Macroevolutionary trends of brain mass in Primates

A distinctive trait in primate evolution is the expansion in brain mass. The potential drivers of this trend and how and whether encephalization influenced diversification dynamics in this group are hotly debated. We assembled a phylogeny accounting for 317 primate species, including both extant and extinct taxa, to identify macroevolutionary trends in brain mass evolution. Our findings show that Primates as a whole follow a macroevolutionary trend for an increase in body mass, relative brain mass and speciation rate over time. Although the trend for increased encephalization (brain mass) applies to all Primates, hominins stand out for their distinctly higher rates. Within hominins, this unique trend applies linearly over time and starts with Australopithecus africanus. The increases in both speciation rate and encephalization begin in the Oligocene, suggesting the two variables are causally associated. The substitution of early, stem Primates belonging to plesiadapiforms with crown Primates seems to be responsible for these macroevolutionary trends. However, our findings also suggest that cognitive capacities favoured speciation in hominins.

Exhaustive search for conservation networks of populations representing genetic diversity

Conservation strategies routinely use optimization methods to identify the smallest number of units required to represent a set of features that need to be conserved, including biomes, species, and populations. In this study, we provide R scripts to facilitate exhaustive search for solutions that represent all of the alleles in networks with the smallest possible number of populations. The script also allows other variables to be added to describe the populations, thereby providing the basis for multi-objective optimization and the construction of Pareto curves by averaging the values in the solutions. We applied this algorithm to an empirical dataset that comprised 23 populations of Eugenia dysenterica, which is a tree species with a widespread distribution in the Cerrado biome. We observed that 15 populations would be necessary to represent all 249 alleles based on 11 microsatellite loci, and that the likelihood of representing all of the alleles with random networks is less than 0.0001. We selected the solution (from two with the smallest number of populations) obtained for the populations with a higher level of climatic stability as the best strategy for in situ conservation of genetic diversity of E. dysenterica. The scripts provided in this study are a simple and efficient alternative to more complex optimization methods, especially when the number of populations is relatively small (i.e., <25 populations).

Multi-objective optimization in systematic conservation planning and the representation of genetic variability among populations

Biodiversity crises have led scientists to develop strategies for achieving conservation goals. The underlying principle of these strategies lies in systematic conservation planning (SCP), in which there are at least 2 conflicting objectives, making it a good candidate for multi-objective optimization. Although SCP is typically applied at the species level (or hierarchically higher), it can be used at lower hierarchical levels, such as using alleles as basic units for analysis, for conservation genetics. Here, we propose a method of SCP using a multi-objective approach. We used non-dominated sorting genetic algorithm II in order to identify the smallest set of local populations of Dipteryx alata (baru) (a Brazilian Cerrado species) for conservation, representing the known genetic diversity and using allele frequency information associated with heterozygosity and Hardy-Weinberg equilibrium. We worked in 3 variations for the problem. First, we reproduced a previous experiment, but using a multi-objective approach. We found that the smallest set of populations needed to represent all alleles under study was 7, corroborating the results of the previous study, but with more distinct solutions. In the 2nd and 3rd variations, we performed simultaneous optimization of 4 and 5 objectives, respectively. We found similar but refined results for 7 populations, and a larger portfolio considering intra-specific diversity and persistence with populations ranging from 8-22. This is the first study to apply multi-objective algorithms to an SCP problem using alleles at the population level as basic units for analysis.

Geographical genetics of Pseudoplatystoma punctifer (Castelnau, 1855) (Siluriformes, Pimelodidae) in the Amazon Basin

Geographical genetics allows the evaluation of evolutionary processes underlying genetic variation within and among local populations and forms the basis for establishing more effective strategies for biodiversity conservation at the population level. In this study, we used explicit spatial analyses to investigate molecular genetic variation (estimated using 7 microsatellite markers) of Pseudoplatystoma punctifer, by using samples obtained from 15 localities along the Madeira River and Solimões, Amazon Basin. A high genetic diversity was observed associated with a relatively low FST (0.057; P < 0.001), but pairwise FST values ranged from zero up to 0.21 when some pairs of populations were compared. These FST values have a relatively low correlation with geographic distances (r = 0.343; P = 0.074 by Mantel test), but a Mantel correlogram revealed that close populations (up to 80 km) tended to be more similar than expected by chance (r = 0.360; P = 0.015). The correlogram also showed a exponential-like decrease of genetic similarity with distance, with a patch-size of around 200 km, compatible with isolation-by-distance and analogous processes related to local constraints of dispersal and spatially structured levels of gene flow. The pattern revealed herein has important implications for establishing strategies to maintain genetic diversity in the species, especially considering the threats due to human impacts caused by building large dams in this river system.

