Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

Molecular phylogeny of the subterranean genus Niphargus (Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids

The subterranean genus Niphargus is one of the most species‐rich genera among freshwater amphipods in the world, distributed in the Western Palearctic. Thus far, taxonomic and phylogenetic research has focused mainly on the European half of the genus range. In this study, 25 populations of Niphargus from Iran, Lebanon and the Crimean Peninsula were investigated. Bayesian inference based on 28S, H3 and COI gene sequences suggests that populations from the area belong to four different clades. Three species from Crimea and one species from Iran are nested at basal nodes, indicating their rather ancient origin. The rest of the species are younger and belong to two separate clades. One Crimean species is a sister‐species to east Romanian species. The second clade includes one species from Lebanon and all but one population from Iran. The origin of this clade corresponds to marine transgression between the Black Sea and Mediterranean approximately 12 Mya. This clade was further investigated taxonomically. Revision of qualitative morphological traits and unilocus species delimitation methods using COI suggest that this clade comprises 12–16 species, of which only three have been described so far. Multilocus coalescence delimitation methods (using fragments of COI, 28S, H3 and ITS) strongly supported 11 of these species. The remaining populations comprise at least two species complexes that require further and more detailed taxonomic research. © 2015 The Linnean Society of London     

An integrative approach to the taxonomy of the pigmented European Pseudomonocelis Meixner, 1943 (Platyhelminthes: Proseriata)

Only a few species belonging to the Proseriata (Platyhelminthes) show a parenchymatic pigmentation, which may aid identification. Among these, Pseudomonocelis agilis has a yellowish body and is provided with a reddish–brown girdle in front of the statocyst. The species is known for limited areas of northern Europe and the Mediterranean. The present study was conducted to assess both the taxonomic status of populations attributed to the species across the unusually wide range for an interstitial flatworm, which lacks an obvious means of dispersal, and the levels of genetic variability within and among populations, by employing an integrative approach that included the analyses, on six populations, of three molecular markers (small subunit ribosomal 18S‐like gene, inter‐simple sequence repeat, allozymes), karyotypes, and 11 morphological characters. Furthermore, crossbreeding experiments were carried out on the Mediterranean populations. The results obtained revealed the existence of four highly divergent genotypic clusters, accompanied by karyological differences, with complete intersterility among the clusters tested. The combination of approaches adopted strongly supports the conclusion that the wide‐ranging European pigmented species P. agilis is actually composed of four species: P. agilis in the Baltic area; Pseudomonocelis cetinae in the Adriatic; and Pseudomonocelis sp. nov. A and Pseudomonocelis sp. nov. B in the western and eastern Mediterranean, respectively. The latter two species are morphologically indistinguishable for the parameters essayed. Reconstruction of the phylogenetic relationships of these taxa, including congeneric and consubfamilial outgroups, showed that pigmentation is a plesiomorphic condition for the genus Pseudomonocelis and that Pseudomonocelis sp. nov. A shares a previously undetected, sister‐group relationship with species of the unpigmented P. ophiocephala complex. The present study thus depicts complex speciation processes in a mesopsammic species, which involves allopatric divergence operating on different scales and ecological shifts, and highlights that the contribution of microturbellarians to marine biodiversity may be seriously underestimated. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 907–922.     

Genetic diversity and differentiation in natural and reintroduced populations of Bencomia exstipulata and comparisons with B. caudata (Rosaceae) in the Canary Islands: an analysis using microsatellites

Variation at five polymorphic microsatellite loci was used to investigate genetic diversity and differentiation of two tetraploid Canarian endemics, Bencomia exstipulata and B. caudata. Data were analysed and are discussed in terms of tetrasomic (autotetraploid) and disomic (allotetraploid) inheritance. In both cases, genetic diversity values were similar to those described in other tetraploid plant species. High genetic differentiation between the only two described natural populations of B. exstipulata was detected (F_ST = 0.411). Bayesian cluster analysis revealed a geographical structure with distinct genetic groups from each island. High genetic differentiation and low genetic diversity of the B. exstipulata population from Tenerife suggest a recent population bottleneck, perhaps caused by the most recent major volcanic eruption, for this natural locality. This may be heightened by possible inbreeding depression and the monoecy of these species. Polymorphic microsatellite loci were also tested across all species in the Bencomia alliance. These reliably amplified the target sequence, suggesting a high degree of conservation of the sequences flanking the microsatellites. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 429–441.     

