Gabriel C. Costa

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.

Predator size, prey size, and dietary niche breadth relationships in marine predators

Based on geographical and home range sizes, physiology, and gape limitation, a positive relationship between predator size and diet breadth is expected. Alternatively, larger predators might avoid smaller prey; in this case no relationship would be found. Here, I used a large data set on the diets of marine predators to describe and identify mechanisms responsible for the relationships among predator body size, diet breadth, and the mean, minimum, maximum, and variance of prey size. I found no relationship between predator size and diet breadth. Mean, minimum, maximum, and variance of prey size were all positively associated with predator size. I found that larger predators increase their minimum and maximum prey size with similar slopes, which explains the lack of relationship between predator size and diet breadth. The results support predictions of the hypothesis that optimal foraging is the main factor constraining the shape of the relationships among predator size, prey size, and diet breadth. Future research should focus on examining the relationship between body size and the breadth of different niche axis across different groups of organisms to assess whether a positive relationship between body size and niche breadth is a general rule in macroecology.

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation.

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species‐richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population‐genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well‐defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.

Gastrointestinal Helminths from Six Species of Frogs and Three Species of Lizards, Sympatric in Pará State, Brazil

Abstract Forty-three frogs representing 6 species (Dendropsophus cachimbo, Scinax fuscomarginatus, Leptodactylus fuscus, Leptodactylus martinezi, Leptodactylus mystaceus, and Leptodactylus rhodomystax) and 35 lizards representing 3 species (Kentropyx calcarata, Leposoma osvaldoi, and Potamites ecpleopus) collected in the Brazilian state of Pará were examined for helminths. One species of Trematoda, Brachycoelium salamandrae, and 12 species of Nematoda, adults of Capillaria recondita, Cosmocerca brasiliense, Cosmocerca podicipinus, Falcaustra belemensis, Falcaustra maculata, Kentropyxia sauria, Oswaldocruzia vaucheri, Physaloptera retusa, Schrankiana formulosa, Schrankiana fuscus, Schrankiana schranki, and juveniles of Acuariidae gen. sp., were found. Only B. salamandrae occurred in both frogs and lizards. There were 1.53 ± 0.13 (x ± 1 SE) helminth species/infected frogs and 28.52 ± 11.7 helminth individuals/infected frogs and 1.12 ± 0.08 helminth species/infected lizards and 6.47 ± 1.58 helminth individuals/infected lizards. Thirteen new host records and 2 new locality records are reported.

Imputation of missing data in life‐history trait datasets: which approach performs the best?

1. Despite efforts in data collection, missing values are commonplace in life-history trait databases. Because these values typically are not missing randomly, the common practice of removingmissing data not only reduces sample size, but also introduces bias that can lead to incorrect conclusions. Imputingmissing values is a potential solution to this problem. Here, we evaluate the performance of four approaches for estimating missing values in trait databases (K-nearest neighbour (kNN), multivariate imputation by chained equations (mice), missForest and Phylopars), and testwhether imputed datasets retain underlying allometric relationships among traits. 2. Starting with a nearly complete trait dataset on the mammalian order Carnivora (using four traits), we artificially removed values so that the percent ofmissing values ranged from 10% to 80%. Using the original values as a reference, we assessed imputation performance using normalized root mean squared error.We also evaluated whether including phylogenetic information improved imputation performance in kNN, mice, and missForest (it is a required input in Phylopars). Finally, we evaluated the extent to which the allometric relationship between two traits (body mass and longevity) was conserved for imputed datasets by looking at the difference (bias) between the slope of the original and the imputed datasets or datasets with missing values removed. 3. Three of the tested approaches (mice, missForest and Phylopars), resulted in qualitatively equivalent imputation performance, and all had significantly lower errors than kNN. Adding phylogenetic information into the imputation algorithms improved estimation of missing values for all tested traits. The allometric relationship between body mass and longevity was conserved when up to 60% of data were missing, either with or without phylogenetic information, depending on the approach. This relationship was less biased in imputed datasets compared to datasets withmissing values removed, especially whenmore than 30%of values weremissing. 4. Imputations provide valuable alternatives to removing missing observations in trait databases as they produce low errors and retain relationships among traits. Although we must continue to prioritize data collection on species traits, imputations can provide a valuable solution for conducting macroecological and evolutionary studies using life-history trait databases.

Niche expansion and the niche variation hypothesis: does the degree of individual variation increase in depauperate assemblages?

