Speciation on the Azores islands: congruent patterns in shell morphology, genital anatomy, and molecular markers in endemic land snails (Gastropoda, Leptaxinae)

Morphological data, in combination with molecular data, may provide invaluable insights into speciation processes on archipelagos. Land snails offer ample opportunities to evalutate adaptive and non-adaptive speciation scenarios. However, studies investigating processes of differentiation and speciation on the Azores are scarce. The present study comprises a morphometrical analysis of shell and genital characters in a group of Azorean land snails (Pulmonata, Leptaxinae). Geographical isolation appears to be an important mechanism underlying morphological and molecular differentiation in the Azorean Leptaxini, instead of adaptive radiation through ecological differentiation. Nevertheless, we could not exclude the occurrence of ecological speciation on the oldest island (Santa Maria) where two species that markedly differ in shell-shape co-occur.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 166–176.     

Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective

Historical relationships were inferred for the oriental lizards of the genus Takydromus Daudin 1802 (Lacertidae) on the basis of DNA sequences. Of the 17 species currently recognized for the genus, 13 species represented by 42 specimens from 29 localities were examined. Maximum-likelihood and maximum-parsimony analyses of data for 829 aligned sites from parts of the mitochondrial 12S and 16S rRNA genes yielded relationships that, while showing no substantial discrepancy with each other, were strikingly different from a currently prevailing phylogenetic hypothesis from a parsimony analysis of morphological characters. Based on the results of these molecular analyses, supplemented by results of the morphological analysis that offered robust evidence for positions of two additional species ( T. khasiensis and T. sylvaticus ), the following interrelationships were hypothesized as the most preferred phylogeny: ( kuehnei ( sexlineatus khasiensis ))( tachydromoides (( smaragdinus ( sauteri ( dorsalis sylvaticus ))) ( amurensis ((( formosanus wolteri ) hsuehshanensis )( toyamai ( septentrionalis stejnegeri )))))). These interrelationships indicate: (1) invalidity of Platyplacopus Boulenger 1917 , which was recently resurrected as a subgenus of Takydromus on the basis of the morphological analysis; (2) homoplasy in states of some morphological characters, such as green dorsal coloration, that were considered as synapomorphs of certain nodes in the morphological analysis; and (3) involvement of the genus in a series of vicariances in both the continental and insular parts of eastern Eurasia. Due to the paucity of available samples, phylogenetic status of T. intermedius and T. haughtonianus remain to be examined in future studies.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 493–509.     

Systematics of two deep-water species from the Indo-West Pacific: Struvea gardineri A.Gepp & E.Gepp and Phyllodictyon orientale (A.Gepp & E.Gepp) Kraft & M.J.Wynne (Siphonocladales, Chlorophyta)

Two rare and ill-known subtidal species of stalked, net-forming green algae, Struvea gardineri A.Gepp & E.Gepp and Phyllodictyon orientale (A.Gepp & E.Gepp) Kraft & M.J.Wynne, are re-described on the basis of the examination of type material and recent collections from the Maldives, Seychelles, and Socotra Island in the tropical Indian Ocean. The taxonomic position of both species is re-appraised on the basis of morphological data (cell division, branching pattern, tenacular cells, crystalline cell inclusions, cell shape, and cell dimensions) and molecular phylogenetic evidence (partial large subunit nuclear ribosomal DNA sequences). On the basis of the occurrence of segregative cell division in young plants of S. gardineri , this species is returned to its original genus, Struvea . Cell division in P. orientale takes place exclusively by centripetal wall ingrowths, confirming its placement in the genus Phyllodictyon as currently defined. However, morphological observations and molecular phylogenetic studies indicate that the delineation of genera on the basis of modes of cell division is problematic, and that the genera Struvea and Phyllodictyon , as presently conceived, almost certainly do not represent natural groups.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 115–132.     

