Disentangling the morphological stasis in two rotifer species of the <Emphasis Type="Italic">Brachionus plicatilis</Emphasis> species complex

The taxonomic uncertainty surrounding cryptic species complexes has traditionally been resolved using lengthy experimental approaches, while, since the advent of PCR based techniques the number of cryptic species described in a variety of taxa is increasing steadily. Here we formally describe a new rotifer species of the Brachionus plicatilis complex: Brachionus manjavacas n.sp., disentangling what was known as a morphological stasis. Detailed morphological analyses demonstrated significant differences in body shape and size between B. manjavacas and B. plicatilis s.s., analysed by geometric morphometrics; unfortunately these statistical differences are not taxonomically reliable because of wide overlaps. Size and asymmetry of masticatory apparatus, named trophi, observed by SEM, gave similar results, with taxonomic ambiguity. Only the shape of small pieces of the trophi, named satellites, were consistently different between the species. On a strictly classical taxonomical basis it is absolutely useful to name new species on morphological bases, as we did, and to assess their status as distinct entities. Nevertheless, the two species are broadly similar; therefore, we do not suggest using the small differences in shape of satellites of trophi to identify the species for further ecological studies, but to continue discriminating them on genetic marker bases. Handling editor: K. Martens     

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.     

Species‐diagnostic microsatellite loci for the fig wasp genus Pegoscapus

To obtain tools for the estimation of inbreeding and assignment of offspring to matrilines, we developed 13 microsatellite loci from the fig wasps that pollinate Ficus obtusifolia. Based on morphological studies, it was thought that a single species (Pegoscapus hoffmeyeri) pollinated this fig. However, our data revealed the presence of two coexisting cryptic species. Several diagnostic microsatellite markers may be used to distinguish these two cryptic species. The new microsatellites can be used across a wide range of fig‐pollinating wasp species for both evolutionary and population genetic studies.     

The endosymbiont community as taxonomic character: a novel approach to resolving the Bemisia tabaci complex

In this issue of Molecular Ecology, Gueguen et al. (2010) describe their novel approach to resolving cryptic genetic diversity in the Bemisia tabaci complex (Hemiptera: Aleyrodidae.) Complexes of cryptic species present a challenge to both morphological and molecular taxonomy – the former presumed, as shared morphology normally defines species as cryptic, but the latter also problematic when host DNA sequence data is either inconclusive or unaccompanied by independent evidence. Endosymbiont associations with insect hosts have, historically, complicated efforts to develop a robust molecular taxonomy, but the approach of Gueguen et al. takes advantage of endosymbiont community composition to help rather than hinder the task of resolving taxonomic distinctions within the B. tabaci complex.     

GENETIC POLYMORPHISM IN THE MORPHOLOGICALLY REDUCED DWARF MISTLETOES (ARCEUTHOBIUM,VISCACEAE): AN ELECTROPHORETIC STUDY

Arceuthobium is a well defined genus of obligate parasites of conifers. Assessment of taxonomic and phylogenetic relationships in this group is difficult owing to morphological reductions and complex host relationships. In the present study, genetic relationships within and among 19 taxa were examined using starch gel electrophoresis of triploid seed endosperm tissue. Allelic frequency data for eleven polymorphic loci were derived from analysis of 40 natural populations collected from the U.S. and Mexico. The genus showed remarkably high levels of genetic diversity: averaged across the 19 taxa, 66.7% of the loci were polymorphic with an average of 2.23 alleles per locus. This level of polymorphism is approximately double the average value reported for many dicotyledons and stands in contrast to the overall uniform morphology of these parasites. Unweighted pair group cluster analysis (UPGMA) of genetic similarity measures was conducted for all sampled populations and the results compared to a phenetic system of classification for the genus. Similarities between the two studies include the recognition of two subgenera based upon the segregation of the verticillately branched Arceuthobium americanum from the remainder of the taxa examined. Analysis of isozyme data supported a grouping of six taxa: A. vaginatum ssp. cryptopodum, A. vaginatum ssp. durangense, A. gillii, A. rubrum, A. divaricatum, and A. douglasii. The placement of the latter three taxa in other groups by phenetic criteria provides evidence for molecular divergence not seen using morphological features. The Campylopodum group of taxa comprised eleven members that were linked at similarity values of 80% or greater. Populations were not unambiguously grouped according to species as defined by the phenetic study or at similarity levels comparable to other well defined species in this study. This group is either not reproductively isolated or molecular differentiation is cryptic due to rapid adaptive radiation onto numerous host tree species.     

