Multivariate analysis of leaf shape patterns in Asian species of the Uvaria group (Annonaceae)

Multivariate analysis of leaf radian measurements was used to investigate variation in leaf shape among 34 Asian species of the Uvaria group, a large palaeotropical group of climbing Annonaceae characterized by imbricate petals and stellate hairs. Raw data were normalized by conversion into 15 ratio characters and using the log₁₀ transformation. All species surveyed showed a unique leaf-shape 'bauplan'. The ratio character with the greatest discriminating power in both the Principal Components Analysis and Discriminant Analysis (DA) results was a measure of the shape of the leaf base. Ratio characters with the highest factor loadings for principal components 1 and 2 clearly separated the sampled taxa when plotted against one another and provided support for the retention of several taxa as distinct species or varieties. Classification of cases into taxa using DA yielded a correct classification rate of only 52% for the ratio-transformed data; however, division of taxa in the dataset into smaller subgroups defined by discrete morphological characters significantly increased the accuracy of case identification to between 67 and 100% of cases correctly classified, depending on the group. Case identification using DA on log₁₀-transformed data was higher than for the ratio values in the entire dataset (61.7%) and the larger subgroups. However, the rate of correct case assignment was lower in the smaller groups than for the ratio data.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 231–242.     

Evolutionary distinctiveness and conservation priority of the endangered Najas ancistrocarpa (Hydrocharitaceae)

Phylogeny is vitally important to evaluate evolutionary distinctiveness and conservation priorities of species. Najas ancistrocarpa is one of the rarest and least known East Asian species of the c. 30–40 species of the aquatic plant genus Najas (Hydrocharitaceae). We used a recently discovered collection of this nationally and regionally endangered species in Japan and East Asia to assess whether N. ancistrocarpa is a distinct species or an untypical form of other Najas species and to evaluate its conservation priority in a phylogenetic context. The sample set of our previous study, exploring worldwide phylogeny of the genus was used with N. ancistrocarpa to delimit species boundaries in Najas and obtain conservation priority scores, calculated by multiplying evolutionary distinctiveness and global extinction risks converted from Red List categories. We performed molecular phylogenetic analyses of plastid (ptDNA) and nuclear (ITS) DNA datasets, STACEY species delimitation analysis using the multilocus dataset and a measurement of conservation priority with Tuatara. Najas ancistrocarpa was consistently placed in ptDNA and ITS trees. Species delimitation analysis objectively assessed that N. ancistrocarpa is phylogenetically distinct. Phylogenetic conservation prioritization ranked N. ancistrocarpa the second highest priority species of the genus Najas. Overall, in terms of biodiversity conservation, N. ancistrocarpa represents an important Najas species in Japan and probably the world.     

An extraordinary new rheophyte in the genus Leptactina (Rubiaceae, Pavetteae) from Rio Muni (Equatorial Guinea)

A distinctive new species of Rubiaceae from Rio Muni, Equatorial Guinea, is described and illustrated. Leptactina rheophytica is the only rheophyte known in the genus. Its diagnostic characters are elucidated, its taxonomic affinities are discussed, and notes on its conservation status are provided.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 109–113.     

Multivariate morphometric and allozymic analysis of theConospermum taxifolium (Proteaceae) species complex

A morphometric analysis of 18 attributes of 110 plants of theConospermum taxifolium complex suggests that it consists of three polythetically distinct taxa, corresponding to the traditional concepts ofC. taxifolium Smith s. str.,C. ericifolium Smith andC. ellipticum Smith. Discrimination is possible on the basis of leaf but not flower attributes. Analysis of allozymic variation indicates that the taxa are also genotypically differentiated.C. ericifolium andC. ellipticum are geographically isolated from each other but not fromC. taxifolium, andC. taxifolium is usually ecologically segregated from the other two taxa. Where this ecological segregation breaks down, morphological intermediates sometimes occur as the result of hybridization.     

