An integrative approach to species delimitation in Benthomangelia (Mollusca: Conoidea)

DNA sequences are currently used to propose primary hypotheses of species delimitation, especially when morphological variability is difficult to assess. In an integrative taxonomy framework, these hypotheses are then compared with other characters, such as morphology or geography, to produce robust species delimitations. For this purpose, the cytochrome oxidase subunit I (COI) gene has been sequenced for almost 50 specimens of the genus Benthomangelia , a deep-sea marine gastropod genus, collected in the South-West Pacific. Five genetic groups, displaying low and high genetic distances respectively within and between groups, were defined. COI hypotheses were compared with both the results obtained with the independent nuclear 28S gene and with an elliptic Fourier analysis of the shape of the last whorl of the shell. 28S gene analysis confirmed the same well-supported groups as COI, and elliptic Fourier analysis identified several morphological characters that vary similarly to genetic variability.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 696–708.     

An integrative approach to species delimitation in Echinodorus (Alismataceae) and the description of two new species

Summary  Taxonomy of the genus Echinodorus is partially revisited in the light of current understanding of the phylogenetic relationships of the genus. As a result of new taxonomy, the species status of some previously synonymised taxa are restored, other names are synonymised, and some nomenclatural problems unnoticed by previous authors are resolved. Two new species, Echinodorus reptilis and E. emersus are described. The subgeneric divisions of the genus are not accepted, and all subspecific taxa are either rejected or established as species. As a result, 28 species based on a phylogenetic species concept are now recognised in Echinodorus and an identification key to these species is provided.     

Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas

Background

The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal “barcoding gene”. An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.

Methods and Findings

A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a “barcode gap” using percent of pairwise sequence divergence (uncorrected p-distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups.

Conclusions

The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a “species”.     

Methods for species delimitation in bumblebees (Hymenoptera,Apidae, Bombus): towards an integrative approach

Delimitation of closely related species is often hindered by the lack of discrete diagnostic morphological characters. This is exemplified in bumblebees (genus Bombus). There have been many attempts to clarify bumblebee taxonomy by using alternative features to discrete morphological characters such as wing shape, DNA, or eco‐chemical traits. Nevertheless each approach has its own limitations. Recent studies have used a multisource approach to gather different lines of speciation evidence in order to draw a strongly supported taxonomic hypothesis in bumblebees. Yet, the resulting taxonomic status is not independent of selected evidence and of consensus methodology (i.e. unanimous procedure, majority, different weighting of evidence). In this article, we compare taxonomic conclusions for a group of taxonomically doubtful species (the Bombus lapidarius‐group) obtained from the four commonly used lines of evidence for species delimitation in bumblebees (geometric morphometric of wing shape, genetic differentiation assessment, sequence‐based species delimitation methods and differentiation of cephalic labial gland secretions). We ultimately aim to assess the usefulness of these lines of evidence as components of an integrative decision framework to delimit bumblebee species. Our results show that analyses based on wing shape do not delineate any obvious cluster. In contrast, nuclear/mitochondrial, sequence‐based species delimitation methods, and analyses based on cephalic labial gland secretions are congruent with each other. This allows setting up an integrative decision framework to establish strongly supported species and subspecies status within bumblebees.     

A taxonomic revision and species delimitation of the genus Purpuraria Enderlein, 1929 (Orthoptera: Pamphagidae) using an integrative approach

Recent studies on the endemic Canarian genus Purpuraria have shown that the taxonomy of its only recognized species (P. erna) is probably erroneous. In this study, an integrative revision of the genus is performed, based on a large number of specimens and geographical sampling. As a result, (1) the diagnostic characters at the genus level are re‐described, (2) Purpuraria magna n. sp. based on morphological, morphometric and genetic data is described and (3) the taxonomic status of a formerly described subspecies is clarified. Intraspecific and interspecific morphometric differences have been found, indicating that the genus is undergoing a process of morphological diversification. Nevertheless, the possibility of interspecific mating between individuals of the two species is suggested, because no significant differences have been found between their respective calling songs. Genetic analyses using mitochondrial and nuclear DNA sequences suggest that P. erna and P. magna are recent species with evidences of secondary contact episodes in the past.     

Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae,Mygalomorphae, Theraphosidae) within the United States

This systematic study documents the taxonomy, diversity, and distribution of the tarantula spider genus Aphonopelma Pocock, 1901 within the United States. By employing phylogenomic, morphological, and geospatial data, we evaluated all 55 nominal species in the United States to examine the evolutionary history of Aphonopelma and the group’s taxonomy by implementing an integrative approach to species delimitation. Based on our analyses, we now recognize only 29 distinct species in the United States. We propose 33 new synonymies (Aphonopelma apacheum, Aphonopelma minchi, Aphonopelma rothi, Aphonopelma schmidti, Aphonopelma stahnkei = Aphonopelma chalcodes; Aphonopelma arnoldi = Aphonopelma armada; Aphonopelma behlei, Aphonopelma vogelae = Aphonopelma marxi; Aphonopelma breenei = Aphonopelma anax; Aphonopelma chambersi, Aphonopelma clarum, Aphonopelma cryptethum, Aphonopelma sandersoni, Aphonopelma sullivani = Aphonopelma eutylenum; Aphonopelma clarki, Aphonopelma coloradanum, Aphonopelma echinum, Aphonopelma gurleyi, Aphonopelma harlingenum, Aphonopelma odelli, Aphonopelma waconum, Aphonopelma wichitanum = Aphonopelma hentzi; Aphonopelma heterops = Aphonopelma moderatum; Aphonopelma jungi, Aphonopelma punzoi = Aphonopelma vorhiesi; Aphonopelma brunnius, Aphonopelma chamberlini, Aphonopelma iviei, Aphonopelma lithodomum, Aphonopelma smithi, Aphonopelma zionis = Aphonopelma iodius; Aphonopelma phanum, Aphonopelma reversum = Aphonopelma steindachneri), 14 new species (Aphonopelma atomicum sp. n., Aphonopelma catalina sp. n., Aphonopelma chiricahua sp. n., Aphonopelma icenoglei sp. n., Aphonopelma johnnycashi sp. n., Aphonopelma madera sp. n., Aphonopelma mareki sp. n., Aphonopelma moellendorfi sp. n., Aphonopelma parvum sp. n., Aphonopelma peloncillo sp. n., Aphonopelma prenticei sp. n., Aphonopelma saguaro sp. n., Aphonopelma superstitionense sp. n., and Aphonopelma xwalxwal sp. n.), and seven nomina dubia (Aphonopelma baergi, Aphonopelma cratium, Aphonopelma hollyi, Aphonopelma mordax, Aphonopelma radinum, Aphonopelma rusticum, Aphonopelma texense). Our proposed species tree based on Anchored Enrichment data delimits five major lineages: a monotypic group confined to California, a western group, an eastern group, a group primarily distributed in high-elevation areas, and a group that comprises several miniaturized species. Multiple species are distributed throughout two biodiversity hotspots in the United States (i.e., California Floristic Province and Madrean Pine-Oak Woodlands). Keys are provided for identification of both males and females. By conducting the most comprehensive sampling of a single theraphosid genus to date, this research significantly broadens the scope of prior molecular and morphological investigations, finally bringing a modern understanding of species delimitation in this dynamic and charismatic group of spiders.     

Species delimitation based on integrative approach suggests reallocation of genus in Hypostomini catfish (Siluriformes,Loricariidae)

Hydrobiologia - Integrative approaches are particularly useful to resolve taxonomic uncertainties in species-rich groups that have undergone explosive radiation, such as Hypostomini (suckermouth...     

Three new species of Melloleitaoina Gerschman & Schiapelli, 1960 (Araneae,Mygalomorphae, Theraphosidae) from northern Argentina

Three new species of the monotypic genus Melloleitaoina Gerschman & Schiapelli, 1960 are described from northern Argentina: M. mutquina sp. n., M. uru sp. n. and M. yupanqui sp. n. The female specimen originally described as M. crassifemur is not conspecific with the male holotype and thus is removed from this species and described as M. uru sp. n.; M. crassifemur is redescribed. All species are diagnosed, illustrated and a key to species is provided.     