Phylogenetic inheritance of genetic variability produced by neutral models of evolution

The amount of genetic variability in species and populations has been mainly related to microevolutionary forces operating in natural populations and the influence of phylogenetic processes for the distribution of genetic variability has been neglected. To investigate how the current genetic variability distribution depends on the genetic variability of ancestral species, we simulated the evolution of heterozygosity on a pre-determined phylogeny under three neutral models of evolution: genetic drift, drift vs mutation and drift vs migration. The distribution of genetic variability resulting from the simulations was used to estimate the phylogenetic signal by the phylogenetic comparative method of autocorrelation. Phylogenetic signal in genetic variability was observed for each of the three models, and its intensity was generally higher and persisted longer when forces of drift, mutation and migration were reduced. The prediction of a phylogenetic signal in genetic variability has consequences for: population genetics, which must consider biological processes acting at the species level influencing the amount and distribution of genetic variability; the macroevolutionary theory, by giving a theoretical basis for species selection by suggesting a heritability of genetic variability between species, and the meta-analyses of genetic variability, which must deal with the non-independence of species. The patterns observed in phylogenetic signal produced by different models of evolution can be used further to compare with data obtained from molecular markers. This is the first study that analyzes the theoretical expectations for the existence of a phylogenetic signal in a population genetic trait.

Autoregressive modelling of species richness in the Brazilian Cerrado

Spatial autocorrelation is the lack of independence between pairs of observations at given distances within a geographical space, a phenomenon commonly found in ecological data. Taking into account spatial autocorrelation when evaluating problems in geographical ecology, including gradients in species richness, is important to describe both the spatial structure in data and to correct the bias in Type I errors of standard statistical analyses. However, to effectively solve these problems it is necessary to establish the best way to incorporate the spatial structure to be used in the models. In this paper, we applied autoregressive models based on different types of connections and distances between 181 cells covering the Cerrado region of Central Brazil to study the spatial variation in mammal and bird species richness across the biome. Spatial structure was stronger for birds than for mammals, with R(2) values ranging from 0.77 to 0.94 for mammals and from 0.77 to 0.97 for birds, for models based on different definitions of spatial structures. According to the Akaike Information Criterion (AIC), the best autoregressive model was obtained by using the rook connection. In general, these results furnish guidelines for future modelling of species richness patterns in relation to environmental predictors and other variables expressing human occupation in the biome.

Transferability of short tandem repeat markers for two wild Canid species inhabiting the Brazilian Cerrado

The maned wolf (Chrysocyon brachyurus) and the crab-eating fox (Cerdocyon thous) are two wild-canid species found in the Brazilian Cerrado. We tested cross-amplification and transferability of 29 short tandem repeat primers originally developed for cattle and domestic dogs and cats on 38 individuals of each of these two species, collected in the Emas National Park, which is the largest national park in the Cerrado region. Six of these primers were successfully transferred (CSSM-038, PEZ-05, PEZ-12, LOCO-13, LOCO-15, and PEZ-20); five of which were found to be polymorphic. Genetic parameter values (number of alleles per locus, observed and expected heterozygosities, and fixation indices) were within the expected range reported for canid populations worldwide.

Phylogenetic autocorrelation and evolutionary interpretation of the higher-taxon approach for biodiversity analyses