Extensive genetic divergence in the East Asian natricine snake,Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations

We investigated intraspecific phylogenetic relationships in the natricine snake, Rhabdophis tigrinus. A partial sequence of mitochondrial cytochrome b gene (990 bp) was sequenced for 220 individuals from 112 populations. The phylogeny indicated monophyly of the Japanese populations against the continental and Taiwanese populations, sister relationships of the Japanese and continental populations, and monophyly of the whole species. The results strongly suggested substantial genetic divergences among population assemblages from those three regions. We thus consider both lateralis from the continent, which is often synonymized to R. tigrinus, and formosanus from Taiwan, which is usually regarded as a subspecies of the latter, as distinct full species based on the evolutionary species concept. In the Japanese populations, haplotypes were classified to in two major clades (I and II) that were parapatric to each other. Clade I consisted of three distinct subclades (I‐A, I‐B, and I‐C), of which the former two were parapatric with each other, whereas the latter was sympatric with each of the former two subclades. The geographical haplotype structure exhibited by the Japanese populations is likely to have resulted from a series of allopatric differentiations with rapid range extensions of resultant lineages, leading to secondary contact or further admixture of mitochondrial haplotype clades and subclades. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 395–408.     

The genus Cyrtomium (Pteridophyta: Dryopteridaceae) in Africa and Madagascar

The fern genus Cyrtomium (Dryopteridaceae) in Africa and Madagascar is reviewed. Until now, a single Cyrtomium species ascribed to either C. caryotideum or C. micropterum (the latter often considered to be a variety of the former) was recognized for the region. This study shows that three Cyrtomium species occur in the region. One, C. falcatum, is not native to the African or Madagascan region, but has become naturalized in various parts of South Africa and Réunion. Two, formerly considered as a single taxon and confused with C. caryotideum and Indian forms thereof, are described as new – C. luctuosum from Madagascar, East, West and South Africa and C. pseudocaryotideum from South Africa. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 449–465.     

Phylogeography of Rhinichthys cataractae (Teleostei: Cyprinidae): pre‐glacial colonization across the Continental Divide and Pleistocene diversification within the Rio Grande drainage

The longnose dace, Rhinichthys cataractae, is a primary freshwater fish inhabiting riffle habitats in small headwater rivers and streams across the North American continent, including drainages east and west of the Continental Divide. The mitochondrially encoded cytochrome b gene (1140 bp) and 2298–2346 bp of the nuclear‐encoded genes S7 and RAG1 were obtained from 87 individuals of R. cataractae (collected from 17 sites throughout its range) and from several close relatives. Phylogenetic analyses recovered a monophyletic R. cataractae species‐group that contained Rhinichthys evermanni, Rhinichthys sp. ‘Millicoma dace’, and a non‐exclusive R. cataractae. Within the R. cataractae species‐group, two well‐supported lineages were identified, including a western lineage (containing R. evermanni, R. sp. ‘Millicoma dace’ and individuals of R. cataractae from Pacific slope drainages) and an eastern lineage (containing individuals of R. cataractae from Arctic, Atlantic, and Gulf slope drainages). Within the eastern lineage of R. cataractae, two well‐supported groups were recovered: a south‐eastern group, containing individuals from the Atlantic slope, southern tributaries to the Mississippi River, and the Rio Grande drainage; and a north‐eastern group, containing individuals from the Arctic slope and northern tributaries to the Mississippi River. Estimates of the timing of divergence within the R. cataractae species‐group, combined with ancestral area‐reconstruction methods, indicate a separation between the eastern and western lineages during the Pliocene to early‐Pleistocene, with a direction of colonization from the west of the Continental Divide eastward. Within the southern portion of its range, R. cataractae likely entered the Rio Grande drainage during the Pleistocene via stream capture events between the Arkansas River (Mississippi River drainage) and headwaters of the Rio Grande. A close relationship between populations of R. cataractae in the Rio Grande drainage and the adjacent Canadian River (Mississippi River drainage) is consistent with hypothesized stream capture events between the Pecos (Rio Grande drainage) and Canadian rivers during the late‐Pleistocene. The population of R. cataractae in the lower Rio Grande may have become separated from other populations in the Rio Grande drainage (upper Rio Grande and Pecos River) and Canadian River during the late‐Pleistocene, well before initiation of recent and significant anthropogenic disturbance within the Rio Grande drainage. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 317–333.     

