Phylogenetics and differentiation among the western taxa of the Erebia tyndarus group (Lepidoptera: Nymphalidae)

The phylogenetic relationships among six members of the 'tyndarus' group in the Erebia genus of Satyrid butterflies, i.e. E. tyndarus, E. cassioides, E. nivalis, E. calcaria, E. hispania and E. ottomana were analysed using data from 19 presumptive enzyme loci, as well as 440 and 429 bp, respectively, from the mitochondrial large ribosomal subunit (16S) and subunit 1 from the NADH dehydrogenase (ND1) genes. The two types of molecular data (allozymes and mtDNA) yielded largely congruent tree topologies. The two basal, independent lineages formed by E. ottomana and E. hispania are contrasted by a group of Genétically closely related taxa, suggestive of a recent radiation associated with allopatric speciation, and competitive exclusion. The time of divergence for the radiation event is similar for both allozymes and mtDNA with an estimation of 440000 years ago. The lineages involved in this radiation do not comply with all the criteria necessary to assign to each of them full species rank, but they can no more be included in one single species unit. Such situations involving more than two alio- or parapatric lineages may explain why polytomies are so often met in phylogenetic reconstructions, after the lineages have reached full species rank. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 319–332.     

Evolution of mosaic hybrid zone between invasive and endemic species of Cyprinidae through space and time

Hybridization phenomena can be considered in different ways. Hybridization studies can be used to elucidate some aspects of speciation and adaptation. However, hybridization may be a threat to endemic species. Here, we studied bidirectional introgression between two sympatric species of Cyprinidae: Chondrostoma toxostoma toxostoma and C. nasus nasus . Analysis of morphology, allozymes and mtDNA sequences revealed that the hybridization between these two cyprinids takes different forms in the same river. The mosaic hybrid zone (so called because of the absence of a simple cline) appeared to be partitioned due to the proportions of the two species along a spatial scale. The proportion of each hybrid group in this zone was unstable over a 5-year period. We propose various protection/conservation states for the C. t. toxostoma populations based on the level of introgressive hybridization and the genetic structure of both species in 'pure' populations.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 135–155.     

DNA phylogeny supports revised classification of Salmothymus obtusirostris

Salmothymus obtusirostris (soft-muzzled trout) is endemic to the South Adriatic drainage. Owing to its unusual appearance, which resembles both trout and grayling, it has been initially classified as a separate genus. However, this classification is ambiguous and has never been firmly established. We have studied mtDNA (control region and cytochrome b gene) and nuclear DNA (a part of LDH C*1 gene) variation between soft-muzzled trout from the upper part of the River Neretva, Bosnia and Herzegovina, and other salmonid representatives in order to examine how the current classification is congruent with molecular data. On the basis of sequence identity of mtDNA control region among several genera (i.e. Salmo , Oncorhynchus , Salvelinus , Acantholingua , Brachymystax , Thymallus and Coregonus ) a close relationship between Salmothymus , Salmo and Acantholingua was established. Phylogenetic analysis on a combined data set of mitochondrial and nuclear DNA, supported by 100% bootstraping, indicated that S. obtusirostris and A. ohridana are sister taxa which exhibit a closer relationship to S. trutta than to S. salar . This finding refutes the current classification, which recognizes S. obtusirostris as separate genus, and instead suggests its reclassification on the species level as Salmo obtusirostris .  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 399–411.     

Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes)

In studies of phylogeography and taxonomy, strong emphasis is usually placed on the study of mitochondrial (mt)DNA. In the present study, we present a remarkable case in which highly phenotypically divergent species have almost no divergence in mtDNA. Yellowhammers ( Emberiza citrinella Linnaeus) and pine buntings ( Emberiza leucocephalos S. G. Gmelin) differ noticeably in appearance and song but hybridize in some areas of contact. They share a variety of closely-related mtDNA haplotypes, with little divergence in frequencies, indicating a mitochondrial divergence time sometime during or after the last major glacial period. By contrast, nuclear DNA (amplified fragment length polymorphism markers and CHD1Z gene sequences) differs more strongly between the species, and these differences can be used to identify intermediate genetic signatures of hybrids. The combined amount of mitochondrial diversity within yellowhammers and pine buntings is very low compared to other Emberiza species pairs, whereas the level of variation at the nuclear gene CHD1Z is comparable to that within other species pairs. Although it is difficult to completely reject the possibility that the two species split extremely recently and experienced rapid nuclear and phenotypic differentiation, we argue that the evidence better supports another possibility: the two species are older and mtDNA has recently introgressed between them, most likely as a result of a selective sweep. Mismatches between mitochondrial and nuclear phylogeographic patterns may occur more commonly than previously considered, and could have important implications for the fields of phylogeography and taxonomy.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 422–438.     

Pollen morphology and phylogenetic relationships in neotropical Phyllanthus (Euphorbiaceae)

In order to provide new insights into phylogenetic relationships among the neotropical taxa of Phyllanthus , 28 illustrations are provided of the pollen grains of 22 selected species studied from 11 sections of the subgenera represented in the neotropics. Special attention has been given to subgenus Conami because of its variability in pollen morphology: of eight species illustrated, the apertures are diploporate colpi in three species and pores in five species; exine ornamentation is vermiculate in two species and pilate in the other six species. The six species in the neotropical sections Pityrocladus and Microglochidion (subgenus Emblica ) are characterized by prolate grains with an increased number of colpi (4–8). Of particular interest are species in which the pollen exine is clypeate (with exine shields); clypeate pollen grains are illustrated in two species of subgenus Xylophylla and in one species of section Cyclanthera that has unique exine shields with single central pila. The pollen of the one Brazilian phylloclade-bearing species illustrated (in section Choretropsis ) has 3-colporate grains with reticulate exine, typical for subgenus Phyllanthus , and very different from the clypeate grains of the West Indian phylloclade-bearing species in section Xylophylla . This pollen evidence clearly demonstrates homoplasy in the origin of phylloclades in Phyllanthus . Pollen morphological data suggest that the neotropical taxa of Phyllanthus have arisen following colonization from Africa (subgenus Kirganelia ) and Asia (subgenus Emblica ). © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 325–338.     

Mitochondrial DNA in the hybrid zone between Mus musculus musculus and Mus musculus domesticus: a comparison of two transects

We studied mtDNA introgression across the contact zone between Mus musculus musculus and M. m. domesticus in two independent transects in the Czech Republic and Bavaria, Germany. A total of 1270 mice from 98 localities in the Czech transect and 456 mice from 41 localities in the Bavarian transect were examined for presence or absence of a Bam HI restriction site in the mt-Nd1 gene. Using this simple mtDNA marker, variants that belonged to the M. m. domesticus lineage (presence of restriction site) could be unequivocally distinguished from those belonging to the M. m. musculus lineage (absence of restriction site). The extent of introgression of mtDNA, three autosomal allozymes and the X chromosome was compared. The introgression of X markers was more limited than was that of the allozymes and mtDNA. In the Czech transect, the centre for the mtDNA cline was shifted about 3.6 km to the west relative to the X chromosome cline, with asymmetric introgression from M. m. musculus to M. m. domesticus . Interestingly, in the Bavarian transect, the centre of the mtDNA cline was shifted about 10.9 km to the east relative to the X chromosome cline, with asymmetric introgression from M. m. domesticus to M. m. musculus, opposite in direction to that observed in the Czech transect.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 363–378.     

A multidisciplinary approach to discriminating different taxa in the species complex Pachycondyla villosa (Formicidae)

A multidisciplinary approach provides new evidence that strongly supports the differentiation of three taxa previously confounded in a single species, Pachycondyla villosa . All specimens studied were collected in the same location at Ilhéus, Bahia, Brazil. Bivariate plots of petiole heights vs. petiole lengths and isozyme patterns clearly differentiate the three taxa. Chain lengths and chemical structures of cuticular hydrocarbons are characteristic of each taxon. This congruent evidence shows that there are three different valid species. Ecological hypotheses are discussed to explain the benefits of these species remaining sympatric. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 249–259.     

Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West

The plethodontid genus Batrachoseps , the slender salamanders, is the most diverse clade of salamanders in western North America, but it has posed taxonomic difficulties because it contains many morphologically cryptic species. A segment of the mitochondrial DNA gene cytochrome b was studied for 278 individuals densely sampled from throughout the range of all 18 described species and several undescribed species. Phylogenetic analyses of the mtDNA data identify six major clades, one corresponding to the subgenus Plethopsis and five within a monophyletic subgenus Batrachoseps. All major clades and most species within these clades display strong phylogeographic structuring. Comparisons of mtDNA and allozyme data show that several allozymically cohesive groups are not monophyletic with respect to mtDNA. We suggest that this phenomenon results from fragmentation of populations, divergence in allopatry, and then recontact and gradual merging of units caused predominantly by male-mediated gene flow. The mtDNA offers evidence that populations were once more isolated than they are now, while the patterns of allozyme variation reflect recent and current interactions among populations. The complex patterns of morphological, allozymic and mtDNA variation associated with the constantly changing geological landscape give insight into the nature of processes responsible for species formation in Batrachoseps .  © 2002 The Linnean Society of London. Biological Journal of the Linnean Society , 2002, 76 , 361–391.     

Markedly discordant mitochondrial DNA and allozyme phylogenies of tube-nosed fruit bats, Nyctimene, at the Australian–Oriental biogeographical interface

Australo-Papuan tube-nosed fruit bats of the genus Nyctimene reach their most westerly distribution on the island archipelagos of eastern Indonesia. A recent morphological examination indicates three species occur on Moluccan islands. Both allozyme electrophoresis and mitochondrial DNA (mtDNA) sequencing reveal there are only two species present, Nyctimene cephalotes and Nyctimene albiventer , but there is considerable disparity between the results obtained from the two genetic data sets. Allozyme data indicate N. albiventer occurs on Wokam, which sits on the Australian continental shelf and was joined to Australo-Papua during the last glacial maximum, and N. cephalotes on the other Moluccan islands, all of which are off the continental shelf. Divergence of these two species is dated at approximately 1.5 Mya. By contrast, the mtDNA gene tree shows two deep clades, one containing all specimens from Wokam and Yamdena, and the second all the specimens from the other islands. This especially marked incongruence between the two genetic data sets is ascribed to either a single introgression event of N. albiventer mtDNA into N. cephalotes on Yamdena at around 100 000 ya or lineage sorting of very old mtDNA lineages that coalesce a rather long time before the speciation event. These results highlight that caution should be exercised when relying on mtDNA as barcodes in species taxonomy. The continental-associated N. albiventer on Wokam has higher levels of allozyme heterozygosity and mtDNA nucleotide diversity than the N. cephalotes populations occurring on the more remote islands, indicating that this colonizing species has experienced bottlenecks and/or a low effective population size since speciation.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 589–602.     

Molecular and morphological data reveal cryptic taxonomic diversity in the terrestrial slug complex Arion subfuscus/fuscus (Mollusca, Pulmonata, Arionidae) in continental north-west Europe

