Guarino R. Colli

The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees

The superfamily Colubroidea (> 2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5814bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean=67% per species), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.

Coming to America: multiple origins of New World geckos

Geckos in the Western Hemisphere provide an excellent model to study faunal assembly at a continental scale. We generated a time‐calibrated phylogeny, including exemplars of all New World gecko genera, to produce a biogeographical scenario for the New World geckos. Patterns of New World gecko origins are consistent with almost every biogeographical scenario utilized by a terrestrial vertebrate with different New World lineages showing evidence of vicariance, dispersal via temporary land bridge, overseas dispersal or anthropogenic introductions. We also recovered a strong relationship between clade age and species diversity, with older New World lineages having more species than more recently arrived lineages. Our data provide the first phylogenetic hypothesis for all New World geckos and highlight the intricate origins and ongoing organization of continental faunas. The phylogenetic and biogeographical hypotheses presented here provide an historical framework to further pursue research on the diversification and assembly of the New World herpetofauna.

Sampling bias and the use of ecological niche modeling in conservation planning: a field evaluation in a biodiversity hotspot

Ecological niche modeling (ENM) has become an important tool in conservation biology. Despite its recent success, several basic issues related to algorithm performance are still being debated. We assess the ability of two of the most popular algorithms, GARP and Maxent, to predict distributions when sampling is geographically biased. We use an extensive data set collected in the Brazilian Cerrado, a biodiversity hotspot in South America. We found that both algorithms give richness predictions that are very similar to other traditionally used richness estimators. Also, both algorithms correctly predicted the presence of most species collected during fieldwork, and failed to predict species collected only in very few cases (usually species with very few known localities, i.e., <5). We also found that Maxent tends to be more sensitive to sampling bias than GARP. However, Maxent performs better when sampling is poor (e.g., low number of data points). Our results indicates that ENM, even when provided with limited and geographically biased localities, is a very useful technique to estimate richness and composition of unsampled areas. We conclude that data generated by ENM maximize the utility of existing biodiversity data, providing a very useful first evaluation. However, for reliable conservation decisions ENM data must be followed by well-designed field inventories, especially for the detection of restricted range, rare species.

DEEP DIVERSIFICATION AND LONG-TERM PERSISTENCE IN THE SOUTH AMERICAN 'DRY DIAGONAL': INTEGRATING CONTINENT-WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS

The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range‐wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American ‘dry diagonal’ biomes. Our approach couples traditional and model‐based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the ‘dry diagonal’ biomes. We recover extremely high genetic diversity and suggest that eight well‐supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low‐vagility species complexes, characterized by strong genetic structure and pre‐Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.

Use of naturally and anthropogenically disturbed habitats in Amazonian rainforest by the teiid lizard Ameiva ameiva

Abstract We studied the effects of natural and anthropogenic habitat disturbances on environmental temperatures and their consequent effects on thermoregulation and habitat use of Ameiva ameiva in a complex habitat matrix of primary tropical forest and several types of disturbed forest in Amazonian Brazil. Data on Ameiva ameiva from other regions in Brazil with habitats that have little canopy coverage are compared with data from rain forest sites to determine if activity of rain forest Ameiva is temporally or spatially limited by the thermal opportunities available in shaded environments. Ameiva ameiva preferentially used disturbed habitats in rain forest regions. These sites had significantly higher environmental temperatures than did surrounding undisturbed rain forest. Environmental temperature distributions indicate that the closed canopy rain forest is a thermally marginal habitat for Ameiva ameiva and that high temperatures resulting from forest clearing are likely to enable Ameiva ameiva to increase foraging activity in adjacent forest edges above what is possible in the continuous interior forest. Ameiva ameiva from rain forest, cerrado and savanna regions of Brazil had significantly lower body temperatures than Ameiva from caatinga, an open habitat type with little canopy coverage. This difference is probably due to high ambient temperatures and the high availability of basking sites in open habitats and suggests a thermal constraint on habitat use and time of activity for Ameiva in closed canopy habitats.

Lizard Assemblages from Natural Cerrado Enclaves in Southwestern Amazonia: The Role of Stochastic Extinctions and Isolation1

Abstract We used null model analyses to investigate the existence of structure in lizard assemblages from open vegetation enclaves in Rondônia, southwestern Amazonia, in relation to species richness, species co-occurrence, diet, and size overlap. These enclaves presumably have been isolated since the Holocene, providing a history of long-term isolation. We assumed that the presence of structure in lizard assemblages from the Rondônia enclaves is consistent with the notion that extinctions are a deterministic process, some species being more prone to extinction than others. We grouped enclaves into four categories: latosoil cerrado, sandy cerrado, transitional forest, and rocky field. We collected 14 Cerrado lizard species, consisting of five families in all sampled areas. Analyses of species richness, co-occurrence, diet overlap, and size overlap patterns suggested lack of organization in the assemblages. The assemblages from the rocky fields of Guajará–Mirim and the sandy cerrados in Vilhena were significantly structured in diet overlap, whereas the remaining assemblages lacked structure. This probably resulted from phylogenetic inertia and not from ecological interactions. Our results suggest that extinctions proceeded in a stochastic fashion and that historical factors had a dominant role in shaping lizard assemblages in detriment of present-day ecological factors. In addition, we identified endemic species in the enclaves as well as a tight association between unique ecogeographic features of the landscape and species occurrences. We propose that conservation measures in the region must adequately preserve these features to ensure the survival of the species.

