Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae)

Leptodactylus fuscus is a neotropical frog ranging from Panamá to Argentina, to the east of the Andes mountains, and also inhabiting Margarita, Trinidad, and the Tobago islands. We performed phylogenetic analyses of 12S rRNA, 16S rRNA, tRNA-Leu, and ND1 mitochondrial (mt) DNA sequences from specimens collected across the geographic distribution of L. fuscus to examine two alternative hypotheses: (i) L. fuscus is a single, widely distributed species, or (ii) L. fuscus is a species complex. We tested statistically for geographic association and partitioning of genetic variation among mtDNA clades. The mtDNA data supported the hypothesis of several cryptic species within L. fuscus. Unlinked mtDNA and nuclear markers supported independently the distinctness of a 'northern' phylogenetic unit. In addition, the mtDNA data divided the southern populations into two clades that showed no sister relationship to each other, consistent with high differentiation and lack of gene flow among southern populations as suggested by allozyme data. Concordance between mtDNA and allozyme patterns suggests that cryptic speciation has occurred in L. fuscus without morphological or call differentiation. This study illustrates a case in which lineage splitting during the speciation process took place without divergence in reproductive isolation mechanisms (e.g. advertisement call in frogs), contrary to expectations predicted using a biological species framework.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 325–341. No claim to original US government works.     

Multivariate analyses of morphological characters of Leptolaena Thouars s.l. subgenera Mediusella and Xerochlamys (Sarcolaenaceae)

Leptolaena Thouars is one of the first described genera within Sarcolaenaceae, but represents the last great species-level taxonomic challenge in this endemic Malagasy plant family. As currently circumscribed, this genus comprises three subgenera, two of which, Mediusella Cavaco and Xerochlamys (Baker) Cavaco, exhibit patterns of morphological variation that have been understood differently and have led to an unstable taxonomy, such that a consensus on the delimitation of species has yet to be reached. Principal component analysis of morphological characters was performed on 211 herbarium specimens in order to evaluate the morphological variation within the two subgenera and to clarify historically problematical species boundaries. The results showed that ten entities could be distinguished on the basis of vegetative, floral, and fruit characters, and that they provide a robust basis for proposing a new species-level taxonomic framework.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 559–574.     

The importance of phylogeny and ecology in microgeographical variation in the morphology of four Canarian species of Aeonium (Crassulaceae)

The relative importance of natural selection in the diversification of organisms can be assessed indirectly using matrix correspondence. The present study determines the environmental and genetic correlates of microgeographical variation in the growth form, leaf form and flower morphology in populations of four Aeonium species from section Leuconium using partial regression methods. The phylogeny of the four species and the other 12 species in the section was deduced from amplified fragment length polymorphism (AFLP). Pubescence of floral organs and flower size correlate with the phylogeny while traits related to growth form, leaf form, flower construction and inflorescence size correlate with ecological factors. The variation in the latter four traits may therefore reflect selection by current ecological conditions while variation in pubescence and flower size may reflect historical events like neutral mutations, founder events and drift. Additionally, the morphological analyses revealed a large amount of variation in all traits within populations. This suggests a possible influence of microhabitat on the variation in morphology of Aeonium in the Canary Islands.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 76 , 521–533.     

Amplified fragment length polymorphism genetic fingerprinting challenges the taxonomic status of the near-endemic species Chara curta Nolte ex Kütz. (Characeae)

Amplified fragment length polymorphism (AFLP) genetic fingerprinting of 14 accessions of Chara curta and Chara aspera Willd., sampled across a range of habitats and morphologies in Britain, suggests that these taxa are part of the variation within a single species complex. Two primer combinations generating 397 fragments (97% of which were polymorphic), analysed by Jaccard's similarity coefficient and principal co-ordinate analysis, did not recover groups which reflect the current taxonomy. By contrast with the genetic study, a Gower general similarity coefficient and principal co-ordinate analysis of 52 morphological characters recovered the currently recognized species groups. A Mantel test showed no significant correlation between the genetic data and the morphological data, supporting the hypothesis that phenotypic variability in Chara L. is either to some extent environmentally induced or represents developmental stages. Implications for the conservation status of C. curta in Britain are discussed.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 467–476.     