Adaptive modifications of carapace outlines in the Cytheroidea (Ostracoda: Crustacea)

Shell outlines of 202 extant cytheroidean ostracods were analysed in dorsal, lateral, and posterior views by elliptic Fourier analysis. The results obtained confirm that the exterior morphology is related to ecological factors as well as phylogenetic constraints. Phytal species living on tall seagrass and benthic species burrowing in sediments are characterized and differentiated from the species crawling on sediments by the presence of slender shells with tapered venters. With reference to reconstruction of ancestral state of outline traits on the molecular phylogeny, the hypothetical ancestor of cytheroidean ostracods is presumed to have had an average-shaped shell. Morphological plasticity of the shell outline was observed in many families. The phytal species living on tall seagrass appear to have evolved convergently with species from other habitats, acquiring slim shell outlines during the Cenozoic period. The present analysis also reveals the phylogenetic constraints on the morphological evolution of the Trachyleberididae in their adaptation to a burrowing habit.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 810–821.     

Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data

Representatives of the genus Praomys occur throughout the African intertropical zone. It is unclear how many species this genus contains, nor do we know the exact distribution ranges and phylogenetic relationships of these taxa. Using molecular (16S rRNA gene sequencing) and morphological (multivariate craniometry) analyses we clarify the taxonomy and phylogenetic relationships among the Praomys occurring in Africa's lowland tropical rainforests. We studied most species known from this area, based on specimens collected in seven countries (Guinea, Ivory Coast, Cameroon, Central African Republic, Gabon, Congo Republic and Democratic Republic of Congo). In our study, Praomys appears to be monophyletic. Our results identify two species complexes: the jacksoni complex includes at least two species ( P. jacksoni and P. mutoni ) and the tullbergi complex contains at least four species ( P. tullbergi , P. rostratus , P. misonnei , P. petteri ). Although the 16S rRNA gene appears insufficient to resolve the phylogenetic relationships among all the members of the tullbergi species complex, it is suitable for the identification of most of the studied species, and its use has allowed us to redefine the geographical limits of several species.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 145 , 539–553.     

Comparative osteology of the Danio (Cyprinidae: Ostariophysi) axial skeleton with comments on Danio relationships based on molecules and morphology

Danio is a diverse group of small, colourful and easily bred freshwater fishes native to Southern Asia. Biological interest in danios has increased in recent years because the zebrafish, Danio rerio , has become an important model organism, particularly for studies of vertebrate developmental biology and genetics. Though several phylogenetic studies of Danio have been done on a subset of Danio species, the resulting phylogenies conflict in detail. To examine the utility of osteology for systematics of this group at the species level, we studied the axial skeleton for 11 species of Danio. We analyse our morphological data alone and combined with DNA sequence data for five gene sequences generated in earlier phylogenetic studies. The axial skeleton of Danio exhibits 14 characters that prove useful in phylogenetic analysis. Both molecular and morphological data support the monophyly of the danios included in our analysis and both data sets support the monophyly of two subclades: a deep-bodied group and a slender-bodied group. Separate analysis of molecular and morphological data sets show that the molecular data resolves relationships within the slender subclade whereas the topology of the deep-bodied subclade is determined by morphological data.  © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 135 , 529–546.     

Evidence for speciational change in the evolution of ratites (Aves: Palaeognathae)

To perform a comparative analysis of character associations framed in a phylogenetic context (e.g. independent contrasts), a model of character evolution must be assumed. According to phyletic gradualism, morphological change accumulates gradually over time within lineages, and speciation events do not have a major role. Under speciational models, morphological change is assumed to occur during or just after cladogenesis in both daughter species, and the resulting morphologies do not change over long periods of time (stasis), until the next cladogenetic event. A novel method is presented for comparing these models of character evolution that uses permutational multiple phylogenetic regressions. The addition of divergence times to well-corroborated phylogenetic trees and the utilization of the method developed in this paper allows the estimation of relative frequency of gradual change and speciational change from living organisms. This method is applied to a dataset from ratites with the conclusion that, for a range of morphological features, change tends to have been speciational rather than gradual.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 99–106.     

