An integrative approach to species delineation incorporating different species concepts: a case study of Limnadopsis (Branchiopoda: Spinicaudata)

The unambiguous delineation and identification of species remain central problems in systematic and taxonomic studies. Species delineation depends on the data utilized and the species concept applied. In recent years, morphology‐based species delineation has been complemented by DNA sequence data, leading to an integrative taxonomy. Such integrative approaches, however, are hampered by the partial incongruence of the various data types with certain species concepts. In this study, we delineated Australian Limnadopsis species employing one mitochondrial (cytochrome c oxidase subunit I, COI) and one nuclear (elongation factor 1α, EF1α) marker and a morphological character apparently part of the specific mate recognition complex, and therefore potentially indicative of reproductive isolation. By integrating the data over various species concepts (e.g. the ‘biological’, ‘Hennigian’, ‘recognition’, ‘phylogenetic’ and ‘evolutionary’ species concepts), the delineation of most species becomes straightforward and unambiguous. Conflicts are particularly interesting as they reveal different aspects of speciation considering the various species concepts. Our study emphasizes the benefits of a truly integrative approach to taxonomy. By combining molecular data with morphological characters indicative of reproductive isolation, it is possible to delineate species integrating not only different data types, but also different underlying species concepts. Overall, 11 Limnadopsis species could be delineated, including all eight currently recognized species, and three so far undescribed species. Most species were congruently delineated under all species concepts. A strict application of the evolutionary species concept, however, would have further split L. parvispinus into two species on the basis of the COI data. In addition, Limnadopsis tatei is consistently split into two sympatrically occurring species under all applied species concepts. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 575–599.     

Phylogenetic,Spatial, and Species‐Trait Patterns across Environmental Gradients: the Case of Hydropsyche (Trichoptera) along the Loire River

When Illies published his concept on the longitudinal zonation of lotic invertebrates five decades ago (Illies, J., 1961: Internat. Rev. ges. Hydrobiol. 46 : 205–213), he defined a research topic that currently interests many ecologists because he linked speciation and phylogeny with spatial distribution and trait adaptation to environmental conditions prevailing along rivers. We tested these ideas analyzing nine species of the caddisfly genus Hydropsyche from the Loire River (France). A morphology‐based phylogeny illustrated that the oldest of our species occurred in the headwater and that specific phylogenetic distances from the root location in the tree were significantly related to the specific longitudinal occurrences in the Loire. Furthermore, traits such as oxygen consumption, optimal velocity for filter‐net‐building, and larval size were significantly related to the specific phylogenetic distances, indicating meaningful, gradual adaptations to environmental gradients prevailing along European rivers (particularly in water temperature, near‐bottom flow, sediment porosity). Thus, joining phylogeny, spatial distribution, and species traits provided insights into a central topic of contemporary ecology, the spatial patterns of speciation, taxonomic community structure (species distributions), and niche adaptation (traits). (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Pre‐ and post‐mating reproductive barriers drive divergence of five sympatric species of Naryciinae moths (Lepidoptera: Psychidae)

The biological species concept suggests that species can be separated on the basis of reproductive isolation. However, because natural interbreeding capabilities are often unknown, differences in morphology are generally used to separate species. Alternatively, genetic dissimilarity is used to separate morphologically similar species. Many genetic markers, including the maternally inherited mitochondrial cytochrome oxidase I sequence, cannot show interbreeding and therefore species status of groups may remain unresolved. In species of the genera Dahlica and Siederia (Lepidoptera: Psychidae: Naryciinae) the lack of morphological distinction and unknown interbreeding has led to unclear and unresolved taxonomic status. Mitochondrial DNA sequences suggest five sexual species to occur in Finland. However, their species status remains unconfirmed, due to a lack of knowledge on interbreeding, unclear morphological distinction and the limited variation in mitochondrial DNA. We combine three methods, a cross‐mating experiment, an analysis of mitochondrial and nuclear DNA, and a detailed male genital morphological examination, to establish the species status of the five suspected species. All suspected species exhibit intraspecies mating preference, although several interspecies pairs readily produce offspring. The genetic analysis, however, fails to show hybrids or introgression, suggesting that both pre‐ and post‐copulation mechanisms isolate the species reproductively. Morphological analysis of the male genitalia confirms that the species have diverged. Our results highlight the need of combining behavioural, morphological and genetic methods to determine species status in challenging taxonomic groups. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 584–605.     

