Molecular systematics and historical biogeography of tree boas (Corallus spp.)

Inferring the evolutionary and biogeographic history of taxa occurring in a particular region is one way to determine the processes by which the biodiversity of that region originated. Tree boas of the genus Corallus are an ancient clade and occur throughout Central and South America and the Lesser Antilles, making it an excellent group for investigating Neotropical biogeography. Using sequenced portions of two mitochondrial and three nuclear loci for individuals of all recognized species of Corallus, we infer phylogenetic relationships, present the first molecular analysis of the phylogenetic placement of the enigmatic C. cropanii, develop a time-calibrated phylogeny, and explore the biogeographic history of the genus. We found that Corallus diversified within mainland South America, via over-water dispersals to the Lesser Antilles and Central America, and via the traditionally recognized Panamanian land bridge. Divergence time estimates reject the South American Caribbean-Track as a general biogeographic model for Corallus and implicate a role for events during the Oligocene and Miocene in diversification such as marine incursions and the uplift of the Andes. Our findings also suggest that recognition of the island endemic species, C. grenadensis and C. cookii, is questionable as they are nested within the widely distributed species, C. hortulanus. Our results highlight the importance of using widespread taxa when forming and testing biogeographic hypotheses in complex regions and further illustrate the difficulty of forming broadly applicable hypotheses regarding patterns of diversification in the Neotropical region.     

Molecular phylogeny of the western South Atlantic Sciaenidae based on mitochondrial and nuclear data

Fragments of mitochondrial (COI and rRNA 16S) and nuclear (Tmo-4C4) genes were sequenced to evaluate the phylogenetic relationships among 15 genera of the western South Atlantic Sciaenidae, two freshwater genera and the northwest Pacific Larimichthys crocea.Our results suggest a great diversification for the western Atlantic assemblage; the monophyly of Macrodon, Menticirrhus and Plagioscion genera; the distinctiveness of Bardiella, Stellifer and Ophioscion as belonging to the same clade; the possible existence of two distinct groups in Stellifer; the closer relationship between Lonchurus and Paralonchurus; the non-monophyly of Cynoscion; and the remarkable diversification of Larimus breviceps populations in the Brazilian coast. This is the most comprehensive study evaluating the phylogenetic relationships of the western Atlantic sciaenid and provides a guide for future studies within this family.     

Molecular phylogenetics and biogeography of Neotropical piping guans (Aves: Galliformes): Pipile Bonaparte, 1856 is synonym of Aburria Reichenbach, 1853

The Cracidae are Neotropical galliform birds with 11 genera currently recognized. To investigate the questioned validity of Pipile Bonaparte, 1856 and the monotypic Aburria Reichenbach, 1853 as separate genera, we gathered data from 2727 bp of mitochondrial DNA (cytochrome b, ND2 and control region) and 151 osteological characters. Our phylogenetic analyses of DNA sequences indicated that Aburria aburri is embedded within Pipile. Also, genetic distances between Aburria and any Pipile species are equivalent to the distances estimated for other congeneric cracid species, which genus status is not doubtful. Although the osteological characters do not have phylogenetic signal to solve the phylogenetic relationships at species level, five synapomorphies were found for Aburria and Pipile. Therefore, we suggest that Pipile should be merged with Aburria, which is the oldest described genus. We estimated that speciation in this group occurred in the Plio-Pleistocene, concordant with other birds, primates and rodents that have similar geographic distribution, and proposed a diversification hypothesis based on the occurrence of sea transgressions and the formation of the Amazon Lagoon. Therefore, we conclude that these palaeogeographic events may have contributed to Neotropical taxa diversification to a greater extent than previously suspected.     

Evolutionary diversification of the lizard genus Bassiana (Scincidae) across Southern Australia

Background

Relatively recent (Plio-Pleistocene) climatic variations had strong impacts on the fauna and flora of temperate-zone North America and Europe; genetic analyses suggest that many lineages were restricted to unglaciated refuges during this time, and have expanded their ranges since then. Temperate-zone Australia experienced less severe glaciation, suggesting that patterns of genetic structure among species may reflect older (aridity-driven) divergence events rather than Plio-Pleistocene (thermally-mediated) divergences. The lizard genus Bassiana (Squamata, Scincidae) contains three species that occur across a wide area of southern Australia (including Tasmania), rendering them ideally-suited to studies on the impact of past climatic fluctuations.