The Ecology of Cnemidophorus ocellifer (Squamata, Teiidae) in a Neotropical Savanna

Abstract We studied the ecology of the lizard Cnemidophorus ocellifer Spix 1825 in the central Brazilian Cerrado. Cnemidophorus ocellifer was active on open ground, in sandy soils and rocky fields, during the hottest hours of the day. Mean body temperatures (37.5°C) were high, relative to sympatric lizard species, and more associated with substrate temperatures than with air temperatures. The thermal ecology of C. ocellifer seems to be tightly associated with an active mode of foraging. Termites were the most important prey, and there was no significant association between head dimensions and prey dimensions. Cnemidophorus ocellifer showed strong sexual dimorphism in body size and shape, with males having larger bodies and head dimensions, and females having longer and thicker bodies. Clutch size averaged 2.1 and was positively correlated with female SVL. Females were reproductively active during the dry season (May to September) and recruitment occurred from July to November. Males were reproductively active throughout the year, peaking from March to August, coinciding with the period of female reproduction. The reproductive cycle in C. ocellifer may be determined by the greater availability of direct sunlight and its physiological effects upon breeding activities, such as courtship and mating, during the dry season.

Niche partitioning and morphology of two syntopic Tropidurus (Sauria : Tropiduridae) in Mato Grosso, Brazil

TIMMIS, W. H. 1969. Observations on Pacific boas at Sydney Zoo. Int. Zool. Y. B., Vol. 9:53. UNDERWOOD, G. 1970. A systematic analysis of boid snakes. Linn. Soc. Symp. Ser. No. 3:151-175. VITT, L. J., AND J. D. CONGDON. 1978. Body shape, reproductive effort, and relative clutch mass in lizards: resolution of a paradox. Amer. Natur. 112: 595-608. WYNN, A. H., AND G. R. ZUG. 1985. Observations on the reproductive biology of Candoia carinata (Serpentes, Boidae). The Snake 17:15-24.

Geographical Variation in the Ecology of Populations of Some Brazilian Species of Cnemidophorus (Squamata, Teiidae)

Abstract We investigated geographical variation in ecological parameters among populations of Cnemidophorus cryptus, Cnemidophorus gramivagus, Cnemidophorus lemniscatus, Cnemidophorus ocellifer, and Cnemidophorus parecis, from three Brazilian biomes (Cerrado, Caatinga, and Amazonian Savannas). Lizards used mainly the open ground, with a high similarity in microhabitat use among populations. Differences in microhabitat use probably resulted from the availability of microhabitats and not from microhabitat preferences. Body temperatures were high and little influenced by environmental temperatures, there being no differences among populations. There were significant differences in diet among populations, with C. ocellifer from Caatinga and Cerrado consuming large quantities of termites, whereas Amazonian Savanna species used primarily ants and insect larvae. The data on reproductive seasonality indicated cyclical reproduction in seasonal biomes and continuous reproduction in unpredictable climate regions. We found significant differences in mean clutch size among populations, independent of body size, with C. lemniscatus having the smallest clutch size (1.50) and C. ocellifer from Cerrado the largest (2.10). There were fewer differences in clutch size among species from Amazonian Savannas, than between populations of C. ocellifer from Caatinga and Cerrado. Apparently, populations under seasonal climates concentrate their reproductive effort during the short reproductive season, producing larger clutches, whereas those under more stable or unpredictable climates reproduce continuously, yielding smaller clutches, corroborating the hypothesis that environmental conditions exert an important influence upon life-history parameters. There were significant differences in body shape among populations, but most of the variation was related to sex. We also observed significant differences in body size among populations, seemingly unrelated to differences in community structure, but the highly conservative morphology of Cnemidophorus species suggests the presence of historical constraints.

ECOLOGY OF THE WORM-LIZARD AMPHISBAENA ALBA IN THE CERRADO OF CENTRAL BRAZIL

Due to their secretive habits, very little is known about the ecology of amphisbaenians. Based on a large series of specimens from the Cerrado of central Brazil, the diet composition, reproduction, and sexual dimorphism of Amphisbaena alba are described. Amphisbaena alba displayed a relatively diverse diet, even ingesting vertebrates and plant material. Beetles, ants, and spiders dominated the diet numerically, whereas ants, insect larvae, and beetles were more important volumetrically. No association was observed between prey size and body dimensions. The smallest reproductive male was 422 mm SVL (snout-vent length), and the smallest reproductive female was 457 mm SVL. Clutch size ranged from 8-16, one of the largest known for amphisbaenians, and is possibly influenced by the large body size of A. alba. Reproduction is apparently seasonal and restricted to the dry season. No intersexual differences were observed, either in morphometric or meristic characters, presumably because of functional constraints related to fossoriality.