With eyes wide open: a revision of species within and closely related to the Pocillopora damicornis species complex (Scleractinia; Pocilloporidae) using morphology and genetics

Molecular studies have been instrumental for refining species boundaries in the coral genus Pocillopora and revealing hidden species diversity within the extensively studied global species Pocillopora damicornis. Here we formally revise the taxonomic status of species closely related to and within the P. damicornis species complex, taking into account both genetic evidence and new data on morphometrics, including fine‐scale corallite and coenosteum structure. We found that mitochondrial molecular phylogenies are congruent with groups based on gross‐morphology, therefore reflecting species‐level differentiation. However, high levels of gross morphological plasticity and shared morphological characteristics mask clear separation for some groups. Fine‐scale morphological variation, particularly the shape and type of columella, was useful for differentiating between clades and provides an excellent signature of the evolutionary relationships among genetic lineages. As introgressive hybridization and incomplete lineage sorting complicate the delineation of species within the genus on the basis of a single species concept, the Unified Species Concept may represent a suitable approach in revising Pocillopora taxonomy. Eight species are herein described (P. damicornis, P. acuta, P. aliciae, P. verrucosa, P. meandrina, P. eydouxi, P. cf. brevicornis), including a novel taxon – P ocillopora bairdi sp. nov. (Schmidt‐Roach, this study). Citation synonyms and type materials are presented. © 2014 The Linnean Society of London     

Teleomorph-anamorph relationships and reclassification of <Emphasis Type="Italic">Cordyceps cuboidea</Emphasis> and its allied species

Based on morphological characteristics and molecular phylogeny, we reclassified Cordyceps cuboidea and allied species C. alboperitheciata, C. prolifica, and Ophiocordyceps ryogamiensis. We investigated their teleomorph-anamorph relationships and revealed that these four species have Hirsutella-like anamorphs with morphological differences between them. By analyzing their molecular phylogeny, inferred from DNA sequences of internal transcribed spacer (ITS) and large subunit (LSU) D1/D2 region of rDNA, they were separated into four close-knit clades. Although C. prolifica and O. ryogamiensis formed their own clades, isolates of C. cuboidea separated into two clades, i.e., a true C. cuboidea clade and one resembling a new species, the O. paracuboidea clade. The latter two species are distinguished by the fruiting region of the stroma. In addition, C. alboperitheciata is regarded as a synonym of C. cuboidea. From the morphology, teleomorph-anamorph relationships, and molecular phylogeny, we concluded these species should be assigned to the genus Ophiocordyceps.     

Systematic studies of the antarctic species of the phyllophoraceae (Gigartinales,Rhodophyta) based on rbcL sequence analysis

The taxonomic placement of four antarctic species of the marine red algal family Phyllophoraceae (Gigartinales) is assessed within a preliminary molecular phylogeny of the family based on direct sequence analysis of the chloroplast gene rbcL. Parsimony analysis of rbcL sequences indicates that Gymnogongrus antarcticus and Gymnogongrus turquetii cluster in a clade consisting predominantly of southern hemisphere species currently placed in Gymnogongrus and Ahnfeltiopsis, whereas Phyllophora ahnfeltioides and Phyllophora antarctica cluster in a separate clade that is widely divergent from the northern hemisphere Phyllophora clade. Results from molecular and morphological data challenge the current taxonomic concept that type of life history is a phylogenetically valid criterion for recognition of genera in the Phyllophoraceae.     

