Canarian land snail diversity: conflict between anatomical and molecular data on the phylogenetic placement of five new species of Napaeus (Gastropoda, Pulmonata, Enidae)

Five new species of land snail (family Enidae) are described from La Gomera (Canary Islands) of which the majority, on the basis of anatomy alone, could be incorporated within a new supraspecific taxon. In addition to the morphological study of these new species, a region of the 16S mitochondrial gene is sequenced from three of the new species and a range of species of Napaeus from within its two subgenera ( Napaeinus and Napaeus ) . There is a disparity between the morphological and preliminary molecular phylogenetic data. Possible explanations for this conflict are discussed, as well as the evolutionary relationships among these different taxa, and it is suggested that this group may be an excellent model for further studies of adaptation and diversification.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 169–187.     

Phylogenetic relationships in the subgenus Mus (genus Mus, family Muridae, subfamily Murinae): examining gene trees and species trees

Over eight kilobases (kb) of sequence from eight genes including two mitochondrial loci, Cyt b and 12S, and six nuclear loci, B2m , Zp3 , Tcp1, Sry, Smcx and Smcy , were used to investigate phylogenetic relationships among 11 taxa representing eight species within the rodent genus Mus . Particular attention was given to discerning relationships among species within the subgenus Mus including members of a Palearctic clade ( M. musculus , M. spicilegus , M. macedonicus and M. spretus ) and members of an Asian clade ( M. caroli , M. cookii and M. cervicolor ), as previous studies using different datasets have produced different topologies for taxa within these two groups. While parsimony analyses of the combined eight-gene dataset yielded a single, fully resolved tree, support values were lower for nodes resolving relationships within the Palearctic and Asian clades than they were elsewhere in the tree. In addition, a maximum likelihood analysis of the same eight-gene dataset yielded different topologies for both the Palearctic and the Asian clades. Both observations are indicative of clade instability. The nature of this instability was explored through a comparison with our previous study in which we included the two mitochondrial loci and only four of the six nuclear genes, and through an analysis of partitioned data, specifically mitochondrial vs. nuclear genes. This study underscores the importance of considering among-site rate variation in phylogeny reconstruction. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 653–662.     

Comparative vegetative anatomy and systematics of the Oncidiinae (Maxillarieae, Orchidaceae)

Subtribe Oncidiinae comprises a vegetatively heterogeneous assemblage of species that has persistently been incapable of organization. Anatomy was considered to be a possible means to resolve the perplexity of relationships amongst the constituent taxa. The consistent occurrence of a foliar hypodermis, homogeneous mesophyll, conical silica bodies in stegmata, and ubiquitous fibre bundles in leaves provides a matrix for linking the taxa, as do the parenchymatous pith and O-thickened endodermal cell walls in roots. However, the strict consensus of the 40 genera studied was completely unresolved, suggesting that vegetative characters alone are insufficient to assess the relationships amongst these taxa, a conclusion also reached for the remainder of Maxillarieae.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 91–107.     

Genetic differentiation and gene flow of two sparidae subspecies, Diplodus sargus sargus and Diplodus sargus cadenati in Atlantic and south-west Mediterranean populations

A total of nine enzymes coded by 14 loci were assayed for each of six populations (from the north-eastern Atlantic and the Mediterranean) of two sea bream subspecies ( Diplodus sargus sargus and Diplodus sargus cadenati ). Diagnostic alleles were observed for each subspecies, although there were several common alleles. Estimates of variance in allele frequencies among samples ( F _ST) revealed significant differences ( P  < 0.05) among both subspecies. Genetic divergence was found between Atlantic and Mediterranean samples: values for genetic distances were higher than 0.163. Furthermore, D. sargus cadenati populations displayed a higher mean weight and length than D. sargus sargus populations and significant differences in growth were found among subspecies and populations. These results are discussed in terms of levels of gene flow and its respective relationships with water circulation in the Strait of Gibraltar and geological events.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 705–717.     