Phylogenetics, zoogeography, and the role of dispersal and vicariance in the evolution of the Rana catesbeiana (Anura: Ranidae) species group

The Rana catesbeiana species group consists of seven species, each variously distributed across eastern North America. We estimated the evolutionary relationships among 31 exemplars and used the phylogenetic hypothesis to examine the potential modes of speciation and relative role of dispersal in the evolution and zoogeography of this species group. Phylogenetic relationships based on 1554 combined base pairs of the cytochrome b and ND2 mitochondrial genes suggest that the species are closely related, having undergone rapid radiation from a common ancestor during the late Miocene or Pliocene. A Pleistocene origin for the rare R. okaloosae is suggested by its pattern of paraphyly with R. clamitans and by its geographically restricted distribution, although hybridization as the explanation for paraphyly cannot be ruled out. Dispersal–vicariance analysis suggested a Coastal Plain biogeographical region origin of the species group, supporting the notion that the region was an important centre of anuran diversification, with post-speciation dispersal playing a major role in explaining the distribution of the widespread species, R. catesbeiana , R. clamitans, and R. septentrionalis . High sea levels during the late Tertiary, greatly reducing and insularizing parts of the southern Coastal Plain region may have played a major role in the diversification of this group.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80 , 601–624.     

Molecular phylogeny of the genus Tibicina (Hemiptera, Cicadidae): rapid radiation and acoustic behaviour

To estimate the potential contribution of ethological and ecological parameters to the mechanisms of species formation and species isolation in the Palearctic cicada genus Tibicina , we constructed a molecular phylogenetic hypothesis of extant Tibicina species. Seven mitochondrial genes and a fragment of a nuclear gene were sequenced (3046 bp). Mitochondrial genes included 547 informative sites but the nuclear gene was too conserved to be included in the analysis. The tree was characterized by a basal polytomy indicating that Tibicina species arose rapidly. Such rapid radiation might explain the low divergence in the acoustic communication observed between species. Parameters describing habitat selection and acoustic communication were mapped onto the tree. A shift in habitat selection accompanied by acoustic changes might have contributed to one speciation event. The stochastic distribution of the same acoustic characters on the other branches of the tree implies, however, that the subtle acoustic differences between species could be the result of previous speciation events and independent evolutionary histories, rather than having contributed themselves in the speciation and isolation processes.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 611–626.     

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.     

Systematics of the spider genus Metabus O. P.-Cambridge, 1899 (Araneoidea: Tetragnathidae) with additions to the tetragnathid fauna of Chile and comments on the phylogeny of Tetragnathidae

The spider genus Metabus (Tetragnathidae) previously included nine species: the type M. gravidus O. P.-Cambridge, 1899 – junior synonym of Leucauge ocellata (Keyserling) – from Central America and eight species from Chile. In this paper, the classification of the Metabus species-complex is revised, and two new genera, with three new species and five new combinations, are described. Allende gen. nov. is created for four Chilean species not congeneric with the type of Metabus : the type A. puyehuensis sp. nov. , A. patagiatus (Simon) comb. nov. , A. nigrohumeralis (F. O. P.-Cambridge) comb. nov. and A. longipes (Nicolet) comb. nov. Further additions to the Chilean fauna are under the new genus Mollemeta gen. nov. – created for M. edwardsi (Simon) comb. nov. – and three new species of Chrysometa : C. acinosa sp. nov. , C. levii sp. nov. and C. maitae sp. nov. Metabus now includes four species: M. ocellatus (Keyserling) comb. nov. , M. debilis (O. P.-Cambridge) comb. nov. , M. ebanoverde sp. nov. and M. conacyt sp. nov. All of these species were included in a phylogenetic analysis of 38 tetragnathid and 12 orbicularian outgroup terminals scored for 105 morphological and behavioural characters. The results suggest that Metabus as previously circumscribed is polyphyletic. The phylogenetic relationships within tetragnathids are briefly discussed. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 285–335.     