A multivariate morphometric analysis and systematic review of Pseudonaja (Serpentes,Elapidae, Hydrophiinae)

Pseudonaja is a clade of seven nominal species of elapid snakes distributed throughout Australia and in southern New Guinea. The species‐level systematics of this group is generally considered to be problematic. A recent phylogenetic analysis of mitochondrial DNA sequences for a geographically extensive series of Pseudonaja specimens revealed nine major clades, of which six largely coincide with nominal species (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta and P. textilis). The three remaining clades are composed of specimens currently referred to P. nuchalis. This paper presents a multivariate analysis of 30 morphometric variables recorded for 220 specimens, representing the P. affinis, P. inframacula, P. textilis and three P. nuchalis clades (P. guttata, P. ingrami and P. modesta are well‐demarcated species and, accordingly, were not considered). The morphometric data readily separate these putative lineages, affording compelling evidence that they constitute evolutionary species. The names aspidorhyncha and mengdeni are resurrected for two of the three species presently recognized as P. nuchalis. These species, P. affinis, P. inframacula, P. nuchalis and P. textilis are redescribed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 171–197.     

Variation in the Festuca brachyphylla (Poaceae) complex in Svalbard, elucidated by chromosome numbers and isozymes

Contrasting with former taxonomic treatments, chromosome numbers and isozyme data support the delimitation of the seminiferous representatives of the Festuca brachyphylla complex in Svalbard into four species: F. baffinensis, F. brachyphylla, F. hyperborea and F. edlundiae. Unique enzyme markers were found for all species. Festuca brachyphylla proved hexaploid, and the others, tetraploid. The chromosome numbers of F. hyperborea and F brachyphylla (as circumscribed at present) are new to Svalbard. Festuca baffinensis is the most distinct species within the complex, probably representing a separate evolutionary lineage. The three other species seem closely related, showing mutually equidistant relationships. Some deviating plants found on disturbed ground might represent hybrid derivatives or an introduced foreign strain of the elsewhere variable F. brachyphylla. Materials of diploid F. ovina from northern Fennoscandia was enzymatically closely related to the F brachyphylla complex in Svalbard. Festuca brachyphylla, F. edlundiae , and F. hyperborea all had a stronger affinity to F ovina than to F baffinensis , indicating that the F brachyphylla complex is an artificial taxonomic group. There are reasons to believe that the origin of the polyploid taxa of the F brachyphylla complex can be traced to diploid species of the F. brachyphylla and F ovina complexes.     

Single-locus DNA barcoding and species delimitation of the sandfly subgenus Evandromyia (Aldamyia)

Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies – E. carmelinoi, E. evandroi, E. lenti and E. piperiformis – were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex.     

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages

Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.     

Multivariate morphometric study of theCardamine pratensis group (Cruciferae) in the Carpathian and Pannonian area

A multivariate morphometric study of theCardamine pratensis group is presented, based on 84 population samples collected from the Carpathian and Pannonian area in the Czech Republic, Slovakia, Poland, Ukraine, Hungary, and Romania. Among the multivariate methods, principal component analysis, cluster analysis, and classificatory and canonical discriminant analysis were used. The analysis of chromosome numbers from all populations studied showed wide variation. The morphometric study showed that not all groups of populations characterised by their chromosome numbers and geographical criteria are morphologically, and thus taxonomically, distinguishable. Besides the morphologically well characterised speciesCardamine dentata andC. rivularis, the following species were recognised in the area studied:C. matthioli, C. majovskii andC. pratensis. Within the last species, besides the typical populations, two diploid types are provisionally recognised: type ucranica and type rivularis auct..     

Floral organogenesis of Potamogeton distinctus A. Benn. (Potamogetonaceae)

The floral organogenesis of Potamogeton distinctus A. Benn. was observed under the scanning electron microscope (SEM). The floral buds are first initiated on the lower portion of inflorescence in alternating whorls of three. Each of the floral buds is subtended by a bract primordium during the early stages. The primordia of the floral appendages arise on the floral bud acropetally. Two lateral tepals are first initiated and then two median ones soon after. Stamens are normally initiated as elongate primordia opposite the tepals, with the two lateral stamens preceding the median ones. The two carpel primordia arise alternating with the stamens. In some flowers, one of the two gynoecial primordia becomes inactive soon after they are initiated, or only one carpel primordium is initiated. The present observation of the gynoecial development supports the viewpoint that the evolution of flower in Potamogeton involves a reduction in number of parts. The existence of bract primordium during the early stages in many species of Potamogeton indicates that the absence of bractin mature flowers should be the result of reduction.     

