp. n., M. erymanthius sp. n., M. luteomaculatus sp. n., M. naxius sp. n., and M. peloponnesius sp. n. We discuss the possible influence of Aegean paleogeographical history on the speciation of this complex.     

Revision of the Cales noacki species complex (Hymenoptera,Chalcidoidea, Aphelinidae)

The genus Cales (Hymenoptera: Aphelinidae) includes 13 species worldwide, of which 10 form a highly morphologically uniform species complex with a native range in the Neotropical region. We recognize ten species previously attributed to a single Neotropical species, Cales noacki Howard, which in the strict sense is a species broadly disseminated to control woolly whitefly. A neotype is designated for C. noacki, and it is redescribed based on specimens molecularly determined to be conspecific with the neotype. Newly described species include: C. bicolor Mottern, n.sp ., C. breviclava Mottern, n.sp ., C. brevisensillum Mottern n.sp ., C. curvigladius Mottern, n.sp ., C. longiseta Mottern, n.sp ., C. multisensillum Mottern n.sp ., C. noyesi Mottern, n.sp ., C. parvigladius Mottern, n.sp . and C. rosei Mottern, n.sp . Species are delimited based on a combination of morphological and molecular data (28S‐D2 rDNA and COI). Additional specimens are included in the phylogenetic analyses and although these likely represent several new species, we lack sufficient specimen sampling to describe them at this time. Cales are highly morphologically conserved and character‐poor, resulting in several cryptic species. A molecular phylogeny of the known Neotropical species based on 28S‐D2–5 rDNA and a 390‐bp segment of COI is included, and identification keys to males and females are provided. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:7FEB0479‐9B2E‐48E8‐8603‐4B7C2759D4EC .     

Molecular phylogeny and DNA barcoding confirm cryptic species in the African freshwater oyster Etheria elliptica Lamarck, 1807 (Bivalvia: Etheriidae)

Recent molecular approaches to taxonomy have led to a steady increase in the identification of cryptic species. Within the Etheriidae, the species Etheria elliptica (freshwater oyster) is widespread and common and exists in most of the major African drainages. Within the African freshwater ecosystems, there are major threats to biodiversity and cryptic species complicate conservation strategies; unknown species exist and no conservation status has been assigned. Our objective here was to determine if E. elliptica from several locations in the Congo drainage are correctly classified as representing a single species. We analysed the genetic diversity at two mitochondrial loci (COI and 16S) and two nuclear loci (H3 and 28S), and estimated evolutionary relationships using phylogenetic and DNA barcoding techniques. Bayesian inference yielded three cryptic species of Etheria, and mismatch analysis revealed discrete differences between the cryptic species. We identified three cryptic species within these collections, and evidence indicates that the third species may resolve further with more sampling. In conclusion, the taxonomic history of E. elliptica makes finding cryptic species unsurprising. However, molecular studies such as this may finally help to resolve the number of species within this genus.     

Cryptic,adaptive radiation of endoparasitic snails: sibling species of <Emphasis Type="Italic">Leptoconchus</Emphasis> (Gastropoda: Coralliophilidae) in corals

Coral reefs are renowned as complex ecosystems with an extremely large biodiversity. Parasite-host relationships contribute substantially to this, but are poorly known. We describe the results of a study in which approximately 60,000 corals were searched for parasitic Leptoconchus snails (Gastropoda: Coralliophilidae) in Indo-West Pacific waters of Egypt, the Maldives, Thailand, Palau and Indonesia. We discovered an adaptive radiation of 14 snail species, each of which lives in species-specific association with one or more of 24 mushroom coral species. The 14 snail species are described as new to science under the names Leptoconchus inactiniformis sp. nov., L. inalbechi sp. nov., L. incrassa sp. nov., L. incycloseris sp. nov., L. infungites sp. nov., L. ingrandifungi sp. nov., L. ingranulosa sp. nov., L. inlimax sp. nov., L. inpileus sp. nov., L. inpleuractis sp. nov., L. inscruposa sp. nov., L. inscutaria sp. nov., L. intalpina sp. nov., and L. massini sp. nov. Their separation is based on indisputable molecular differences, whereas the rudimentary shell characters or impoverished anatomical details do not allow identification. The coral hosts also serve to distinguish the snail species, as none of the former was found to contain more than one of the latter. The complexity of coral reefs is still underrated, as is shown here by the application of DNA taxonomy as an indispensable approach to unravel cryptic radiations, which must be known in order to understand the functioning of the ecosystem.     

Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow‐endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus)

Species delimitation is fundamental for biological studies, yet precise delimitation is not an easy task, and every involved approach has an inherent failure rate. Integrative taxonomy, a method that merges multiple lines of evidence, can profoundly contribute to reliable alpha‐taxonomy and shed light on the processes behind speciation. In this study, we explored and validated species limits in a group of closely related Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps. Without a priori species hypotheses, we used multiple sources of inference, including mitochondrial and multilocus nuclear DNA, morphometrics and chemistry. The results of these discovery approaches revealed morphological crypsis and multiple new species within two of the five hitherto known species. Based on our analyses, we discussed the most plausible evolutionary scenarios, invoked the most reasonable species hypotheses and validated the new species limits. Building upon the achieved rigour, three new species, Megabunus cryptobergomas Muster and Wachter sp. nov., Megabunus coelodonta Muster and Steiner sp. nov., and Megabunus lentipes Muster and Komposch sp. nov., are formally described. In addition, we provide a dichotomous morphological key to the Megabunus species of the Alps. Our work demonstrates the suitability of integrative, discovery‐based approaches in combination with validation approaches to precisely characterize species and enabled us to implement nomenclatural consequences for this genus.     

Cryptic species complexes,widespread species and conservation: lessons from Amazonian frogs of the Leptodactylus marmoratus group (Anura: Leptodactylidae)

Morphologically cryptic species act as a wild card when it comes to biodiversity assessments and conservation, with the capacity to dramatically alter our understanding of the biological landscape at the taxonomic, ecological, biogeographic, evolutionary, and conservation levels. We discuss the potential effects that cryptic species may have on biodiversity assessments and conservation, as well as some of the current issues involving the treatment of cryptic species both at taxonomic and conservation levels. In addition, using a combination of advertisement call and morphological data, we describe a new species of the Leptodactylus marmoratus group from the upper Amazon basin, and we assess how cryptic species can affect conservation assessments of species in the Leptodactylus marmoratus group by examining how recent findings affect our understanding of the distribution of what is assumed to be a widespread Amazonian species, Leptodactylus andreae.     

An African bat in Europe,Plecotus gaisleri: Biogeographic and ecological insights from molecular taxonomy and Species Distribution Models

Because of the high risk of going unnoticed, cryptic species represent a major challenge to biodiversity assessments, and this is particularly true for taxa that include many such species, for example, bats. Long‐eared bats from the genus Plecotus comprise numerous cryptic species occurring in the Mediterranean Region and present complex phylogenetic relationships and often unclear distributions, particularly at the edge of their known ranges and on islands. Here, we combine Species Distribution Models (SDMs), field surveys and molecular analyses to shed light on the presence of a cryptic long‐eared bat species from North Africa, Plecotus gaisleri, on the islands of the Sicily Channel, providing strong evidence that this species also occurs in Europe, at least on the islands of the Western Mediterranean Sea that act as a crossroad between the Old Continent and Africa. Species Distribution Models built using African records of P. gaisleri and projected to the Sicily Channel Islands showed that all these islands are potentially suitable for the species. Molecular identification of Plecotus captured on Pantelleria, and recent data from Malta and Gozo, confirmed the species' presence on two of the islands in question. Besides confirming that P. gaisleri occurs on Pantelleria, haplotype network reconstructions highlighted moderate structuring between insular and continental populations of this species. Our results remark the role of Italy as a bat diversity hotspot in the Mediterranean and also highlight the need to include P. gaisleri in European faunal checklists and conservation directives, confirming the usefulness of combining different approaches to explore the presence of cryptic species outside their known ranges—a fundamental step to informing conservation.     

