Phylogenetic relationships and biogeography of midwife toads (Discoglossidae: Alytes)

Aim To devise a robust phylogenetic hypothesis for midwife toads (Alytes: Anura: Discoglossidae) and to discuss its implications for the reconstruction of the biogeographical history of the group. Location Western Palearctic. Methods Analysis of sequences of mitochondrial DNA (cytochrome b and 16S RNA, 861 bp) and 29 characters of cranial osteology of all species and subspecies within Alytes. Results Phylogenetic analyses support a sister group relationship between Alytes dickhilleni and A. muletensis, and of this clade with A. maurus. The monophyly of A. obstetricans is controversial; in particular, the phylogenetic position of A. obstetricans almogavarii is uncertain. The estimated dates for the cladogenetic events within Alytes are congruent with those derived from independent analyses (allozymes), except for the differentiation of A. o. almogavarii and the split between A. dickhilleni and A. muletensis. Main conclusions The phylogeny based on the analysis of morphological and mtDNA data differs from previous hypotheses in the positions of A. o. almogavarii and A. maurus. Events associated with the radiation of Alytes are the formation of large inland saline lakes in Iberia c. 16 Ma and the 11 ° C dramatic decrease in average annual temperature during the Middle–Late Badenian transition c. 14–13.5 Ma (A.cisternasii vs. the ancestor of the remaining clades), the structuring of the Neo‐Pyrenees and the reopening of the Betic Strait c. 10–8 Ma(A. o. almogavarii vs. A. obstetricans and vs. the subgenus Baleaphryne), the opening of the Gibraltar Strait at the end of the Messinian Salinity Crisis at c. 5.3 Ma (A. maurus vs. the ancestor of the A. dickhilleni A. muletensis clade) and a transmarine colonization event at c. 3 Ma (the ancestor of A. muletensis vs. A. dickhilleni). Following the new hypothesis, A. maurus, previously considered a subspecies of A. obstetricans, deserves species status. Second, A. o. almogavarii is a well‐differentiated lineage that was isolated from other A. obstetricans more than c. 5 Ma, but later lost its genetic and specific identity following secondary contact, hybridization and introgression with the main stock. The presence of a marked morphological and genetic diversity within A. obstetricans renders reconstruction of the evolutionary history of the genus more complicated than previously appreciated.     

Positive Darwinian selection results in resistance to cardioactive toxins in true toads (Anura: Bufonidae)

Members of the Family Bufonidae, true toads, are famous for their endogenously synthesized cardioactive steroids that serve as defensive toxins. Evolution of resistance to these toxins is not understood. We sequenced a key region of the toxin''s binding site in the Na⁺/K⁺ ATPase for relevant taxa representing Hyloidea (including bufonids), Ranoidea and Archaeobatrachia and tested for positive selection in a phylogenetic context. Bufonidae were distinct from other Hyloidea at 4–6 of 12 sites and, with one exception, had a homologous amino acid sequence. Melanophryniscus stelzneri had a distinct sequence, consistent with other independent evidence for a differentiated toxin. Tests within Bufonidae detected positive selection within the binding region, providing, to our knowledge, the first evidence of this type for positive selection within Amphibia. There was no evidence for positive selection on Bufonidae or M. stelzneri lineages. Sequence change in Leptodactylus ocellatus, a leptodactylid predator of Bufonidae, provides a molecular basis for predator resistance possibly associated with gene duplication.     

Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence

Despite the considerable research that has focused on the evolutionary relationships and biogeography of the genus Bufo, an evolutionary synthesis of the entire group has not yet emerged. In the present study, almost 4 kb of DNA sequence data from mitochondrial (12S, tRNA^Val, and 16S) and nuclear (POMC; Rag-1) genes, and 83 characters from morphology were analysed to infer a phylogeny of South American toads. Phylogenies were reconstructed with parsimony and maximum likelihood and Bayesian model-based methods. The results of the analysis of morphological data support the hypothesis that within Bufo , some skull characters (e.g. frontoparietal width), correlated with the amount of cranial ossification, are prone to homoplasy. Unique and unreversed morphological synapomorphies are presented that can be used to diagnose recognized species groups of South American toads. The results of all phylogenetic analyses support the monophyly of most species groups of South American Bufo . In most DNA-only and combined analyses, the South American (minus the B. guttatus and part of the ' B. spinulosus ' groups), North American, Central American, and African lineages form generally well-supported clades: ((((((((South America) (North America + Central America)) Eurasia) Africa) Eurasia) South America) West Indies) South America). This result confirms and extends prior studies recovering South American Bufo as polyphyletic. The biogeographical results indicate that: (1) The origin of Bufo predates the fragmentation of Gondwana; (2) Central and North American species compose the sister group to a large, 'derived' clade of South American Bufo ; and (3) Eurasian species form the sister group to the New World clade.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 407–452.     

Phylogenetic patterns of diversification in a clade of Neotropical frogs (Anura: Aromobatidae: Mannophryne)

We used partial sequences of mitochondrial 16S and cytochrome oxidase I genes to perform a phylogenetic study of collared frogs (Anura: Aromobatidae: Mannophryne ), a genus endemic to Venezuela and the islands of Trinidad and Tobago. We analysed 1.2 kb from 13 of the 15 described species of Mannophryne . Maximum parsimony, maximum likelihood and Bayesian analyses support the monophyly of Mannophryne . Mannophryne consists of three deeply differentiated clades that split from each other in a relatively short period of time. The diversification of Mannophryne occurred well before the glacial-interglacial periods of the Quaternary. Our data support the taxonomic validity of M. olmonae , a species endemic to Tobago Island. Mannophryne olmonae is more closely related to the continental species Mannophryne riveroi than to the Trinidad island endemic Mannophryne trinitatis . As in most tropical clades of frogs, molecular evidence indicates that species richness in Mannophryne is largely underestimated and, consequently, current priorities for conservation are inadequate.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 185–199.     

Molecular diversification of salamanders of the tropical American genus Bolitoglossa (Caudata: Plethodontidae) and its evolutionary and biogeographical implications

The largest genus of salamanders, Bolitoglossa (Plethodontidae), is widespread in tropical America, where it occurs in diverse habitats and elevations, from high elevation grasslands to lowland rain forest . It has the most extensive geographical range of any salamander genus. While most species occur in Middle America, it ranges throughout most of tropical South America as well. Phylogenetic analysis of 1196 bp of two mitochondrial genes (cytochrome b , 16S RNA) from 55 species offers strong support for the monophyly of the genus and sorts the species into a number of clades. Taking into account morphology, distribution, general ecology, and prior systematic and taxonomic studies, we recognize seven subgenera, four of them new: Bolitoglossa Duméril, Bibron et Duméril, 1854, Eladinea Miranda Ribeiro, 1937, Magnadigita Taylor, 1944, Mayamandra , Nanotriton , Oaxakia and Pachymandra . All South American and some lower Middle American species are included in a single well -supported clade, Eladinea . At the species level our analyses uncover the existence of large genetic diversity within morphologically homogeneous taxa. We propose the new combination: B. (Eladinea) paraensis (Unterstein, 1930) stat. nov. , for Brazilian salamanders previously included under B. altamazonica . We evaluate evidence for the multiple colonization of the tropical lowlands by morphologically derived species groups. South America was invaded by members of one clade, Eladinea , which we infer to have dispersed to South America prior to closure of the Panamanian Portal. Despite the relatively long history of salamanders in South America, that continent now accounts for a relatively small proportion of the lineages and species of neotropical salamanders.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81 , 325–346.     

Evolution and biogeography of the genus Tarentola (Sauria: Gekkonidae) in the Canary Islands,inferred from mitochondrial DNA sequences

Sequences from fragments of the 12S ribosomal RNA and cytochrome b mitochondrial genes were used to analyze phylogenetic relationships among geckos of genus Tarentola from the Canary Islands. A surprisingly high level of within island differentiation was found in T. delalandii in Tenerife and T. boettgeri in Gran Canaria. Molecular differentiation between populations of T. angustimentalis on Lanzarote and Fuerteventura, and between Moroccan and Iberian Peninsula T. mauritanica, also indicate that at least two subspecies should be recognized within each of them. Phylogenetic relationships among these species reveals a higher level of differentiation and a more complex colonization pattern than those found for the endemic genus Gallotia. Lack of evidence for the presence of T. boettgeri bischoffi on the island of Madeira does not seem to support the origin of T. delalandii, T. gomerensis and the canarian subspecies of T. boettgeri from this island, whereas molecular data confirms that T. angustimentalis is a sister species of the continental T. mauritanica. Several independent colonization events from the continent and the extinction of some species are probably responsible for the current distribution of Tarentola in the Canary Islands.     

