Craniodental characters and the relationships of Procyonidae (Mammalia: Carnivora)

Recent phylogenies of Procyonidae based on molecular data differ significantly from previous morphology‐based phylogenies in all generic sister taxon relationships. I have compiled the most comprehensive dataset of craniodental morphology that incorporates previous morphological characters, and with the aid of high‐resolution X‐ray computed tomography, new characters. This expanded craniodental analysis is based on 78 characters and yields new phylogenetic results regarding the ingroup relationships of Procyonidae. These results include Bassariscus astutus as the least derived member of Procyonidae and Ailurus fulgens nested well within the clade. Additionally, there are some similarities to previous morphological analyses of Procyonidae. Although the characters used to unite and diagnose Procyonidae vary depending on the phylogenetic analysis and have ambiguous taxonomic distribution amongst both Procyonidae and Musteloidea, there is significant morphological support for clades within Procyonidae. In addition to the strength of the morphological support within the clade, the disparate topographical regions of the skull from which the characters are derived may indicate that these synapomorphies are indeed the result of homology rather than adaptive convergence, as suggested by analyses based on molecular data. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 669–713.     

Leaf morphology and anatomy of Camellia section Camellia (Theaceae)

The delimitations of species in Camellia section Camellia have been disputed for many years, resulting from uncertain relationships among species. Leaf morphological and anatomical characters for 54 species and three varieties in this section were investigated to reveal the relationships. Principal component analysis and cluster analysis were conducted using the transformed data for quantitative and qualitative characters from leaf morphology and anatomy. Combining the results of statistical analysis with comparative leaf characters of morphology and anatomy, we discussed the taxonomic treatment of section Camellia by Chang compared with that of Ming and we conclude that section Camellia consists of c. 50 species. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 456–476.     

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 phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.     

Barcoding,molecular taxonomy,and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

We tested the efficiency of cytochrome oxidase I (COI)‐barcoding as a taxonomic tool to discriminate and identify sympatric shrew species on Mount Nimba (Guinea). We identified 148 specimens at the species level using morphological characters and comparison with type specimens, including several taxa from Mount Nimba. We identified ten morphospecies and tested aspects of genetic diversity and monophyly using genetic data from three mitochondrial (16S, cytochrome b, and COI) and one nuclear marker (the breast cancer gene, BRCA). Nine morphospecies were validated under the phylogenetic and genetic species concepts, including the recently diverged species Crocidura buettikoferi, Crocidura theresae, and Crocidura grandiceps. Under the same concepts, our analyses revealed the presence of two cryptic species amongst animals identified as Crocidura muricauda. We then tested the efficiency of barcoding thanks to commonly used phenetic methods, with the 148 specimens representing 11 potentially valid species based on morphological and molecular data. We show that COI‐barcoding is a powerful tool for shrew identification and can be used for taxonomic surveys. The comparison of genetic divergence values shows the presence of a barcoding gap (i.e. difference between the highest intraspecific and the lowest interspecific genetic divergence values). Given that only a few COI sequences are available for Afrotropical shrews, our work is an important step forward toward their enrichment. We also tested the efficiency of the three other sequenced markers and found that cytochrome b is as efficient as COI for barcoding shrews. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 672–687.     

Multivariate morphometric analysis of the Potamogeton compressus group (Potamogetonaceae)

The Potamogeton compressus group is a complex of three to five closely related species with a circumpolar distribution in the Northern Hemisphere. Multivariate morphometric analyses (principal component analysis, cluster analysis, canonical and classificatory discriminant analyses) were used to elucidate the patterns of variation within this group and to test the morphological differentiation of the species recognized in the current literature. From the entire distribution range, 156 specimens of the group were included in the numerical methods. Results from morphological comparison are discussed in relation to molecular data, reproductive behaviour and geographical distribution. Morphometric analyses provided evidence that this complex can be clearly divided into three groups, one of which was subdivided mainly on the basis of allopatric occurrence and genetic differentiation. These groups correspond to four species accepted here: P. acutifolius (temperate regions of Europe), P. compressus (boreal and temperate regions of Europe and Asia), P. manchuriensis (northeastern China and Russian Far East) and P. zosteriformis (boreal and temperate regions of North America). Two species, P. acutifolius and P. compressus, are partly sympatric, but clearly differentiated morphologically and genetically, and effectively isolated reproductively. Endemic P. manchuriensis is characterized by a unique combination of characters and an occurrence in a limited geographical area. Allopatric P. zosteriformis is weakly differentiated morphologically from P. compressus, but differs markedly in molecular markers correlated with geographical differentiation. It may represent a cryptic species. In contrast, a recently suggested concept of southern Siberian P. henningii was not supported by our analyses. Plants so named are considered here as slender phenotypes of the widespread and variable P. compressus. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 112–130.     

