High Levels Of Cryptic Diversity Research Articles

Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa

Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.

From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam

BackgroundPrompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam.MethodsIn this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time.ResultsCombined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group.ConclusionThis study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.Graphical abstract

A new pale-ventered nurse frog (Aromobatidae: Allobates) from southwestern Brazilian Amazonia

Abstract We use integrative taxonomy to formally describe a candidate species of nurse frog of the genus Allobates from southwestern Brazilian Amazonia. The new species nests within a clade that has been defined historically as A. gasconi, but it has an 8.8–11.0% genetic distance for 16S to samples from the type locality of A. gasconi. The new species differs from congeners mainly by males having a translucent white throat and vocal sac; advertisement calls with a duration of 42–60 ms, two notes separated by an inter-note interval of 8–23 ms, and a dominant frequency of 4,953–6,331 Hz; and exotrophic tadpoles with 2 pyramidal papillae on each end of the upper lip and 10–13 pyramidal and cylindrical papillae surrounding the lower lip. Phylogenetic analyses based on mitochondrial DNA suggest that A. gasconi sensu lato as defined previously represents a complex of as many as seven species, corroborating studies that have shown high levels of cryptic diversity within Allobates.

Unveiling the evolutionary relationships and the high cryptic diversity in Andean rainfrogs (Craugastoridae: Pristimantis myersi group).

Pristimantis is the most diverse genus of terrestrial frogs. Historically, it has been divided into several phenetic groups in order to facilitate species identification. However, in light of phylogenetic analysis, many of these groups have been shown to be non-monophyletic, denoting a high degree of morphological convergence and limited number of diagnostic traits. In this study, we focus on the Pristimantis myersi group, an assemblage of small rainfrogs distributed throughout the Andes of Ecuador and Colombia, whose external morphology is highly conserved, and its species diversity and evolutionary relationships largely unknown. We inferred a new phylogenetic hypothesis for the frog genus Pristimantis, including all available sequences of the mtDNA 16S rRNA, as well as new DNA sequences from 175 specimens. Our sampling included 19 of the 24 species currently recognized as part of the Pristimantis myersi group. Our new evolutionary hypothesis recovered the P. myersi group as non-monophyletic and composed of 16 species. Therefore, we exclude P. albujai, P. bicantus, P. sambalan, and P. nelsongalloi in order to preserve the monophyly of the group. We discovered at least eight candidate species, most of them hidden under the names of P. leoni, P. hectus, P. festae, P. gladiator, and P. ocreatus. Our results reveal the occurrence of a high level of cryptic diversity to the species level within the P. myersi group and highlight the need to redefine some of its species and reassess their conservation status. We suggest that the conservation status of six species within the group need to be re-evaluated because they exhibit smaller distributions than previously thought; these species are: P. festae, P. gladiator, P. hectus, P. leoni, P. ocreatus, and P. pyrrhomerus. Finally, given that the Pristimantis myersi group, as defined in this work, is monophyletic and morphologically diagnosable, and that Trachyphrynus is an available name for the clade containing P. myersi, we implement Trachyphrynus as a formal subgenus name for the Pristimantis myersi group.

Cryptic diversity in Zoraptera: Latinozoros barberi (Gurney, 1938) is a complex of at least three species (Zoraptera: Spiralizoridae).

The order Zoraptera contains relatively few species, but current molecular phylogenetic studies suggest an unexpectedly high level of cryptic diversity in the order with many overlooked species based on morphology alone. Latinozoros Kukalova-Peck & Peck, 1993 represents the only genus of monotypic Latinozorinae (Zoraptera: Spiralizoridae) with only one species described, L. barberi (Gurney, 1938), until now. Although this species has been repeatedly reported from a number of locations in South and Central America, it is likely a complex of unrecognized species. Here, we present a molecular phylogenetic reconstruction revealing three genetically distinct lineages in Latinozoros, and we also present detailed morphological comparisons that prove the species status of Latinozoros cacaoensis sp. nov. from French Guiana and L. gimmeli sp. nov. from the Dominican Republic, Trinidad and Panama. The results indicate that the species previously referred to L. barberi is actually a species complex that includes L. barberi, the new species described here, and perhaps other species.

Cryptic Genetic Diversity in the Coastal Isopod Alloniscus oahuensis from the Pacific Ocean.

