Integrative methods reveal multiple drivers of diversification in rice paddy snakes.

Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.

Phylogenetic, morphological and niche differentiation unveil new species limits for the big brown bat (Eptesicus fuscus).

Phylogeographic accounts of mammals across fragmented landscapes show high levels of genetic, morphological and ecological variation. The big brown bat (Eptesicus fuscus) widely spans mainland landmasses from Canada to Ecuador and Colombia, and the insular Caribbean through The Bahamas and Greater and Lesser Antilles. Given the distribution of E. fuscus, we hypothesized that insular lineages could represent a different species aided by isolation. We assessed species limits by capitalizing on available mitochondrial and genomic data. Novel morphological and spatial datasets were produced to examine limits phenotypically and whether ecological niches could be associated with differences between groups. Phylogenetics strongly supported the Caribbean as unique compared to the mainland. Genomic data indicated high levels of genetic structure within the Caribbean and no detectable admixture of the Caribbean with continental lineages. Similarly, the Caribbean group shows high phenotypic disparity, and niche models revealed differences in habitat suitability between groups, concordant with the phylogenetic results. This study uncovered signals of divergence supporting the Caribbean clade of E. fuscus as unique through an integrative framework. We endorse re-evaluating the taxonomic status of Caribbean big brown bats as Eptesicus dutertreus. This recognition can help promote local conservation plans for insular lineages of big brown bats.

Presence of the Eucalyptus snout beetle in Ecuador and potential invasion risk in South America.

Eucalyptus snout beetles are a complex of at least eight cryptic species (Curculionidae: Gonipterus scutellatus complex), native to mainland Australia and Tasmania, that defoliate Eucalyptus trees and are considered important pests. Since the 19th century, three species of the complex have been introduced to other continents. Here, we document the presence of Eucalyptus snout beetles in Ecuador. We used DNA data for species identification and unambiguously demonstrated that the Ecuadorian specimens belong to the species Gonipterus platensis, which has low genetic diversity compared with other species in the complex. We analyzed G. platensis' potential distribution in South America with ecological niche models and found several areas of high to intermediate climatic suitability, even in countries where the pest has not been registered, like Peru and Bolivia. Accurate identification of species in the G. scutellatus complex and understanding of their potential distribution are essential tools for improved management and prevention tactics.

Los gorgojos del eucalipto son un complejo de al menos ocho especies crípticas (Curculionidae: complejo Gonipterus scutellatus), nativos de Australia continental y Tasmania, que defolian árboles de eucalipto y son considerados como plagas de importancia. Desde el siglo 19, tres especies de este complejo se han introducido a otros continentes. En este trabajo reportamos la presencia de gorgojos del eucalipto en Ecuador. Usamos datos genéticos para la identificación específica y demostramos claramente que los especímenes ecuatorianos pertenecen a la especie Gonipterus platensis, la cual tiene baja diversidad genética comparada con otras especies en el complejo. Analizamos la distribución potencial de G. platensis en América del Sur con modelos de nicho ecológico y encontramos varias áreas con idoneidad ambiental alta a intermedia, incluso en países donde esta especie no ha sido registrada, como Perú y Bolivia. La correcta identificación de las especies del complejo Gonipterus scutellatus y una mejor comprensión de su distribución potencial constituyen herramientas fundamentales para optimizar medidas de manejo y prevención.

Environmentally driven phenotypic convergence and niche conservatism accompany speciation in hoary bats.