The niche expansion and niche variation hypotheses predict that release from interspecific competition will promote niche expansion in depauperate assemblages. Niche expansion can occur by different mechanisms, including an increase in within‐individual, among‐individual, or bimodal variation (sexual dimorphism). Here we explore whether populations with larger niche breadth have a higher degree of diet variation. We also test whether populations from depauperate lizard assemblages differ in dietary resource use with respect to variation within and/or among individuals and sexual dimorphism. We found support for the niche expansion and niche variation hypotheses. Populations in assemblages with low phylogenetic diversity had a higher degree of individual variation, suggesting a tendency for niche expansion. We also found evidence suggesting that the mechanism causing niche expansion is an increase in variation among individuals rather than an increase in within‐individual variation or an increase in bimodal variation due to sexual dimorphism.

A CRITICALLY ENDANGERED NEW SPECIES OF CNEMIDOPHORUS (SQUAMATA, TEIIDAE) FROM A CERRADO ENCLAVE IN SOUTHWESTERN AMAZONIA, BRAZIL

We describe a new species of Cnemidophorus from a Cerrado enclave in southwestern Amazonia, Rondônia state, Brazil. This species is apparently endemic to Cerrado enclaves in the vicinity of the city of Vilhena, a region under intensive anthropic pressure due to the expansion of soybean plantations. A discriminant analysis indicated that femoral pores and scales around the tail are the best discriminators among Brazilian species of Cnemidophorus. A naïve Bayesian network constructed with categorical (mostly coloration) variables indicated that the new species had high conditional probabilities of dorsolateral fields absent, vertebral field spotted, and paravertebral lines absent. The analyses revealed clear distinctions between species of Cnemidophorus that range north and south of the the Amazon River. The new species may have evolved as a result of vicariance, following the isolation of peripheral enclaves of Cerrado in southwestern Amazonia after the late Pleniglacial. The restricted range in small areas, under extreme human pressure around Vilhena, makes this species one of the most critically endangered elements of the Brazilian herpetofauna.

Reproduction, Body Size, and Diet of Polychrus acutirostris (Squamata: Polychrotidae) in Two Contrasting Environments in Brazil

Abstract We compared reproduction, diet, and body size of Polychrus acutirostris (Squamata: Polychrotidae) from the Cerrado and Caatinga biomes in Brazil. Because these two biomes have widely different climates, we predicted that lizards in Caatinga would produce smaller clutches in response to rainfall unpredictability. We also expected reproductive timing to differ between biomes, with lizards occurring in the Cerrado producing a single clutch in association with the predictable rains of October–November. Contrary to expectations, clutches had fewer (although larger) eggs in Cerrado. Reproductive period was remarkably similar (peak of female reproductive activity in November), but female reproduction started 1 month earlier in Cerrado. Diet composition was also similar, with the exception of spiders, that exhibited a high index of relative importance in Cerrado but were nearly absent in Caatinga lizard diets. Lizards from both biomes ingested a large proportion of plant material, as well as soft-bodied arboreal arthropods, such as orthopterans, and mostly slow-moving, large arboreal insects. Rainfall predictability in the Cerrado therefore did not influence Polychrus reproduction or diet in the same manner as in other lizard species. The large number of small eggs in the Caatinga suggests that the competitive environment for offspring is either unpredictable or that mortality is high but random. Rain forest Polychrus lizards produce few large eggs, suggesting that the competitive environment for offspring is predictably intense and mortality is non-random. Cerrado Polychrus lizards seem intermediate between Caatinga and rain forest Polychrus lizards, producing fewer and larger eggs than their conspecifics in the Caatinga but relatively more and smaller eggs than rain forest Polychrus species.

ECOLOGY OF AN AMAZONIAN SAVANNA LIZARD ASSEMBLAGE IN MONTE ALEGRE, PARÁ STATE, BRAZIL

Abstract We describe the lizard assemblage from an Amazonian savanna in the region of Monte Alegre, Pará, Brazil, using ecological, morphological, and life history data, and examining the role of history in the assemblage. The lizard assemblage in Monte Alegre contained seven species. Microhabitat niche breadth was low for all species in the assemblage and niche overlap varied from none to almost complete. The least overlap in microhabitat occurred among more distantly related species and the greatest overlap occurred among teiids. Lizards were active between 9:00 and 17:00 h. Active foragers tended to be active during the hottest hours of day, whereas sit and wait foragers were more commonly observed later in the day, when temperatures were lower. Analysis of body temperatures identified two statistically homogeneous groups, one with teiids and another with the remaining species. Dietary overlap was highest among teiids. Pseudocommunity analyses showed that neither mean dietary overlap nor mean microhabitat overlap differed statistically from random, indicating lack of structure. Factor scores of morphological variables per species revealed clusters corresponding to lizard families. An examination of ecological traits mapped onto a tree depicting phylogenetic relationships among species and comparisons with related species from other biomes clearly indicated the role of history in the Monte Alegre lizard assemblage. This result was corroborated by Canonical Phylogenetic Ordination analysis.

Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well‐delimited lineages (Northeast and Southwest) that have diverged along the Cerrado–Caatinga border during the Mid‐Late Miocene (6–14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado–Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.