A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887

The systematic biology of the subgenus Daphnia s . s . remains confused. Prior attempts at resolution used chiefly postabdominal claw morphology, chromosome numbers and rRNA gene sequences as characters for higher-level relations. Still, several taxa, such as Daphnia curvirostris Eylmann, 1878, have unclear affiliations. We addressed the position of D. curvirostris in this genus by estimating phylogenetic trees from a rapidly evolving protein coding gene (ND2), conducting broad geographical comparisons and carrying out detailed morphological comparisons. The Japanese ' curvirostris' was found to be a new divergent lineage in the subgenus Daphnia , and to possess distinctive morphological characteristics from D. curvirostris . We described this new species as Daphnia tanakai sp. nov. , and redescribed D. curvirostris . The polymorphic postabdominal claw morphology and the distinctive chromosome number of D. tanakai sp. nov. provided evidence for rapid evolution of these traits. Our new morphological, chromosomal and genetic assessment of Daphnia weakened the argument for division of the subgenus Daphnia ( Daphnia ) O. F. Müller, 1785 sensu Johnson, 1952, into two further subgenera.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 385–405.     

Morphological, mitochondrial DNA and allozyme evolution in representative amphibians and reptiles inhabiting each side of the Strait of Gibraltar

Patterns of differentiation in morphology, mitochondrial DNA and allozymes in amphibians and reptiles inhabiting northern and southern shores of the Strait of Gibraltar are not concordant, suggesting that each taxon was affected differently by events preceding or following the formation of the Strait of Gibraltar. Mitochondrial DNA and allozyme differentiation between Discoglossus jeanneae and Discoglossus scovazzi (Anura, Discoglossidae), Rana perezi and Rana saharica (Anura, Ranidae), and Blanus cinereus and Blanus tingitanus (Squamata, Amphisbaenia, Amphisbaenidae) is substantial, whereas morphological differentiation is moderate in Rana and Blanus , but is substantial in Discoglossus . Differentiation in mitochondrial DNA and morphology between Timon ( Lacerta ) lepidus and Timon ( Lacerta ) tangitanus (Squamata, Lacertoidea, Lacertidae) is considerable, but allozyme differentiation is low. In members of type-I and -II Podarcis vaucheri (Squamata, Lacertoidea, Lacertidae), morphology and mitochondrial DNA are moderately differentiated, but allozyme differentiation is low. Spanish and Moroccan populations of Hyla meridionalis (Anura, Hylidae), Mauremys leprosa (Testudines, Geoemydidae), and Macroprotodon brevis (Squamata, Serpentes, Colubridae) demonstrate little allozyme and mitochondrial DNA differentiation, but whereas morphological differentiation between Mauremys and Macroprotodon populations is moderate, Hyla demonstrate substantial morphological differentiation between continental populations. These data suggest that sex-limited mitochondrial markers are reflective of ancient phylogenetic history, whereas biparentally inherited allozyme markers and morphological characteristics reflect more recent population structure and movement.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 445–461.     

Mitochondrial gene diversity in Cepaea– population structure, history and positive selection

Previous studies on the geographical distributions of both shell polymorphisms and mitochondrial haplotypes in Cepaea land snails have suggested varying contributions of natural selection, random genetic drift and population history to the origin and persistence of variation. We combine previous studies of polymorphism within two species of Cepaea , with new molecular data from two mitochondrial genes. The distributions of mitochondrial variants suggest that elements of population history may have been influential in creating patterns of diversity. However, some patterns of amino acid substitution that are found in a protein coding gene are also consistent with the action of diversifying selection. This suggests the possibility that in addition to stochastic processes such as repeated founder events, local extinctions and random genetic drift within a structured population, adaptive molecular change may have affected mitochondrial diversity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 167–184.     

Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae)

We used morphological, vocal and molecular (one mitochondrial and two nuclear loci) data to re-evaluate the taxonomic status of the taxa acanthizoides , concolor , and brunnescens in the Cettia acanthizoides (J. Verreaux, 1871) complex. We conclude that all three are valid taxa, and that acanthizoides of China and concolor of Taiwan are best treated as conspecific, whereas brunnescens of the Himalayas is better considered as a separate species. The degree of morphological, vocal, and genetic differentiation is variably congruent among all taxa; the recently separated acanthizoides and concolor differ slightly in plumage and structure but are indistinguishable in vocalizations, whereas the earlier diverged brunnescens and acanthizoides/concolor differ only slightly more in morphology but to a much greater degree in vocalizations. We stress the essential nature of taxonomic revisions as a prerequisite for the biodiversity estimates required for conservation planning.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 437–452.     

