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.     

Phylogenetic resolution and systematics of the Asian tree frogs,Rhacophorus (Rhacophoridae,Amphibia)

Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, South‐east Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well‐supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.     

PHYLOGENETIC ANALYSIS OF PSEUDOCHLORODESMIS STRAINS REVEALS CRYPTIC DIVERSITY ABOVE THE FAMILY LEVEL IN THE SIPHONOUS GREEN ALGAE (BRYOPSIDALES,CHLOROPHYTA)1

The genus Pseudochlorodesmis (Bryopsidales) is composed of diminutive siphons of extreme morphological simplicity. The discovery of Pseudochlorodesmis‐like juveniles in more complex Bryopsidales (e.g., the Halimeda microthallus stage) jeopardized the recognition of this genus. Confronted with this uncertainty, taxonomists transferred many simple siphons into a new genus, Siphonogramen. In this study, we used a multimarker approach to clarify the phylogenetic and taxonomic affinities of the Pseudochlorodesmis‐Siphonogramen (PS) complex within the more morphologically complex bryopsidalean taxa. Our analyses reveal a new layer of diversity largely distinct from the lineages containing the structurally complex genera. The PS complex shows profound cryptic diversity exceeding the family level. We discuss a potential link between thallus complexity and the prevalence and profundity of cryptic diversity. For taxonomic simplicity and as a first step toward clarifying the taxonomy of these simple siphons, we propose to maintain Pseudochlorodesmis as a form genus and subsume Siphonogramen and Botryodesmis therein.     

Genetic analysis of an endemic archipelagic lizard reveals sympatric cryptic lineages and taxonomic discordance

The importance of genetic data in biodiversity conservation is well established, and knowledge of standing genetic variation within and between populations is important for designing conservation strategies. We investigated partitioning of genetic diversity in an endemic lizard (Leiocephalus psammodromus) distributed in the Turks and Caicos archipelago using mtDNA and AFLP data from 259 individuals sampled across 13 islands. Current taxonomy identifies six or more subspecies of L. psammodromus within the archipelago, several of which have undergone recent drastic reductions in range due to extirpation. However, our results indicate the presence of two independent lineages, one on each of the Turks and Caicos banks, and a third sympatric cryptic lineage on both banks. These lineages do not correspond to current taxonomy and alter our understanding of diversity and conservation of this species. Gross morphological data (mass and snout-vent length) indicate some variation in female size among lineages, indicating the possibility of cryptic morphological variation. Instead of initiating separate conservation measures for nominate subspecies, we recommend a more thorough investigation of the morphology and genetics of this group and a more inclusive conservation program. Our surprising results indicate that other endemic squamates in the Bahamas Archipelago might also exhibit sympatric cryptic diversity that does not correspond to current taxonomic understanding and could have significant impacts on our approach to conservation in this region.     

Hidden diversity of Euscorpius (Scorpiones: Euscorpiidae) in Greece revealed by multilocus species‐delimitation approaches

Phylogenetic analysis of the genus Euscorpius (Scorpiones: Euscorpiidae) across the Mediterranean region (86 specimens, 77 localities, four DNA markers: 16S rDNA, COI, COII, and ITS1), focusing on Greek fauna, revealed high variation, deep clade divergences, many cryptic lineages, paraphyly at subgenus level, and sympatry of several new and formerly known lineages. Numerous specimens from mainland and insular Greece, undoubtedly the least studied region of the genus' distribution, have been included. The reconstructed phylogeny covers representative taxa and populations across the entire genus of Euscorpius. The deepest clades detected within Euscorpius correspond (partially) to its current subgeneric division, outlining subgenera Tetratrichobothrius and Alpiscorpius. The rest of the genus falls into several clades, including subgenus Polytrichobothrius and a paraphyletic subgenus Euscorpius s.s. Several cryptic lineages are recovered, especially on the islands. The inadequacy of the morphological characters used in the taxonomy of the genus to delineate species is discussed. Finally, the time frame of differentiation of Euscorpius in the study region is estimated and the distributional patterns of the lineages are contrasted with those of other highly diversified invertebrate genera occurring in the study region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 728–748.     