Tracing geographical patterns of population differentiation in a widespread mangrove gastropod: genetic and geometric morphometrics surveys along the eastern African coast

In the present study, we assessed the inter‐ and intrapopulation genetic and morphological variation of Cerithidea decollata along the eastern coast of Africa. The population structure of C. decollata along the latitudinal gradient was examined by sequencing 420 bp of the mitochondrial cytochrome c oxidase I (COI) gene in 172 snails from 29 sites, in a combined analysis with geometric morphometrics in 1799 snails from 32 sites. Analysis of molecular variance and spatial analysis of molecular variance showed a moderate spatial population differentiation from Kenya to the Republic of South Africa, suggesting genetic divergence between the northern, central, and southern regions. This structure appears to be the result of life‐history traits combined with oceanographic features. Haplotype network and mismatch analysis suggest a recent population expansion during the Holsteinian interglacial period in the northern region and several colonization events in the central and southern regions. The morphometric approach suggests that morphological variation in shell shape is somewhat independent of the genetic divergence, revealing an overlap of shape across the latitudinal gradient but significant differences among‐population at a local level. This may indicate that similar ecological pressures are acting along the coast, leading to the occurrence of similar morphological characters. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 647–663.     

An integrative approach to characterize cryptic species in the Thoracostoma trachygaster Hope, 1967 complex (Nematoda: Leptosomatidae)

Nematode diversity may seriously be underestimated when taking into account cryptic speciation. Thoracostoma trachygaster is commonly found in kelp holdfasts along the California coastline and was recently shown to consist of at least two distinct molecular clades (I and II). Here, we provide detailed morphological analysis of both clades, based on measurements taken from video vouchers of respectively eight and 16 individuals from the previous study, as well as 80 newly collected specimens from four Californian beaches. The latter were vouchered, measured, and then subjected to molecular analyses of the mitochondrial cytochrome oxidase c subunit I (COI) gene, and the ribosomal D2D3 and internal transcribed spacer (ITS) regions. This integrative approach shows that the three molecular clades are phylogenetically and morphologically distinct species, but a combination of morphological characters is needed to distinguish them. Two new species, Thoracostoma fatimae sp. nov. and Thoracostoma igniferum sp. nov. , are identified and described. The spicule length of T. fatimae sp. nov. is significantly shorter than that of T. trachygaster. Thoracostoma igniferum sp. nov. can be distinguished by the irregular posterior edge of the cephalic capsule and the two internal subdorsal tropis‐like projections in the wall of the cephalic capsule, which are lacking in T. fatimae sp. nov. and T. trachygaster. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 18–35.     

Taxonomic revision of the genus Galictis (Carnivora: Mustelidae): species delimitation,morphological diagnosis,and refined mapping of geographical distribution

Although critical for enabling in‐depth evolutionary, ecological, or conservation‐orientated studies, taxonomic knowledge is still scarce for many groups of organisms, including mammals of the order Carnivora. For some of these taxa, even basic aspects such as species limits and geographical distribution are still uncertain. This is the case for the Neotropical mustelid genus Galictis, considered one of the least studied carnivoran genera in the Americas. To address this issue, we performed a comprehensive assessment of morphological and molecular characters to test the number of species within Galictis, and to characterize their distinctiveness and evolutionary history. In addition, we reviewed and consolidated the available information on the taxonomy of this genus, so as to provide a historical framework upon which we could interpret our data. Our analyses demonstrated that two Galictis species can be clearly delimited and diagnosed using metric and nonmetric morphological characters as well as DNA sequences from mitochondrial and nuclear gene segments. On the basis of this clarified species‐level delimitation, we reassessed the geographical range of each Galictis taxon, identifying possible areas of sympatry between them. These results provide a solid taxonomic framework for Galictis, enabling the development of additional studies focusing on this poorly known taxon. © 2013 The Linnean Society of London, Zoological Journal of the Linnean Society, 2013, 167 , 449–472.     

