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.     

Application of parsimony analysis of endemicity to Mexican gymnosperm distributions: grid-cells, biogeographical provinces and track analysis

Parsimony analysis of endemicity (PAE) was used to analyse the distributional patterns of 124 species of Mexican gymnosperms, using two different sample units: grid-cells and biogeographical provinces. PAE analyses were based on distributional data from herbarium specimens and specialized literature. Two data matrices were constructed for 60 grid-cells of 2° and 14 biogeographical provinces. The analysis of the 2° grid-cell matrix led to 7084 cladograms. The strict consensus cladogram showed several clades equivalent to the results obtained with the biogeographical provinces. Three clades agree with some principal regions of distribution of Mexican pines, previously identified by several authors, located at the northern portion of the Baja California peninsula, the Sierra Madre Occidental, and the Sierra Madre Oriental. These areas represent important centres of species diversity and endemism for Mexican gymnosperms. The analysis of the province matrix led to two most parsimonious cladograms, which only differed in the position of the Sierra Madre Occidental province. The iterative procedure PAE with progressive character elimination was applied to identify generalized tracks, where clades of provinces were considered equivalent to generalized tracks, and each time a cladogram was obtained, species defining its clades were deleted and a new run was undertaken. We found five generalized tracks, mainly located in montane provinces. The distribution patterns of gymnosperms agree with the existence of several Mexican biogeographical provinces, and a different historical biogeography of the Mexican peninsulas from the rest of the country is evident.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 405–417.     

Biogeographical patterns of the avifaunas of the Caribbean Basin Islands: a parsimony perspective

We analyzed the avifaunas of the Caribbean islands and nearby continental areas and their relationships using Parsimony Analysis of Endemicity (PAE), in order to assess biogeographical patterns and their concordance with geological and phylogenetic evidence. Using distributional information of birds obtained from published literature, a presence/absence matrix for 695 genera and 2026 species of land and freshwater birds was constructed and analyzed. Three different analyses were performed: for species, for genera, and for species and genera combined. In the combined analysis, the Lesser Antilles appear paraphyletic at the base of the cladogram. Then, two major clades are identified: South America (Andes, Venezuelan lowlands, Dutch West Indies and Trinidad and Tobago) and North America, including the Greater Antilles in a clade that is the sister area to Yucatan and the Central American countries nested from north to south. PAE results support Caribbean vicariant models and cladistic biogeographical hypotheses on area relationships, and show relative congruence with available phylogenetic data. Bird biogeography on the Caribbean islands appears to have been caused by both vicariance and dispersal processes. © The Willi Hennig Society 2007.     

Biogeographic analysis of endemic cacti of the Sierra Madre Oriental, Mexico

The distribution of cacti species that inhabit the Sierra Madre Oriental (SMO) was analysed. Grid-cells were analysed using parsimony analysis of endemicity (PAE) and endemism indices. Areas characterized by their diagnostic species were determined, aiming to propose areas for the conservation of threatened cacti. Distributional data were obtained from 1936 herbarium specimens, electronic information, and from field collections. Eight areas of endemism and three main clades were obtained from the grid-cell analysis. Areas obtained from the endemism indices are very similar to those obtained with the PAE, but differ in the association of grid-cells. PAE showed endemism patterns indicating that southern and central sections of the SMO province are the areas richest in geographically-restricted species. The results obtained with different endemism indices detected more or less the same areas, although the importance level is different. The corrected weighted endemism index can be considered as a reliable measure of endemism because it is unrelated to species richness. A regionalization of the SMO in three subprovinces is suggested, supported by characteristic cacti taxa and the existence of natural barriers.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 373–389.     