Evolutionary Patterns in Pearl Oysters of the Genus <Emphasis Type="Italic">Pinctada</Emphasis> (Bivalvia: Pteriidae)

Pearl oysters belonging to the genus Pinctada (Bivalvia: Pteriidae) are widely distributed between the Indo-Pacific and western Atlantic. The existence of both widely distributed and more restricted species makes this group a suitable model to study diversification patterns and prevailing modes of speciation. Phylogenies of eight out of the 11 currently recognised Pinctada species using mitochondrial (cox1) and nuclear (18S rRNA) data yielded two monophyletic groups that correspond to shell size and presence/absence of hinge teeth. Character trace of these morphological characters onto the molecular phylogeny revealed a strong correlation. Pinctada margaritifera appears polyphyletic with specimens from Mauritius grouping in a different clade from others of the French Polynesia and Japan. Hence, P. margaritifera might represent a species complex, and specimens from Mauritius could represent a different species. Regarding the putative species complex Pinctada fucata/Pinctada martensii/Pinctada radiata/Pinctada imbricata, our molecular analyses question the taxonomic validity of the morphological characters used to discriminate P. fucata and P. martensii that exhibited the lowest genetic divergence and are most likely conspecific as they clustered together. P. radiata and P. imbricata were recovered as monophyletic. The absence of overlapping distributions between sister lineages and the observed isolation by distance suggests that allopatry is the prevailing speciation mode in Pinctada. Bayesian dating analysis indicated a Miocene origin for the genus, which is consistent with the fossil record. The northward movement of the Australian plate throughout the Miocene played an important role in the diversification process within Pinctada.     

Phylogeny and systematics of Sphaeriusidae (Coleoptera: Myxophaga): minute living fossils with underestimated past and present-day diversity

Sphaeriusidae (Coleoptera: Myxophaga) is a group of shiny, blackish and hemispherical riparian beetles, known for their miniaturized bodies. They are worldwide in distribution, but very limited information is available about taxonomic and morphological diversity, and natural and evolutionary history. The aim of this study is to help fill in these gaps. We examined the external morphology of modern representatives using scanning electron microscopy (SEM), and reconstructed the phylogeny of the family using five DNA markers (cytochrome oxidase I, 18S rRNA, 28S rRNA, CAD and wingless). Our results suggest a larger morphological diversity than previously expected, corresponding to the deep genetic divergences of principal lineages. We also examined two inclusions in 99-million-year-old Burmese amber. The integration of all evidence allows us to recognize three genera: the extinct genus †Burmasporum Kirejtshuk, the newly defined genus Bezesporum gen.nov. preserved in Burmese amber (B. burmiticum sp.nov. ) and present in the modern fauna of Southeast Asia, and the genus Sphaerius Waltl with a world-wide distribution. Sphaerius species are morphologically highly uniform, with the exception of species from Australia and South Africa, which share some characteristics with Bezesporum gen.nov. despite being resolved as deeply nested lineages of Sphaerius by DNA data. The presence of Bezesporum gen.nov. in Burmese amber and in recent fauna indicates that Sphaeriusidae largely maintained their specific morphology and specialized riparian lifestyle for at least 100 million years. Therefore, they can be considered an exceptionally conserved group, with a minimum of evolutionary changes over a long period. Our study also demonstrates that the species numbers and fine-scale morphological diversity of Sphaeriusidae are larger than expected in both the past and present-day faunas. Both were apparently underestimated due to the minute body size and cryptic habits of these beetles.     

Cryptic species in the Andean hemiparasite Quinchamalium chilense (Schoepfiaceae: Santalales)

The integration of different characters (e.g. morphological, ecological, and molecular) is now recognized as important in species delimitation. In particular, genetic distances between homologous genes have been suggested as one of the main tools to identify species, especially in the case of cryptic species. Quinchamalium is morphologically variable and occupies a diverse set of biomes across its distribution in the Southern Andes. Recent work based on morphology has synonymized the entire genus as a single morphospecies, Quinchamalium chilense. This widely distributed taxon presents the opportunity to find potential cryptic species. The main objective of this study was to test the existence of cryptic species, based mainly on phylogenetic gene trees, genetic distances, and geographic patterns of haplotypes from molecular markers of the nuclear (ITS) and chloroplast (trnL-F) genomes, considering climatic and morphological characteristics. The ITS phylogeny and corresponding haplotype network resulted in three lineages with strong genetic differentiation and distinct geographic patterns. These lineages were informally named Desert, Matorral, and Mountain, based on their geographic distribution in different biomes. The trnL-F chloroplast phylogeny did not distinguish Desert from Matorral, and the haplotype network showed overlap between these last two lineages. Overall, we hypothesize the existence of two cryptic species within Quinchamalium chilense (Mountain and Matorral–Desert) that correspond to genetic, climatic, and morphological differences.     