The importance and abundance of cryptic species among invertebrate taxa is well documented. Nowadays, taxonomic, phylogenetic and conservation biological studies frequently use molecular markers to delineate cryptic taxa. Such studies, however, often face the problem of the differential resolution of the molecular markers and techniques involved. This issue is explored in the present study of cryptic taxa within the terrestrial slug complex Arion subfuscus/fuscus in continental north-west Europe. To this end, morphological, allozyme and mitochondrial 16S rDNA sequence data have been jointly evaluated. Using allozyme data and gonad type, two distinct groups were consistently delineated, even under sympatric conditions. The 16S rDNA data strongly supported both those groups and even suggested the presence of three distinct taxa within one of them. However, in view of: (1) the allopatric distribution of three OTUs, (2) the lack of allozyme or morphological differentiation, and (3) the extremely high degree of intraspecific mtDNA variation reported in pulmonate gastropods, they are, for the time being, not regarded as valid species under the biological species concept. By means of 16S rDNA and allozyme data, the position of type and topotype material of A. subfuscus s.s. and A. fuscus relative to the newly defined OTUs was determined, thus clarifying the nomenclature of this species complex. Additionally, gonad type proved to be a useful character for distinguishing the two species in north-west Europe.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 23–38.     

Chromosome numbers in the tribes Anthemideae and Inuleae (Asteraceae)

Twenty-two chromosome counts of 19 taxa (21 populations) in the tribe Anthemideae and one member (one population) of the tribe Inuleae of the family Asteraceae are reported. The Anthemideae studied belong to the subtribes Artemisiinae (14 Artemisia taxa, and one species each of the genera Dendranthema , Filifolium and Neopallasia ) and Tanacetinae (one species each of the genera Lepidolopha and Tanacetopsis ). From the Inuleae, we studied one Inula species. Five counts are new reports (including two at generic level), six are not consistent with previous counts and the remainder are confirmations of very limited (one to four records) previous data. Most of populations of Anthemideae studied have the basic chromosome number x  = 9, with ploidy levels ranging from 2 x to 10 x . Dysploidy is also present, with two x  = 8 diploid taxa. The species of Inuleae studied is a diploid with x  = 10, also indicating dysploidy, other members of the same genus Inula having basic numbers of x  = 9 or 8.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 77–85.     

Natural hybridization does not dissolve species boundaries in commercially important sea cucumbers

The study of species boundaries in areas of sympatry provides important insight into speciation processes. We investigated whether (i) two sympatric holothurians, Holothuria scabra and H. s. var. versicolor constituted species, and (ii) specimens of intermediate phenotype hybrids. Results from allozyme and 16S mtDNA sequence analyses indicated these two sea cucumbers to be distinct but young biological and phylogenetic species. Several private allozyme alleles existed and a Bayesian analysis grouped varieties into separate clusters. MtDNA sequences hardly varied within each taxon, and nine single bp changes were diagnostic between these two taxa. Allozyme allele frequencies in individuals of intermediate phenotype were intermediate to those of H. scabra and H. s.  var.  versicolor , most private alleles were present and heterozygote frequencies were higher than in either species. Ancestry coefficients modelled for these individuals were close to 0.5, indicating that the two taxa contributed equally to their genome. MtDNA sequences were identical to those of either species. We conclude that individuals of intermediate phenotype represent F1 hybrids. The presence of hybrids demonstrates that the opportunity for introgression exists, but is not realized, as backcrossing and introgression were not supported by the data. Thus, the genetic integrity of either holothurian species remains intact through an unknown postzygotic mechanism, possibly hybrid sterility.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 261–270.     

A new species of Acantholimon Boiss. (Plumbaginaceae) from Turkey

A new species, Acantholimon avanosicum Dogan & Akaydin in the Plumbaginaceae is described and illustrated. The species grows on argillaceous slopes in Central Anatolia, Turkey. The diagnostic morphological characters that distinguish it from closely related taxa are discussed. A revised key to Acantholimon species in Turkey with densely distichous simple spikes is presented. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 365–368.     

Morphological and pollen differentiation in Solanum cardiophyllum ssp. cardiophyllum and S. cardiophyllum ssp. ehrenbergii

A multivariate analysis to differentiate morphologically the populations of wild potatoes Solanum cardiophyllum ssp. cardiophyllum and S. cardiophyllum ssp. ehrenbergii was carried out. An analysis of the morphology and the viability of pollen of these potato populations was also made. The results of the morphometric analysis indicate that both subspecies are phenetically different. The pollen grain shape and size in ssp. cardiophyllum are different in northern and southern populations. Pollen diameter is significantly different between subspecies. Based on these results we propose that these taxa should be considered as two separate species.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 415–426.     