The isopod sub-order Oniscidea includes over 3,700 species and is known to occur in all terrestrial environments, except those at extreme elevations and polar latitudes. Current estimates of the biodiversity of the Oniscidea may be underestimates, as recent molecular studies have uncovered high levels of cryptic diversity in several taxa in the sub-order. High levels of cryptic diversity have been found in coastal species, species from remote and isolated regions, and species with complex taxonomic histories. Alloniscus oahuensis is a good candidate to harbor cryptic diversity, as it is a coastal isopod species with a geographic range that spans several remote and isolated archipelagos in the Pacific Ocean and has a complex taxonomic history. In this study, we used sequences for three mitochondrial genes and one nuclear gene to determine whether A. oahuensis harbors highly divergent lineages that may represent cryptic species. By characterizing 60+ A. oahuensis individuals from 17 localities from various Pacific Ocean archipelagos, we uncovered two deeply divergent lineages with disjunct distributions. The levels of genetic divergence observed amongst the two lineages match or exceed those reported across other cryptic species in the Oniscidea, suggesting that A. oahuensis may represent a cryptic species complex in need of a taxonomic revision. The extremely low lineage diversities within A. oahuensis indicate that the lineages may have spread across the Pacific Ocean recently, potentially due to anthropogenic activity.

Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana).

Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.

Cryptic diversity in the macroalgal genus Lobophora (Dictyotales) reveals environmental drivers of algal assemblages

Stress-induced reductions in the world’s coral populations are, in many locations, giving way to an increase in macroalgae, for example the common brown macroalgal genus Lobophora. While many ecological studies report a single species (Lobophora variegata), DNA-based identification methods have recently shown that Lobophora is a highly diverse genus with over 100 reported species. Here, we aim to identify possible ecological differences among Lobophora species by investigating environmental drivers of Lobophora assemblages. We sampled Lobophora thalli from 12 reefs around Palau (Micronesia) at varying depths, wave exposure, and herbivore biomass. Using one mitochondrial marker (cox3) and two chloroplast markers (psbA, rbcL), we uncovered a striking cryptic diversity of 15 species, including 8 undescribed taxa. Associations between potential drivers and Lobophora assemblages varied at two spatial scales. At the larger scale of both island coastlines only a single variable—wave exposure—was found to be important. On a smaller geographic scale, confined to the east coast, all factors—wave exposure, depth and herbivory—were associated with assemblages of Lobophora. Widespread sampling indicates the presence of generalist species, which were found in most sampled habitats, and specialists, which occupy specific habitats. Such high levels of cryptic diversity have important implications for ecological studies. Given that species inhabit different environments, have a variable growth form, and have a threefold difference in thallus thickness, it seems likely that species differ in their function. If these differences manifest in competitive strengths, these results have broad implications for our understanding of coral reef recovery following perturbation.

Inferring Evolutionary Timescales without Independent Timing Information: An Assessment of "Universal" Insect Rates to Calibrate a Collembola (Hexapoda) Molecular Clock.

Previous estimates of nucleotide substitution rates are routinely applied as secondary or “universal” molecular clock calibrations for estimating evolutionary timescales in groups that lack independent timing information. A major limitation of this approach is that rates can vary considerably among taxonomic groups, but the assumption of rate constancy is rarely evaluated prior to using secondary rate calibrations. Here I evaluate whether an insect mitochondrial DNA clock is appropriate for estimating timescales in Collembola—a group of insect-like arthropods characterized by high levels of cryptic diversity. Relative rates of substitution in cytochrome oxidase subunit 1 (COI) were inferred via Bayesian analysis across a topologically constrained Hexapod phylogeny using a relaxed molecular clock model. Rates for Collembola did not differ significantly from the average rate or from the rates estimated for most other groups (25 of 30), suggesting that (1) their apparent cryptic diversity cannot be explained by accelerated rates of molecular evolution and (2) clocks calibrated using “universal” insect rates may be appropriate for estimating evolutionary timescales in this group. However, of the 31 groups investigated, 10 had rates that deviated significantly from the average (6 higher, 4 lower), underscoring the need for caution and careful consideration when applying secondary insect rate calibrations. Lastly, this study exemplifies a relatively simple approach for evaluating rate constancy within a taxonomic group to determine whether the use of secondary rates are appropriate for molecular clock calibrations.