Identifying monophyletic groups within Bugula sensu lato (Bryozoa,Buguloidea)

Species in the genus Bugula are globally distributed. They are most abundant in tropical and temperate shallow waters, but representatives are found in polar regions. Seven species occur in the Arctic and one in the Antarctic and species are represented in continental shelf or greater depths as well. The main characters used to define the genus include bird's head pedunculate avicularia, erect colonies, embryos brooded in globular ooecia and branches comprising two or more series of zooids. Skeletal morphology has been the primary source of taxonomic information for many calcified bryozoan groups, including the Buguloidea. Several morphological characters, however, have been suggested to be homoplastic at distinct taxonomic levels, in the light of molecular phylogenies. Our purpose was to investigate the phylogenetic interrelationships of the genus Bugula, based on molecular phylogenetics and morphology. A Bayesian molecular phylogeny was constructed using original and previously published sequences of the mitochondrial genes cytochrome c oxidase subunit 1 (COI) and the large ribosomal RNA subunit (16S). Morphological characteristics from scanning electron and light microscopy were used to confirm the clades detected by the molecular phylogeny. Our results suggest that the genus is composed of four clades, for which we provide diagnoses: Bugula sensu stricto (30 species), Bugulina (24 species), Crisularia (23 species) and the monotypic Virididentula gen. n. Ten species could not be assigned to any of those genera, so they remain as genus incertae sedis. Our findings highlight the importance of using molecular phylogenies in association with morphological characters in systematic revisions of bryozoan taxa.     

Molecular identification of <Emphasis Type="Italic">Schoenoplectiella</Emphasis> species (Cyperaceae) by use of microsatellite markers

Over the past few decades, use of molecular markers for species delimitation has drastically increased. Schoenoplectiella Lye has been recognized as a taxonomically difficult genus because of its morphological simplicity and frequent interspecific hybridization. The main objective of this study was to clarify the taxonomic identities of eight Schoenoplectiella species by use of molecular markers. We also evaluated the genetic relationships among S. × trapezoidea, known as a natural hybrid, and its close relatives. We used six microsatellite markers for 44 individuals from 31 natural populations of eight Schoenoplectiella species in South Korea. Six microsatellite marker combinations generated 59 amplification-detectable bands, of which 33 were specifically detected in one or more individuals of each species. Cluster analysis revealed that the grouping was consistent with the taxonomically recognized species. Our results do not support the hybrid origin of S. × trapezoidea. Rather, they suggest that this species is more closely related to S. hotarui. The informative microsatellite markers enabled us to clarify the distinctions among Schoenoplectiella species from South Korea and to identify the genetic relationships among these species. The molecular signatures found suitable for accurate identification of Schoenoplectiella species can be reliably used for studies of the phylogeny and evolution of this genus.     

On the integrated frameworks of species concepts: Mayden’s hierarchy of species concepts and de Queiroz’s unified concept of species

Richard L. Mayden and Kevin de Queiroz have devised and developed ‘a hierarchy of species concepts’ and ‘a unified species concept’, respectively. Although their integrated frameworks of species concepts are rather different as to how to integrate the diverse modern concepts of species, the end result is that they are likely to agree on species recognition in nature, because they virtually share the same major components (i.e. evolutionary or lineage concept of species; same way of delimiting species), and have the same important consequences. Both the hierarchical and unified frameworks, however, are interpreted to have shortcoming regarding the way of integrating the modern species concepts. I reformulate these ideas into a framework of species concepts as follows: It treats the idea of species as population‐level evolutionary lineages (sensu Wiley 1978 ) as the concept for species category, and it adopts the contingent biological properties of species (e.g. internal reproductive isolation, diagnosability, monophyly) as operational criteria in delimiting species. I also suggest that existing and revised versions of the integrated framework of species concepts all are not new species concepts, but versions of the evolutionary species concept, because they treat the evolutionary (or lineage) species concept as the concept for species category.     