A species complex within the isopod genus Haploniscus (Crustacea: Malacostraca: Peracarida) from the Southern Ocean deep sea: a morphological and molecular approach

Seven new species of the genus Haploniscus from the deep Scotia and Weddell Seas are presented, combining morphological and molecular data (mitochondrial 16S rDNA and nuclear 18S rDNA). Haploniscus cassilatus sp. nov. , H. cucullus sp. nov. , H. weddellensis sp. nov. , H. procerus sp. nov. and H. kyrbasia sp. nov. are characterized by a prominent rostral process, the size and shape of which vary among species. The rostrum of H. microkorys sp. nov. is distinctly smaller than that of the former species, while H. nudifrons sp. nov. does not possess a rostrum. The status of the latter as separate species is obvious, owing to the stronger morphological differences. DNA was sequenced from three of the other five species. Genetic distances together with the more subtle morphological variation justify the erection of separate species. Overall morphological variations between these species are small yet noticeable and include, among others, the rostrum, the shape of the pleotelson and setation of pereopods. Our molecular data sets reveal detailed phylogenetic insights within the Haploniscus cucullus complex, supporting the monophyly of all species. We found p -distances of at least 0.0732 (16S rDNA) and 0.0140 (complete 18S rDNA) between pairs of species and show that both genes can be used as a marker for DNA taxonomy.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 655–706.     

Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolution

Phylogenetic relationships among 15 species in the family Salangidae were constructed based on the complete cytochrome b sequence (1141 bp). We confirmed the monophyly of the family Salangidae and defined four primitive lineages within this family: (I) Protosalanx , Neosalanx anderssoni , Neosalanx tangkahkeii , and Neosalanx argentea ; (II) Neosalanx reganius , Neosalanx jordani , Neosalanx oligodontis , and Neosalanx  sp.; (III) Hemisalanx , Salanx , Leucosoma , and Salangichthys ishikawae ; and (IV) Salangichthys microdon . A major finding of our study is the key basal placement of Sg. microdon . According to the tentative estimation, the divergence of the four lineages appears to have been initiated in the early Miocene (21 Mya), with most speciation events occurring 1.05–9.90 Mya. Taxonomic revisions on subfamilial, generic, and specific levels were carried out based on phylogenetic relationships and genetic distance, taking into account some key morphological characters. The speciation mechanism in Salangidae is also discussed, and the evidence shows that geographical isolation, water mass, as well as some ecological factors, may not always play important roles in the speciation of temperate estuarine fish. In the most cases, sympatric salangids are not monophyletic, indicating that their coexistence reflects secondary contact rather than sympatric speciation.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 327–342.     

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.     

Systematics and biogeography of the New World species of Trichadenotecnum Enderlein (Insecta: Psocodea: 'Psocoptera': Psocidae)

The taxonomy of the New World species of the genus Trichadenotecnum is revised. A total of 44 species, including 29 new species, were treated. These species are classified into 12 monophyletic species groups, eight of them newly proposed here. Two species previously assigned to Trichadenotecnum , T. pichincha New & Thornton and T. sylvaticum Turner, are recognized as not belonging to this genus. Phylogenetic relationships among 16 previously and presently proposed species groups are estimated based on a data matrix of 58 morphological characters. Trees from these analyses support monophyly of Trichadenotecnum and the proposed species groups. The New World species were divided into three major clades. Based on the phylogenetic hypothesis and distributional pattern of the species groups, the biogeographical history of the New World Trichadenotecnum is discussed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 651–723.     

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.     

Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morhological tools

Correct taxonomy is a prerequisite for biological research, but currently it is undergoing a serious crisis, resulting in the neglect of many highly diverse groups of organisms. In nematodes, species delimitation remains problematic due to their high morphological plasticity. Evolutionary approaches using DNA sequences can potentially overcome the problems caused by morphology, but they are also affected by theoretical flaws. A holistic approach with a combination of morphological and molecular methods can therefore produce a straightforward delimitation of species. The present study investigates the taxonomic status of some highly divergent mitochondrial haplotypes in the Rhabditis ( Pellioditis ) marina species complex by using a combination of molecular and morphological tools. We used three molecular markers (COI, ITS, D2D3) and performed phylogenetic analyses. Subsequently, morphometric data from nearly all lineages were analysed with multivariate techniques. We included R. ( P. ) mediterranea and R. (R.) nidrosiensis to infer species status of the observed lineages. The results showed that highly divergent genotypic clusters were accompanied by morphological differences, and we created a graphical polytomous key for future identifications. This study indisputably demonstrates that R. ( P. ) marina and R. ( P. ) mediterranea belong to a huge species complex and that biodiversity in free-living marine nematodes may be seriously underestimated.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 1–15.     