Parsimony Analysis of Endemicity (PAE) of Mexican hydrological basins based on helminth parasites of freshwater fishes

Aim The distributional patterns of helminthological fauna of freshwater fishes were analysed to postulate a general hypothesis on the relationships of some Mexican hydrological systems. Location Eight hydrological systems of central and eastern Mexico were studied and compared with records from Nicaragua. Methods A Parsimony Analysis of Endemicity (PAE) was applied to the presence/absence of ninety‐two helminth parasite taxa (Monogeneans, Digeneans, Cestodes, Acanthocephalans and Nematodes) of freshwater fishes, from eight Mexican hydrological systems, using the Hennig86 program. Results The results represent the first attempt for a biogeographical analysis through application of the PAE method to the distributional patterns of helminth parasites of freshwater fishes in Mexico. A single most parsimonious cladogram was obtained, which grouped all the Neotropical systems in accordance with previous proposals based on other plant and animal taxa. Main conclusions The most basal systems were Santiago and Lerma basins, which exhibited Nearctic affinities. The remaining areas of the cladogram showed Neotropical affinities. All the southeastern systems were grouped in a clade with the Nicaragua system, providing support for a ‘Mesoamerican province’ based on helminth parasites of cichlids. The cladogram also suggests that the treatment of the Lerma‐Santiago basin as a single biogeographical unit is inaccurate and that they should be treated as separate systems.     

The importance of looking at small-scale patterns when inferring Gondwanan biogeography: a case study of the centipede Paralamyctes (Chilopoda, Lithobiomorpha, Henicopidae)

Gondwanan biogeography has fascinated zoologists and botanists for over a century, but most biogeographical work has used continent-scale areas as analytical units. More finely resolved patterns, as can be obtained from small invertebrates with limited dispersal abilities, will be obscured in those studies. A common case is treating Australia as a single biogeographical region. In the present study, the necessity of splitting Australia into multiple microareas is demonstrated using centipedes as an example. The lithobiomorph centipede Paralamyctes is distributed on fragments of Gondwana, with species in southern Africa, Madagascar, southern India, Patagonia, eastern Australia, and New Zealand. A cladogram for Paralamyctes is based on morphology and sequences for four molecular markers for 30 terminals that sample 20 of 26 known ingroup species and four outgroups. Analysis with direct optimization across a range of indel costs and transversion : transition cost ratios identifies two main clades: Paralamyctes ( Paralamyctes ) unites species from southern Africa, Madagascar, tropical and warm temperate Australia, and New Zealand. The other group includes the temperate Australian/New Zealand Paralamyctes ( Haasiella ) and Paralamyctes ( Thingathinga ) and a Chilean clade. Subtree analysis finds that different parts of Australia have closest affinities to other Gondwanan fragments, and some of these relationships (such as that between north Queensland and New Zealand) are based on taxonomically stable clades. Area delimitation for large continental fragments should use sufficiently fine resolution to test the 'monophyly' of those fragments and attempt to eliminate spurious geographical paralogy.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 65–78.     

Species diversity and endemism in the Daphnia of Argentina: a genetic investigation

Although the temperate regions of South America are known to have a diverse daphniid fauna, there has been no genetic evaluation of the existing taxonomic system or of the affinities between the North and South American faunas. The present study analyses mitochondrial DNA sequences and allozyme variation to investigate species diversity in 176 Daphnia populations from Argentina. This work established the presence of at least 15 species in Argentina, six of which are either undescribed or are currently misidentified and two of which represent range extensions of North American taxa. Eleven of the Argentine species appear endemic to South America, while the remaining four also occur in North America. In the latter cases, the close genetic similarity between populations from North and South America indicates the recent exchange of propagules between the continents. While biological interactions and habitat availability have undoubtedly contributed to the observed species distributions, chance dispersal has apparently played a dominant role in structuring large-scale biogeographical patterns in this genus and probably in other passively-dispersed organisms.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 171−205.     

Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca)

Phylogenetic relationships among assumed Gondwanan aquatic inland invertebrate fauna are generally largely neglected, and biogeographical hypotheses for these organisms are generally inferred from historic (palaeogeographical) and contemporary distribution patterns. The distribution of the monogeneric thermophilic freshwater fairy shrimp family Streptocephalidae ( Streptocephalus ) provides a particularly useful framework to test the three contrasting biogeographical scenarios proposed for the evolution of this group: (1) the genus evolved in Laurasia and subsequently dispersed into Africa and North America; (2) the genus evolved and dispersed out of Africa and (3) the current distribution of the genus is the result of vicariance following the fragmentation of Gondwana. In the present study, the phylogenetic relationships of species in this genus are examined with the use of two mitochondrial genes (12S rRNA and COI mtDNA), while the phylogenetic relationships among the North American species and selected African taxa was investigated using the nuclear fragment (5.8S-ITS-1-18S). Phylogenetic results indicate that Streptocephalus probably evolved in Gondwana and that the current distribution patterns are a consequence of a combination of vicariance and limited dispersal. The implications for the evolution of continental freshwater crustaceans are discussed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 313–327.     

Historical biogeography of Hexabathynella , a cosmopolitan genus of groundwater Syncarida (Crustacea, Bathynellacea, Parabathynellidae)

Hexabathynella is the only cosmopolitan genus of the order Bathynellacea (Crustacea). The known species number 18, found in Europe (9), Africa (1), South America (2), North America (3) and Australia and New Zealand (3). Phylogenetic analysis suggests that the least derived species are those from South America and the most derived those from the Iberian Peninsula, North America and Australia. The five species with the most plesiomorphic characters occur in salt or brackish water, which supports a marine origin for the genus. Phylogenetic and biogeographical analyses suggest that the distribution of the genus can be explained by dispersion and a double vicariant biogeographical model based on plate tectonics and the evolution of the Tethys during the Mesozoic and Cenozoic.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 457–466.     

Colonization, population expansion, and lineage turnover: phylogeography of Mesoamerican characiform fish

We present a phylogeographical analysis of four genera of Mesoamerican primary freshwater fish ( Brycon , Bryconamericus , Eretmobrycon , and Cyphocharax ). Three hundred and thirty-nine individuals were genotyped into one of 31 operational taxonomic units (OTUs) based on the nucleotide sequence of their mitochondrial ATPase 6 & 8 genes (842–839 bp). Contrary to inference based on the species-level taxonomy of these genera, molecular data identified only a single case of sympatry between closely related OTUs, despite extensive parapatry. Polytomies dominate the mtDNA-based phylogenies and demonstrate multiple, noncontemporaneous waves of rapid expansion across Mesoamerica from South American sources. Analyses based on genetic distances observed among congeneric species of Mesoamerican primary freshwater fishes in comparison to divergence between transisthmian marine fishes permit the strong inference that the Pliocene rise of the Panama land bridge provided the first opportunity for the colonization of Mesoamerica by Characiform fishes. We develop a priority-effect model, based on the assumption that genetically closely related OTUs share similar ecological niches, to reconcile the general lack of contemporary sympatry between closely related OTUs with the substantial historical connectivity among Mesoamerican drainages demonstrated by the rapid expansion of Brycon , Bryconamericus , and Cyphocharax . Finally, in most cases, we infer that the westerly limits of freshwater fish distributions in Mesoamerica are more consistent with being defined by ecological factors rather than by dispersal limitation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 235–255.     

Historical legacies in the geographical diversity patterns of New World palm (Arecaceae) subfamilies

The extent to which species richness patterns of the major palm subfamilies in the Americas are controlled by lineage history was studied. Based on the fossil record, we suggest that the subfamily Coryphoideae has followed a boreotropical dispersal route into Central and South America, whereas Calamoideae (tribe Lepidocaryeae), Ceroxyloideae and Arecoideae have Gondwana/South America-biased histories. However, Arecoideae has been present and diverse in both South and Central America at least since the early Tertiary. We used regression analyses to evaluate the relative importance of environmental factors and spatial variables (as substitutes for historical or other non-environmental factors) as determinants of geographical variation in species richness for each subfamily. Given the different lineage histories, we hypothesized that: (1) coryphoid richness should be least strongly controlled by the modern environment and exhibit a strong non-environmental bias towards Central and North America, reflecting its boreotropical invasion route, (2) calamoid species richness should exhibit a non-environmental bias towards South America, reflecting its long African–South American history, and (3) arecoid species richness should be most strongly environmentally determined, reflecting the long arecoid residency in both Central and South America. The regression analyses confirmed the hypothesized effects of lineage history on the geographical patterns in species richness. Hence, modern species richness patterns in the New World palm subfamilies strongly reflect their divergent biogeographical histories.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 113–125.     