Molecular systematics,taxonomy and biogeography of the genus Cavia (Rodentia: Caviidae)

Phylogenetic analyses were conducted on cytochrome b sequence data of the most geographically and taxonomically broad sampling of Cavia taxa to date. Primary objectives included providing the first extensive molecular phylogenetic framework for the genus, testing the taxonomic and systematic hypotheses of previous authors and providing insight into the evolutionary and biogeographic history of the genus. Support was found for the morphologically defined species C. aperea, C. tschudii, C. magna and C. fulgida and the taxonomic placement of taxa previously subject to conflicting taxonomic opinions (e.g. C. nana, C. anolaimae and C. guianae) was further resolved. Additionally, we elevate the Ecuadorian C. a. patzelti to species status, restrict the distributional limits and suggest taxonomic affiliations of some C. tschudii subspecies, and provide strong evidence for the geographic origin of guinea pig domestication. Finally, we provide an estimated evolutionary timeline for the genus Cavia, which appears to extend well into the late Miocene.     

Late Cenozoic diversification of the austral genus Lagenophora (Astereae,Asteraceae)

Lagenophora (Astereae, Asteraceae) has 14 species in New Zealand, Australia, Asia, southern South America, Gough Island and Tristan da Cunha. Phylogenetic relationships in Lagenophora were inferred using nuclear and plastid DNA regions. Reconstruction of spatio‐temporal evolution was estimated using parsimony, Bayesian inference and likelihood methods, a Bayesian relaxed molecular clock and ancestral area and habitat reconstructions. Our results support a narrow taxonomic concept of Lagenophora including only a core group of species with one clade diversifying in New Zealand and another in South America. The split between the New Zealand and South American Lagenophora dates from 11.2 Mya [6.1–17.4 95% highest posterior density (HPD)]. The inferred ancestral habitats were openings in beech forest and subalpine tussockland. The biogeographical analyses infer a complex ancestral area for Lagenophora involving New Zealand and southern South America. Thus, the estimated divergence times and biogeographical reconstructions provide circumstantial evidence that Antarctica may have served as a corridor for migration until the expansion of the continental ice during the late Cenozoic. The extant distribution of Lagenophora reflects a complex history that could also have involved direct long‐distance dispersal across southern oceans. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 78–95.     

The history of a nearctic colonization: molecular phylogenetics and biogeography of the Nearctic toads (Bufo)

Previous hypotheses of phylogenetic relationships among Nearctic toads (Bufonidae) and their congeners suggest contradictory biogeographic histories. These hypotheses argue that the Nearctic Bufo are: (1) a polyphyletic assemblage resulting from multiple colonizations from Africa; (2) a paraphyletic assemblage resulting from a single colonization event from South America with subsequent dispersal into Eurasia; or (3) a monophyletic group derived from the Neotropics. We obtained approximately 2.5 kb of mitochondrial DNA sequence data for the 12S, 16S, and intervening valine tRNA gene from 82 individuals representing 56 species and used parametric bootstrapping to test hypotheses of the biogeographic history of the Nearctic Bufo. We find that the Nearctic species of Bufo are monophyletic and nested within a large clade of New World Bufo to the exclusion of Eurasian and African taxa. This suggests that Nearctic Bufo result from a single colonization from the Neotropics. More generally, we demonstrate the utility of parametric bootstrapping for testing alternative biogeographic hypotheses. Through parametric bootstrapping, we refute several previously published biogeographic hypotheses regarding Bufo. These previous studies may have been influenced by homoplasy in osteological characters. Given the Neotropical origin for Nearctic Bufo, we examine current distributional patterns to assess whether the Nearctic-Neotropical boundary is a broad transition zone or a narrow boundary. We also survey fossil and paleogeographic evidence to examine potential Tertiary and Cretaceous dispersal routes, including the Paleocene Isthmian Link, the Antillean and Aves Ridges, and the current Central American Land Bridge, that may have allowed colonization of the Nearctic.     

