The complete mitochondrial genome of Anomaloglossus baeobatrachus (Amphibia: Anura: Aromobatidae)

The complete mitogenome of the rocket frog Anomaloglossus baeobatrachus was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA), providing the first mitogenome for this genus. The genome was 17,572 bp long and presents the typical organization found in other neobatrachian anurans. A phylogenetic analysis including A. baeobatrachus and all other available mitogenomes of Hyloidea provided relationships in accordance with previous phylogenetic studies.

Comparative phylogeography of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) in Florida: Testing the maritime discontinuity in coastal plants

PREMISE OF THE STUDY

Previous studies of the comparative phylogeography of coastal and marine species in the southeastern United States revealed that phylogenetically diverse taxa share a phylogeographic break at the southern tip of Florida (the maritime discontinuity). These studies have focused nearly exclusively on animals; few coastal plant species in Florida have been analyzed phylogeographically. We investigated phylogeographic patterns of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle), two coastal trees that occur on both coasts of the peninsula of Florida.

METHODS

We sampled and genotyped 150 individuals each of A. germinans and R. mangle, using eight microsatellite loci per species. We used observed and expected heterozygosity to quantify genetic diversity in each sampling location and allele frequencies to identify putative phylogeographic breaks and measure gene flow using BayesAss and Migrate-n. We tested the hypothesis that both species would exhibit a phylogeographic break at the southern tip of Florida.

KEY RESULTS

We did not find any significant phylogeographic breaks in either species. Rhizophora mangle exhibits greater genetic structure than A. germinans, contrary to expectations based on propagule dispersal capability. However, directional gene flow from the Gulf to the Atlantic was more pronounced in R. mangle, indicating that the Gulf Stream may affect genetic patterns in R. mangle more than in A. germinans.

CONCLUSIONS

The high dispersal capability of these species may lead to high genetic connectivity between sampling locations and little geographic structure. We also identified several locations that, based on genetic data, should be the focus of conservation efforts.

Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru

A new species of the genus Amazophrynella (Anura, Bufonidae) is described from the departments of Madre de Dios, Cusco and Junin in Peru. An integrative taxonomy approach is used. A morphological diagnosis, morphometrics comparisons, description of the advertisement call, and the phylogenetic relationships of the new species are provided. Amazophrynella javierbustamantei sp. n. differs from other species of Amazophrynella by: intermediate body-size (snout-vent length 14.9 mm in males, n = 26 and 19.6 mm in females, n = 20), tuberculate skin texture of body, greatest hand length of the Amazophrynella spp. (3.6 mm in males, n = 26 and 4.6 mm in females, n = 20), venter coloration yellowish, tiny rounded black points covering the venter, and thirteen molecular autapomorphies in the 16S RNA gene. Its distribution varies from 215 to 708 m a.s.l. This discovery highlights the importance of the remnant forest in preserving the biodiversity in Peru, and increase in seven the species formally described in the genus Amazophrynella.

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system

Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.

Phylogeographic Structure of the White-Footed Mouse and the Deer Mouse, Two Lyme Disease Reservoir Hosts in Québec

Modification of a species range is one of many consequences of climate change and is driving the emergence of Lyme disease in eastern Canada. The primary reservoir host of the bacteria responsible for Lyme disease, Borrelia burgdorferi, is the white-footed mouse (Peromyscus leucopus), whose range is rapidly shifting north into southern Québec. The deer mouse, P. maniculatus, is occurring over most Québec province and is a less competent host for B. burgdorferi. Here, we compared the phylogeographic structure of both Peromyscus species in Québec. Using a combination of multiple mitochondrial DNA markers and phylogeographic methods, we detected an ongoing and rapid expansion of P. leucopus, while P. maniculatus appears more stable. Haplotype and populations networks indicated that populations of P. maniculatus exhibit more genetic structure than P. leucopus across the study area. Furthermore, significant and consistent genetic divergences between populations of the two species on both sides of the St. Lawrence River suggest that distinct lineages of P. leucopus and P. maniculatus with different ancestral origins colonized Southern Québec following the Last Glacial Maximum. The phylogeographic structure of pathogens is expected to mirror the structure observed in their reservoir hosts. As different strains of Borrelia burgdorferi may be associated with different levels of pathogenicity and immune responses of their hosts, our results are helpful at better understanding the pattern of spread of Lyme disease in a zone of emergence, and associated risk for human populations.

High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America

Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.