Phylogeny and evolutionary history of the Aplodontoidea (Mammalia: Rodentia)

Athough over a hundred species of fossil aplodontoids have been described since the extant species, Aplodontia rufa (the mountain beaver), was first described by Rafinesque in 1817, a thorough survey of the relationships among all the species in this clade has not been undertaken since McGrew's study in 1941. Here, a complete phylogenetic analysis of all published species of aplodontoids is used to reconstruct the evolutionary relationships within the clade, and to present an updated classification of the Aplodontoidea. Several of the traditionally recognized subfamilies are found to be paraphyletic, namely the Prosciurinae, the Allomyinae, and the Meniscomyinae. Others, however, including the Aplodontinae and the Mylagaulidae, appear to be monophyletic. These latter two taxa, which include all of the hypsodont members of the aplodontoid clade, seem to be sister taxa. The history of the aplodontoid clade shows several episodes of rapid diversification in the Early Oligocene, the Late Oligocene, and the Early to Middle Miocene. The Ansomyinae and Aplodontinae show comparatively low speciation rates. The patterns of change in morphology and evolutionary rates suggest a need for a more detailed study of the causes of diversification, extinction, and ecological change in this lineage.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 769–838.     

Mitochondrial DNA phylogeny of the woodpecker genus Veniliornis (Picidae, Picinae) and related genera implies convergent evolution of plumage patterns

The woodpecker genus Veniliornis comprises 12 species, all restricted to the New World tropics. The seemingly distantly related genus Picoides is broadly distributed in Eurasia and North America with two putative species, P. lignarius and P. mixtus , occurring in South America. The two genera are clearly distinct with respect to general plumage colouration and patterning as well as habitat utilization and thus traditionally have been placed in different tribes. Phylogenetic analyses of mtDNA sequences from the COI and cyt b genes indicated that both genera are reciprocally paraphyletic. The two South American species of Picoides belong to a clade comprising most species of Veniliornis , but V. fumigatus of Central and north-western South America belongs to a clade comprising species of Picoides . The mtDNA tree also indicated that Veniliornis is not closely related to the genus Piculus, as is implicit in current classifications. Misclassifications involving Veniliornis at both the generic and tribal levels appear to result from convergent evolution of plumage traits in specific forest types. We infer that the common ancestor of Veniliornis entered South America approximately at the time the Isthmus of Panama was formed, and diversification within South America was rapid.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 611–624.     

Taxonomic relationships between Pachycerus and Rhabdorrhynchus (Coleoptera: Curculionidae: Lixinae), with descriptions of two new species of Rhabdorrhynchus from the Arabian Peninsula

Taxonomic relationships between Rhabdorrhynchus and Pachycerus are discussed, and two new species of Rhabdorrhynchus are described: Rhabdorrhynchus sauditus (type locality: Saudi Arabia, As Shāqqah al Yamānīyah, 19°42'N, 40°48'E) and Rhabdorrhynchus emir (type locality: United Arab Emirates, Jebel Ali, 24°59'N, 55°43'E). Some hypotheses on the distribution of the new species in the Arabian Peninsula, based on a biogeographical analysis, are proposed.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 152 , 25–37.     

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.     