Species that are geographically widespread may exist across environmentally heterogeneous landscapes that could influence patterns of occupation and phylogeographic structure. Previous studies have suggested that geographic range size should be positively correlated with niche breadth, allowing widespread species to sustain viable populations over diverse environmental gradients. We examined the congruence of phenotypic and phylogenetic divergence with the environmental factors that help maintain species level diversity in the geographically widespread hoary bats (Lasiurus cinereus sensu lato) across their distribution. Genetic sequences were analyzed using multiple phylogenetic and species delimitation methods, and phenotypic data were analyzed using supervised and unsupervised machine learning approaches. Spatial data from environmental, geographic, and topographic features were analyzed in a multiple regression analysis to determine their relative effect on phenotypic diversity. Ecological niches of each hoary bat species were examined in environmental space to quantify niche overlap, equivalency, and the magnitude of niche differentiation. Phylogenetic and species delimitation analyses support existence of three geographically structured species of hoary bat, each of which is phenotypically distinct. However, the Hawaiian hoary bat is morphologically more similar to the South American species than to the North American species despite a closer phylogenetic relationship to the latter. Multiple regression and niche analyses revealed higher environmental similarities between the South American and Hawaiian species. Hoary bats thus exhibit a pattern of phenotypic variation that disagrees with well-supported genetic divergences, instead indicating phenotypic convergence driven by similar environmental features and relatively conserved niches occupied in tropical latitudes.

Effect of land use, habitat suitability, and hurricanes on the population connectivity of an endemic insular bat.

Urbanization and natural disasters can disrupt landscape connectivity, effectively isolating populations and increasing the risk of local extirpation particularly in island systems. To understand how fragmentation affects corridors among forested areas, we used circuit theory to model the landscape connectivity of the endemic bat Stenoderma rufum within Puerto Rico. Our models combined species occurrences, land use, habitat suitability, and vegetation cover data that were used either as resistance (land use) or conductance layers (habitat suitability and vegetation cover). Urbanization affected connectivity overall from east to west and underscored protected and rustic areas for the maintenance of forest corridors. Suitable habitat provided a reliable measure of connectivity among potential movement corridors that connected more isolated areas. We found that intense hurricanes that disrupt forest integrity can affect connectivity of suitable habitat. Some of the largest protected areas in the east of Puerto Rico are at an increasing risk of becoming disconnected from more continuous forest patches. Given the increasing rate of urbanization, this pattern could also apply to other vertebrates. Our findings show the importance of maintaining forest integrity, emphasizing the considerable conservation value of rustic areas for the preservation of local biodiversity.

Population structure of a widespread bat (Tadarida brasiliensis) in an island system.

Dispersal is a driving factor in the creation and maintenance of biodiversity, yet little is known about the effects of habitat variation and geography on dispersal and population connectivity in most mammalian groups. Bats of the family Molossidae are fast-flying mammals thought to have potentially high dispersal ability, and recent studies have indicated gene flow across hundreds of kilometers in continental North American populations of the Brazilian free-tailed bat, Tadarida brasiliensis. We examined the population genetics, phylogeography, and morphology of this species in Florida and across islands of The Bahamas, which are part of an island archipelago in the West Indies. Previous studies indicate that bats in the family Phyllostomidae, which are possibly less mobile than members of the family Molossidae, exhibit population structuring across The Bahamas. We hypothesized that T. brasiliensis would show high population connectivity throughout the islands and that T. brasiliensis would show higher connectivity than two species of phyllostomid bats that have been previously examined in The Bahamas. Contrary to our predictions, T. brasiliensis shows high population structure between two groups of islands in The Bahamas, similar to the structure exhibited by one species of phyllostomid bat. Phylogenetic and morphological analyses suggest that this structure may be the result of ancient divergence between two populations of T. brasiliensis that subsequently came into contact in The Bahamas. Our findings additionally suggest that there may be cryptic species within T. brasiliensis in The Bahamas and the West Indies more broadly.

The bat community of Haiti and evidence for its long-term persistence at high elevations.

