Phylogeography of the livebearer Xenophallus umbratilis (Teleostei: Poeciliidae): glacial cycles and sea level change predict diversification of a freshwater tropical fish

The biogeography of Central America is viewed as a classic case study in understanding the impact of vicariant events on patterns of biotic dispersal. While many biogeographers have focused on community composition and geographical limits of species at broad scales across Central America, much less work has focused on post-colonization diversification patterns at finer scales. The livebearing freshwater fish Xenophallus umbratilis presents an ideal system for determining the impact of recent Earth history events on biodiversity in northern Costa Rica. Here, we test the hypotheses that marine inundation of the San Carlos and northern Limón basins during the Pliocene and Pleistocene has caused genetic fragmentation among X. umbratilis populations, despite contemporary freshwater connections. To test this idea, we collected mitochondrial (cytochrome b ) sequence data in 162 individuals taken from 27 localities across northern Costa Rica. We employed a variety of analytical approaches, including: maximum parsimony and maximum likelihood, analysis of molecular variance, and demographic analysis of population size through time. We found four major clades within X. umbratilis , each geographically isolated with no shared haplotypes across drainages. Oddly, clades that occupy adjacent drainages are not always sister taxa in the phylogeny, suggesting that colonization in this species is more complex than a simple model of isolation by distance. All our results are consistent with the hypothesis that changes in sea level associated with glacial eustatic cycles have had an important effect in shaping diversification patterns in this species.     

Historical biogeography of New World emballonurid bats (tribe Diclidurini): taxon pulse diversification

Aim To reconstruct the biogeographical history of New World emballonurid bats (tribe Diclidurini). Although bats are the second most species‐rich order of mammals, they have not contributed substantially to our understanding of the historical biogeography of mammals in the Neotropics because of a poor fossil record. In addition, being the only group of mammals that fly, bats typically have large distributions with relatively few species endemic to restricted areas that are amenable to vicariant biogeographical approaches. Location Central and South America. Methods Phylogenetic analysis for comparing trees (PACT) is a new algorithm that incorporates all spatial information from taxon area cladograms into a general area cladogram. There were nine biogeographical areas identified in Central and South America for New World emballonurid bats. Molecular dating was used to incorporate the temporal aspect of historical biogeography. This method was compared with dispersal–vicariance analysis (DIVA), which assumes vicariance as the default mode of speciation. Results Of the 45 speciation events in a fully resolved phylogeny, eight that were hypothesized by DIVA as vicariance were considered by PACT as two peripheral isolations and six within‐area events. DIVA was less parsimonious because it required six more post‐speciation dispersal events in addition to the 73 hypothesized by PACT. DIVA reconstructed a widely distributed ancestor, suggesting that most dispersal events occurred earlier, whereas the ancestral area for PACT based on character optimization was the Northern Amazon, suggesting that dispersal events were more recent phenomena. Main conclusions The general area cladogram from PACT indicated that within‐area events, and not vicariance, provide the major mode of speciation for New World emballonurid bats. There was no biological evidence supporting or rejecting sympatric speciation in New World emballonurid bats. However, the geological history, combined with fluctuations in temperature and sea level, suggested within‐area speciation in a changing and heterogeneous environment in the Northern Amazon during the Miocene. This scenario is similar to the taxon‐pulse hypothesis of biotic diversification, which posits repeated episodes of range expansions and contractions from a stable core area such as the Guiana Shield within the Northern Amazon.     

Evidence for selection on coloration in a Panamanian poison frog: a coalescent‐based approach