Patterns of Amazonian area relationships based on raw distributions of papilionid butterflies (Lepidoptera: Papilioninae)

Diversifications within a biota are due to several factors. Although some of these are untestable with current analytical methods, hierarchical congruence obtained with different cladistic methods and based on independent taxa are undoubtedly important. In the recent past, most hypotheses of historical biogeography (e.g. refugial, riverine, disturbance, vicariance) were tested on the Amazonian biota, selecting a number of diverse organisms such as plants, anurans, lizards, butterflies, birds and monkeys. In this study we used parsimony analysis of endemicity to infer historical relationships among 16 interfluvial areas in the Amazonian lowlands based on raw distributions of 114 Papilioninae (Lepidoptera). The analysis yielded two most parsimonious trees of area relationships. One tree was characterized by two main clusters of areas which showed a separation of Guyanan + south-east Amazonian interfluvial areas from western Amazonian interfluvial areas. The second tree showed the Guyanan interfluvial areas basal to a cluster which included all the other interfluvial areas. This latter cluster was subdivided into two main groups of areas separating the south-east Amazonian and the western Amazonian interfluvial areas. This result is discussed in the light of previous hypotheses obtained with the same method using some vertebrate taxa in the Amazonian lowlands. Likewise, comparisons with other hypotheses on lineages of birds, mammals and butterflies obtained applying cladistic biogeographical methods are made. The two alternative vicariant patterns presented for papilionid butterflies are strictly congruent with those for birds.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 345–357.     

Molecular systematics of North American phoxinin genera (Actinopterygii: Cyprinidae) inferred from mitochondrial 12S and 16S ribosomal RNA sequences

The cyprinid fish fauna of North America is relatively large, with approximately 300 species, and all but one of these are considered phoxinins. The phylogenetic relationships of the North American phoxinins continue to pose difficulties for systematists. Results of morphological analyses are not consistent owing to differences interpreting and coding characters. Herein, we present phylogenetic analyses of mitochondrial 12S and 16S ribosomal RNA sequence data for representatives of nearly all genera of North American phoxinins. The data were analysed using parsimony, weighted parsimony, maximum likelihood and bayesian analyses. Results from weighted parsimony, likelihood and the bayesian analysis are largely consistent as they all account for differing substitution rates between transitions and transversions. Several major clades within the fauna can be recognized and are strongly supported by all analyses. These include the western clade, creek chub–plagopterin clade and the open posterior myodome clade. The shiner clade is nested in the open posterior myodome clade and is the most species-rich clade of North American phoxinins. Relationships within this clade were not well resolved by our analyses. This may reflect the inability of the mitochondrial RNA genes to resolve recent speciation events or taxon sampling within the shiner clade.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 63–80.     

Sophora sect. Edwardsia (Fabaceae): further evidence from nrDNA sequence data of a recent and rapid radiation around the Southern Oceans

Phylogenetic relationships are inferred from nuclear ribosomal internal transcribed spacer sequences for species belonging to Sophora sect. Edwardsia from South America, New Zealand, Lord Howe Island, Hawai'i, La Réunion, Easter Island, and Raivavae Island (French Polynesia). Results support the monophyly of sect. Edwardsia , but relationships among the species from this section are poorly resolved due to most species having identical sequences. The origin of Sophora sect. Edwardsia is discussed, as competing hypotheses have proposed the group originated in South America from a North American ancestor, or in the north-west Pacific. We suggest sect. Edwardsia may have arisen in the north-west Pacific from a Eurasian ancestor.  © The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 435–441.     

Phylogeography and morphological variability in land snails: the Sicilian Marmorana (Pulmonata, Helicidae)

Land snails have long been recognized as suitable organisms for studying phenotypic differentiation and phylogeny in relation to geographical distribution. Morphological data (shell and anatomy biometry on different geographical scales) and partial sequences from mitochondrial genes (cytochrome oxidase subunit I , 16S rDNA) were used to test whether morphological patterns match phylogeny in a diversified group of Sicilian rock-dwelling land snails belonging to the genus Marmorana . The taxonomic implications of the three character sets (shell and anatomical biometry and molecular data) were also considered. The inferred phylogenetic relationships do not match morphological (shell and genitalia) patterns. This result may significantly modify the current taxonomy. Mitochondrial based reconstructions define several supported clades well correlated with geographic distribution and populations were found to be distributed parapatrically. The progressive decline in mitochondrial DNA sequence similarity over a distance of 250 km is consistent with a model of isolation by distance, a pattern previously recognized for other groups of land snails. For one clade of Marmorana , colonization along Mediterranean trade routes appears to be a possibility.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 809–823.