Morphometric analysis of the Taxus wallichiana complex (Taxaceae) based on herbarium material

We used morphological and geographical data of 128 herbarium specimens of the Taxus wallichiana complex in eastern Asia to investigate their utilization in discriminating and identifying taxa included in the complex. One bud scale and 26 leaf characters were used to separate T. fuana , T. wallichiana var. wallichiana , T. wallichiana var. mairei , T. wallichiana var. chinensis and T. sumatrana by K-means clustering and dendrograms using Ward's distance. Out of the 27 characters examined 21 were found to be well correlated with geographical patterns. T. fuana was morphologically the most distant taxon, while T. sumatrana clustered among the T. wallichiana varieties. After correcting misidentifications of the specimens in T. wallichiana , its varieties occupied discrete geographical ranges, except for some limited sympatry of varieties mairei and chinensis east of the Tanaka–Kaiyong line and the Sichuan Basin, China. Our analysis demonstrates the importance of consistency in character selection and definition in the identification of morphologically difficult taxa and the power of combining morphometric and geographical data in clarifying their spatial distribution.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 307–335.     

Combining molecular, morphological and ecological data to infer species boundaries in a cryptic tropical pitviper

Few operational methods exist for delimiting species boundaries, and these usually require sampling strategies that are unrealistic for widespread organisms that occur at low densities. Here we apply molecular, morphological and ecological species delimitation criteria to a wide-ranging, fragmented group of Asian green pitvipers, the Popeia popeiorum complex. A mitochondrial DNA phylogeny for the group indicates two well-differentiated clades, corresponding mainly to northern and southern parts of its range. Strong phylogeographical structure within each clade suggests isolation in forest refugia during the Pliocene and a southward colonization of the Sunda islands during the Pleistocene. Multivariate analysis of morphological characters reveals a generally conserved pattern of geographical variation, incongruent with the recovered phylogenetic history. We compare groups delineated by mtDNA variation to morphological and ecological divisions in the complex, and discuss the implications of these for the taxonomy of the group. Discordance between species boundaries inferred from different criteria suggests that combining independent sources of data provides the most reliable estimation of species boundaries in organisms that are difficult to sample in large numbers.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 343–364.     

Geographic allozyme variation in the Japanese clouded salamander, Hynobius nebulosus (Amphibia: Urodela)

Using starch gel electrophoresis, geographical enzyme variation was surveyed in 46 populations of the Japanese salamander Hynobius nebulosus , which occurs widely in western Japan. This species exhibits substantial local genetic differentiation and is more diverse in inland regions than on small islands. In several different analyses, two groups of populations, one from Kyushu Island to the westernmost part of Chugoku district, Honshu (western group), and another from Shikoku through Kinki to Chubu district, Honshu (eastern group), were consistently recognized. Most of the remaining populations were placed in two less clearly-defined groups: the montane group from the Chugoku Mountains and the Chugoku group from the coastal regions of Chugoku district. The divergence patterns of H. nebulosus are thought to be related to the geological history of its range. The populations near the boundary of the western group were found to share several alleles that were predominant on both sides of the boundary, indicating past secondary contact. Differentiation in the montane group did not follow the isolation by distance model, probably because several populations included were genetically mixed with lowland populations of the Chugoku group.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 311–330.     

A multivariate analysis of the fringe-toed lizards of the Acanthodactylus scutellatus group (Squamata: Lacertidae): systematic and biogeographical implications