An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago

The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.     

Revisiting species delimitation within the genus Oxystele using DNA barcoding approach

The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.     

A new species of the genus Chaetopelma Ausserer, 1871 (Araneae: Theraphosidae) from Turkey

A new species of Chaetopelma Ausserer, 1871 is described from Hatay province, Turkey. Differences between the new species and related species are discussed. The characteristic features of this species are described and illustrated.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:99C21605-5308-4363-8420-02F6151B4457     

Coalescent-based species delimitation in an integrative taxonomy

The statistical rigor of species delimitation has increased dramatically over the past decade. Coalescent theory provides powerful models for population genetic inference, and is now increasingly important in phylogenetics and speciation research. By applying probabilistic models, coalescent-based species delimitation provides clear and objective testing of alternative hypotheses of evolutionary independence. As acquisition of multilocus data becomes increasingly automated, coalescent-based species delimitation will improve the discovery, resolution, consistency, and stability of the taxonomy of species. Along with other tools and data types, coalescent-based species delimitation will play an important role in an integrative taxonomy that emphasizes the identification of species limits and the processes that have promoted lineage diversification.     

Intraspecific non-sexual interactions of Grammostola schulzei (Araneae: Theraphosidae) under laboratory conditions

Intraspecific interactions of araneomorph spiders have received considerable attention, but there are few detailed studies on intraspecific interactions of mygalomorph spiders. Moreover, a thorough understanding of theraphosid biology and ecology is necessary from a conservation standpoint because natural populations may be threatened by habitat disturbances and captures for pet commerce. We described the behavior of conspecific individuals of Grammostola schulzei during non-sexual interactions, under laboratory conditions. Pairs of individuals involving adult males, adult females and juveniles were confronted and observed in resident and intruder conditions, totalizing 115 trials. When confronted two adult females, they retreated or grappled, and performed gaping display with bite attempts, usually resulted in severe injury of the intruder spiders. When confronted females with large juveniles, we frequently observed cannibalism on juveniles. Juveniles exposed to females or to other juveniles retreated or made leg tapping with forelegs and palpal drumming, which are common displays of courting adult males. Adult males courted and clasped some juveniles, but juveniles avoided or reject clasping. The behaviors observed during intraspecific interactions could play an important role determining spatial distribution and could lead to behavioral adaptations of territoriality.     

An integrative systematic approach to species diversity and distribution in the genus Mesophyllum (Corallinales,Rhodophyta) in Atlantic and Mediterranean Europe

For the first time, a comprehensive assessment of Mesophyllum species diversity and their distribution in Atlantic Europe and the Mediterranean Sea is presented based on molecular (COI-5P, psbA) and morphological data. The distribution ranges were redefined for the four species collected in this study: M. alternans, M. expansum, M. macroblastum and M. sphaericum. Mesophyllum sphaericum, which was previously known only from a single maerl bed in Galicia (NW Spain), is reported from the Mediterranean Sea. The known range of M. expansum (Mediterranean and Macaronesia) was extended to the Atlantic Iberian Peninsula. The occurrence of M. alternans was confirmed along the Atlantic French coast south to Algarve (southern Portugal). Mesophyllum lichenoides was only recorded from the Atlantic, whereas M. macroblastum appears to be restricted to the Mediterranean Sea. A positive correlation was observed between maximum Sea Surface Temperature (SSTmax) and the depth at which M. expansum was collected, suggesting that this species may compensate for higher SST by growing in deeper habitats where the temperature is lower. The latter indicates that geographic shifts in the distribution of coastal species as a result of global warming can possibly be mitigated by changes in the depth profile at which these species occur. Mesophyllum expansum, an important builder of Mediterranean coralligenous habitats, may be a good target species to assess its response to climate change.     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

A polyphasic approach to the delimitation of diatom species: a case study for the genus Pinnularia (Bacillariophyta)