Fairy shrimps in distress: a molecular taxonomic review of the diverse fairy shrimp genus Branchinella (Anostraca: Thamnocephalidae) in Australia in the light of ongoing environmental change

Australia, and especially South-Western Australia, is a diversity hotspot for large branchiopod crustaceans. A significant proportion of this diversity is found in the anostracans (Crustacea, Anostraca) and particularly in the diverse genus Branchinella with at least 34 species. Members of this genus are found exclusively in temporary aquatic habitats which are increasingly threatened by secondary salinization and other anthropogenic pressures. The development of adequate conservation strategies is therefore considered a priority. To define conservation units, however, thorough knowledge of the taxonomy and phylogenetic position of extant lineages is essential. We reconstructed a large scale phylogeny of the Australian Branchinella by analyzing the 16S mitochondrial gene of 31 presumed species, complemented with analysis of morphological structures holding taxonomic information. Results revealed the presence of at least three new cryptic species. On the other hand, some Branchinella lineages, surviving in environments subjected to contrasting selection regimes, appeared to be conspecific. This suggests substantial physiological plasticity or important adaptive variation present in some species, potentially enabling them to better cope with environmental change, such as secondary salinization. Overall, these results further illustrate the benefits of combining molecular markers and classic morphological taxonomy and phylogeny to assess biodiversity and define conservation units in cryptic groups.     

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.     

The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland,Australia

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.     

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.     

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.     

Taxonomic assessment of sharks,rays and guitarfishes (Chondrichthyes: Elasmobranchii) from south‐eastern Arabia,using the NADH dehydrogenase subunit 2 (NADH2) gene

An 829‐bp fragment of the NADH dehydrogenase subunit 2 (NADH2) gene was used to assess the taxonomic status of 1487 elasmobranch specimens, representing 52 putative species. Strong evidence was found for the existence of an undescribed Echinorhinus species and for cryptic speciation within Rhynchobatus djiddensis. The results also provide strong molecular support for the existence of two previously reported, but undescribed, guitarfish species. Potential, but less conclusive, cryptic lineage diversification was also noted in Carcharhinus leucas, Loxodon macrorhinus, Iago omanensis and Gymnura poecilura. A complex situation was found in the genus Himantura, with potentially three distinct lineages evident, one of which is probably an undescribed species, in the H. gerrardi complex. One dasyatid specimen could not be identified, but appears to be closely related to Dasyatis ushiei, while Himantura leoparda and Carcharhinus longimanus are reported from Oman for the first time. The results of the present study also reinforce previously reported geographical divisions within certain putative species, which has important implications for fishery management and conservation. © 2015 The Linnean Society of London     

Tracing the radiation of Maniola (Nymphalidae) butterflies: new insights from phylogeography hint at one single incompletely differentiated species complex

The use of DNA sequence data often leads to the recognition of cryptic species within putatively well‐known taxa. The opposite case, detecting less diversity than originally described, has, however, far more rarely been documented. Maniola jurtina, the Meadow Brown butterfly, occurs all over Europe, whereas all other six species in the genus Maniola are restricted to the Mediterranean area. Among them, three are island endemics on Sardinia, Cyprus, and Chios, respectively. Maniola species are almost indistinguishable morphologically, and hybridization seems to occur occasionally. To clarify species boundaries and diversification history of the genus, we reconstructed the phylogeography and phylogeny of all seven species within Maniola analyzing 138 individuals from across its range using mitochondrial and nuclear genetic markers. Examination of variation in mitochondrial and nuclear DNA surprisingly revealed a case of taxonomic “oversplitting”. The topology of the recovered phylogenetic tree is not consistent with accepted taxonomy, but rather reveals haplotype clades that are incongruent with nominal species boundaries: instead of seven species, we recognized only two major, yet incompletely segregated, lineages. Our results are consistent with the hypothesis that Maniola originated in Africa. We suggest that one lineage dispersed over the Strait of Gibraltar and the Iberian Peninsula to the west of Europe, while the other lineage spreads eastward through Asia Minor and over the Bosporus to Eastern Europe.     