Conflicting patterns of genetic and morphological variation in European Gentianella section Gentianella

Genetics in European Gentianella Moench sect. Gentianella were investigated using internal transcribed spacer (ITS) nrDNA, trn L-F cpDNA and Amplified Fragment Length Polymorphisms (AFLP) fingerprint data to analyse relationships within the section. Both a cladistic and a phenetic approach, as well as nonhierarchical analysis (PCA) and partitioning of molecular variance (AMOVA), were used. Sequence data did not resolve groups within the section. They reflected, however, geographical isolation between central European and eastern Carpathian ( G. lutescens and G. bulgarica ) as well as Caucasian samples ( G. caucasea ). AFLP data revealed a strong differentiation within G. germanica between populations of the Alps and north-western middle Europe, although there is hardly any morphological differentiation of taxonomic significance. Morphological similarities between G. aspera and G. pilosa were not reflected in genetics, and no support was found for G. aspera . Genetic similarities were not in line with morphology in G. lutescens and G. bulgarica . AFLP data only partly resolve relationships among taxa. High genetic similarities, as well as partitioning of molecular variance among taxa/populations of eastern middle Europe ( G. austriaca , G. bohemica , G. germanica , G. stiriaca ) and intermediate morphological characters in G. bohemica and G. stiriaca , might indicate reticulate evolution. The overall low sequence divergence within the section points to a very young origin of all taxa.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 175–187.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

Genetic variation within and between Iliamna corei and I. remota (Malvaceae): implications for species delimitation

Iliamna corei and I. remota are classified as endangered species; however, their designation as separate species has been questioned. In order to address this problem, intersimple sequence repeat (ISSR) data were generated to examine patterns of genetic differentiation within and between these two taxa. ISSRs were used to screen individuals for genetic diversity of I. corei from the single known natural population and two garden populations, and individuals of I. remota from the six natural populations and four garden populations. Using ten primers, 140 informative markers were generated. Ninety-four percent of loci detected revealed polymorphisms. Cluster analysis (neighbour-joining, NJ) revealed that the two species are genetically distinct and that the Illinois populations of I. remota were genetically distinct from the Virginia populations of I. remota . Ordination by Principal Coordinate Analysis (PCoA) supported the findings of the NJ, with a separation of I. corei and I. remota . Analysis of Molecular Variance (AMOVA) revealed that the majority of variation detected was within populations, which is consistent with other self-incompatible plants. The results indicate a correlation between the geographical distributions of the species and gene flow.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 345–354.     

Lineage diversification on an evolving landscape: phylogeography of the California newt, Taricha torosa (Caudata: Salamandridae)

We used mitochondrial cytochrome  b sequences (up to 778 bp) and starch gel electrophoresis (45 loci) to examine the phylogeographical history of 39 populations of the California newt, Taricha torosa . Phylogenetic and population genetic methods were integrated to infer history at deep and shallow time depths. Using a molecular clock, the subspecies T. t. torosa and T. t. sierrae were estimated to have diverged 7–13 Mya. Within T. t. torosa, genetically differentiated groups were identified along coastal California, in southern California, and in the southern Sierra Nevada. The coastal group exhibited isolation by distance, but a lack of genetic variation north of present-day Monterey was indicative of a recent range expansion. In southern California, a disjunct population in central San Diego County was genetically diverged from coastal populations to the north (Nei's genetic distance of 0.113). However, mtDNA and protein data were geographically discordant regarding the boundary between the coastal and southern Californian groups, and a biogeographical scenario was developed to account for this discordance. The southern Sierran clade of T. t. torosa was weakly diverged from coastal populations for mtDNA sequence variation, yet was strongly differentiated for allozyme variation (Nei's genetic distance of 0.17–0.20). Populations of T. t. sierrae exhibited substantial population structure, and showed a steeper pattern of isolation by distance than did coastal populations of T. t. torosa . These results are interpreted in consideration of the known geomorphological history of California.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 213–239.     

Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae)

Phylogeographical and population genetics methods are used to reconstruct the diversification history of two species of the genus Xiphorhynchus (Aves: Dendrocolaptidae) associated with seasonally flooded forest types in Amazonia. Sequences of the mitochondrial gene cytochrome b were assessed for 21 and 30 individuals, belonging to eight and ten populations, of Xiphorhynchus kienerii and Xiphorhynchus obsoletus , respectively. Uncorrected genetic distances among unique haplotypes recovered ranged only from 0.01% to 0.4% for both species. Over 90% of the genetic variation detected in both species was partitioned within populations, and therefore was not structured geographically. Mismatch distributions and values of Tajima's D -tests indicate that both X. kienerii and X. obsoletus have had small evolutionary effective population sizes, but experienced a recent demographic expansion. These demographic expansions are tentatively dated as occurring over the last 18 000 years BP, a time frame which coincides with the establishment of the early and mid-Holocene age floodplain forest in most of central and eastern Amazonia, following a period of increased river stages throughout the basin. Based on phylogenetic, phylogeographical, and populations genetics data obtained for X. kienerii and X. obsoletus , an evolutionary scenario is proposed to account for the historical diversification of floodplain specialist species in Amazonia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 383–395.     

Phylogeography and conservation genetics of endangered European Margaritiferidae (Bivalvia: Unionoidea)

Margaritifera margaritifera and M. auricularia are among the most endangered freshwater mussels in the world, and the only species of the genus found in Europe. Our genetic study explores allozymic variability (27 loci) and differentiation at the mitochondrial sequence level (partial COI and 16S rRNA gene sequences). The Spanish M. auricularia population showed genetic parameters of variation that were of the same order as those of other freshwater molluscs (though at the lower end of the range), probably permitting its potential recovery. The difference between this species and M. margaritifera was clearly established (ten diagnostic allozymic loci, Nei = 0.462, and mean nucleotide divergence around 9.4%). The M. margaritifera populations analysed showed a certain degree of population genetic structure (according to allozyme data) that was not, however, related to a geographical cline. Nevertheless, two mitochondrial lineages (albeit very closely related) were identified: a northern lineage extending from Ireland to the Kola Peninsula including the western Atlantic coast, and a second cluster distributed from Ireland to the Iberian Peninsula. The phylogenetic relationships between these two species and other related taxa were established. The putative M. m. durrovensis could be considered an 'ecophenotype'. Palaeobiogeographical scenarios are presented and indicate unexpected 'recent' gene flow between M. margaritifera populations that were theoretically isolated in the early Tertiary.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society 2003, 78, 235–252.     

Polyploidy in Aconitum subgenus Lycoctonum (Ranunculaceae)

Chromosome numbers and morphology in 22 populations belonging to 11 taxa of Aconitum subgenus Lycoctonum (Ranunculaceae) from China were studied. Some taxa were diploid, with 2 n  = 16, but four species and two varieties were found to be tetraploid, with 2 n  = 32. They are concentrated in the Hengduan Mountains region in south-west China, indicating that polyploidy could have played an important role in the speciation of the subgenus in this region, one of the areas of the world with a high concentration of endemic species. The relationships of some of the species are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 343–353.     

Subdivided population structure and phylogeography of an endangered freshwater snail, Notopala sublineata (Conrad, 1850) (Gastropoda: Viviparidae), in Western Queensland, Australia

Populations of the Australian freshwater snail Notopala sublineata (Conrad, 1850) have declined rapidly over the last decade, but are still abundant in most river systems of Western Queensland. These rivers are characterized by the unpredictable and highly variable nature of their climatic and hydrological regimes, with episodic periods of very large flow and many periods of little or no flow. We used mitochondrial sequences and allozymes to investigate the genetic structure and infer patterns of dispersal of N. sublineata within this unique environment. We sampled 24 waterholes throughout the four major catchments of the Lake Eyre Basin. Based on a 457-bp fragment of the mitochondrial cytochrome oxidase subunit I gene, we identified 55 haplotypes in a sample of 256 individuals. Both nuclear and mitochondrial genetic datasets indicated high levels of genetic subdivision and restricted gene flow among populations within and among catchments. The mitochondrial haplotypes clustered into two main geographical clades, corresponding with two groups of adjacent catchments: Cooper–Bulloo and Diamantina–Georgina, which appear to have diverged 300 000 years ago. Populations of N. sublineata within these adjacent catchments seem to have diverged relatively recently, roughly 130 000 years ago. Contemporary dispersal seems to be absent between catchments but we suggest that climate fluctuations during the Pleistocene resulted in extensive floods that promoted historical movement of aquatic organisms across catchment boundaries.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 1–16.     