Cryptic diversity,intraspecific phenetic plasticity and recent geographical translocations in Branchiomma (Sabellidae,Annelida)

The importance of identifying biological diversity accurately and efficiently is becoming more evident. It is therefore critical to determine the species boundaries between closely related taxa and to establish diagnostic characters that allow us to define species. This is not an easy task when species exhibit high intraspecific phenotypic plasticity or when distinct evolutionary lineages with an unusually large amount of genetic distinctiveness show no apparent morphological diversity (cryptic species). These phenomena appear to be common in the genus of fan worms Branchiomma (Sabellidae, Annelida), and consequently, taxonomic errors are widespread in the group. Moreover, some Branchiomma species have been unintentionally translocated outside the area where natural range extension is expected, increasing the taxonomic problems. We have performed a range of analytical methods including genetic distances, Bayesian inference, maximum likelihood, maximum parsimony, statistical parsimony analyses and general mixed Yule coalescent model to clarify the taxonomic status and assess the species boundaries of Branchiomma in Australia. This study shows that the traditional diagnostic morphological features are greatly homoplastic. Results also indicate that the diversity of Branchiomma in Australia is higher than previously reported and evidence some cases of high phenetic plasticity (in features previously considered as stable within species), high intraspecific genetic variability, cryptic species and several unexpected cases of translocations.     

Ecological and genetic evidence for cryptic ecotypes in a rare sexually deceptive orchid,Drakaea elastica

Species with specialized ecological interactions present significant conservation challenges. In plants that attract pollinators with pollinator‐specific chemical signals, geographical variation in pollinator species may indicate the presence of cryptic plant taxa. We investigated this phenomenon in the rare sexually deceptive orchid Drakaea elastica using a molecular phylogenetic analysis to resolve pollinator species boundaries, pollinator choice experiments and a population genetic study of the orchid. Pollinator choice experiments demonstrated the existence of two ecotypes within D. elastica, each attracting their own related but phylogenetically distinct pollinator species. Despite the presence of ecotypes, population genetic differentiation was low across populations at six microsatellite loci (F_ST = 0.026). However, Bayesian STRUCTURE analysis revealed two genetic clusters, broadly congruent with the ecotype distributions. These ecotypes may represent adaptation to regional variation in pollinator availability and perhaps the early stages of speciation, with pronounced morphological and genetic differences yet to evolve. Resolution of the taxonomic status of the D. elastica ecotypes is required as this has implications for conservation efforts and allocation of management funding. Furthermore, any reintroduction programmes must incorporate knowledge of ecotype distribution and pollinator availability to ensure reproductive success in restored populations. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 124–140.     

New polymorphic microsatellite loci,cross‐species amplification and PCR multiplexing in the black aphid,Aphis fabae Scopoli

Aphis fabae includes four morphological cryptic subspecies, which are mostly identified by their partially distinct secondary host range. To determine the extent of gene flow and isolation between these four taxa, we isolated and characterized 12 microsatellite loci from Aphis fabae fabae and tested cross‐species amplification of eight loci from the closely related species Aphis gossypii. Using eight previously described microsatellite loci, we have developed the polymerase chain reaction (PCR) multiplexing of 24 loci, which were separated in tree sets and five PCRs. These sets of microsatellite loci provide high throughput capacity for large‐scale population genetic studies at a minimum cost.     

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.     

Taxonomic implications for diaptomid copepods based on contrasting patterns of mitochondrial DNA sequence divergences in four morphospecies

Morphological identification methods do not provide reliable and meaningful species identifications for taxa where morphological differences among distinct species are either absent or overlooked (i.e., cryptic species). For example, due to the minute nature of the morphological characters used to delineate diaptomid copepod species and the apparent potential for copepod speciation to occur with little or no morphological change (i.e., morphological stasis), morphological identifications of diaptomid species may not adequately capture their true species diversity. Here, we present results from a geographic survey of mtDNA sequences from populations across the geographic ranges of four North American diaptomid species—Leptodiaptomus minutus, Skistodiaptomus pallidus, Skistodiaptomus reighardi, and Onychodiaptomus sanguineus. Shallow mitochondrial DNA sequence divergences (maximum of 1.1%) among haplotypes of L. minutus from across its geographic range suggest that current morphological identification techniques reliably identify this species. In contrast, we found large mitochondrial DNA sequence divergences (14–22%) among populations within the currently recognized morphospecies of S. pallidus, S. reighardi, and O. sanguineus. However, pairwise sequence divergences within four distinct S. pallidus clades and within populations of S. reighardi and O. sanguineus were similarly low (maximum of 1.5%) as found within L. minutus as a whole. Thus, the S. pallidus, S. reighardi, and O. sanguineus morphospecies may be considered best as cryptic species complexes. Our study therefore indicates that morphological identifications, while sufficient for some species, likely underestimate the true species diversity of diaptomid copepods. As such, we stress the need for extensive taxonomic revision that integrates genetic, morphological, reproductive, and ecological analyses of this diverse and important group of freshwater zooplankton. Furthermore, we believe an extensive taxonomic revision will shed important insight into major questions regarding the roles of geography, phylogeny, and habitat on the frequency of cryptic species on earth. Handling editor: S. I. Dodson     