The taxonomy of the fringe-toed lizards of the Acanthodactylus scutellatus group has long been unstable and no consensus exists on the systematic status of its various forms. A multivariate analysis of morphological characters, performed on over 1000 specimens from most of the African range of this group, allowed us to clarify the specific allocation of most of the Saharan populations included in this species group. Based on comparisons of morphology between allopatric and sympatric populations of this complex, we propose the recognition of six biological species. Our results confirm the specific status of Acanthodactylus aureus , A. dumerili , A. scutellatus, A. longipes and the recently described A. taghitensis . In addition, we re-validate A. senegalensis (occurring from Mauritania and Mali south to Senegal), which has been treated as a synonym of A. dumerili by previous authors. Acanthodactylus longipes is reported for the first time from coastal Mauritania, and A. taghitensis (previously known only from a very small region in Algeria) is reported from continental Mauritania. The systematic section of this paper includes a full list of examined material, diagnosis and known distribution of each species, in addition to some information on geographical variation and ecology. A key for specific identification is provided as an appendix.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 117−155.     

Genetic variation and structure in native populations of the fire ant Solenopsis invicta: evolutionary and demographic implications

We studied population genetic variation and structure in the fire ant Solenopsis invicta using nuclear genotypic and mitochondrial DNA (mtDNA) sequence data obtained from samples collected throughout its native range. Geographic populations are strongly differentiated at both genomes, with such structure more pronounced in Brazil than in Argentina. Higher-level regional structure is evident from the occurrence of isolation-by-distance patterns among populations, the recognition of clusters of genetically similar, geographically adjacent populations by ordination analysis, and the detection of an mtDNA discontinuity between Argentina and Brazil coinciding with a previously identified landform of biogeographical relevance. Multiple lines of evidence from both genomes suggest that the ancestors of the ants we studied resembled extant northern Argentine S. invicta , and that existing Brazilian populations were established more recently by serial long-distance colonizations and/or range expansions. The most compelling evidence for this is the corresponding increase in F _K (a measure of divergence from a hypothetical ancestor) and decrease in genetic diversity with distance from the Corrientes population in northern Argentina. Relatively deep sequence divergence among several mtDNA clades, coupled with geographical partitioning of many of them, suggests prolonged occupation of South America by S. invicta in more-or-less isolated regional populations. Such populations appear, in some cases, to have come into secondary contact without regaining the capacity to freely interbreed. We conclude that nominal S. invicta in its native range comprises multiple entities that are sufficiently genetically isolated and diverged to have embarked on independent evolutionary paths.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 541–560.     

Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae)

Land snails have long been recognized as suitable organisms for studying phenotypic differentiation and phylogeny in relation to geographical distribution. Morphological data (shell and anatomy biometry on different geographical scales) and partial sequences from mitochondrial genes (cytochrome oxidase subunit I , 16S rDNA) were used to test whether morphological patterns match phylogeny in a diversified group of Sicilian rock-dwelling land snails belonging to the genus Marmorana . The taxonomic implications of the three character sets (shell and anatomical biometry and molecular data) were also considered. The inferred phylogenetic relationships do not match morphological (shell and genitalia) patterns. This result may significantly modify the current taxonomy. Mitochondrial based reconstructions define several supported clades well correlated with geographic distribution and populations were found to be distributed parapatrically. The progressive decline in mitochondrial DNA sequence similarity over a distance of 250 km is consistent with a model of isolation by distance, a pattern previously recognized for other groups of land snails. For one clade of Marmorana , colonization along Mediterranean trade routes appears to be a possibility.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 809–823.     

Morphological and geographic variation of the cycad Dioon edule Lindl. (Zamiaceae): ecological and evolutionary implications

The relationship in geographical distribution and morphological variation of leaflet width and length (diagnostic trait), between and within populations of Dioon edule Lindl., has been investigated throughout its known range in eastern Mexico (from the states of Nuevo León to Veracruz, north to south, respectively). A total of 1832 leaflets were measured for width and length from 154 plants distributed amongst five populations using four leaflet replicas from each of three leaves per plant. For leaflet width and length the variation among populations indicated significant stat-istical differences ( F _4,147 = 125.83; P  < 0.0001; R ² = 92.17% and F _4,147 = 9.04; P  < 0.001; R ² = 26.8%), respectively. With respect to leaflet width, the multiple range test showed three groups with a north to south distributional relationship along the range of the species. The correlation coefficient among paired populations, respect to geographical distance and the absolute value of the mean difference of leaflet width in each population, was positive, and different from zero ( r  = 0.82; P  = 0.013). A great variation of important ecological and evolutionary parameters was shown.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 465–470.     