Integrative analyses unveil speciation linked to host plant shift in Spialia butterflies

Discovering cryptic species in well‐studied areas and taxonomic groups can have profound implications in understanding eco‐evolutionary processes and in nature conservation because such groups often involve research models and act as flagship taxa for nature management. In this study, we use an array of techniques to study the butterflies in the Spialia sertorius species group (Lepidoptera, Hesperiidae). The integration of genetic, chemical, cytogenetic, morphological, ecological and microbiological data indicates that the sertorius species complex includes at least five species that differentiated during the last three million years. As a result, we propose the restitution of the species status for two taxa often treated as subspecies, Spialia ali (Oberthür, 1881) stat. rest. and Spialia therapne (Rambur, 1832) stat. rest., and describe a new cryptic species Spialia rosae Hernández‐Roldán, Dapporto, Dinc?, Vicente & Vila sp. nov. Spialia sertorius (Hoffmannsegg, 1804) and S. rosae are sympatric and synmorphic, but show constant differences in mitochondrial DNA, chemical profiles and ecology, suggesting that S. rosae represents a case of ecological speciation involving larval host plant and altitudinal shift, and apparently associated with Wolbachia infection. This study exemplifies how a multidisciplinary approach can reveal elusive cases of hidden diversity.     

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.     

Detecting cryptic species in sympatry and allopatry: analysis of hidden diversity in Polyommatus (Agrodiaetus) butterflies (Lepidoptera: Lycaenidae)

Modern multilocus molecular techniques are a powerful tool in the detection and analysis of cryptic taxa. However, its shortcoming is that with allopatric populations it reveals phylogenetic lineages, not biological species. The increasing power of coalescent multilocus analysis leads to the situation in which nearly every geographically isolated or semi‐isolated population can be identified as a lineage and therefore raised to species rank. It leads to artificial taxonomic inflation and as a consequence creates an unnecessary burden on the conservation of biodiversity. To solve this problem, we suggest combining modern lineage delimitation techniques with the biological species concept. We discuss several explicit principles on how genetic markers can be used to detect cryptic entities that have properties of biological species (i.e. of actually or potentially reproductively isolated taxa). Using these principles we rearranged the taxonomy of the butterfly species close to Polyommatus (Agrodiaetus) ripartii. The subgenus Agrodiaetus is a model system in evolutionary research, but its taxonomy is poorly elaborated because, as a rule, most of its species are morphologically poorly differentiated. The taxon P. (A.) valiabadi has been supposed to be one of the few exceptions from this rule due to its accurately distinguishable wing pattern. We discovered that in fact traditionally recognized P. valiabadi is a triplet of cryptic species, strongly differentiated by their karyotypes and mitochondrial haplotypes.     

Loricaria cuffyi (Siluriformes: Loricariidae), a new species of loricariin catfish from the Guiana Shield

Loricaria cuffyi n. sp. is described based on 36 specimens from the Essequibo and upper Negro River drainages in western Guyana and the upper Orinoco River drainage in Venezuela. The new species can be distinguished from sympatric and geographically proximate congeners by a postorbital notch that is inconspicuous, shallow and rounded, odontode ridges on the dorsum of head and predorsal weakly developed, abdominal plates tightly joined and completely covering the median abdominal space and pectoral girdle, higher anterior lateral plate counts, and coloration characteristics. The distribution of the new species adds to an interesting and well-documented biogeographical pattern exhibited by other Guiana Shield loricariids influenced by the proto-Berbice during the Cenozoic and recent configuration of drainages in the Guiana Shield. We present an update on the taxonomy of Loricaria, and discuss the biogeography and conservation status of the new species.     