Methodology/Principal Findings

We performed molecular phylogenetic and dating analyses using two partial mitochondrial genes (ND2 and ND4) of 97 samples of Bassiana spp. Our results reveal a pattern of diversification beginning in the Middle Miocene, with intraspecific diversification arising from 5.7 to 1.7 million years ago in the Upper Miocene-Lower Pleistocene.

Conclusions/Significance

In contrast to the temperate-zone Northern Hemisphere biota, patterns of evolutionary diversification within southern Australian taxa appear to reflect geologically ancient events, mostly relating to east-west discontinuities imposed by aridity rather than (as is the case in Europe and North America) relatively recent recolonisation of northern regions from unglaciated refugia to the south.     

Cytogenetic and Molecular Data Demonstrate that the Bryconinae (Ostariophysi,Bryconidae) Species from Southeastern Brazil Form a Phylogenetic and Phylogeographic Unit

Brycon spp. occur in Neotropical watersheds to the west and east of the Andes, and as they are sensitive to anthropogenic changes, many these species are endangered in southeastern Brazil. Coastal rivers in southeastern Brazil are characterized by the presence of relatively few freshwater fish species and high endemism of this fauna. The objective of this study was to examine whether Brycon spp. occurring in the coastal basins of southeastern Brazil are monophyletic, using cytogenetic data, mitochondrial, and nuclear molecular markers. All the species showed a diploid number of 50 chromosomes, a conserved number within the subfamily Bryconinae. However, the karyotypic formulas were unique to most species, including Brycon devillei (26m+22sm+2st), Brycon ferox (26m+12sm+12st), Brycon insignis (22m+20sm+8st), Brycon opalinus, and Brycon vermelha (24m+20sm+6st), indicating the prevalence of pericentric and paracentric inversions in the chromosomal evolution of these species. All of them had nucleolar organizer regions in the first pair of subtelocentric chromosomes and no equilocal distribution of heterochromatin in the first pair of chromosomes of the karyotype. These two features, not seen in any other Brycon spp. examined to date, indicate that Bryconinae species from the Brazilian southeastern coastal basins, including the monotypic genus Henochilus, are monophyletic. Also, this is the first study that reports NOR location and C-banding patterns as synapomorphies for a Neotropical fish species group. The monophyly was also supported by a phylogenetic analysis of 16S rDNA (16S), cytochrome oxidase subunit I (COI), alpha-myosin (MYH6) genes and S72 intron molecular data. Our results partially corroborate the “Brycon acuminatus” group proposed by Howes in 1982: our proposed clade keeps B. devillei, B. ferox, and B. insignis; but it also includes B. opalinus, B. vermelha, and H. weatlandii whereas it excludes B. nattereri. The phylogeographic unit formed by Bryconinae species in southeastern Brazil reflects the long and isolated paleohydrological history of these coastal basins relative to the continental watersheds.     

Molecular systematics of the genus Troglophilus (Rhaphidophoridae,Orthoptera) in Turkey: mitochondrial 16S rDNA evidences

This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus.Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.     

DNA barcode detects high genetic structure within neotropical bird species

Background

Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna.

Methods and Findings

Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520) of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21) or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20). Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism.

Conclusions

The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent geological periods.     