Accurate accounts of both living and fossil mammal communities are critical for creating biodiversity inventories and understanding patterns of changing species diversity through time. We combined data from from14 new fossil localities with literature accounts and museum records to document the bat biodiversity of Haiti through time. We also report an assemblage of late-Holocene (1600-600 Cal BP) bat fossils from a montane cave (Trouing Jean Paul, ~1825m) in southern Haiti. The nearly 3000 chiropteran fossils from Trouing Jean Paul represent 15 species of bats including nine species endemic to the Caribbean islands. The fossil bat assemblage from Trouing Jean Paul is dominated by species still found on Hispaniola (15 of 15 species), much as with the fossil bird assemblage from the same locality (22 of 23 species). Thus, both groups of volant vertebrates demonstrate long-term resilience, at least at high elevations, to the past 16 centuries of human presence on the island.

Vertebrate community on an ice-age Caribbean island.

We report 95 vertebrate taxa (13 fishes, 11 reptiles, 63 birds, 8 mammals) from late Pleistocene bone deposits in Sawmill Sink, Abaco, The Bahamas. The >5,000 fossils were recovered by scuba divers on ledges at depths of 27-35 m below sea level. Of the 95 species, 39 (41%) no longer occur on Abaco (4 reptiles, 31 birds, 4 mammals). We estimate that 17 of the 39 losses (all of them birds) are linked to changes during the Pleistocene-Holocene Transition (PHT) (∼ 15-9 ka) in climate (becoming more warm and moist), habitat (expansion of broadleaf forest at the expense of pine woodland), sea level (rising from -80 m to nearly modern levels), and island area (receding from ∼ 17,000 km(2) to 1,214 km(2)). The remaining 22 losses likely are related to the presence of humans on Abaco for the past 1,000 y. Thus, the late Holocene arrival of people probably depleted more populations than the dramatic physical and biological changes associated with the PHT.

Fossils reject climate change as the cause of extinction of Caribbean bats.

We combined novel radiocarbon dates of bat fossils with time-scaled ecological niche models (ENM) to study bat extinctions in the Caribbean. Radiocarbon-dated fossils show that late Quaternary losses of bat populations took place during the late Holocene (<4 ka) rather than late Pleistocene (>10 ka). All bat radiocarbon dates from Abaco (Bahamas) that represent extirpated populations are younger than 4 ka. We include data on six bat species, three of which are Caribbean endemics, and include nectarivores as well as insectivores. Climate-based ENMs from the Last Glacial Maximum to the present reflect overall stability in distributions, with suitable climatic habitat being present over time. In the absence of radiocarbon dates, bat extinctions had been presumed to take place during the last glacial-interglacial transition (ca. 10 ka). Now we see that extirpation of bats on these tropical islands is more complex than previously thought and primarily postdates the major climate changes that took place during the late Pleistocene-Holocene transition.

Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence.

We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma-830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial-interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence.

Population distribution models: species distributions are better modeled using biologically relevant data partitions.

BACKGROUND: Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions. RESULTS: Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit. CONCLUSIONS: Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications.

Ectoparasitic assemblages on mormoopid bats (Chiroptera: Mormoopidae) from Puerto Rico.

We performed the first quantitative survey of ectoparasitic assemblages on three species of mormoopid bats living on the Caribbean island of Puerto Rico: Mormoops blainvillii Leach (n=40), Pteronotus quadridens Gundlach (n=40), and Pteronotus parnellii Gray (n=9). We examined bats for parasites primarily on 8-10 May and 24-27 July 2002 at Culebrones Cave, near Arecibo, Puerto Rico. Only 50% of M. blainvillii were infested with at least one parasite, compared with 85-100% for Pteronotus; infested individuals of both species of Pteronotus also harbored a greater number of parasites than did M. blainvillii. The assemblage on M. blainvillii was less diverse than in the other species and more dominated by a single group of parasites, the chiggers. Chirodiscid ear mites and spinturnicid wing mites were common on both species of Pteronotus but absent from M. blainvillii. All P. parnellii harbored streblid flies, but none typically was found on P. quadridens or M. blainvillii. Adult female M. blainvillii and P. quadridens sheltered a greater number of ectoparasites than did males. All host-parasite combinations represented new associations for Puerto Rico.