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     

European cave shrimp species (Decapoda: Caridea: Atyidae), redefined after a phylogenetic study; redefinition of some taxa,a new genus and four new Troglocaris species

Endemic atyids of southern Europe have been ascribed to Dugastella, and to subterranean Typhlatya and Troglocaris: Dugastella is epigean, and Typhlatya and Troglocaris are subterranean. An extensive collection from all centres of distribution in southern Europe (excepting the Caucasus) was morphologically examined. A taxonomic redefinition of the group, at different levels, is based on recently published and newly generated molecular phylogeny, whereas newly established taxa have also been morphologically defined. The accordance between the phylogenetic tree and the geographical distributions suggested that a re‐evaluation of some traditionally used morphological characters should generate the most parsimonious solution: this enabled a novel taxonomic division. Gallocaris gen. nov. is erected for the French Troglocaris inermis Fage, 1937, which is more closely related to the epigean Dugastella valentina (Ferrer Galdiano, 1924) than to its supposed congeners. Both western Mediterranean Typhlatya species are closely related to their Caribbean congeners. All other European cave shrimps constitute a monophylum, Troglocaris, which is divisible into subgenera (already with available names): the holo‐Dinaric Troglocaris (Troglocaris) Dormitzer, 1853, south‐eastern mero‐Dinaric Troglocaris (Troglocaridella) Babi?, 1922, and Troglocaris (Spelaeocaris) Matja?i?, 1956, and the Caucasian Troglocaris (Xiphocaridinella) Sadovsky, 1930. Four new species are described: Troglocaris (Troglocaris) bosnica sp. nov. , Troglocaris (Spelaeocaris) prasence sp. nov. , Troglocaris (Spelaeocaris) kapelana sp. nov. , and Troglocaris (Spelaeocaris) neglecta sp. nov. The distribution of all established species is shown, and the value of the morphological characters is discussed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 786–818.     

An integrative approach for species delimitation in the spider genus Grammostola (Theraphosidae,Mygalomorphae)

The mygalomorph genus Grammostola (family Theraphosidae) is endemic to South America. The species Grammostola anthracina is one of the largest spiders in Uruguay and reputed to be the longest lived tarantula in the world. This nominal species has two distinct colour morphs comprising black and reddish‐brown forms with controversial taxonomic status. Here, we present a phylogenetic study based on molecular characters (cytochrome c oxidase subunit I) of haplotypes of G. anthracina and closely related species. Our analysis together with new morphological data and biogeographical information indicates that the two morphs of G. anthracina constitute different species that are not sister to each other. Consequently, a new species, Grammostola quirogai is described, diagnosed and illustrated to encompass the black morph. Phylogenetic relationships and new taxonomic characters for Grammostola species included in this study are discussed.     

Expanded molecular phylogeny of the genus Bicyclus (Lepidoptera: Nymphalidae) shows the importance of increased sampling for detecting semi-cryptic species and highlights potentials for future studies

The genus Bicyclus is one of the largest groups of African butterflies, but due to the generally cryptic nature and seasonal variation of adult wing patterns, there has been a lot of systematic confusion. With a large research community working with the model species Bicyclus anynana there has been increasing interest in the evolutionary history of the genus. A previous phylogeny started to unravel interesting patterns, but only included 61% of the then known species. With a range of new species having been described in the last decade there has been a need for an updated phylogeny for the genus. We present the most complete phylogeny of Bicyclus yet, including 93% of the currently 103 recognized species and make a range of taxonomic revisions. We revise the status of four previous subspecies and synonymized taxa that in the light of the new genetic data are raised to species level. We also subsume two subspecies and describe a new species, Bicyclus collinsi sp. nov., based on both genetic and morphological evidence. A further new taxon is identified, but not described at this point due to lack of morphological data. Our phylogeny lays a solid foundation for better understanding the evolution of Bicyclus and highlights key species-groups and complexes with intriguing ecological patterns making them prime candidates for future studies.

http://zoobank.org/urn:lsid:zoobank.org:pub:2F775351-097E-4CD7-8F8F-A90B26D52DE8