The taxonomy of the endemic golden palm civet of Sri Lanka

Two species of palm civet are currently known from Sri Lanka: the widespread common species, Paradoxurus hermaphroditus (Pallas, 1777), and the endemic golden species, Paradoxurus zeylonensis (Pallas, 1778). The latter has two ‘morphs’, one golden and one dark brown, both of which are recorded from all three major biotic zones in Sri Lanka (wet zone, dry zone, and cloud forest). We have examined specimens of both ‘morphs’ from all zones, and conclude that there are actually several species involved: names are available for two of them, we describe a third as a new species, and we draw attention to a probable fourth species, based on two distinctive specimens, the provenance of which are unfortunately unknown. The name zeylonensis probably does not apply to a golden palm civet at all. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 238–251.     

When rare species become endangered: cryptic speciation in myrmecophilous hoverflies

The myrmecophilous hoverfly, Microdon mutabilis, is listed as a ‘Rare’ or ‘Nationally Notable Species’ in UK Red Data Books. As an obligate social parasite, feeding only from ant colonies, its life‐style satisfies theoretical conditions under which cryptic speciation is predicted to evolve; namely, strong selection for nonmorphological adaptations that enhance its exploitation of a local subspecies or populations of its host. Samples of larvae and pupae in Ireland, Scotland and England showed that M. mutabilis exploits a single and different host ant species on different sites across its range. In nine southern English colonies, 95.6% of infested nests were of Myrmica scabrinodis whereas in six Irish and two Scottish colonies 100% and 94.2%, respectively, of the infested nests were of Formica lemani, despite M. scabrinodis being common at all sites. Although the adults from ‘scabrinodis’ (and lemani) populations are cryptic, morphometric measurements of pupae showed consistent diagnostic characters that were sufficiently distinct for these ecotypes to be classed as separate species. We conclude that M. mutabilis is the ‘lemani‐type’ and designate the ‘scabrinodis‐type’ as a new species, Microdon myrmicae spec. nov. Thus, one of the listed threatened species of the British Isles becomes two species, each possessing about half the number of populations and occupying half the range of the original ‘species’. Each also inhabits a different serai stage within grassland or heathland, and will require a different management regime if its declining populations are to be conserved. ‘M. mutabilis’ is reported with other host ant species on the European continent. In the light of our results, these may prove to be additional cryptic species. We suggest that cryptic speciation is apt to evolve in species, such as myrmecophiles, endoparasites and koinobiont parasitoids, whose life‐styles result in strong selection on their physiological or behavioural characters. The implications for Red Data Book classifications and for practical conservation are discussed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75 , 291–300.     

Morphometric analysis and taxonomic revision of the Vriesea paraibica complex (Bromeliaceae)

The species related to Vriesea paraibica (Bromeliaceae, Tillandsioideae) have controversial taxonomic limits. For several decades, this group has been identified in herbarium collections as V. × morreniana, an artificial hybrid that does not grow in natural habitats. The aim of this study was to assess the morphological variation in the V. paraibica complex through morphometric analyses of natural populations. Two sets of analyses were performed: the first involved six natural populations (G1) and the second was carried out on taxa that emerged from the first analysis, but using material from herbarium collections (G2). Univariate ANOVA was used, as well as discriminant analysis of 16 morphometric variables in G1 and 18 in G2. The results of the analyses of the two groups were similar and led to the selection of diagnostic traits of four species. Lengths of the lower and median floral bracts were significant for the separation of red and yellow floral bracts. Vriesea paraibica and V. interrogatoria have red bracts; these two species are differentiated by the widths of the lower and median portions of the inflorescence and by scape length. These structures are larger in the former and smaller in the latter. Of the species with yellow floral bracts, V. eltoniana is distinguished by longer leaf blades and scapes and V. flava is characterized by its shorter sepal lengths. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 163–181.     