Integration of molecular, ecological, morphological and endosymbiont data for species delimitation within the Pnigalio soemius complex (Hymenoptera: Eulophidae)

Integrative taxonomy is a recently developed approach that uses multiple lines of evidence such as molecular, morphological, ecological and geographical data to test species limits, and it stands as one of the most promising approaches to species delimitation in taxonomically difficult groups. The Pnigalio soemius complex (Hymenoptera: Eulophidae) represents an interesting taxonomical and ecological study case, as it is characterized by a lack of informative morphological characters, deep mitochondrial divergence, and is susceptible to infection by parthenogenesis‐inducing Rickettsia. We tested the effectiveness of an integrative taxonomy approach in delimiting species within the P. soemius complex. We analysed two molecular markers (COI and ITS2) using different methods, performed multivariate analysis on morphometric data and exploited ecological data such as host–plant system associations, geographical separation, and the prevalence, type and effects of endosymbiont infection. The challenge of resolving different levels of resolution in the data was met by setting up a formal procedure of data integration within and between conflicting independent lines of evidence. An iterative corroboration process of multiple sources of data eventually indicated the existence of several cryptic species that can be treated as stable taxonomic hypotheses. Furthermore, the integrative approach confirmed a trend towards host specificity within the presumed polyphagous P. soemius and suggested that Rickettsia could have played a major role in the reproductive isolation and genetic diversification of at least two species.     

Gen‐morph species concept—A new and integrative species concept for outbreeding organisms

The present article briefly reviewed the prevailing species concepts, especially biological, genetic, evolutionary, phylogenetic, ecological, and several taxonomic species concepts. The former five reflect the properties of species from diverse aspects and in different degrees, while taxonomic species concepts all contain more or less subjective elements, except for Hedberg's taxonomic method (not species concept). So far, there is no species concept that is both theoretically rational and practically operable. The present article outlined recent studies on the genus Paeonia L. (Paeoniaceae) in biology, particularly in morphology, biogeography, molecular phylogeny, and reproductive behavior, which provided insight into the relationship between variation of morphological characteristics and phylogeny. Taking the study on Paeonia L. as a case, referring to studies on some other plant groups, and incorporating the merits of the prevailing species concepts into our consideration, “gen‐morph species concept” is proposed here formally as new for outbreeding organisms. The new species concept has three special features: (i) a bridge linking morphological aspect with genetic and other aspects of species; (ii) proposal of a concrete morphological criterion for species definition, and (iii) considering quantitative and qualitative characteristics as equally valuable for species definition and introducing statistics into the concept to handle such characteristics. Therefore, the gen‐morph species concept is an integrative species concept, both theoretically objective and practically operable.     

Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua

Nitzschia inconspicua is an ecologically important diatom species, which is believed to have a widespread distribution and to be tolerant to salinity and to organic or nutrient pollution. However, its identification is not straightforward and there is no information on genetic and ecophysiological diversity within the species. We used morphological, molecular (rbcL and LSU D1–D3), ecophysiological and reproductive data to investigate whether N. inconspicua constitutes a single species with a broad ecological tolerance or two or more cryptic species with shared or different ecological preferences. Molecular genetic data for clones from upstream and deltaic sites in the Ebro River basin (Catalonia, Spain) revealed seven N. inconspicua rbcL + LSU genotypes grouped into three major clades. Two of the clades were related to other Nitzschia and Denticula species, making N. inconspicua paraphyletic and suggesting the need for taxonomic revision. Most clones were observed to be automictic, exhibiting paedogamy, and so the biological species concept cannot be used to establish species boundaries. Although there were morphological differences among clones, we found no consistent differences among genotypes belonging to different clades, which are definable only through sequence data. Nevertheless, separating the genotypes could be important for ecological purposes because two different ecophysiological responses were encountered among them.     