Genetic variation and evolution in the genus Apodemus (Muridae: Rodentia)

Genetic variation was studied using protein electrophoresis of 28–38 gene loci in 1347 specimens of Apodemus agrar-ius, A. peninsulae, A. flavicollis, A. sylvaticus, A. alpicola, A. uralensis, A . cf. hyrcanicus, A. hermonensis, A. m. mystacinus and A. m. epimelas , representing 121 populations from Europe, the Middle East, and North Africa. Mean values of heterozygosity per locus for each species ranged from 0.02 to 0.04. Mean values of Nel's genetic distance ( D ) between the taxa ranged from 0.06 (between A. flavicollis and A. alpicola) to 1.34 (between A. uralensis and A. agrarius ). The highest values of D were found between A. agrarius and other Apodemus species (0.62-1.34). These values correspond to those generally observed between genera in small mammals. Our data show that A. agrarius and A. peninsulae are sister species, well-differentiated from other taxa. High genetic distance between A. m. mystacinus and A. m. epimelas leads us to consider them distinct species and sister taxa to other Western Palaearctic species of the subgenus Sylvaemus . The data also suggest a recent separation of members of the latter group from a common ancestor, and subsequent rapid radiation, making it difficult to infer phylogenetic relationships. Some taxonomic implications of the results are discussed further.© 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 395–419.     

Continental scale patterns of biodiversity: can higher taxa accurately predict African plant distributions?

The distribution maps of a total of 3563 species, which represent 8.9% of the known African angiosperm flora, were entered into cells representing a one-degree latitude–longitude grid of Sub-Saharan Africa. The computer programme WORLDMAP was used to explore continental scale patterns of biodiversity. The maps were used to assess the use of higher taxa as a surrogate measure for predicting patterns of species richness. Genera were found to predict species richness distributions most closely, with higher taxa (families, orders, subclasses) exhibiting progressively worse correlations. However in two areas, the Cape Region of South Africa and coastal Cameroon, there was a higher species to genus ratio than in other areas of Africa. In the Cape Region this meant that generic richness failed to predict species richness. Hotspots, defined as the 5% of grid cells with the highest scores for richness and range-size rarity, were identified for species and higher taxa. Whilst a high percentage of species richness hotspots were predicted by higher taxa, there were important exceptions like the Cape Region. Species range-size rarity hotspots were not well predicted by higher taxa. Hotspots of higher taxa (families and orders) do not therefore accurately predict the location of species hotspots. Higher taxa appear to provide a powerful and accurate tool that can be used to predict large scale patterns of species biodiversity in Sub-Saharan Africa. However care must be taken when using taxa higher than genera, especially if selecting areas of highest conservation priority. The special case of the Cape Region indicates the danger of extending predictive generalizations as the ecological mechanisms that promote and retain species may not be the same in all places. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 225–235.     

Limited mitochondrial DNA introgression in a Bombina hybrid zone

We analysed the variation at mitochondrial DNA (mtDNA) and six allozyme loci in two transects across a hybrid zone between the fire-bellied toads Bombina bombina and Bombina variegata in southern Poland. The mtDNA cline was narrower than allozyme clines in one transect (Przemyśl, β = 0.435, w  = 3.42 km) and shifted to the B .  bombina side in both (near Kraków by 1.32 km, α = 0.437, and near Przemyśl by 0.97 km, α = 0.319). Cytonuclear associations were weak. Narrowed mtDNA clines could be a by-product of female demography and lowered effective population size of mtDNA. Alternatively, restricted mtDNA introgression is a likely result of negative epistasis in recombinants augmented by environment-dependent selection because divergence of Bombina mitochondrial and nuclear genomes is large. The shift of the mtDNA cline, contrary to expectations from initial mating preferences and fecundity differences between the species, suggests that on the B .  bombina side of the zone hybrid females with B .  variegata mtDNA have a higher chance of leaving progeny.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 295–306.     