Morphological correlates of ant eating in horned lizards (Phrynosoma)

The North American horned lizards ( Phrynosoma ) represent a morphologically specialized group of ant-eating lizards. Although variation in dietary fidelity is observed among the species, all appear to possess morphological specializations thought to be related to their ant-eating diets. Previous studies have examined morphological specialization in Phrynosoma , but they have not taken into account the phylogenetic relationships of its member species. In the present study, the morphological characteristics of the head, jaws and teeth that are thought to be important in prey capture and prey processing were examined to test whether variation in cranial morphology is associated with diet in lizards of the genus Phrynosoma . It is suggested that lizards of the genus Phrynosoma are indeed morphologically specialized and that ant-eating is associated with reduced dentition and an overall reduction in the robustness of morphological structures important in prey processing. Although this trend holds for the highly myrmecophagous species of Phrynosoma , a robust cranial morphology is apparent in the short-horned lizard clade ( Phrynosoma ditmarsi , Phrynosoma douglasii , Phrynosoma hernandesi , Phrynosoma orbiculare ), implying the ability to process a variety of dietary items. The present study suggests that additional feeding specializations exist within an already specialized clade (i.e. the short-horned lizard clade) and highlights the need for more detailed dietary and behavioural studies of feeding behaviour in this uniquely specialized group of lizards.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 13–24.     

Distribution and genetic divergence of two parapatric sibling ant species in Central Europe

The two sibling ant species Temnothorax nylanderi and Temnothorax crassispinus are widely distributed throughout deciduous forests in Europe. Their resemblance in morphology and similar ecological requirements suggest that they evolved from the same ancestral species in different glacial refugia and re-immigrated into Central Europe after the last ice age. Here, we show that the two species are parapatrically distributed in south-eastern Germany and hybridize along a narrow contact zone close to the continental divide. Phylogeographical data based on the mitochondrial genes cytochrome oxidase subunit I and cytochrome b suggest that the dominant haplotypes for T. nylanderi and T. crassispinus might have diverged already 1.5–2 Mya. Intraspecific variability is extremely low in both species, which might be explained by severe bottlenecks during rapid postglacial expansion into Central Europe.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 223–234.     

Ecological and evolutionary factors in the morphological diversification of South American spiny rats

Understanding the processes underlying morphological diversification is a central goal in ecology and evolutionary biology and requires the integration of information about phylogenetic divergence and ecological niche diversity. In the present study, we use geometric morphometrics and comparative methods to investigate morphological diversification in Neotropical spiny rats of the family Echimyidae. Morphological diversification is studied as shape variation in the skull, comprising a structure composed of four distinct units: vault, base, orognathofacial complex, and mandible. We demonstrate association among patterns of variation in shape in different cranial units, levels of phylogenetic divergence, and ecological niche diversification. At the lower level of phylogenetic divergence, there is significant and positive concordance between patterns of phylogenetic divergence and cranial shape variation in all cranial units. This concordance may be attributable to the phylogenetic and shape distances being calculated between species that occupy the same niche. At higher phylogenetic levels of divergence and with ecological niche diversity, there is significant concordance between shape variation in all four cranial units and the ecological niches. In particular, the orognathofacial complex revealed the most significant association between shape variation and ecological niche diversity. This association may be explained by the great functional importance of the orognathofacial complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 646–660.     

Labile ecotypes accompany rapid cladogenesis in an adaptive radiation of Mandarina (Bradybaenidae) land snails

The endemic land snail genus Mandarina of the oceanic Bonin Islands shows exceptionally diverse morphological and ecological traits. Previous studies have already provided evidence that speciation on different islands of the three main archipelagos was such that similar ecotypes evolved independently in different lineages and islands. Here we present data to show that the same species can have different ecotypes. As most of the characters involved are inherited, then variation between ecotypes must represent genetic differences between populations. We then show that the radiation on the Bonin Islands is derived from a single colonization event, and use a mitochondrial phylogeny to provide evidence for a burst of cladogenesis soon after colonization. As divergent selection has previously been implicated in causing differences between Mandarina species, and theory predicts that most of the speciation should have taken place early in their history, then the study adds to the evidence for an adaptive radiation by ecological speciation in Mandarina . However, while the diversity of ecotypes present at each site is dependent on the regime of natural selection and competition, geography still must have an important role.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 269–282.     

Geographical variation and diversification in the flightless leaf beetles of the Chrysolina angusticollis species complex (Chrysomelidae, Coleoptera) in northern Japan

Geographical variation and differentiation of flightless leaf beetles of the Chrysolina angusticollis species complex were analysed. Nine morphological groups were recognized on the basis of metric characters relating to body size, shape of hind wing and shape of male genitalia, and binary characters relating to females' elytral surface and larval pubescence. The nine groups were essentially parapatric or allopatric to each other. Five groups occupied a continuous geographical range each, whereas another four groups were disjunctively distributed. Morphometric distance and geographical distance between populations were significantly correlated. Analyses based on 13 allozyme loci demonstrated that six out of the nine morphological groups were further divided into more than one genetically distinct group each. Genetic similarity between populations was significantly correlated with morphometric similarity and geographical closeness. Disjunctively distributed populations of a single morphological group more often resembled geographically adjacent populations of different morphological groups than geographically remote populations of the same group. In a morphological group that occupied a wide continuous range, remote populations substantially differed genetically from each other. The results suggest that there exist at least 19 morphologically and/or genetically differentiated units in the C. angusticollis complex in northern Japan. The C. angusticollis complex is likely a superspecies composed of a number of semispecies. We postulate that the diversification of this species complex might have resulted from the repeated range contraction and expansion during the ice ages. Movement of tension zones that separate two adjacent forms might contribute to enhance their geographical differentiation.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 557–578.     