Species diversity of the genus Osmundea (Ceramiales,Rhodophyta) in the Macaronesian region

Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first‐order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI‐5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra‐ and interspecific relationships. Subsequently, one or several sequences of plastid‐encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as “Osmundea sp.1,” which is a sister taxon of O. hybrida.     

Reef‐building coralline algae from the Southwest Atlantic: filling gaps with the recognition of Harveylithon (Corallinaceae,Rhodophyta) on the Brazilian coast

The Southwest Atlantic is notable for having extensive reef areas cemented by nongeniculate coralline red algae. Based on an analysis of four genetic markers and morpho‐anatomical features, we clarify the species of Harveylithon in the tropical and warm temperate Southwest Atlantic. Species delimitation methods (mBGD, ABGD, SPN, and PTP), using three markers (psbA, rbcL, and COI), support the recognition of three new species: H. catarinense sp. nov., H. maris‐bahiensis sp. nov., and H. riosmenum sp. nov., previously incorrectly called Hydrolithon samoënse. Our findings highlight the importance of using an approach with several lines of evidence to solve the taxonomic status of the cryptic species.     

Fruits and seeds of Ruppia (Potamogetonaceae) from the Pliocene of Yushe Basin, Shanxi, northern China and their ecological implications

Numerous fruits and seeds of Ruppia are reported from the Upper Pliocene (2.3–3.5 Myr ago) Zhangcun Formation in Yushe Basin, Shanxi, northern China. They are the first fossil Ruppia from China and demonstrate the importance of fruit and seed fossils in recording genera not represented by fossil leaves. These Ruppia are characterized by possessing a small oval endocarp, smooth endocarp surface, distinct elliptical external depressions, distinct apical mucro, slightly curved seed shape and conspicuous globose hilum. A new species, R. yushensis Zhao, Collinson and Li, is described from these endocarp and seed features. Comparison with the two European Miocene species, R. palaeomaritima Negru and R. maritime-miocenica Szafer, indicates the existence at that time of three different geographical and stratigraphical species. R. yushensis constitutes the first Pliocene record of Ruppia and extends the range of fossils of this genus from Europe to eastern Asia. R. yushensis is the only aquatic plant in the uppermost middle part of the Zhangcun Formation. This monotypic occurrence indicates a brackish, clear, tranquil and shallow lake in this region in the Late Pliocene. The smooth endocarp surface further suggests a warm temperate or temperate palaeoclimate.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 317–329.     

Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae,Rhodophyta)

The simple and convergent morphologies of many red algae make these species difficult to identify using traditional morphological characters. Many cryptic species have been described in recent years based on molecular datasets, and this has led to the application of an integrative taxonomy approach in species delimitation. Here, we performed several species delimitation methods (mBGD, ABGD, SPN, PTP, GMYCs and GMYCm) based on two different loci (COI-5P and rbcL) in species of the Hypnea cornuta complex. These methods were combined with morphological and phylogenetic data, extensive sampling, analysis of topotype material, and historically relevant herbarium samples. Our findings demonstrate that the groups morphologically assigned to H. cornuta and H. stellulifera consist of five different cryptic species. H. cornuta is a polyphyletic taxon composed of three well-separated lineages, thus requiring sequencing of type or topotype specimens to determine which one is Hypnea cornuta sensu stricto. We have revealed that the distribution of H. stellulifera is limited to Asia, while the Brazilian specimens initially assigned to this species were clarified as a new endemic species: Hypnea cryptica sp. nov. Our results indicated that only an integrative approach combining several lines of evidence, including morphology, nomenclature history, molecular data, biogeography and ecology can correctly solve the taxonomic status of widely distributed cryptic species.     

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure , principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large‐scale ecological data for niche‐based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic‐scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.