Leaf morphometric variation in Quercus affinis and Q. laurina (Fagaceae), two hybridizing Mexican red oaks

Leaf variation was examined in two hybridizing Mexican red oaks, Quercus affinis and Q. laurina . Data of nine traits were obtained for ten randomly chosen leaves in each of 512 individuals from 16 populations sampled along a geographical gradient, including the distribution area of both species and a putative area of secondary contact and hybridization. A cluster analysis recognized two main groups of populations, which were congruent with the taxonomic assignment of the predominant morphological type within the populations and were thus labelled ' Q. affinis -like' and ' Q. laurina -like' population groups. A nested analysis of variance revealed that the largest proportion of the total variation was contained within populations, as among-tree variation (28–54%, depending on the trait), and as intra-individual variation (17–56%). However, differences between the two groups of populations (3–27%) and among populations within groups (5–21%) were also significant for the nine traits. A distinct pattern of change across populations was observed for each trait. Variation was particularly pronounced along the geographical gradient for petiole length and leaf-margin teeth number, possibly implying selection on these two traits. Results suggest that phenotypic plasticity, gene flow, hybridization and natural selection have shaped foliar variation in this oak complex. © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 427–435.     

Glacial history of high alpine Ranunculus glacialis (Ranunculaceae) in the European Alps in a comparative phylogeographical context

There is considerable controversy concerning the fate of Alpine plants during Pleistocene glaciations. While some studies have found evidence for nunatak survival, others have explained the present genetic patterns by survival only in peripheral refugia. We investigated 75 populations of high alpine Ranunculus glacialis from its entire Alpine distribution. Phylogeographical analyses of AFLP data revealed four groups of populations. Two of them, located in the western Alps, were genetically isolated from each other and from the eastern groups, whereas the two eastern Alpine groups were genetically more similar to each other. This suggests longer isolation and/or lower levels of gene flow in the two western groups. As all groups are close to, or overlap with, presumed glacial refugia, invoking glacial survival on nunataks is unnecessary to explain the present genetic pattern. Similar to the phylogeographical patterns of R. glacialis , the previously investigated alpine Phyteuma globulariifolium and Androsace alpina , which are also confined to siliceous bedrock, showed strong geographical affinities to peripheral refugial areas and there were large-scale congruencies in the location of these refugia for all three species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 183–195.     

Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences

Salamander populations of the Plethodon jordani species complex form a challenging system for applying the general lineage concept of species to diagnose population-level lineages. The present study reports and analyses mitochondrial-DNA haplotypes (∼1200 nucleotide bases from the genes encoding ND2, tRNA^Trp, and tRNA^Ala from 438 salamanders) from 100 populations representing six species of the P. jordani complex ( Plethodon amplus , Plethodon cheoah , Plethodon jordani , Plethodon meridianus , Plethodon metcalfi , and Plethodon montanus ) with comparative analyses of previously published allozymic data to reconstruct the evolutionary history of this group and to diagnose species lineages. Analyses of mitochondrial haplotypic data include nested-cladistic analysis of phylogeography, analysis of molecular variance, hierarchical analysis of nucleotide-diversity measures, and likelihood-based estimates of recent temporal changes in population size. New analyses of allozymic data include multidimensional scaling and principal component analyses, and both data sets are analysed and compared for congruent genetic structure using Mantel correlation tests. These analyses in combination identify the six named species as distinct evolutionary lineages despite sporadic genetic exchanges among them and some discordance between mitochondrial DNA and allozymic markers. Sexual isolation is not complete for any pair of these six species, but they replace each other geographically and appear to block the geographical spreading of their neighbours. The P. jordani complex is a strong study system for investigating the genetic and ecological processes responsible for vicariant speciation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 25–51.     