Molecular phylogeny and divergence of major clades in the Puntius complex (Teleostei: Cypriniformes)

Puntius sensu lato (s.l.) was one of the most speciose genera in the family Cyprinidae. There are around 120 valid species widely distributed in South-East and South Asia, and South China. Puntius has long been known as an artificial assemblage and ‘catch-all’ genus in which a large number of small, unrelated cyprinids have been placed. With new species and genera being described each year, obtaining detailed knowledge of the phylogenetic relationships of this complex is critically important in the assessment of a natural classification. In the present study, two mitochondrial and four nuclear genes were used to examine the inter-specific and inter-generic relationships of the Puntius complex and to test the monophyly of the current genera. Divergence time analysis was performed to explore the origin, evolution, and divergence of major clades in Puntius s.l. Results revealed that the genera Puntius seusu stricto (s.s.), Systomus, Pethia, Haludaria, Desmopuntius and Puntigrus were monophyletic with high support. However, monophyly of Barbodes, Striuntius and Sahyadria was not supported. Dawkinsia and Sahyadria formed a highly supported clade. Puntius semifasciolatus and P. snyderi from South China and Taiwan represent a new lineage. Inferences from divergence time analysis indicated that Puntius s.l. likely dated to early Miocene. Major clades in Puntius s.l. diverged during Miocene as well.     

Multiple origins of Locusta migratoria (Orthoptera: Acrididae) in the Japanese Archipelago and the presence of two major clades in the world: evidence from a molecular approach

Phylogenetic relationships among migratory locust (Locusta migratoria) populations in different climatic regions were analysed by sequencing four mitochondrial DNA regions, with special reference to the origin of Japanese populations. The populations are clearly separated into two clades: one consists of individuals from temperate and cold‐temperate areas of Japan and the Chinese continent, and the other comprises those from subtropical islands of Japan, Hainan Island in China, Timol Leste, Australia, Ethiopia, France, and some individuals from Tsushima Island and Honshu of Japan. The divergence time between the two clades is estimated to be 0.86–1.89 Mya. The phylogenetic analysis revealed that Japanese L. migratoria populations were composed of individuals of six different origins: (1) Hokkaido populations possibly from the Russian continent; (2) Honshu–Kyushu populations from the Chinese continent; (3) Southwest Island populations from Hainan Island or adjacent areas; (4) Ogasawara populations that might have originated from Micronesia; (5) part of the Tsushima population that originated from somewhere in the Asian tropics; and (6) a possible relict population of ancient southern haplotypes that exists in western areas of northern Honshu. The Tsugaru Straits and Tokara Straits have acted as effective geographical barriers, as in other organisms, isolating locust populations for a few thousand years. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 570–581.     

Mitochondrial phylogeny and biogeography of the genus Gobio (Teleostei: Cyprinidae) in Turkey

Species of the cyprinid genus Gobio Cuvier, 1816 are widely distributed in freshwater lakes and rivers in Turkey, which is a hotspot for freshwater fish diversity and endemism. The mitochondrial 16S, coxI and cytb genes were sequenced for 217 individuals representing 15 species of Gobio from Turkey. A total of 23 haplotypes were identified for each mitochondrial gene. The genetic distance matrices show that Turkish Gobio species are clustered into three groups (northwestern, central and northeastern Anatolia). Phylogenetic trees constructed with combined dataset by using maximum parsimony, maximum likelihood and Bayesian inference methods revealed that the Turkish Gobio species belongs to three well-supported groups in accordance with their geographic distribution: Group I comprises species found in Central Anatolia, Group II species ranging from eastern Thrace to western Anatolia (northwestern Group) and Group III contains only one species from Western Transcaucasia (northeastern Group). The estimated divergence times between the three Gobio groups, calculated using a conventional 1% rate of mutation for a fish mitochondrial cytb gene per million years, coincide with the late Miocene period in which the tectonic uplift of Anatolia and global climate fluctuations occurred. The relatively low genetic distance between Gobio species in the Turkish Lake District indicate that they are not good species.     