Diversity and Systematics of Schizomavella Species (Bryozoa: Bitectiporidae) from the Bathyal NE Atlantic

Eight NE Atlantic and Mediterranean species, which were originally assigned to the genus Schizoporella (Family Schizoporellidae) when introduced, are redescribed and stabilized by typification. Seven of these species are transferred to the bitectiporid genus Schizomavella: S. fischeri, S. glebula, S. neptuni, S. obsoleta, S. richardi, S. triaviculata, and S. triaviculata var. paucimandibulata, which is here raised to species rank. The eighth species, Schizoporella fayalensis, is transferred to the lanceoporid genus Stephanotheca. Schizomavella obsoleta and S. glebula are considered junior subjective synonyms of S. fischeri and S. richardi, respectively. Two new species are described: Schizomavella rectangularis n. sp. from the Strait of Gibraltar, and Schizomavella phterocopa n. sp. from the Great Meteor Bank. A new subgenus, Calvetomavella n. subgen. is established as a result of a phylogenetic analysis based on morphological characters; it includes S. neptuni, S. triaviculata, S. paucimandibulata and S. phterocopa n. sp., together with Schizomavella discoidea and Schizomavella noronhai. The rest of the species remain in the nominotypical subgenus Schizomavella.     

Neotropical diversification: the effects of a complex history on diversity within the poison frog genus Dendrobates

Aim We study the Neotropical poison frogs of the genus Dendrobates Wagler, 1830 in order to clarify their phylogenetic relationships and biogeographical history. The genus Dendrobates is an excellent taxon for examining patterns of Neotropical diversification as the four major species groups appear to correspond roughly to distinct geographical regions: (1) trans‐Andean, (2) Andean foreland, (3) Brazilian Shield and (4) Guianan Shield/Central America. In order to test the agreement of five of the most prominent hypotheses of Amazonian diversification, phylogenetic patterns were examined for agreement with patterns predicted by these hypotheses. Location Central and South America Methods The phylogenetic relationships of the genus Dendrobates were examined from novel and existing (GenBank) sequences of four mitochondrial loci totalling c. 1400 bp from 40 specimens of 22 different species using maximum parsimony and Bayesian methods. Results were compared with traditional taxonomic arrangements by means of SH tests. Phylogenetic relationships and genetic distances were used to test the adequacy of various diversification hypotheses. Results Phylogenetic analyses support the restructuring of two species groups of Dendrobates and the creation of a new species group. Statistical tests of the traditional taxonomic arrangement indicate a significantly bad fit to the molecular data. This restructuring has important implications for the understanding of the historical biogeography of Dendrobates. Biogeographical patterns within this genus suggest that a complex interaction of biotic and abiotic factors since the Eocene have produced the diversity observed today. Main conclusions The current classification of Dendrobates into discrete species groups does not accurately reflect evolutionary history. Data presented here strongly support a monophyletic Brazilian Shield lineage whose members have previously been split among the quinquevittatus and tinctorius groups. Furthermore, previous attempts at elucidating the historical biogeography of this genus were compromised by incomplete sampling and conclusions drawn from a paraphyletic ingroup. Our findings demonstrate a role for numerous hypotheses of diversification (e.g. river, refuge, disturbance–vicariance) in the history of Dendrobates, supporting previous warnings about the dangers of over‐simplification in the study of Neotropical diversification.     

Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification

Background  

The family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. Despite great morphological and ecological diversity, the evolutionary relationships in the family have been poorly explored at all taxonomic levels. Using sequences from four mitochondrial genes (12S, ATP8, ATP6, and ND6), we reconstructed the phylogeny of the Neotropical forest hawk genus Leucopternis and most of the allied genera of Neotropical buteonines. Our goals were to infer the evolutionary relationships among species of Leucopternis, estimate their relationships to other buteonine genera, evaluate the phylogenetic significance of the white and black plumage patterns common to most Leucopternis species, and assess general patterns of diversification of the group with respect to species' affiliations with Neotropical regions and habitats.     

Evolution of the Northern Rockweed,Fucus distichus,in a Regime of Glacial Cycling: Implications for Benthic Algal Phylogenetics