Infraspecific variation and phylogeography of the high-polyploid Iberian endemic Anthoxanthum amarum Brot. (Poaceae; Pooideae) assessed by random amplified polymorphic DNA markers (RAPDs) and morphology

High morphological and ecological diversity has been observed in the north-west Iberian Peninsula endemic Anthoxanthum amarum Brot., for which two different morphotypes (northern and southern) have been described on the basis of qualitative traits and geographical origin. In the present study, a combined molecular and morphological method was applied to ten populations of this species with the following aims: (1) to assess whether the variation observed was taxonomically meaningful; (2) to assess the influence of the environment on the variation in the morphological characters; and (3) to track the potential phylogeographical information deduced from our random amplified polymorphic DNA marker (RAPD) data in order to draw inferences about the past history of this species in the north-west Iberian Peninsula. To achieve these aims, 26 macromorphological characters were recorded in 279 specimens, and 77 RAPD phenotypes were identified in the 79 plants studied. The association analyses performed using the morphological and molecular data showed that no clear separation existed between the morphs, and a strong correlation between qualitative characters and the environment was detected. Moreover, both the multivariate analyses and the assignment test based on RAPD data revealed that the genetic variation was hierarchically structured, and three genetically distinct groups could be identified. Two of these clusters might correspond to different expansion routes proposed in the literature for different plant species in the north-west Iberian Peninsula.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 179–192.     

Morphological variation of the Oncocyclus irises (Iris: Iridaceae) in the southern Levant

Morphological traits of Iris section Oncocyclus (Siems.) Baker in the southern Levant (Israel, Jordan, The Palestinian Authority and Sinai/Egypt) were analysed in order to clarify taxonomic relationships among taxa and the validity of diagnostic characters. Floral and vegetative characters were measured in 42 populations belonging to nine species during the peak of the flowering season in 1998–2000. Pearson's Coefficient of Racial Likelihood (CRL) was used to calculate morphological distances between populations. Twelve of the measured populations, distributed along the north-south aridity gradient in Israel, were further explored for morphological changes along the gradient. Cluster analysis revealed two major clusters: the first includes most of the dark-coloured Iris populations, with populations of I. petrana Dinsmore and I. mariae W. Barbey forming a subcluster; the second consists of all the light-coloured populations but also some dark-coloured populations. Pearson's CRL and geographical distance were significantly correlated among the dark-coloured populations. Along the geographical gradient, flower, stem and leaf size traits decrease towards the south, probably as an adaptation to aridity. This suggests that natural selection promoted the differences between populations. Almost no discrete phenotypic groups exist within the Oncocyclus species of the southern Levant except for variation in the floral colours. Most of the suggested diagnostic characters proved unreliable in that they varied continuously across populations. The taxonomical difficulties encountered in this study reflect the special evolutionary state of the Oncocyclus irises as a group in the course of speciation.  © 2002 The Linnean Society of London. Botanical Journal of the Linnean Society , 2002, 139 , 369–382.     

Patterns of morphological evolution in Marmota (Rodentia, Sciuridae): geometric morphometrics of the cranium in the context of marmot phylogeny, ecology and conservation