Aim The strawberry poison frog, Oophaga pumilio, has undergone a remarkable radiation of colour morphs in the Bocas del Toro archipelago in Panama. This species shows extreme variation in colour and pattern between populations that have been geographically isolated for < 10,000 years. While previous research has suggested the involvement of divergent selection, to date no quantitative test has examined this hypothesis. Location Bocas del Toro archipelago, Panama. Methods We use a combination of population genetics, phylogeography and phenotypic analyses to test for divergent selection in coloration in O. pumilio. Tissue samples of 88 individuals from 15 distinct populations were collected. Using these data, we developed a gene tree using the mitochondrial DNA (mtDNA) d‐loop region. Using parameters derived from our mtDNA phylogeny, we predicted the coalescence of a hypothetical nuclear gene underlying coloration. We collected spectral reflectance and body size measurements on 94 individuals from four of the populations and performed a quantitative analysis of phenotypic divergence. Results The mtDNA d‐loop tree revealed considerable polyphyly across populations. Coalescent reconstructions of gene trees within population trees revealed incomplete genotypic sorting among populations. The quantitative analysis of phenotypic divergence revealed complete lineage sorting by colour, but not by body size: populations showed non‐overlapping variation in spectral reflectance measures of body coloration, while variation in body size did not separate populations. Simulations of the coalescent using parameter values derived from our empirical analyses demonstrated that the level of sorting among populations seen in colour cannot reasonably be attributed to drift. Main conclusions These results imply that divergence in colour, but not body size, is occurring at a faster rate than expected under neutral processes. Our study provides the first quantitative support for the claim that strong diversifying selection underlies colour variation in the strawberry poison frog.     

NEOSQUIRREL: a data set of ecological knowledge on Neotropical squirrels

1. The squirrels (Sciuridae), with 292 species, make up the second most diverse family of rodents. Squirrels play important roles as seed and spore dispersers and seed predators in all regions where they occur. In Neotropical regions, around 28 species of squirrel are recognised. However, our knowledge of the ecology of the Neotropical Sciuridae is severely incomplete, lacking in the most basic ecological information for most species.
2. We reviewed the literature in English, Spanish, and Portuguese, for all squirrel species in the Neotropical biogeographic region, summarising ecological interactions between squirrels and the local biota, population density records, the number of publications, and the distribution of study sites.
3. We found information for 20 squirrel species (71% of the recognised species), from 15 countries, in 48 publications containing 126 population density records and 155 publications containing 649 ecological interactions. The most studied species were Guerlinguetus brasiliensis, Notosciurus granatensis, and Sciurus variegatoides, with 53% of all publications, whereas for eight species of Microsciurus, we found no publications. The density of Neotropical squirrels varied from 0.08 to 100 individuals per km² and was negatively correlated with forest area.
4. Neotropical squirrels were recorded eating 174 plant taxa, five fungus taxa, four invertebrate taxa, and one species of vertebrate. Palms were common in the diet of squirrels (30 palm species, 27% of feeding records). Squirrels cached 28 plant species, of which 15 were palms.
5. Sixty‐five taxa of parasites are documented to occur in Neotropical squirrels, and the most common were Enderleinellus lice. Zoonotic parasites, including trypanosomes, Leptospira spp., Leishmania spp., and plague were also reported.
6. Our review reveals the main information gaps in the current knowledge about the ecology of Neotropical Sciuridae and maps the geographic distribution of the available information throughout South and Central America. Squirrels often thrive in small forest fragments and fulfil important roles as seed dispersers and prey for mesopredators.

     

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae)

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short‐tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Chocó, Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.     

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.     

Systematic revision of Neotropical Achalcus and a related new genus (Diptera: Dolichopodidae, Achalcinae) with comments on their phylogeny, ecology and zoogeography