Geological habitat template overrides late Quaternary climate change as a determinant of range dynamics and phylogeography in some habitat‐specialist water beetles

Aim We investigated the roles of lithology and climate in constraining the ranges of four co‐distributed species of Iberian saline‐habitat specialist water beetles (Ochthebius glaber, Ochthebius notabilis, Enochrus falcarius and Nebrioporus baeticus) across the late Quaternary and in shaping their geographical genetic structure. The aim was to improve our understanding of the effects of past climate changes on the biota of arid Mediterranean environments and of the relative importance of history and landscape on phylogeographical patterns. Location Iberian Peninsula, Mediterranean. Methods We combined species distribution modelling (SDM) and comparative phylogeography. We used a multi‐model inference and model‐averaging approach both for assessment of range determinants (climate and lithology) and for provision of spatially explicit estimates of the species current and Last Glacial Maximum (LGM) potential ranges. Potential LGM distributions were then contrasted with the phylogeographical and population expansion patterns as assessed using mitochondrial DNA sequence data. We also evaluated the relative importance of geographical distance, habitat resistance and historical isolation for genetic structure in a causal modelling framework. Results Lithology poses a strong constraint on the distribution of Iberian saline‐habitat specialist water beetles, with a variable, but generally moderate, additional influence by climate. The degree to which potential LGM distributions were reduced and fragmented decreased with increasing importance of lithology. These SDM‐based suitability predictions were mostly congruent with phylogeographical and population genetic patterns across the study species, with stronger geographical structure in the genetic diversity of the more temperature‐sensitive species (O. glaber and E. falcarius). Furthermore, while historical isolation was the only factor explaining genetic structure in the more temperature‐sensitive species, lithology‐controlled landscape configuration also played an important role for those species with more lithology‐determined ranges (O. notabilis and N. baeticus). Main conclusions Our data show that lithology is an important constraint on the distribution and range dynamics of endemic Iberian saline‐habitat water beetles, in interaction with climate and long‐term climate change, and overrides the latter in importance for some species. Hence, geological landscape structure and long‐term history may codetermine the overall range and the distribution of genetic lineages in endemic species with specialized edaphic requirements.     

Using DNA taxonomy to investigate the ecological determinants of plankton diversity: explaining the occurrence of Synchaeta spp. (Rotifera,Monogononta) in mountain lakes

1. The occurrence of unresolved complexes of cryptic species may hinder the identification of the main ecological drivers of biodiversity when different cryptic taxa have different ecological requirements. 2. We assessed factors influencing the occurrence of Synchaeta species (monogonont rotifers) in 17 waterbodies of the Trentino‐South Tyrol region in the Eastern Alps. To do so, we compared the results of using unresolved complexes of cryptic species, as is common practice in limnological studies based on morphological taxonomy, and having resolved cryptic complexes, made possible by DNA taxonomy. 3. To identify cryptic species, we used the generalised mixed Yule coalescent (GMYC) model. We investigated the relationship between the environment and the occurrence of Synchaeta spp. by multivariate ordination using two definitions of the units of diversity, namely (i) unresolved species complexes (morphospecies) and (ii) putative cryptic species (GMYC entities). Our expectation was that resolving complexes of cryptic species could provide more information than using morphospecies. 4. As expected, DNA taxonomy provided greater taxonomic resolution than morphological taxonomy. Further, environmental‐based multivariate ordination on cryptic species explained a significantly higher proportion of variance than that based on morphospecies. Occurrence of GMYC entities was related to total phosphorus (TP), whereas no relationship could be found between morphospecies and the environment. Moreover, different cryptic species within the same morphospecies showed different, and even opposite, preferences for TP. In addition, the wide geographical distribution of haplotypes and cryptic species indicated the absence of barriers to dispersal in Synchaeta.     