Marmots are of great interest for both sociobiologists studying the evolution of mammal societies and conservationists trying to protect them from extinction. In contrast, their phylogeny and morphological evolution are poorly understood and studied. Recently, a phylogenetic analysis using cytochrome b provided the first reconstruction of marmot evolutionary history and suggested that a high level of sociality evolved at least twice independently in the two proposed marmot subgenera. A morphological analysis of the marmot mandible supported this subgeneric classification and showed interesting, and unexpected, patterns in the evolution of marmot skeletal characters. In the present study we investigated a more complex, and potentially informative structure, the ventral cranium. Geometric morphometric techniques were applied in the first analysis of cranial morphology including all marmot species. Three main phenetic groups were found, which reflect phylogeny (subgenus Petromarmota , and Palaearctic subgenus Marmota ) or geographical distribution (Palaearctic vs. Nearctic subgenus Marmota ). Convergence in skeletal characters due to size similarities, a common finding in the sciurid skeleton according to traditional morphological analyses, did not occur in the marmot ventral cranium. Despite a genetic distance between Marmota vancouverensis and Marmota caligata similar to that among different populations of the latter species, the Vancouver Island marmot had the most atypical ventral cranium in the subgenus Petromarmota . This finding confirmed results obtained with the mandible, and emphasized the uniqueness of M. vancouverensis and the usefulness of complementing molecular analyses with morphological studies for a thorough characterization of population divergence, and a careful planning of conservation strategies.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 385–407     

Revision of Pseudonereis (Polychaeta, Nereididae)

A taxonomic revision of Pseudonereis (Polychaeta, Nereididae) shows that some of the described taxa are very similar in most morphological characteristics. The revision includes all ten taxa considered valid, and are redescribed from type material. Lectotypes are designated for Pseudonereis anomala Gravier, 1901, Pseudonereis noodti (Hartmann-Schröder, 1962) and Pseudonereis trimaculata Horst, 1924. The widely geographically distributed and well-known P. gallapagensis Kinberg, 1865 and P. variegata ( Grube, 1857 ) show striking morphological resemblance to less well-known taxa with similar distribution. Paragnath variation in populations of P. anomala is discussed relating to its geographical distribution. Pseudonereis trimaculata is recorded from Australia for the first time. Taxa belonging to Pseudonereis are predominantly tropical and subtropical. A cladistic analysis using parsimony is included to test for monophyly of Pseudonereis . A monophyletic clade including all Pseudonereis taxa is given low bootstrap support. This clade is supported by the synapomorphies: presence of paragnaths in closely spaced comb-like rows on the maxillary ring on the pharynx, and presence of p-bar paragnaths in Areas II–IV and VII–VIII. Several of the included taxa share the shield-shaped paragnath in Area VI, which serves to distinguish Pseudonereis spp. from Perinereis spp. Paragnaths of the type p-bars and shield-shaped bar is described for the first time; the latter character is different from the smooth bar-shaped paragnaths in Area VI as has previously been described in these taxa.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 145–176.     

Fluvial range expansion, allopatry, and parallel evolution in a Danubian snail lineage (Neritidae: Theodoxus)

The snails Theodoxus danubialis and Theodoxus prevostianus form a single clade native to freshwaters of south-eastern Europe whose inter- and intraspecific relationships remain unresolved. The present study utilized a phylogeographical approach to clarify the relationship of these species as well as to reconstruct the evolutionary and demographic history of populations in the western portion of their range. Phylogenetic, population genetic, and nested clade analyses reveal a clade that has distributed itself upriver from a lower Danube River source population and become genetically distinct primarily through range expansion and localized allopatric divergence. Notably, this geographical pattern is replicated phylogenetically in the form of two cytochrome c oxidase subunit I (CO I) lineages that are present simultaneously in individual snails. Haplotypes from polymorphic individuals form two distinct clades, both of which show phylogenetic and nucleotide substitution patterns consistent with a mitochondrial origin, and whose common ancestor must have occurred in a lower Danube source population. Separated allopatrically from their Danubian relatives, populations of T. danubialis in northern Italy have also undergone substantial range expansion, much more recently than Danube watershed lineages. In addition to repeated patterns of range expansion, parallelism is found in T. prevostianus , which is shown to be a nonmonophyletic taxon of remarkable morphological and ecological similarity.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 603–617.     