ADAPTIVE RADIATION AND GENETIC DIFFERENTIATION IN HAWAIIAN BIDENS

The genus Bidens (Asteraceae) has undergone extensive adaptive radiation on the Hawaiian Islands. The 19 species and eight subspecies endemic to Hawaii exhibit much more morphological and ecological differentiation than the continental members of the genus. However, the Hawaiian taxa have the same chromosome number and retain the capacity to interbreed in all possible combinations. Twenty-two populations of 15 Hawaiian taxa and four populations of American taxa were compared at 21 loci controlling eight enzyme systems. Populations of Hawaiian taxa are highly polymorphic. However, little genetic differentiation has occurred among taxa in spite of the high levels of genetic variability. Genetic identities calculated for pairs of populations show that populations of the same taxon are genetically more similar than are populations belonging to different taxa, but all values are high. The level of genetic differentiation that has occurred among the species of Hawaiian Bidens is comparable to the level of genetic differences found among populations within single continental plant species. Moreover, there is no correlation between the isozyme data and morphological data. No groups of taxa are evident in the genetic data, although morphological groups exist. Genetic differentiation at isozyme loci has not occurred at the same rate as the acquisition of presumably adaptive morphological and ecological characters in Hawaiian Bidens. Adaptive radiation may be limited to a few genes controlling morphological and ecological characters.     

A new species of Borgatomelissa Patiny, 2000 from eastern Morocco: Borgatomelissa flavimaura n. sp. (Hymenoptera,Andrenidae)

Until now, two species of Borgatomelissa Patiny, 2000 have been described, both from loci typici located in the Near East and eastern Africa. Borgatomelissa brevipennis (Walker, 1871), the most widespread taxon, has also been found in the southern Sahelo-Sudanian belt of the Sahara. A third species from eastern Morocco is described in the present study: Borgatomelissa flavimaura n. sp. In addition to taxonomic insights, the new species sheds a new light on the biogeography of the genus.     

Leaf gall polymorphism and molecular phylogeny of a new Bruggmanniella species (Diptera: Cecidomyiidae: Asphondyliini) associated with Litsea acuminata (Lauraceae) in Taiwan,with ecological comparisons and a species description

Two types of cecidomyiid leaf galls, cup‐shaped and umbrella‐shaped, occur on Litsea acuminata (Lauraceae) in Taiwan. Based on the concept of gall shapes as “extended phenotypes” of gall inducers, these two types could be induced by different gall midge species. However, galls with intermediate shapes between the two types were recently discovered, which implies that possible genetic exchanges occur between the gall inducers of both types. To clarify the taxonomic status of gall midges responsible for the two types of galls on L. acuminata, we undertook taxonomic, molecular phylogenetic and ecological studies. Our findings show that the two gall types are induced by the same Bruggmanniella species and the species is new to science. We describe the species forming this range of galls as Bruggmanniella litseae sp. n. , and compare their geographical distribution, galling position and morphometry. Based on our results, a possible evolutionary scenario of B. litseae sp. n. is discussed.     

Integrative insect taxonomy based on morphology,mitochondrial DNA,and hyperspectral reflectance profiling

Integrative taxonomy is considered a reliable taxonomic approach of closely related and cryptic species by integrating different sources of taxonomic data (genetic, ecological, and morphological characters). In order to infer the boundaries of seven species of the evacanthine leafhopper genus Bundera Distant, 1908 (Hemiptera: Cicadellidae), an integrated analysis based on morphology, mitochondrial DNA, and hyperspectral reflectance profiling (37 spectral bands from 411–870 nm) was conducted. Despite their morphological similarities, the genetic distances of the cytochrome c oxidase subunit I (COI) gene among the tested species are relatively large (5.8–17.3%). The species‐specific divergence of five morphologically similar species (Bundera pellucida and Bundera spp. 1–4) was revealed in mitochondrial DNA data and reflectance profiling. A key to identifying males is provided, and their morphological characters are described. Average reflectance profiles from the dorsal side of specimens were classified based on linear discriminant analysis. Cross‐validation of reflectance‐based classification revealed that the seven species could be distinguished with 91.3% classification accuracy. This study verified the feasibility of using hyperspectral imaging data in insect classification, and our work provides a good example of using integrative taxonomy in studies of closely related and cryptic species. © 2015 The Linnean Society of London