A revision of the species of the subfamily Achalcinae of the Neotropical region is presented. A new genus, Australachalcus gen. nov. , is erected based on the presence of six dorsocentral bristles and synapomorphies in the hypopygium. Eight new Achalcus species ( bilineatus , brevicornis , costaricensis , cyanocephalus , maculipennis , micromorphoides , niger , tibialis ) and eight new Australachalcus species ( acornis , browni , cummingi , incisicornis , pseudorobustus , robustus , setosus , variabilis ) are described, and Achalcus albipalpus Parent, A. brevinervis Van Duzee, A. longicornis Van Duzee and Enlinia edwardsae (Van Duzee) are newly referred to Australachalcus and redescribed. A key to males of all species and females of eight species is provided. One Palaearctic species, Achalcus melanotrichus Mik, and nine New Zealand Achalcus species ( chaetifemoratus , luteipes , medius , minor , minusculus , minutus , nigroscutatus , relictus , separatus ) described by Parent are also transferred to Australachalcus . In Neotropical Achalcinae, three Achalcus and more than four different Australachalcus species groups can be distinguished, whereas all Holarctic Achalcus species belong to the single A. flavicollis species group. In the Neotropics, Australachalcus is nearly entirely confined to Chile, whereas Achalcus is recorded from Costa Rica, Venezuela, Ecuador, Colombia, Peru and Chile, with no or little overlap in distribution between the separate species groups. Beyond Chile, most achalcine species treated here were collected at higher altitudes. Most Chilean species are only active during the southern summer, whereas in Costa Rica achalcine representatives are encountered throughout the year.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 27–73.     

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.     

Systematics of the Neotropical caddisfly genus Notidobiella Schmid (Trichoptera, Sericostomatidae), with the description of 3 new species

Three new species of Notidobiella Schmid (Insecta: Trichoptera) are described from South America: Notidobiella amazonianasp. n. (Brazil), Notidobiella brasilianasp. n. (Brazil), and Notidobiella ecuadorensissp. n. (Ecuador). In addition, the 3 previously described species in the genus, Notidobiella chacayana Schmid, Notidobiella inermis Flint, and Notidobiella parallelipipeda Schmid, all endemic to southern Chile, are redescribed and illustrated, including the females of each species for the first time, and a key to males of the species in the genus is provided. The occurrence of Notidobiella in Brazil and Ecuador represents a significant extension of the range of the genus beyond southern Chile where it previously was thought to be endemic. The biogeography of Sericostomatidae and other austral South American Trichoptera is reviewed. The presence of the family in South America may not be part of a "transantarctic" exchange, but instead may represent an earlier occurence in the region. The distribution of Notidobiella in tropical South America likely represents recent dispersal from southern South America to the north.     

Evidence of history in explaining diversity patterns in tropical riverine fish

Aim Documentation of the ongoing effect of rain forest refuges at the last glacial maximum (LGM) on patterns of tropical freshwater fish diversity. Location Tropical South and Central America, and West Africa. Methods LGM rain forest regions and species richness by drainage were compiled from published data. GIS mapping was applied to compile drainage area and contemporary primary productivity. We used multiple regression analyses, applied separately for Tropical South America, Central America and West Africa, to assess differences in species richness between drainages that were connected and disconnected to rain forest refuge zones during the LGM. Spatial autocorrelation of the residuals was tested using Moran's I statistic. We added an intercontinental comparison to our analyses to see if a historical signal would persist even when a regional historical effect (climate at the LGM) had already been accounted for. Results Both area and history (contact with LGM rain forest refuge) explained the greatest proportions of variance in the geographical pattern of riverine species richness. In the three examined regions, we found highest richness in drainages that were connected to the rain forest refuges. No significant residual spatial autocorrelation was detected after considering area, primary productivity and LGM rain forest refuges. These results show that past climatic events still affect West African and Latin American regional and continental freshwater fish richness. At the continental scale, we found South American rivers more species‐rich than expected on the basis of their area, productivity and connectedness to rain forest refuge. Conversely, Central American rivers were less species‐diverse than expected by the grouped model. African rivers were intermediate. Therefore, a historical signal persists even when a regional historical effect (climate at the LGM) had already been accounted for. Main conclusions It has been hypothesized that past climatic events have limited impact on species richness because species have tracked environmental changes through range shifts. However, when considering organisms with physically constrained dispersal (such as freshwater fish), past events leave a perceptible imprint on present species diversity. Furthermore, we considered regions that have comparable contemporary climatic and environmental characteristics, explaining the absence of a productivity effect. From the LGM to the present day (a time scale of 18,000 years), extinction processes should have played a predominant role in shaping the current diversity pattern. By contrast, the continental effects could reflect historical contingencies explained by differences in speciation and extinction rates between continents at higher time scales (millions of years).     