Biogeographical connections between the Maghreb and the Mediterranean peninsulas of southern Europe

The glacial–interglacial cycles have caused severe range modifications of species' distributions. In Europe, thermophilic species had to retreat into geographically distinct southern refugia during glaciations. This process produced strong genetic imprints, which are still detectable by the present pattern of genetic differentiation and the distribution of regional diversity. To reveal the biogeographical imprints in the western Mediterranean, we analysed 26 populations of the butterfly Maniola jurtina spread over large areas of its European and North African distribution range. The samples were analysed using allozyme electrophoresis. We detected three genetic groups, divided into Western Europe, Central/Eastern Europe, and Italy with the Maghreb. The North African samples randomly cluster within the Italian samples. Even the population sampled in Morocco is genetically closely related to these samples and not to the geographically neighbouring Iberian ones. Parameters of genetic diversity showed similar values over the whole study area. The observed genetic pattern reflects possible glacial refugia in Europe located in the Iberian Peninsula and the Balkans. For North Africa and Italy, our data reveal a colonization of Africa originating from Italy.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 693–703.     

Distinct geographical structure across species units evidenced by chloroplast DNA haplotypes and nuclear ribosomal ITS genotypes of Corylopsis (Hamamelidaceae) in the Japanese islands

The geographical distribution of chloroplast DNA (cpDNA) haplotypes and nuclear ribosomal internal transcribed spacer (nrITS) genotypes of Japanese Corylopsis (Hamamelidaceae), which consists of four species, was investigated. Two hundred and five individuals belonging to four species from 30 populations, covering the entire geographical range, were studied. Based on approximately 1108 bp of the three non-coding regions of cpDNA, nine haplotypes were detected, and each was distinguished from adjacent haplotypes by one substitution. Based on approximately 507-bp nrITS sequences, 47 genotypes were detected, for which three clades were identified in the phylogenetic analysis. There was inconsistency between the cpDNA haplotypes, nrITS genotypes, and classification of Corylopsis taxa, possibly because of incomplete lineage sorting or introgressive hybridization. The distribution of the haplotypes was highly structured geographically, and N _ST (0.893) was significantly greater than G _ST (0.819), implying that the current distribution of Corylopsis species was structured phylogeographically during Quaternary climatic oscillations. The haplotype composition and results of analysis of molecular variance showed that the populations in Hokuriku were highly divergent, suggesting that they are long-term persistent populations arising from refugia during the Quaternary climatic oscillations. Refugial populations in Chugoku and Shikoku may have lost genetic diversity because of a bottleneck resulting from a small population size, followed by post-glacial range expansion. Pre-existing refugia may have been so small that the subsequent range expansion replaced the pre-existing genetic structure.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 501–518.     

Taxonomic studies on Senecio aquaticus (Asteraceae). A recommendation for the taxonomic status of Aquaticus and Barbareifolius

Aquaticus and Barbareifolius are two subgroups of Senecio aquaticus s. l. (Asteraceae) that have been recognized at various taxonomic levels in European taxonomic literature. In this paper we present the results of morphological studies on S. aquaticus s. l. in order to establish the taxonomic status of these two subgroups. Using multivariate morphometric techniques (discriminant analysis and principal component analysis), we examined the diagnostic potential of 60 macro-morphological characters and studied the delimitation of Aquaticus and Barbareifolius. Seven of the characters studied were included in the discriminant function of the stepwise discriminant analysis and are therefore considered to be the most reliable diagnostic characters of Aquaticus and Barbareifolius. Barbareifolius has, amongst other distinguishing traits, a more divaricate inflorescence than Aquaticus. Because both subgroups are distinct but overlapping clusters in multivariate morphometric space, and because clear differences in their geographical distribution are absent, we recommend the taxonomic status of variety to both groups. Following the rules of nomenclature, Aquaticus and Barbareifolius should therefore be named S. aquaticus Hill var. aquaticus and S. aquaticus Hill var. barbareifolius (Krock.) Wimm. & Grab.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 489–498.