Systematics and phylogeography of Acanthodactylus schreiberi and its relationships with Acanthodactylus boskianus (Reptilia: Squamata: Lacertidae)

Acanthodactylus is a widespread lacertid genus occurring from the Iberian Peninsula and western North Africa to western India including the Middle East, Cyprus, and the Arabian Peninsula. The genus is in dire need of a taxonomic revision, and the phylogenetic relationships amongst and within its species remain unclear. In particular, the taxonomy and relationship of the allopatric, narrow‐ranged Acanthodactylus schreiberi and its close relative, the widespread Acanthodactylus boskianus asper, are poorly understood. We estimated the phylogenetic and phylogeographical structure of A. schreiberi across its distribution range, and evaluated its relationships to A. b. asper, using mitochondrial and nuclear data. The phylogenetic results indicate that both species are paraphyletic, with A. schreiberi nested within A. b. asper, and the subspecies A. schreiberi syriacus nested within a distinct lineage of A. b. asper. We suggest that the group is in need of a taxonomic revision because the identified lineages and genetic diversity are incongruent with the currently recognized taxonomy. We tentatively conclude that A. schreiberi is restricted to Cyprus and Turkey, reduced to a single form, and that the populations in Lebanon and Israel belong to A. b. asper. © 2014 The Linnean Society of London     

Genetic and chaetal variation in Nais worms (Annelida,Clitellata, Naididae)

The genus Nais is a group of oligochaetous clitellates, common in eutrophic freshwater habitats. About 30 species are described. Species identification is based primarily on chaetal characters, which are often subtle, inconsistent, and even overlapping between nominal species. We investigated the correlation between genetic variation and chaetal morphology in this genus. Eighty‐one individuals from Europe, North America, and China were included in the study. Seventy‐five of these were preserved as vouchers. They were scrutinized with regard to chaetal morphology, and ten different morphotypes were identified. Three molecular markers, two mitochondrial (the COI gene and 16S rDNA) and one nuclear (the ITS region), were used to establish the genetic lineages in the material. Genetic variation was found to be largely congruent with chaetal character patterns. However, at least nine separately evolving lineages (all supported by mitochondrial as well as nuclear data) correspond to at most six nominal species. Four morphotypes/lineages are recognized as Nais barbata, Nais christinae, Nais elinguis, and Nais stolci, respectively, whereas five, or possibly more, lineages represent a morphological continuum covering the variation of the Nais communis/variabilis complex. Thus, cryptic speciation is revealed. Our results indicate that a taxonomic revision of the genus will be needed in the future.     

‘Old-forest fungi’ are not always what they seem: the case of Antrodia crassa

Putatively old-forest dependent fungi have acquired a distinct position in biodiversity conservation, acting both as management targets and indicators for other nature values in the forest. Establishing old-forest dependency, however, requires rigorous sampling, taxonomy and identification approaches as exemplified here by a case study on Antrodia crassa. This rarely recorded polypore is considered indicative of old conifer forests in Northern Europe. We demonstrate that the material labelled as A. crassa includes not only frequent misidentifications, but it represents two genetically and ecologically distinct cryptic lineages with partly overlapping distributions. A balanced survey of different successional stages in Estonia indicated that one of those lineages prefers deadwood-rich disturbed habitats, notably clear-cuts, which have been previously undersampled. Because similar problems with cryptic lineages and biased surveys are common in mycological research, lists of ‘old-forest fungi’ should be considered as high-priority working hypotheses for taxonomic and ecological research, rather than well-established management tools.     

钟冠报春苣苔(苦苣苔科)的分类鉴定

原唇柱苣苔属(Chirita Buch.-Ham. ex D. Don)为一个人为界定的属, 2011年在分子系统学研究的基础上对该属及其近缘属开展了系统发育重建工作,其中绝大部分的原唇柱苣苔属唇柱苣苔组(Sect. Gibbosaccus C. B. Clark)的物种被并入了广义报春苣苔属(Primulina Hance)。然而,由于历史原因和早期经典分类学在研究方法上的局限性以及对现报春苣苔属部分物种的营养器官与生殖器官的认知不够,该属下一些物种的分类仍存在一些问题,亟待深入研究。比如,在对中国和越南分布的苦苣苔科植物开展研究的过程中,作者发现两个报春苣苔属的物种——广布于中国西南和华南直至中南半岛中部的钟冠报春苣苔[Primulina swinglei(Merr.)Mich. Möller & A. Weber]命名人和原被认为是中国与广西特有种的疏花报春苣苔[P. laxiflora(W. T. Wang)Yin. Z. Wang]之间的鉴定存在分类学问题,需要进一步厘清两者之间的关系。该文对这两个物种进行了形态比较,同时通过对这两种植物的原始描述对比、植物标本检查、栽培观察以及野外实地观察,确定疏花报春苣苔是钟冠报春苣苔的异名。此外,还明确了钟冠报春苣苔的后选指定模式标本。