Diatoms are one of the most abundant and arguably the most species‐rich group of protists. Diatom species delimitation has often been based exclusively on the recognition of morphological discontinuities without investigation of other lines of evidence. Even though DNA sequences and reproductive experiments have revealed several examples of (pseudo)cryptic diversity, our understanding of diatom species boundaries and diversity remains limited. The cosmopolitan pennate raphid diatom genus Pinnularia represents one of the most taxon‐rich diatom genera. In this study, we focused on the delimitation of species in one of the major clades of the genus, the Pinnularia subgibba group, based on 105 strains from a worldwide origin. We compared genetic distances between the sequences of seven molecular markers and selected the most variable pair, the mitochondrial cox1 and nuclear encoded LSU rDNA, to formulate a primary hypothesis on the species limits using three single‐locus automated species delimitation methods. We compared the DNA‐based primary hypotheses with morphology and with other available lines of evidence. The results indicate that our data set comprised 15 species of the P. subgibba group. The vast majority of these taxa have an uncertain taxonomic identity, suggesting that several may be unknown to science and/or members of (pseudo)cryptic species complexes within the P. subgibba group.     

Theraphosidae phylogeny: relationships of the ‘Ischnocolinae’ genera (Araneae,Mygalomorphae)

The mygalomorph spider subfamily ‘Ischnocolinae’ was originally established as a group based on the presence of divided tarsal scopula. Later, the divided condition of the scopula was considered the plesiomorphic state, which could not support the monophyly of ‘Ischnocolinae’. In Raven 1985, the subfamily was considered paraphyletic, pending a phylogenetic analysis to reinvestigate monophyletic groups. This study comprises such a phylogenetic analysis, based on morphological data, that includes representatives of all genera currently included in ‘Ischnocolinae’ as well as representatives of all other nine Theraphosidae subfamilies (Thrigmopoeinae, Ornithoctoninae, Eumenophorinae, Stromatopelminae, Harpactirinae, Selenogyrinae, Theraphosinae, Aviculariinae and Selenocosmiinae). The family Theraphosidae is considered monophyletic and expanded to include three additional genera previously considered as possible Barychelidae, namely Brachionopus (as Harpactirinae), Trichopelma and Reichlingia (as Ischnocolinae sensu stricto) while ‘Ischnocolinae’ as previously defined does not appear as monophyletic. However, two monophyletic groups were defined as subfamilies to include some former ‘Ischnocolinae’ representatives. The first group includes Acanthopelma rufescens, Trichopelma nitidum, Reichlingia annae, Ischnocolus spp., Holothele rondoni, Holothele culebrae and Holothele aff culebrae and is hereby named as Ischnocolinae (sensu stricto). The other subgroup comprises Sickius longibulbi, Holothele incei, Holothele aff incei, Guyruita spp., Schismatothele lineata, Hemiercus modestus, Holothele colonica and Holothele sp., together established as Schismatothelinae subfam. nov. Several genera included in former ‘Ischnocolinae’ appear as monophyletic (Catumiri, Oligoxystre, Heterothele, Nesiergus, Chaetopelma, Ischnocolus, Guyruita and Plesiophrictus). However, the genera Holothele, Schismatothele and Hemiercus deserve more attention in order to evaluate their intrarelationships and inclusion of species.     

Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae)

Antrodiaetus riversi (Araneae, Antrodiaetidae) is a dispersal-limited, habitat specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. This species occupies a disjunct distribution, with populations in the Sierra Nevada and Coast Ranges, separated by the inhospitable Central Valley. Previous studies of morphological and allozyme variation have suggested that these populations may constitute cryptic species. We investigated the phylogeography of A. riversi using both nuclear and mitochondrial DNA sequences, collected for a comprehensive population sample. These data reveal the presence of at least five species in the A. riversi complex - these species are deeply diverged, and genealogically exclusive in both nuclear and mitochondrial genomes. Each of these species is characterized by extreme population subdivision and deep phylogeographical structuring, consistent with minimal gene flow across the dissected Californian landscape. Three species are restricted to the Coast Ranges, one to high altitudes of the central Sierran Nevada, and one species is found in both ranges. These species have allopatric distributions, although species parapatry is hypothesized to occur in several areas. Species diversification appears to have pulsed in the Late Miocene/Early Pliocene, a timing consistent with biogeographical reconstructions for many Californian taxa, and a time of turbulent geological activity in the region.