The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China

Little has been published to describe or interpret Asian biodiversity hotspots, including those in the East Himalayan Mountains of Southwest China (HMSC), thus making necessary a review of the current knowledge. The Pliocene and Pleistocene geological and glacial histories of the Asian continent differ from those of Europe and North America, suggesting different mechanisms of speciation and extinction, and, thus, different responses to climate changes during the Quaternary glaciations. This short review summarizes potential drivers in shaping and maintaining high species richness and endemism of birds in the HMSC. The geographical location at the junction of different biogeographical realms, the wide range of habitats and climates along the extensive elevational range, the complex topography and the distinct geological history of this region have probably contributed to the evolution of an exceptionally species-rich and endemic-rich, specialized montane avian fauna. The Mountain systems in the HMSC may have provided refugia where species survived during the glacial periods and barriers for preventing species dispersal after the glacial periods. More studies are required to further test this refugia hypothesis by comparing more cold-tolerent and warm-tolerent species.

The trans-riverine genetic structure of 28 Amazonian frog species is dependent on life history

Among the hypotheses formulated to explain the origin of Amazonian biodiversity, two (the riverine-barrier and the river-refuge hypotheses) focus on the role that rivers play as biotic barriers promoting speciation. However, empirical results have both supported and refuted these hypotheses. This is likely due, at least in part, to river-specific hydrologic characteristics and the biology of the focal species. The rivers of the Guiana Shield represent a model system because they have had more stable courses over time than those of the western Amazon Basin, where most tests of riverine barrier effects have taken place. We tested whether life-history traits (body size, habitat and larval development), expected to be important in determining dispersal ability, of 28 frog species are associated with genetic structure and genetic distances of individuals sampled from both banks of the Oyapock River. Thirteen of these species displayed genetic structure consistent with the river acting as a barrier to dispersal. Surprisingly, body size was not correlated with trans-riverine population structure. However, leaf-litter dwellers and species lacking free-living tadpoles were found to exhibit higher river-associated structure than open habitat/arboreal species and those with exotrophic tadpoles. These results demonstrate that rivers play an important role in structuring the genetic diversity of many frog species though the permeability of such riverine barriers is highly dependent on species-specific traits.

Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA

Quaternary climatic changes have been recognized to influence the distribution patterns and evolutionary histories of extant organisms, but their effects on alpine species are not well understood. To investigate the Pleistocene climatic oscillations on the genetic structure of amphibians, we sequenced one mitochondrial and three nuclear DNA fragments in Nanorana parkeri, a frog endemic to the Tibetan Plateau, across its distribution range in the southern plateau. Mitochondrial cytochrome b (Cytb) and three nuclear genes (c-Myc2, Rhod, and Tyr) revealed two distinct lineages (i.e. the lineages East and West), which were strongly geographically structured. The split of the two divergent lineages was dated back earlier than the Middle Pleistocene, probably being associated with climatic and ecological factors. Species distribution modeling, together with the phylogeographic structuring, supported the hypothesis of multiple refugia for N. parkeri on the Tibetan Plateau during the Pleistocene glaciations, and suggested the Yarlung Zangbo valley and the Kyichu catchment to be the potential refugia. Our findings indicate that Pleistocene climatic changes have had a great impact on the evolution and demographic history of N. parkeri. Our study has important implications for conservation of this and other frog species in the Tibetan Plateau.

Systematics of the Rhinellamargaritifera complex (Anura, Bufonidae) from western Ecuador and Panama with insights in the biogeography of Rhinellaalata

The Rhinellamargaritifera species group consists of 17 species of toads distributed in tropical and subtropical South America and eastern Central America. The identity of some of its species is poorly understood and there are numerous undescribed cryptic species. Among them, the status of Rhinellamargaritifera is one of the most problematic. Its range includes lowland rainforests separated by the Andes, the Chocoan rainforest to the west and the Amazonian rainforest to the east. This distribution is puzzling because the Andes are an old and formidable barrier to gene flow and therefore should generate vicariant speciation between disjunct lowland populations. Herein we clarify the taxonomy of populations of the Rhinellamargaritifera complex from Central America and the Chocó region of South America. The morphological and genetic variation of Rhinellamargaritifera was examined from 39 populations from Chocó, 24 from the upper Amazon region of Ecuador, and 37 from Panama, including the holotype of the Panamanian Rhinellaalata. Phylogenetic analyses were performed based on mitochondrial genes 12S rRNA, 16S rRNA, and cytochrome c oxidase I (COI) and the nuclear gene Tyrosinase (Tyr). The genetic and morphological data show that Panamanian and Chocoan populations are conspecific. In the phylogeny, populations from Chocó and Panama form a well-supported clade. The morphology of the holotype of Rhinellaalata falls within the variation range of Panamanian and Chocoan populations. Based on all this evidence, we assign the populations from western Ecuador and Panama to Rhinellaalata and demonstrate that the unusual distribution pattern of "Rhinellamargaritifera" on both sides of the Andes was an artifact of incorrectly defined species boundaries.