The green-veined white (Pieris napi L.), its Pierine relatives, and the systematics dilemmas of divergent character sets (Lepidoptera, Pieridae)

The butterfly Pieris napi (L.) and relatives exemplify recently evolving taxa, exhibiting variation that makes their evolutionary dynamics interesting, but their systematics difficult. Wing-pattern characters commonly used to distinguish these Holarctic insects display both genetic polymorphism and environmentally-cued polyphenism. Often, these causes of variation are confounded, impairing the characters' phylogenetic usefulness. DNA sequences of four mitochondrial genes offer an independent view of pierine phylogeny. Sampling diverse relatives within family Pieridae assists resolution of the P. napi complex, suggests previous underestimation of clade diversity in subfamily Pierinae, and shows that other genera near Pieris also display confusions of wing-pattern-based phylogenetic inference. The European P. napi is sister to all North American taxa, and is well diverged from them all in sequences. The North American taxa comprise a northern subclade including Pieris oleracea , and questionably distinct Pieris ' angelika ', and a southern subclade including distinct Pieris virginiensis , Pieris marginalis , and Pieris macdunnoughii , and other regional entities yet to be clarified. Weak bootstrap support for some nodes in this group arises from a closeness of sequence identity rather than character conflict; more sequence data and denser geographical sampling may resolve these nodes more clearly. Evidence of reproductive isolation, from other experimental hybridization studies, agrees with the DNA results where these conflict with other divergent character sets. The system offers much promise for a deeper understanding of character evolution in relation to phyletic differentiation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 413–435.     

The molecular systematics of Leiopotherapon unicolor (Günther, 1859): testing for cryptic speciation in Australia's most widespread freshwater fish

Leiopotherapon unicolor is the most widespread freshwater fish species in Australia. A comprehensive allozyme and mitochondrial DNA 16S rRNA data set was assembled from 141 specimens of L. unicolor collected Australia-wide in order to test for cryptic speciation in this far-ranging species. Surprisingly, little genetic diversity was observed within L. unicolor and provided no evidence for the existence of cryptic species within this lineage. In contrast, a small sample set of L. aheneus used as the outgroup showed two highly divergent haplotypes strongly suggestive of cryptic speciation. L. unicolor has a number of ecological and life history attributes that may explain the lack of significant genetic divergence over substantial geographical distances. The occurrence of other widespread fish and crustacean species that also display only limited genetic diversity indicate that climate conditions more favourable to dispersal across central and northern Australia than is suggested by the extent of present-day aridity have occurred in the relatively recent geological past.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 537–552.     

Little genetic differentiation across Europe between early-flowering and late-flowering populations of the rapidly declining orchid Neotinea ustulata

Amplified fragment length polymorphism (AFLP) was used to characterize genetic diversity of the endangered Burnt Orchid, Neotinea (formerly Orchis ) ustulata . Fingerprinting of Estonian and British populations revealed surprisingly little genetic differentiation between populations but larger amounts of diversity within populations, especially in Britain. The resulting mean F _st value of 0.51 is unusually high for an orchid species. Much of the variation follows a west–east cline across Europe, whereas the much-discussed early- and late-flowering taxa of N. ustulata are considered insufficiently distinct to be viewed as separate subspecies. The later flowering N. ustulata var. aestivalis probably evolved independently on two or three occasions, each time diverging from the earlier flowering nominate race. The identity of the genes underpinning phenology in the species, and the potential selective advantages of phenological divergence, merit further study. Overall genetic diversity within populations is sufficiently high to render impoverishment an unlikely cause of their recent, precipitous decline.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 13–25.     

Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?

The sepiids are characterized by their cuttlebone or sepion, an internal shell resulting from secondary mineralization of a chitinous 'gladius'. The various species are identified using a combination of shell criteria and 'soft-part' characters. Using mitochondrial genes, we established phylogenetic relationships of sepiids including the three accepted genera ( Sepia , Sepiella , Metasepia ) and a species complex of uncertain status ( Doratosepion ). We showed the Sepia genus to be paraphyletic and found no direct correlation between geographical distribution and systematics. We mapped, on the molecular tree, shell characteristics commonly used as reliable diagnostic criteria for taxonomy. Due to the plasticity of the shell, these characters did not appear phylogenetically informative. In an attempt to define systematic categories related to phylogenetic relationships, new clear synapomorphies need to be established for each genus, necessitating a revision of the genus Sepia .  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 139–150.