Northern hemisphere rockweeds (Fucus) are thought to have evolved in the North Pacific and then spread to the North Atlantic following the opening of the Bering Strait. They have dispersed and widely speciated in the North Atlantic and its tributary seas. Fucus distichus is likely near the ancestral member of this genus, and studies have shown that there are several species/subspecies in this complex (i.e. F. evanescens and F. gardneri). We used phylogenetic and haplotype analyses to test the phylogenetic relationships and biogeography of F. distichus. Our data and subsequent analyses demonstrate that, unlike previous studies that lacked samples from an extensive geographical area of the Arctic and Subarctic, there is a distinct Arctic haplotype that is the source of subspecies in both the North Pacific and North Atlantic. Fucus distichus occupies a low tide zone habitat, and in Arctic/Subarctic regions it is adapted to the severe stress of sea ice coverage and disturbance during many months per year. We hypothesize that the very large geographic area of Arctic and Subarctic rocky shores available to this species during interglacials, supported by large Arctic/Subarctic fringe areas as well as unglaciated refugia during glacial cycles, provided a robust population and gene pool (described by the Thermogeographic Model). This gene pool dilutes that of the more fragmented and area-limited Temperate/Boreal area populations when they are brought together during glacial cycles. We suggest that similar subspecies complexes for a variety of Arctic/Subarctic shore biota should be examined further in this context, rather than arbitrarily being split up into numerous species.     

Spatial Genetic Structure of the Abundant and Widespread Peatmoss Sphagnum magellanicum Brid.

Spore-producing organisms have small dispersal units enabling them to become widespread across continents. However, barriers to gene flow and cryptic speciation may exist. The common, haploid peatmoss Sphagnum magellanicum occurs in both the Northern and Southern hemisphere, and is commonly used as a model in studies of peatland ecology and peatmoss physiology. Even though it will likely act as a rich source in functional genomics studies in years to come, surprisingly little is known about levels of genetic variability and structuring in this species. Here, we assess for the first time how genetic variation in S. magellanicum is spatially structured across its full distribution range (Northern Hemisphere and South America). The morphologically similar species S. alaskense was included for comparison. In total, 195 plants were genotyped at 15 microsatellite loci. Sequences from two plastid loci (trnG and trnL) were obtained from 30 samples. Our results show that S. alaskense and almost all plants of S. magellanicum in the northern Pacific area are diploids and share the same gene pool. Haploid plants occur in South America, Europe, eastern North America, western North America, and southern Asia, and five genetically differentiated groups with different distribution ranges were found. Our results indicate that S. magellanicum consists of several distinct genetic groups, seemingly with little or no gene flow among them. Noteworthy, the geographical separation of diploids and haploids is strikingly similar to patterns found within other haploid Sphagnum species spanning the Northern Hemisphere. Our results confirm a genetic division between the Beringian and the Atlantic that seems to be a general pattern in Sphagnum taxa. The pattern of strong genetic population structuring throughout the distribution range of morphologically similar plants need to be considered in future functional genomic studies of S. magellanicum.     

Les otolithes des Téléostéens du Plio-Pleistocène belge

The study of approximately twenty three thousand otoliths from Plio-Pleistocene sites in the harbour region of Antwerp, as well as a critical revision of already published material allowed us to identify a teleostean fauna with fourty seven species (including two subspecies and seven species in open nomenclature). Two of these, Ophidion springeri and Uranoscopus septentrionalis are new to science. The fauna is typical for coastal waters slightly warmer than those of the actual North Sea and caracterized by the predominance of Gadidae. Biostratigraphically this fauna is well individualized with respect to preceeding ones (only seven species in common with the Miocene fauna) and those following twenty-three species in common with the extant fauna). The following biostratigraphical subdivision has been recognized in the Upper Miocene and the Plio-Pleistocene of the Antwerp region: (1) an association with «genus? Macrouridarum labiatus, Trisopterus sculptus, Gadiculus benedeni and Trisopterus luscus spectabilis, in the Sands of Deurne (Upper Miocene); (2) an association with Gadiculus benedeni and Merlangius pseudaeglephinus, in the Formation of Kattendijk (Pliocene); (3) an association with Gadiculus verticalis and Merlangius pseudaeglefinus in the Formation of Lillo (Plio-Pleistocene); (4) an association with Gadus morhua and Merlangius pseudaeglefinus in the so called «Icenian deposits not present in Belgium but found in the Netherlands.     