A likelihood inference of historical biogeography in the world's most diverse terrestrial vertebrate genus: diversification of direct-developing frogs (Craugastoridae: Pristimantis) across the Neotropics

The geology of the northern Andean region has driven the evolutionary history of Neotropical fauna through the creation of barriers and connections that have resulted in speciation and dispersal events, respectively. One of the most conspicuous groups of anuran fauna in the Andes and surrounding areas is the direct-developing species of the genus Pristimantis. We investigated the molecular phylogenetic placement of 12 species from the montane Andes of Colombia in a broader geographical context with a new genus-level phylogeny in order to identify the role of Andean orogeny over the last 40million years and the effect of elevational differences in diversification of Pristimantis. We examined the biogeographic history of the genus using ancestral range reconstruction by biogeographic regions and elevational ranges. We recognized the middle elevational band (between 1000 and 3000m) in the Northwestern Andes region of Colombia and Ecuador as a focal point for the origin and radiation of Pristimantis species. Additionally, we found several Andean migrations toward new habitats in Central Andes and Merida Andes for some species groups. We suggest that the paleogeological changes in the Northwestern Andes were the main promoter of speciation in Pristimantis, and may have served as a corridor for the dispersion of lowland species.

Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses?

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns ("concerted-response hypothesis"); (2) independent responses, indicated by spatial incongruence ("independent-response hypothesis"); or (3) multiple responses ("multiple-response hypothesis"), indicated by spatial congruence but temporal incongruence ("pseudocongruence") or spatial and temporal incongruence ("pseudoincongruence"). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co-occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer-scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation-with-migration models estimated incongruent timelines of among-region divergences, with A. cultratus and Xenophallus populations diverging over Miocene-mid-Pleistocene while P. gillii populations diverged over mid-late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B 10] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple-response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer-scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.

A new species of the Rhinella margaritifera species group (Anura, Bufonidae) from the montane forest of the Selva Central, Peru

We describe a new species of the bufonid toad genus Rhinella from transition montane forest of the buffer zones of the Yanachaga-Chemillén National Park and the Pui Pui Protected Forest (eastern slopes of Andes, Selva Central, Peru). The new species belongs to the Rhinella margaritifera species group (confirmed by mtDNA data) and differs from all its members by the absence of tympanic membrane and tympanic annulus. It is characterized by medium size (SVL 57.5-65.5 mm, n = 5), moderately developed cranial crests, absence of neural crest of vertebrae, absence of bone protrusion at angle of jaw, presence of lateral rows of enlarged tubercles, and absence of subgular vocal sac and vocal slits in males. In addition, based on the molecular phylogenetic analyses of selected Rhinella species we propose the monophylum containing R. chavin, R. festae, R. macrorhina, R. manu, R. nesiotes, R. rostrata, and R. yanachaga as a new species group under the name Rhinella festae species group.

Timeframes of speciation, reticulation, and hybridization in the bulldog bat explained through phylogenetic analyses of all genetic transmission elements

Phylogenetic comparisons of the different mammalian genetic transmission elements (mtDNA, X-, Y-, and autosomal DNA) is a powerful approach for understanding the process of speciation in nature. Through such comparisons the unique inheritance pathways of each genetic element and gender-biased processes can link genomic structure to the evolutionary process, especially among lineages which have recently diversified, in which genetic isolation may be incomplete. Bulldog bats of the genus Noctilio are an exemplar lineage, being a young clade, widely distributed, and exhibiting unique feeding ecologies. In addition, currently recognized species are paraphyletic with respect to the mtDNA gene tree and contain morphologically identifiable clades that exhibit mtDNA divergences as great as among many species. To test taxonomic hypotheses and understand the contribution of hybridization to the extant distribution of genetic diversity in Noctilio, we used phylogenetic, coalescent stochastic modeling, and divergence time estimates using sequence data from cytochrome-b, cytochrome c oxidase-I, zinc finger Y, and zinc finger X, as well as evolutionary reconstructions based on amplified fragment length polymorphisms (AFLPs) data. No evidence of ongoing hybridization between the two currently recognized species was identified. However, signatures of an ancient mtDNA capture were recovered in which an mtDNA lineage of one species was captured early in the noctilionid radiation. Among subspecific mtDNA clades, which were generally coincident with morphology and statistically definable as species, signatures of ongoing hybridization were observed in sex chromosome sequences and AFLP. Divergence dating of genetic elements corroborates the diversification of extant Noctilio beginning about 3 Ma, with ongoing hybridization between mitochondrial lineages separated by 2.5 myr. The timeframe of species' divergence within Noctilio supports the hypothesis that shifts in the dietary strategies of gleaning insects (N. albiventris) or fish (N. leporinus) are among the most rapid instances of dietary evolution observed in mammals. This study illustrates the complex evolutionary dynamics shaping gene pools in nature, how comparisons of genetic elements can serve for understanding species boundaries, and the complex considerations for accurate taxonomic assignment.