Ancient introductions of mammals in the Mediterranean Basin and their implications for conservation

• 1 The importance of taxonomy to the determination of conservation priorities and actions is widely accepted. It should be not surprising therefore that the taxonomic treatment of mammal species that have been subject to human actions in antiquity may well influence the contemporary assessment of conservation priorities at various levels.
• 2 As a result of early extinctions caused by humans and protohistoric and historic introductions, we suggest that the Mediterranean Basin and its islands are particularly prone to misdirection of efforts towards biodiversity conservation.
• 3 The two main risks associated with the failure to use an evolutionary and palaeoecological approach to conservation efforts are (i) an underestimation of the conservation importance of distinctive continental taxa vs. the apparent endemicity of island taxa; and (ii) a serious risk for native and endemic island species when anthropochorous mammals, especially ungulates, misguidedly become the focus of conservation actions, particularly inside protected areas.
• 4 Urgent measures, including refinement of mammal taxonomy, the exclusion of known anthropochorous taxa from conservation lists and implementation of protective legislation, are necessary to maintain the uniqueness and richness of the Mediterranean biodiversity hotspot.

     

Uncovering hidden coral diversity: a new cryptic lobophylliid scleractinian from the Indian Ocean

Extant biodiversity can easily be underestimated owing to the presence of cryptic taxa, even among commonly observed species. Scleractinian corals are challenging to identify because of their ecophenotypic variation and morphological plasticity. In addition, molecular analyses have revealed the occurrence of cryptic speciation. Here, we describe a new cryptic lobophylliid genus and species Paraechinophyllia variabilis gen. nov., sp. nov., which is morphologically similar to Echinophyllia aspera and E. orpheensis. The new taxon occurs in Mayotte Island, Madagascar, the Gulf of Aden and the Red Sea. Six molecular markers (COI, 12S, ATP6-NAD4, NAD3-NAD5, histone H3 and ITS) and 46 morphological characters at three different levels (macromorphology, micromorphology and microstructure) were examined. The resulting molecular phylogenetic reconstruction showed that Paraechinophyllia gen. nov. represents a distinct group within the Lobophylliidae that diverged from the lineage leading to Echinophyllia and Oxypora in the Early Miocene, approximately 21.5 Ma. The morphological phylogenetic reconstruction clustered Paraechinophyllia gen. nov., Echinophyllia and Oxypora together in a single clade. A sole morphological character, calice relief, discriminated Paraechinophyllia gen. nov. from the latter two genera, suggesting that limited morphological variation has occurred over a long period. These results highlight the importance of cryptic taxa in reef corals, with implications for population genetics, ecological studies and conservation.     

Biogeographical patterns of algal communities in the Mediterranean Sea: Cystoseira crinita‐dominated assemblages as a case study

Aim The aim of this study was to describe the composition, community structure and biogeographical variation of subtidal algal assemblages dominated by the brown alga Cystoseira crinita across the Mediterranean Sea. Location The Mediterranean coast, from Spain (1°25′ E) to Turkey (30°26′ E). Methods Data on the species composition and structure of assemblages dominated by the species C. crinita were collected from 101 sites in nine regions across the Mediterranean Sea. Multivariate and univariate statistical tools were used to investigate patterns of variation in the composition of the assemblages among sites and regions, and to compare these with previously defined biogeographical regions. Linear regressions of species richness versus longitude and versus latitude were also carried out to test previously formulated hypotheses of biodiversity gradients in the Mediterranean Sea. Results The main features characterizing C. crinita‐dominated assemblages across the Mediterranean included a similar total cover of species, a similar cover of C. crinita, and consistency in the presence of the epiphyte Haliptilon virgatum. Biogeographical variation was detected as shifts in relative abundances of species among regions, partly coinciding with previously described biogeographical sectors. A significant positive correlation was found between species richness and latitude, while no significant correlation was detected between species richness and longitude. Main conclusions The patterns of variation in community structure detected among the studied regions reflected their geographical positions quite well. However, latitude seemed to contribute more to the explanation of biological patterns of diversity than did geographical distances or boundaries, which classically have been used to delimit biogeographical sectors. Moreover, the positive correlation between species richness and latitude reinforced the idea that latitude, and possibly temperature as a related environmental factor, plays a primary role in structuring biogeographical patterns in the Mediterranean Sea. The lack of correlation between species richness and longitude contradicts the notion that there is a decrease in species richness from west to east in the Mediterranean, following the direction of species colonization from the Atlantic.