The two-horned chamaeleons of East Africa

There have been numerous attempts to resolve the taxonomy of the two-horned chamaeleons of East Africa. However, the high levels of intraspecific variation and reported sympatry of morphologically distinct taxa indicate that their current classification is unsatisfactory. Tissue samples were collected from specimens from most mountain massifs (excluding the Nguu) where two-horned chamaeleons are known to occur and were used to sequence partial 12S and 16S rRNA, as well as ND2 mtDNA genes. These specimens and further museum material were used to review morphological variation and to define discriminating characters for each taxon. Phylogenetic analyses of gene sequences show clear genetic divergence between allopatric populations, although two lineages occur in sympatry in the East Usambara Mountains, and is supported by divergent morphology. In light of these results a formal revision of the taxonomy of all East African two-horned chamaeleons is proposed and seven species are recognized ( Kinyongia boehmei , K. fischeri , K. matschiei , K. multituberculata , K. tavetana , K. uluguruensis and K. vosseleri ). These taxa form a monophyletic group except for K. uluguruensis , which seems to be more closely related to one-horned species. Most of these taxa have been previously described and subsequently reduced to synonyms. Two other previously described two-horned taxa are not recognized as valid: Chamaeleo tornieri is considered species inquiriendae , and C. fischeri werneri is placed in synonymy with K. multituberculata . A dichotomous key is provided for the identification of these taxa and some aspects of their conservation, ecology and evolutionary origins are also discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 367–391.     

Morphological differentiation among closely related species with disjunct distributions: a case study of Mediterranean Cyclamen L. subgen. Psilanthum Schwarz (Primulaceae)

In Cyclamen subgenus Psilanthum , previous authors have recognized three species ( C. repandum, C. balearicum and C. creticum ), with C. repandum subdivided into three subspecies (ssp. repandum , ssp. peloponnesiacum and ssp. rhodense ), and two varieties (var. vividum and var. peloponnesiacum ) within C. repandum ssp. peloponnesiacum . To examine the validity of this classification and the degree of morphological differentiation among closely related endemic taxa with disjunct distributions, we undertook analyses of three quantitative and eight qualitative morphological traits of flowers and leaves, most of which have previously been used without statistical comparison in the classification of the different taxa. Cyclamen balearicum showed high levels of morphological differentiation from all other taxa in subgenus Psilanthum consistent with its specific status. In contrast, morphological differentiation between C. creticum and subspecies of C. repandum was similar to that among the three subspecies of C. repandum . When compared with a recent molecular phylogeny of this subgenus, our results suggest that C. creticum may best be described as a geographical subspecies of C. repandum . The two varieties of C. repandum ssp. peloponnesiacum showed few significant differences for individual traits and their overall morphology is very similar to each other. The morphology of plants at three sites on Corsica strongly suggest, consistent with molecular data, the occurrence of hybrid populations between C. balearicum (outside of its previously recognized distribution) and local C. repandum .  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 133–144.     

An analysis and revision of Cyclamen L. with emphasis on subgenus Gyrophoebe O. Schwarz

Studies in the areas of comparative morphology and palynology of the genus Cyclamen L. (Primulaceae) are outlined, and used in combination with observations and analyses of past works and publications and of field data (gathered by the Cyclamen Society and others) to generate new data sets. These are subject to cladistic parsimony analysis for the entire genus, and to phenetic ordinal analysis for subgenus Gyrophoebe O.Schwarz, to reach a conclusion on the validity of the latter classification, and the separation of taxa within it. A phylogeny and subgeneric reclassification is proposed with the reinstatement of Cyclamen elegans Boiss. & Buhse at species level based on the results gathered. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 473–481.