Range limits,large‐scale biogeographic variation,and localized evolutionary dynamics in a polymorphic damselfly

Studies of heritable colour polymorphisms allow investigators to track the genetic dynamics of natural populations. By comparing polymorphic populations over large geographic areas and across generations, issues about both morph stability and evolutionary dynamics can be addressed, increasing our understanding of the potential mechanisms maintaining genetic polymorphisms. In the present study, we investigated population morph frequencies in a sex‐limited heritable colour polymorphic damselfly (Ischnura elegans, Vander Linden), with three discrete female morphs. We compared the frequencies of these three female morphs in 120 different populations from ten European countries at differing latitudes and longitudes. There were pronounced differences in morph frequencies both across the entire European biogeographic range, as well as at a smaller scale within regions. We also found considerable between‐population variation at the local scale within regions, particularly at the edges of the range of this species. We discuss these findings in the context of recent models of adaptive population divergence along the range of a species. This polymorphism is thus highly dynamic, with stable morph frequencies at the core of the species range but fluctuating morph dynamics at the range limits. We finish with a discussion of how local interactions and climatic factors can be expected to have a strong influence on the biogeographic patterns in this species and other sexually selected polymorphisms. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 775–785.     

Putative speciation events in Lamellodiscus (Monogenea: Diplectanidae) assessed by a morphometric approach

In the present study, we used morphometry as a proxy to study the microevolution of generalist Lamellodiscus (Monogenea, Diplectanidae) species, comprising gill parasites of sparid fish. We investigated 147 individuals, belonging to nine described species, regrouped in four morphotypes. Morphometric measurements were taken on sclerotized parts of the attachment organ. The formation of groups on the basis of the global morphometry within a host species, or between several host species, was assessed using both exploratory analyses (principal component analysis and clustering analysis) and statistical tests. We showed that: (1) for three out of four morphotypes, the global morphometry was significantly different according to host species used, and (2) the coexistence of two populations of Lamellodiscus elegans on Diplodus sargus could reflect an ongoing intra‐host speciation event. We suggest that generalist Lamellodiscus are undergoing specialization on their different hosts, which may lead to speciation. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 559–569.     

Potential for parthenogenesis of virgin females in a bisexual population of the geographically parthenogenetic mayfly Ephoron shigae (Insecta: Ephemeroptera,Polymitarcyidae)

The burrowing polymitarcyid mayfly Ephoron shigae is a geographically parthenogenetic species. Interestingly, the distributions of the bisexual and unisexual populations overlap broadly in their respective geographic ranges. In this mayfly, obligatory diploid thelytoky appears within unisexual populations. In the present study, we examined the potential for parthenogenesis or the parthenogenetic ability of females in a bisexual population aiming to understand the emergence of unisexual populations. The results obtained revealed that females in the examined bisexual populations showed a potential for diploid thelytoky as also seen in the unisexual populations, although, in females from bisexual populations, the development success rates of their unfertilized eggs were considerably lower than those of virgin females from unisexual populations. In the three bisexual reproducing species (Ephemera japonica, Ephemera strigata, and Ephemera orientalis) in the closely‐related family Ephemeridae, diploid thelytoky (i.e. tychoparthenogenesis; < 3%) was also observed. However, in this case, the parthenogenetic development success rates of unfertilized eggs were significantly lower than those of virgin females in the bisexual (Hino‐yosui Irrigation Canal) population of E. shigae. Accordingly, we suggest that parthenogenetic ability (i.e. tychoparthenogenesis or facultative parthenogenesis) in bisexual populations of E. shigae may facilitate the evolutionary transition to unisexual populations with fully obligatory parthenogenesis. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 326–334.     