The advertisement call of Scinax funereus (Cope, 1874) (Anura: Hylidae) from Ecuadorian Amazon.

Scinax Wagler currently harbors 72 treefrog species distributed throughout the Neotropical region, occurring from Mexico to Argentina and Uruguay, and also in some Caribbean islands (Frost et al. 2020). The genus has a high level of cryptic diversity, with its actual number of species currently considered to be underestimated (Fouquet et al. 2007, Ferrão et al. 2016). Scinax funereus (Cope) is a medium-sized species described from Moyobamba, San Martín Department, northern Peru, with occurrences reported from the Peruvian and Ecuadorian Amazon (Duellman Wiens 1993), southern Colombia (Lynch 2005), and from the Brazilian states of Acre (Bernarde et al. 2011) and Amazonas (Ramalho et al. 2016). Duellman (1978) reported that the advertisement call of S. funereus "consists of a moderately long, rather high-pitched, single note", but as no call recording was obtained at the time, it was not described. Although Read (2000) published the species' call in the audio form in a compact disc (CD), it was not formally described. Given this, herein we provide the first formal description of the advertisement call of S. funereus.

Cryptic species within the rotifer Lecane bulla (Rotifera: Monogononta: Lecanidae) from North America based on molecular species delimitation

The littoral rotifer Lecane bulla is one of the most eurytopic members of the Lecane genus and is found in a wide variety of water bodies around the world. Taxonomic orthodoxy dictates that all specimens of this widespread taxon represent a single morphospecies. We analyzed a dataset of previously published and newly generated sequences of the mitochondrial COI gene of the L. bulla complex to examine cryptic diversity in the taxon. We undertook phylogenetic analyses and applied 3 methods of species delimitation (ABGD, PTP and GMYC) to identify cryptic species within L. bulla . Our results revealed the existence of 13 cryptic species based on the agreement of the different delimitation methods. Genetic distances between the 13 cryptic species ranged from 4.6 to 16.8%. We found a barcoding gap where the intraspecific divergences (within cryptic species) were smaller than interspecific divergences (among cryptic species), thus supporting the 13 cryptic species delimited by the species delineation methods as independent entities. Our work reveals high levels of cryptic diversity in L. bulla and highlights the need to further studies to resolve the taxonomic status of these cryptic species (and genetic lineages).

Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex

Scolecophidia (worm snakes) are a vertebrate group with high ecomorphological conservatism due to their burrowing lifestyle. The Eurasian or Greek blindsnake Xerotyphlops vermicularis is their only European representative, a species-complex with an old diversification history. However, its systematics and taxonomy has remained untouched. Here, we extend previous work that relied heavily on mitochondrial markers, following a multi-locus approach and applying several species-delimitation methods, including a Bayesian coalescence-based approach (STACEY). Four “species” delimitation analyses based on the mtDNA (ABGD, bGMYC, mPTP, parsimony networks) returned 14, 11, 9 and 10 clusters, respectively. By mitotyping twice as many specimens as before, we have a complete picture of each cluster’s distribution. With the exception of the highly-divergent Levantine lineage, the three independent nuclear markers did not help with phylogenetic resolution, as demonstrated in haplotype networks, concatenated and species-trees, a result of incomplete lineage sorting. The prevailing model from the coalescence-based species-delimitation identified two species: the lineage from the Levant and all others. We formally recognize them as distinct species and resurrect Xerotyphlops syriacus (Jan, 1864) to include the Levantine blindsnakes. Finally, X. vermicularis and X. syriacus may represent species-complexes themselves, since they include high levels of cryptic diversity.

Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage

The Neotropical region harbors an astonishing diversity of species, but still encompasses the least studied biogeographic region of the world. These properties apply for different taxonomic groups, and can be exemplified by drosophilids. In fact, high levels of cryptic diversity have recently been discovered for Neotropical species of the Zygothrica genus group, but relationships among these species, or them and other Drosophilidae species still remains to be addressed. Therefore, the aim of this study was to evaluate the phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica, which together with Paramycodrosophila and Paraliodrosophila compose the Zygothrica genus group. For this, fragments of the mitochondrial cytochrome oxidase subunits I (COI) and II (COII) genes, and the nuclear alpha methyldopa (Amd) and dopa decarboxylase (Ddc) genes were newly characterized for 43 Neotropical specimens of fungus-associated drosophilids, and analyzed in the context of 51 additional Drosophilinae sequences plus one Steganinae outgroup. Based on the resulting phylogeny, the evolution of breeding sites usage was also evaluated through ancestral character reconstructions. Our results revealed the Zygothrica genus group as a monophyletic lineage of Drosophila that branches after the subgenera Sophophora and Drosophila. Within this lineage, Mycodrosophila species seem to encompass the early offshoot, followed by a grade of Hirtodrosophila species, with derived branches mostly occupied by representatives of Zygothrica. This genus, in particular, was subdivided into five major clades, two of which include species of Hirtodrosophila, whose generic status needs to be reevatuated. According to our results, the use of fungi as breeding sites encompasses a symplesiomorphy for the Zygothrica genus group, since one of the recovered clades is currently specialized in using flowers as breeding sites whereas a sole species presents a reversal to the use of fruits of a plant of Gentianales. So, in general, this study supports the paraphyly of Drosophila in relation to fungus-associated Neotropical species of Drosophilidae, providing the first molecular insights into the phylogenetic patterns related to the evolution of this diverse group of species and some of its characteristic traits.

Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

AbstractAimTo investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.LocationCentral Amazonia, Brazil.TaxonSquamata; Gymnophthalmidae; Loxopholis osvaldoi.MethodsWe sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).ResultsWe detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.Main ConclusionsOur results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.

High genetic variation and phylogeographic relations among Palearctic fairy shrimp populations reflect persistence in multiple southern refugia during Pleistocene ice ages and postglacial colonisation

Abstract Intense anthropogenic disturbance threatens temporary pond ecosystems and their associated fauna across the Palearctic. Since fairy shrimps (Crustacea, Branchiopoda) are endemic to temporary ponds, populations are declining due to habitat loss and it is important to define adequate units for conservation. Phylogeographic reconstructions, based on genetic variation, provide valuable information for defining evolutionary and conservation units, especially for organisms with high levels of cryptic diversity like many fairy shrimps. We studied a total of 152 individuals of the fairy shrimp Branchipus schaefferi from 79 populations across the Palearctic and used mitochondrial (CO1) and nuclear (ITS1) DNA data to reconstruct the phylogeography of the species. Our results show that B. schaefferi comprises four highly diverged (10.3–16.5%) evolutionary clades. The present‐day haplotypes within each of the clades probably diverged from lineages that were maintained in separate refugia during the Pleistocene ice ages. While two clades represent distinct geographic regions, the two remaining clades have more wide and overlapping ranges. In addition, the limited number of shared haplotypes among populations from geographically distant regions within three of the clades suggest recent long‐distance dispersal events. Overall, the studied B. schaefferi dataset comprises high levels of genetic differentiation, without a clear morphological signal. Phylogenetic searches and pairwise genetic distances suggest that the studied lineages belong to a complex of four morphologically cryptic species. Since these four evolutionary old clades persist (±2 million years), despite overlapping geographic ranges and since they span a variety of ecological conditions, they should be considered as separate evolutionary significant units for conservation.

A molecular phylogeny for the Pacific monitor lizards (Varanus subgenus Euprepiosaurus) reveals a recent and rapid radiation with high levels of cryptic diversity

Abstract We provide a geographically well-sampled, time-calibrated molecular phylogeny for the Pacific monitor lizards (Varanus: subgenus Euprepiosaurus) based on ND4 and 16S rRNA mitochondrial DNA sequences. Three well-supported clades, or species groups, are retrieved: the Varanus doreanus Group, the V. jobiensis Group and the V. indicus Group. The subgenus is estimated to have originated in the Mid-Miocene, but extant lineage diversification dates from the Late Miocene and Pliocene. A rapid and widespread radiation of the V. indicus Group into the South-West Pacific islands has occurred in the Pleistocene, but colonization onto these islands did not occur in a linear, stepping-stone fashion. Genetically distinct populations – by tradition classified as V. indicus, but seemingly representing distinct species – occur scattered on Tanimbar, several of the Solomon Islands, the Admiralty Islands, the Louisiade Archipelago, Palau and Guam. Our analyses indicate that Varanus jobiensis is a species complex with several divergent lineages that started to separate in the Pliocene and continued in the Pleistocene, the former coinciding with the uplift of the Central Dividing Range on New Guinea. We find that sympatry among species of Euprepiosaurus has not occurred until divergence times of 4.7–5.8 Myr have accrued.

Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot

Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.

Neoprotoparmelia gen. nov. and Maronina (Lecanorales, Protoparmelioideae): species description and generic delimitation using DNA barcodes and phenotypical characters.

Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus Maronina (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages warranted recognition as separate species. Here we study the morphology and chemistry of these taxa and formally describe eight new species based on phenotypical and molecular characters. Further, we evaluate the use of ITS rDNA as a DNA barcode for identifying species in this genus. For the first time, we obtained an ITS sequence of Maroninaaustraliensis, the type species of the genus and showed that it is phylogenetically not closely related to species currently placed in Maronina or Protoparmelia. We assembled a dataset of 66 ITS sequences to assess the interspecies genetic distances amongst the twelve Maronina species using ITS as DNA barcode. We found that Maronina and Protoparmelia form a supported monophyletic group whereas M.australiensis is sister to both. We therefore propose a new genus Neoprotoparmelia to accommodate the tropical-subtropical species within Protoparmelioideae, with Neoprotoparmeliacorallifera as the type, N.amerisidiata, N.australisidiata, N.brasilisidiata, N.capensis, N.crassa, N.pauli, N.plurisporibadia and N.siamisidiata as new species and N.capitata, N.isidiata, N.multifera, N.orientalis and N.pulchra as new proposed combinations. We provide a key to Neoprotoparmelia and confirm the use of ITS for accurately identifying species in this group.

Cryptic diversity in the common flap-necked chameleon Chamaeleo dilepis in South Africa

The spatial genetic structure of a species, and whether distinct genetic lineages are present, is strongly influenced by their biology and habitat requirements. Given habitat specificity and low vagility, many herpetofaunal species are reservoirs for high levels of cryptic diversity; chameleons are a case in hand. The common flap-necked chameleon Chamaeleo dilepis has a large range that spans much of sub-Saharan Africa. Within South Africa, the species is largely confined to the north-eastern and central areas of the country, and occurs from the coastal forests in southern KwaZulu-Natal westwards into Namibia. Their large range, together with anecdotal evidence that there is considerable morphological and phenotypic diversity across the range, suggests a questionable taxonomy with possible cryptic lineages. The aims of the present study were to investigate whether C. dilepis is genetically structured across parts of its South African range, and whether this species (as it currently stands) might include cryptic lineages. To this end, 72 C. dilepis individuals sampled from four localities across South Africa (Gauteng, n = 2; KwaZulu-Natal, n = 2) were sequenced for two mitochondrial markers (ND4 and 16S). The phylogenetic results suggest that C. dilepis is indeed spatially structured. In addition, the large sequence divergence values between groups strongly suggests the presence of cryptic lineages and, pending the inclusion of more data from a larger geographic range, the group may be in need of a taxonomic revision.

Worms in the sand: Systematic revision of the Australian blindsnake Anilios leptosoma (Robb, 1972) species complex (Squamata: Scolecophidia: Typhlopidae) from the Geraldton Sandplain, with description of two new species

The blindsnake genus Anilios (formerly Ramphotyphlops) is the largest and most diverse genus of snakes in Australia with 45 currently recognized species. Recent molecular genetic studies of the genus have identified high levels of cryptic diversity within many taxa, suggesting true species diversity is greatly underestimated. Anilios leptosoma is a slender blindsnake endemic to the mid-west of Western Australia. Although morphological variation has been identified within the species in the past, the systematics and true diversity remained unstudied. Here we use recent molecular data to guide a reappraisal of morphology in order to provide a taxonomic revision of the A. leptosoma species complex. We redescribe A. leptosoma and describe two new species that occur to the south of most of true A. leptosoma’s distribution: A. systenos sp. nov. and A. obtusifrons sp. nov. Anilios systenos sp. nov. is known from the Geraldton region with the furthest record only 100 km to the north-east, a very small range for a species of snake. Anilios obtusifrons sp. nov. has an even smaller distribution, as it is only known from a small coastal area south of Kalbarri and may represent a range-restricted taxa. All species are genetically divergent from each other and can be distinguished by consistent morphological characteristics, including the shape of the snout, the termination point of the rostral cleft and number of mid-body scale rows and ventral scales.