Elliptic Fourier analysis of leaf shape in southern African Strychnos section Densiflorae (Loganiaceae)

Leaves can be a useful source of taxonomic information in plants particularly when flowers and fruits are absent during certain periods of the year. In this study, we applied an elliptic Fourier analysis (EFA)‐based morphometric technique to assess leaf morphological divergence among four species of southern African Strychnos section Densiflorae. Using leaf specimen images from field and herbarium collections, we extracted six shape variables [i.e. principal components (PCs)] from the Fourier coefficients and used these variables to describe leaf outline among the species. Our results indicate that the symmetric component of a leaf is the main source of shape differences accounting for 90.25% of total leaf shape variation and captures the more obvious range of observed shapes. PC1 of the symmetric variables describes a wide range of visually observable leaf shape among the species. MANOVA revealed significant interspecific differences except between S. innocua and S. madagascariensis, which could not be separated by outline analysis. A cross‐validated group classification suggests that S. gerrardii, with a classification rate of 88.4%, is distinct from S. madagascariensis, contrary to some taxonomic treatments. We discuss the value of geometric morphometrics at detecting subtle morphological variations and the evolutionary implications of such variations, which may be undetectable to the human eye. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 542–553.     

Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South‐West Pacific)

The family Galatheidae is among the most diverse families of anomuran decapod crustaceans, and the South‐West Pacific is a biodiversity hot spot for these squat lobsters. Attempts to clarify the taxonomic and evolutionary relationships of the Galatheidae on the basis of morphological and molecular data have revealed the existence of several cryptic species, differentiated only by subtle morphological characters. Despite these efforts, however, relationships among genera are poorly understood, and the family is in need of a detailed systematic review. In this study, we assess material collected in different surveys conducted in the Solomon Islands, as well as comparative material from the Fiji Islands, by examining both the morphology of the specimens and two mitochondrial markers (cytochrome oxidase subunit I, COI, and 16S rRNA). These two sources of data revealed the existence of eight new species of squat lobster, four of which were ascribed to the genus Munida, two to the genus Paramunida, one to the genus Plesionida, and the last species was ascribed to the genus Agononida. These eight species are described along with phylogenetic relationships at the genus level. Our findings support the taxonomic status of the new species, yet the phylogenetic relationships are not yet fully resolved. Further molecular analysis of a larger data set of species, and more conserved genes, will help clarify the systematics of this group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 465–493.     

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     

Leaf epidermal character variation and evolution in Gaultherieae (Ericaceae)

The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum‐likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 686–710.     

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.     

Evidence of incipient speciation in the Neotropical mangrove Pelliciera rhizophorae (Tetrameristaceae) as revealed by molecular,morphological, physiological and climatic characteristics

Two variants of the Neotropical mangrove species Pelliciera rhizophorae distributed along both sides of the Isthmus of Panama were detected by different colouration of the floral bracts and the size of the floral and vegetative structures. These findings raised questions concerning a possible speciation event in P. rhizophorae, for which a series of macro‐ and microscopic morphological traits (reproductive and vegetative structures), molecular markers from plastid DNA and climatic profiles were analyzed. Samples of P. rhizophorae were collected in three localities from the Panamanian Caribbean and Pacific coasts. The data obtained from molecular markers and morphological traits showed significant differences between the variants. The climatic profiles showed contrasting characteristics of rainfall and temperature in their habitats: variant A is found in wetter zones and variant B occupies drier zones. Evidence suggesting that a process of incipient speciation has occurred in P. rhizophorae in response to ecogeographical isolation due to climatic factors is presented. The presence of two geographically separate genetic‐morphological groups, adapted to contrasting climatic conditions, will be the basis for suggesting the existence of incipient lineages in Pelliciera. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 499–510.