A total evidence analysis of the phylogeny of hatchet-faced treefrogs (Anura: Hylidae: Sphaenorhynchus)

The Neotropical hylid genus Sphaenorhynchus includes 15 species of small, greenish treefrogs widespread in the Amazon and Orinoco basins, and in the Atlantic Forest of Brazil. Although some studies have addressed the phylogenetic relationships of the genus with other hylids using a few exemplar species, its internal relationships remain poorly understood. In order to test its monophyly and the relationships among its species, we performed a total evidence phylogenetic analysis of sequences of three mitochondrial and three nuclear genes, and 193 phenotypic characters from all species of Sphaenorhynchus. Our results support the monophyly of Sphaenorhynchus with molecular and phenotypic evidence, with S. pauloalvini as the earliest diverging taxon, followed by S. carneus, as the sister taxon of all remaining species of the genus. We recognize three species groups in Sphaenorhynchus (the S. lacteus, S. planicola and S. platycephalus groups), to facilitate its taxonomic study; only three species (S. carneus, S. pauloalvini and S. prasinus) remain unassigned to any group. Sequence data were not available for only two species (S. bromelicola and S. palustris) for which we scored phenotypic data; wildcard behaviour was detected only in S. bromelicola nested inside the S. platycephalus group. On the basis of the resulting phylogenetic hypothesis, we discuss the evolution of oviposition site and a number of phenotypic characters that could be associated with heterochronic events in the evolutionary history of this group.     

High Levels of Diversity Uncovered in a Widespread Nominal Taxon: Continental Phylogeography of the Neotropical Tree Frog Dendropsophus minutus

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km². One of them occupies an area of almost one million km² encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.     

Out of South America: phylogeny of non‐biting midges in the genus Labrundinia suggests multiple dispersal events to Central and North America

Non‐biting midges of the genus Labrundinia (Chironomidae: Tanypodinae) are minute dipterans with immature stages living in a variety of unpolluted water bodies, from small streams and ponds to lakes and bays. Extensively recorded in ecological studies, the genus comprises 39 species, all except one described from areas outside the Palearctic region. Internal structure among Labrundinia species was postulated by S. S. Roback, who recognized four species groups based on morphological characters of immature stages. We examined phylogenetic relationships among known Labrundinia species using partial DNA sequences of the nuclear protein‐coding gene CAD and morphological characters. Both analyses with Bayesian inference and parsimony methods recovered the monophyly of Labrundinia, strongly supported by five morphological synapomorphies. Internal relationships within the genus partly supported Roback's species groups with the addition of later described species. Biogeographical inferences were obtained by applying Bayesian binary MCMC (BBM) analysis and favoured a scenario where Labrundinia had its initial diversification in the Neotropical region and that current presence in the Nearctic region and southern South America is due to subsequent dispersal.     

Community-level interactions and functional ecology of major workers in the hyperdiverse ground-foraging Pheidole (Hymenoptera, Formicidae) of Amazonian Ecuador

Ants of the genus Pheidole are abundant and hyperdiverse, particularly in Neotropical rainforests. Very little is known, however, about the degree of ecological and behavioral differentiation of coexisting species comprising Pheidole communities. Additionally, the ecological role of the major worker subcaste, thought to be significant to the diversification of Pheidole, is poorly understood. We investigated the ecology and behavior of a ground-foraging Pheidole community of at least 56 species in Amazonian Ecuador. Pheidole species differed strongly in tolerance to flooding, nest site usage, foraging range, major worker foraging, and control of baits, but not in daily activity or ability to discover baits. A molecular phylogeny based on mitochondrial DNA was characterized by poorly resolved basal relationships and long terminal branches, suggesting an ancient diversification of many Pheidole lineages. Comparison of well-supported sister species suggests that both phylogenetic history and ecologically induced differentiation contribute to interspecific variation in Amazonian Pheidole. Ground-nesting species had larger major workers than twig-nesting species, whereas dominant species with stronger recruitment had a higher proportional abundance of major workers at baits. Variation among species suggests the presence of behavioral groups within the Amazonian Pheidole community that appear to segregate according to nest site usage and/or tolerance to flooding disturbance. Our results suggest an important role for major worker differentiation in the diversification of Pheidole.