Persistence across Pleistocene ice ages in Mediterranean and extra-Mediterranean refugia: phylogeographic insights from the common wall lizard

BACKGROUND

Pleistocene climatic oscillations have played a major role in structuring present-day biodiversity. The southern Mediterranean peninsulas have long been recognized as major glacial refugia, from where Northern Europe was post-glacially colonized. However, recent studies have unravelled numerous additional refugia also in northern regions. We investigated the phylogeographic pattern of the widespread Western Palaearctic lizard Podarcis muralis, using a range-wide multilocus approach, to evaluate whether it is concordant with a recent expansion from southern glacial refugia or alternatively from a combination of Mediterranean and northern refugia.

RESULTS

We analyzed DNA sequences of two mitochondrial (cytb and nd4) and three nuclear (acm4, mc1r, and pdc) gene fragments in individuals from 52 localities across the species range, using phylogenetic and phylogeographic methods. The complex phylogeographic pattern observed, with 23 reciprocally monophyletic allo- parapatric lineages having a Pleistocene divergence, suggests a scenario of long-term isolation in multiple ice-age refugia across the species distribution range. Multiple lineages were identified within the three Mediterranean peninsulas - Iberia, Italy and the Balkans - where the highest genetic diversity was observed. Such an unprecedented phylogeographic pattern - here called "refugia within all refugia" - compasses the classical scenario of multiple southern refugia. However, unlike the southern refugia model, various distinct lineages were also found in northern regions, suggesting that additional refugia in France, Northern Italy, Eastern Alps and Central Balkans allowed the long-term persistence of this species throughout Pleistocene glaciations.

CONCLUSIONS

The phylogeography of Podarcis muralis provides a paradigm of temperate species survival in Mediterranean and extra-Mediterranean glacial refugia. Such refugia acted as independent biogeographic compartments for the long-term persistence of this species, for the differentiation of its genetic lineages, and for the short-distance post-glacial re-colonization of neighbouring areas. This finding echoes previous findings from recent phylogeographic studies on species from temperate ecoregions, thus suggesting the need for a reappraisal of the role of northern refugia for glacial persistence and post-glacial assembly of Holarctic biota.

Phylogenetic analysis of Thecosomata Blainville, 1824 (holoplanktonic opisthobranchia) using morphological and molecular data

Thecosomata is a marine zooplankton group, which played an important role in the carbonate cycle in oceans due to their shell composition. So far, there is important discrepancy between the previous morphological-based taxonomies, and subsequently the evolutionary history of Thecosomata. In this study, the remarkable planktonic sampling of TARA Oceans expedition associated with a set of various other missions allowed us to assess the phylogenetic relationships of Thecosomata using morphological and molecular data (28 S and COI genes). The two gene trees showed incongruities (e.g. Hyalocylis, Cavolinia), and high congruence between morphological and 28S trees (e.g. monophyly of Euthecosomata). The monophyly of straight shell species led us to reviving the Orthoconcha, and the split of Limacinidae led us to the revival of Embolus inflata replacing Limacina inflata. The results also jeopardized the Euthecosomata families that are based on plesiomorphic character state as in the case for Creseidae which was not a monophyletic group. Divergence times were also estimated, and suggested that the evolutionary history of Thecosomata was characterized by four major diversifying events. By bringing the knowledge of palaeontology, we propose a new evolutionary scenario for which macro-evolution implying morphological innovations were rhythmed by climatic changes and associated species turn-over that spread from the Eocene to Miocene, and were shaped principally by predation and shell buoyancy.