Maximizing information in systematic revisions: a combined molecular and morphological analysis of a cryptic green pitviper complex (Trimeresurus stejnegeri)

Although the integration of DNA information in taxonomy has been invaluable, logistical problems relating to sampling can seriously limit its applicability. Here we describe the analysis of a morphologically cryptic species complex, in which we maximize the information present by using both a DNA phylogeny and a multivariate morphometric approach. The green pitviper Trimeresurus stejnegeri s.l. is widespread in Asia, with a number of described subspecies (some of which are considered full species by some workers) and two new species that have recently been described from Thailand. The phylogeny indicates three clades, which can also be discerned in the principal component analyses of morphological variation. Combining molecular and morphological information permits evaluation of the taxonomic position of populations not represented in the phylogeny − in particular, the subspecies T. s. chenbihui and T. s. yunnanensis . We discuss nomenclatural issues raised by this analysis, although these cannot be fully resolved until the holotypes of these subspecies can be examined. Finally, we apply a molecular clock calibrated in New World pitvipers, and discuss some of the palaeoclimatic changes that might have impacted upon diversification in this group.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 219–235.     

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.     

The evolutionary pathway of light emission in myodocopid Ostracoda

The evolutionary history of bioluminescence and iridescence in myodocopid ostracods was estimated by phylogenetic analysis of mitochondrial 16S ribosomal RNA sequences. The inferred phylogeny of the myodocopids suggests that the common ancestor of Myodocopida evaluated in this study exhibits iridescence. This type of light emission was once lost and recaptured independently in the descendant lineages. Bioluminescent species also evolved from non-luminous ancestral species. In the suborder Myodocopina, all the bioluminescent species form a monophyletic group, suggesting that bioluminescence evolved only once. Structural differences between two bioluminescent groups in the order Myodocopida suggests independent origins for bioluminescence.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 449–455.     

DNA barcoding to analyse taxonomically complex groups in plants: the case of Thymus (Lamiaceae)

We evaluated the utility of the core barcode regions (matK and rbcL) and the plastid intergenic spacer trnH‐psbA to distinguish between Thymus spp. This is a taxonomically complex group that has been investigated so far mainly using morphological approaches. Thirty‐six samples representing nine different morphospecies were collected and used for molecular analysis. The three markers showed clear amplification and sequencing. However, the genetic variation and the resulting haplotype networks showed that only Thymus capitatus forms a well‐defined ‘barcoding gap’ compared with the other taxa. The identification problems observed in the other Thymus spp. may be related to reduced gene flow among populations, resulting in high intraspecific and low interspecific genetic variation. This situation does not permit the definition of species‐specific barcodes. A second hypothesis suggests that morphological traits used for the delimitation of Thymus spp. do not reflect real biological and molecular species boundaries. If this is the case, the taxonomy of Thymus should be revised through extensive sampling and analyses with different tools (i.e. molecular variability, morphology, geographical distribution, etc.) to define the natural units at the species level. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013 , 171 , 687–699.     

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.     

Intraspecific variation in Anolis sagrei mirrors the adaptive radiation of Greater Antillean anoles

Anolis lizards of the Greater Antilles represent one of the classic examples of vertebrate adaptive radiation. The same morphological types ('ecomorphs') have evolved repeatedly in response to similar ecological pressures on different islands. We tested whether patterns of within species diversification were congruent with between species patterns and the processes leading to the adaptive radiation of Greater Antillean anoles by measuring variation in performance-related morphological characters in the brown anole, Anolis sagrei . We measured morphological and genetic variation in two different habitat types on each of five islands in the Bahamas. We estimated population structure and rates of gene flow within and among islands using eight microsatellite markers. Intraspecific variation in performance-related morphological characters was similar to the pattern of interspecific variation that characterizes the adaptive radiation of this group in the Greater Antilles. For example, limb length was correlated with perch diameter within A. sagrei as has also been shown among species of anole. Morphological divergence in traits has occurred despite relatively high levels of gene flow both within and among islands. These results are discussed in the context of the divergence-with-gene-flow model of speciation. The results provide important intraspecific evidence that the diversification of anoles has been shaped by natural selection and show how ecologically-based selection pressures explain diversification at both the population and species levels.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 189–199.