Variation in spectral reflectance among populations of Dendrobates pumilio, the strawberry poison frog, in the Bocas del Toro Archipelago, Panama

Aim The goal of this study was to quantify levels of variation in spectral reflectance within and among populations of Dendrobates pumilio, the strawberry poison frog from the Bocas del Toro Archipelago. Location This study was carried out in the Bocas del Toro Archipelago, in the Republic of Panama, Central America. Methods Spectral reflectance was measured for samples of individuals from fifteen distinct island and mainland populations, using an Ocean Optics 2000 spectrometer and a BiLink portable computer. Results Our results provide quantitative evidence for extreme polymorphism among populations, and more limited levels of polymorphism within some populations. No obvious signs of sexual dimorphism were found. All the colour morphs appear to have relatively little reflectance in the ultraviolet part of the spectrum. There is some evidence for clinal variation in colour and pattern across some mainland populations. There is also at least one area where distinctly different morphs occur in sympatry, suggesting the possibility of incipient reproductive isolation. We argue that variation in coloration may have been enhanced by sexual selection.     

Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification

Among those few hypotheses of Amazonian diversification amenable to falsification by phylogenetic and population genetics methods, three can be singled out because of their general application to vertebrates: the riverine barrier, the refuge, and the Miocene marine incursion hypotheses. I used phylogenetic and population genetics methods to reconstruct the diversification history of the upland (terra-firme) forest superspecies Xiphorhynchus spixii/elegans (Aves: Dendrocolaptidae) in Amazonia, and to evaluate predictions of the riverine barrier, refuge, and Miocene marine incursion hypotheses. Phylogeographic and population genetics analyses of the X. spixiilelegans superspecies indicated that the main prediction of the riverine barrier hypothesis (that sister lineages occur across major rivers) hold only for populations separated by "clear-water" rivers located on the Brazilian shield, in central and eastern Amazonia; in contrast, "white-water" rivers located in western Amazonia did not represent areas of primary divergence for populations of this superspecies. The main prediction derived from the refuge hypothesis (that populations of the X. spixii/elegans superspecies would show signs of past population bottlenecks and recent demographic expansions) was supported only for populations found in western Amazonia, where paleoecological data have failed to support past rainforest fragmentation and expansion of open vegetation types; conversely, populations from the eastern and central parts of Amazonia, where paleoecological data are consistent with an historical interplay between rainforest and open vegetation types, did not show population genetics attributes expected under the refuge hypothesis. Phylogeographic and population genetics data were consistent with the prediction made by the Miocene marine incursion hypothesis that populations of the X. spixii/elegans superspecies found on the Brazilian shield were older than populations from other parts of Amazonia. In contrast, the phylogeny obtained for lineages of this superspecies falsified the predicted monophyly of Brazilian shield populations, as postulated by the Miocene marine incursion hypothesis. In general, important predictions of both riverine barrier and Miocene marine incursion hypotheses were supported, indicating that they are not mutually exclusive; in fact, the data presented herein suggest that an interaction among geology, sea level changes, and hydrography created opportunities for cladogenesis in the X. spixii/elegans superspecies at different temporal and geographical scales.     

Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally‐dry forests. We use genomic, phenotypic and habitat heterogeneity data coupled with climatic niche modelling. Results suggest the evolutionary history of the species is mainly related to paleoclimatic changes, although changes in the strength of the Amazon river as a barrier to dispersal, current habitat heterogeneity and geographic distance were also relevant. We propose an ancestral distribution in the Guyana Shield, and recent colonization of areas south of the Amazon river at ~380 to 166 kya, and expansion of the distribution to southern Amazonia, Cerrado and the Atlantic Forest. Since then, populations south of the Amazon River have been subjected to cycles of isolation and possibly secondary contact due to climatic changes that affected habitat heterogeneity and population connectivity. Most Amazonian rivers are not associated with long lasting isolation of populations, but some might act as secondary barriers, susceptible to crossing under specific climatic conditions. Morphological variation, while stable in some parts of the distribution, is not a reliable indicator of genetic structure or phylogenetic relationships.