Evolution and phylogeny of the genus Natrix (Serpentes: Colubridae)

Some aspects of the natural history of snakes of the colubrid genus Natrix have been well studied. With their extensive European distribution and relative abundance, their ecology, reproduction and behaviour are well known. Yet other facets of their biology remain poorly understood. These include knowledge of Natrix phylogeny, hypotheses explaining the current distribution of the three extant members of the genus, and their evolution and relationships. In this study we used molecular data, the nucleotide sequences of four protein-coding mitochondrial genes (3806 bp total), to provide a well-supported phylogeny for the genus Natrix . With these molecular data, evidence from the fossil record, and knowledge of palaeogeological events, we used two approaches in designing a time scale which we used to date the major events in Natrix speciation and intraspecific variation. Our data strongly support a phylogeny for the genus in which N. maura is basal with N. natrix and N. tessellata being sister species. The calibrated molecular clock suggests that N. maura diverged from the common ancestor of the three species 18–27 mya and that N. natrix and N. tessellata diverged 13–22 mya. Although the ranges of these estimates are large they support an early Miocene to late Oligocene origin for the three species. Intraspecific divergence is estimated to have commenced 5.3, 6.0 and 6.7 mya with evolutionary rates of 1 : 1.25 : 1.35% per million years for N. maura, N. natrix and N. tessellata , respectively.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 127–143.     

Geometric morphometrics, neural networks and diagnosis of sibling Taterillus species (Rodentia, Gerbillinae)

The lack of diagnostic traits in sibling species means that great quantities of biogeographical and ecological data held in museum collections cannot be utilized effectively, leading to underestimates of biodiversity. In this study we applied neural networks (NN) and canonical variates analyses (CVA) to landmark measurements on the skulls of the West African species Taterillus arenarius , T. petteri , T. gracilis and T. pygargus in an attempt to discriminate species previously identified unambiguously from their karyotypes. Among suggested differences, the relationship between inflation of the tympanic bullae and lower population density is discussed. Cross-validated classification rates did not exceed 73%. Two hypotheses are proposed to explain such high phenotypic similarity: morphological plasticity limited by environmental constraints and the possibility that speciation has been too recent to allow significant morphological divergence.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 319−327.     

A molecular study of phylogenetic relationships and evolution of antipredator strategies in Australian Diplodactylus geckos, subgenus Strophurus

We present phylogenetic analyses of the lizard genus Diplodactylus subgenus Strophurus using 1646 aligned positions of mitochondrial DNA sequences containing 893 parsimony-informative characters for samples of 12 species of Strophurus and 19 additional Australian gecko species. Sequences from three protein-coding genes (ND1, ND2 and COI) and eight intervening transfer RNA genes were examined using parsimony, maximum-likelihood and Bayesian analyses. Species of Strophurus appeared to form a monophyletic group with the possible exception of S. taenicauda . Strophurus has evolved two distinct defence/display characteristics: caudal glands, which expel an unpalatable substance, and striking mouth colours. Caudal glands appeared to have arisen once in a common ancestor of Strophurus , with dermal augmentation of caudal glands characterizing a subclade within the subgenus. Evolution of yellow and dark-blue mouth colours in Strophurus occurred in the context of diurnal activity and may be interpreted as an augmentation of defensive behavioural displays. Molecular divergence suggests that arboreality evolved in a common ancestor of Oedura and Strophurus approximately 29 Mya and that the caudal glands of Strophurus arose approximately 25 Mya.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 123–138.