Systematics, cladistics and biogeography of the American genus Farrodes (Ephemeroptera: Leptophlebiidae: Atalophlebiinae)

Cladistic and biogeographic analyses of the genus Farrodes are presented. Two species groups are delineated within Farrodes: F. caribbianus and F. bimaculatus. Three species formerly placed in other genera– Thraulus caribbianus Traver, Thraulus roundsi Traver and Homothraulus maculatus (Needham & Murphy)–are transferred to Farrodes. The species of the F. caribbianus species group are revised. Three new species are described: F. savagei from Venezuela, F. maya and F. mexicanus from Mexico. Keys to separate the two species groups of Farrodes and the species of the F caribbianus species group are provided. Successive cladistic analyses were carried out on both adult and nymphal characters using Hennig86 and CLADOS. The matrix was composed of all available data (nymphal characters were missing for some species), from nymphal and adult stages separately and on taxa represented by both adult and nymphal characters. Species of the genera Simothraulopsis and Homothraulus (components of the Farrodes lineage) were included in the analyses, and Ecuaphkbia was used as the outgroup. Results of the four analyses are compatible. The historical biogeography of Farrodes , with a distribution from nordiern Argentina to southern Texas, is analysed using the program COMPONENT. Areas of endemism are established, and some of their relationships compared with those of other groups available in the literature.     

Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic Forest

Phylogenetic analyses based on mtDNA cytochrome  b were performed in 42 lizards of the Gymnodactylus darwinii complex from three regions within Brazil's Atlantic Forest. Mainland regions and continental shelf islands in the south-eastern range and mainland areas from the north-east were sampled. The criteria of maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods were explored, with the robustness for nodes assessed by bootstrapping (MP and ML) and posterior probabilities (Bayesian searches). By all methods, three distinctive phylogroups were recovered: a south-eastern clade (SE) and two clades from northern regions (NE₁ and NE₂). The pattern of genetic structure of the major clades coincided with the presence of river systems in the Atlantic Forest, and based on corrected genetic distances between those clades, divergence times were tentatively estimated using mtDNA rates calibrated for squamate reptiles. The putative role of Atlantic Forest rivers in generating differentiation is discussed. We present a hypothesis of species limits for G. darwinii , based on concordant lines of evidence including cytogenetic and mtDNA analyses. Two chromosome races (cytotype A, 2n = 38; and cytotype B, 2n = 40) had distributions concordant with clades SE and NE₁ + NE₂, respectively. These races are interpreted to be full species on the basis of a number of empirical criteria.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 13–26.     

Comparative morphology of pond,stream and phytotelm‐dwelling tadpoles of the South American Redbelly Toads (Anura: Bufonidae: Melanophryniscus)

We present a comprehensive review of larval morphology in the Neotropical toad genus Melanophryniscus. The taxa studied included 23 species with representatives of recognized phenetic groups and different larval ecomorphological guilds: pond, stream, and phytotelm‐dwelling tadpoles. Their external morphology variation is congruent with current phenetic arrangement based on adult features, but also reflects the habitat where larvae develop. Lotic tadpoles (i.e. M. tumifrons group and M. krauczuki) in general exhibit a more depressed body, a longer tail with lower fins, and larger oral discs than lentic forms (i.e. M. stelzneri group, M. moreirae, M. sanmartini, and M. langonei). Despite their peculiar, confined microhabitat, phytotelm larvae do not diverge markedly from non‐arboreal species. The distinctive features of all species are the presence of a pineal end organ and the placement of the intestinal reversal point at the left of the abdomen in typical larval stages. The buccal cavity and musculoskeletal anatomy are quite conserved between species, yet some characteristics differ from those of other bufonids. The presence of one pair of subhyoid muscles is apparently an exclusive trait of Melanophryniscus among Bufonidae. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 417–441.