Morphological and geographic variation of the cycad Dioon edule Lindl. (Zamiaceae): ecological and evolutionary implications

The relationship in geographical distribution and morphological variation of leaflet width and length (diagnostic trait), between and within populations of Dioon edule Lindl., has been investigated throughout its known range in eastern Mexico (from the states of Nuevo León to Veracruz, north to south, respectively). A total of 1832 leaflets were measured for width and length from 154 plants distributed amongst five populations using four leaflet replicas from each of three leaves per plant. For leaflet width and length the variation among populations indicated significant stat-istical differences ( F _4,147 = 125.83; P  < 0.0001; R ² = 92.17% and F _4,147 = 9.04; P  < 0.001; R ² = 26.8%), respectively. With respect to leaflet width, the multiple range test showed three groups with a north to south distributional relationship along the range of the species. The correlation coefficient among paired populations, respect to geographical distance and the absolute value of the mean difference of leaflet width in each population, was positive, and different from zero ( r  = 0.82; P  = 0.013). A great variation of important ecological and evolutionary parameters was shown.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 465–470.     

Unmasking cryptic species: morphometric and phylogenetic analyses of the Ibero‐North African Linaria incarnata complex

Linaria incarnata has been treated as a widely distributed Ibero‐North African species in the latest taxonomic reviews. Morphological and phylogenetic disparity between populations of this species has been previously reported. Here we present new morphological and phylogenetic evidence for the disintegration of L. incarnata into three distinct species: L. incarnata from the western Iberian Peninsula; L . mamorensis sp. nov. from north‐western Morocco; and L. onubensis from south‐western Spain. The relatively poor morphological differentiation between these taxa (which can be regarded as cryptic species) and their distinct phylogenetic positions indicate that characters of the L. incarnata morphotype have been acquired multiple times in the evolution of Linaria section Versicolores. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000–000.     

Phylogeny‐based species delimitations and the evolution of host associations in symbiotic zoanthids (Anthozoa,Zoanthidea) of the wider Caribbean region

Zoanthids are marine cnidarians with simple morphologies that challenge our ability to delineate species. Phylogenetic analyses of internal transcribed spacer (ITS) sequences are consistent with six morphologically described species from the wider Caribbean region, and reveal four additional species that were not previously recognized. Histological examinations of unidentified species reveal cryptic Isozoanthus and Edwardsiidae (Actiniaria) species. Observations of zoanthids in situ reveal geographic distributions that range from regional to trans‐Atlantic. ITS and 16S data are consistent with hypotheses of paraphyly in some higher taxa of zoanthids; however, the clades of zoanthids recovered in both analyses can largely be defined by their host associations, thereby supporting phylogenetic conservatism in zoanthid–host association evolution. The single clear example of a zoanthid switching hosts was accompanied by a compensatory loss of endosymbiosis, which maintained the match in photosynthetic symbioses between zoanthids and sponge hosts. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 223–238.     

How many species of Isothecium (Lembophyllaceae,Bryophyta) are there in Macaronesia? A survey using integrative taxonomy

Species boundaries are sometimes difficult to assess, especially when molecular data do not neatly match morphologically defined units. This study investigates the moss genus Isothecium, with special emphasis on Macaronesian populations. Morphological studies are combined with the analysis of three rapidly evolving markers: nuclear internal transcribed spacer and plastid trnG and trnL‐trnF. The results of the morphological studies suggest that Isothecium is represented by five species in Macaronesia, including a new endemic species from Madeira, I sothecium montanum sp. nov. , which is described here. The molecular results are less conclusive than the morphology results in delimiting species of this genus, even when indels are included as informative. Once possible methodological shortcomings have been discarded, the results can be interpreted as having been caused by incomplete lineage sorting, probably as a consequence of recent speciation. The molecular results also suggest that the origin of the Macaronesian endemics may be explained by at least two independent colonization events. Finally, the delimitation of a new endemic species of Isothecium in Macaronesia indicates that current knowledge on the taxonomy of spore‐producing plants may be far from complete in this hotspot of biodiversity. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00 , 000–000.