Although in most recent broad-scale analyses, diversity is measured by counting the number of species in a given area or spatial unity (species richness), a 'top-down' approach has been used sometimes, counting higher-taxon (genera, family) instead of species with some advantages. However, this higher-taxon approach is quite empirical and the cut-off level is usually arbitrarily defined. In this work, we show that the higher-taxon approach could be theoretically linked with models of phenotypic diversification by means of phylogenetic autocorrelation analysis in such a way that the taxonomic (or phylogenetic) rank to be used could not be necessarily arbitrary. This rank expresses past time in which taxa became independent for a given phenotypic trait or for the evolution of average phenotypes across different traits. We illustrated the approach by evaluating phylogenetic patches for 23 morphological, ecological and behavioural characters in New World terrestrial Carnivora. The higher-taxon counts at 18.8 mya (S(L)) defined by phylogenetic correlograms are highly correlated with species richness (r = 0.899; P < 0.001 with ca. 13 degrees of freedom by taking spatial autocorrelation into account). However, S(L) in North America is usually larger than in South America. Thus, although there are more species in South and Central America, the fast recent diversification that occurred in this region generated species that are "redundant" in relation to lineages that were present at 18.8 my. BP. Therefore, the number of lineages can be comparatively used as a measure of evolutionary diversity under a given model of phenotypic divergence among lower taxonomic units.

Priority areas for anuran conservation using biogeographical data: a comparison of greedy, rarity, and simulated annealing algorithms to define reserve networks in Cerrado

Spatial patterns in biodiversity variation at a regional scale are rarely taken into account when a natural reserve is to be established, despite many available methods for determining them. In this paper, we used dimensions of occurrence of 105 species of Anura (Amphibia) in the cerrado region of central Brazil to create a regional system of potential areas that preserves all regional diversity, using three different algorithms to establish reserve networks: "greedy", rarity, and simulated annealing algorithms. These generated networks based on complementarity with 10, 12, and 8 regions, respectively, widely distributed in the biome, and encompassing various Brazilian states. Although the purpose of these algorithms is to find a small number of regions for which all species are represented at least once, the results showed that 67.6%, 76.2%, and 69.5% of the species were represented in two or more regions in the three networks. Simulated annealing produced the smallest network, but it left out three species (one endemic). On the other hand, while the greedy algorithm produce a smaller solution, the rarity-based algorithm ensured that more species were represented more than once, which can be advantageous because it takes into consideration the high levels of habitat loss in the cerrado. Although usually coarse, these macro-scale approaches can provide overall guidelines for conservation and are useful in determining the focus for more local and effective conservation efforts, which is especially important when dealing with a taxonomic group such as anurans, for which quick and drastic population declines have been reported throughout the world.

Worldwide patterns in species richness of Falconiformes: analytical null models, geometric constraints, and the mid-domain effect

Recently, the hypothesis that the geographic distribution of species could be influenced by the shape of the domain edges, the so-called Mid-Domain Effect (MDE), has been included as one of the five credible hypotheses for explaining spatial gradients in species richness, despite all the unsuccessful current attempts to prove empirically the validity of MDE. We used data on spatial worldwide distributions of Falconiformes to evaluate the validity of MDE assumptions, incorporated into two different sorts of null models at a global level and separately across five domains/landmasses. Species richness values predicted by the null models of the MDE and those values predicted by Net Primary Productivity, a surrogate variable expressing the effect of available energy, were compared in order to evaluate which hypothesis better predicts the observed values. Our tests showed that MDE continues to lack empirical support, regardless of its current acceptability, and so, does not deserve to be classified as one possible explanation of species richness gradients.

Macroecological analyses support an overkill scenario for late Pleistocene extinctions

The extinction of megafauna at the end of Pleistocene has been traditionally explained by environmental changes or overexploitation by human hunting (overkill). Despite difficulties in choosing between these alternative (and not mutually exclusive) scenarios, the plausibility of the overkill hypothesis can be established by ecological models of predator-prey interactions. In this paper, I have developed a macroecological model for the overkill hypothesis, in which prey population dynamic parameters, including abundance, geographic extent, and food supply for hunters, were derived from empirical allometric relationships with body mass. The last output correctly predicts the final destiny (survival or extinction) for 73% of the species considered, a value only slightly smaller than those obtained by more complex models based on detailed archaeological and ecological data for each species. This illustrates the high selectivity of Pleistocene extinction in relation to body mass and confers more plausibility on the overkill scenario.

Rapoport effect in South American Carnivora (Mammalia): null models under geometric and phylogenetic constraints

Rapoport effect predicts that species geographic range sizes will increase toward higher latitudes, probably reflecting adaptations to extreme climatic conditions that increase species tolerance. Recently, studies about spatial patterns in species richness and geographic range size may be associated with the geometry of species' ranges. In this context, null models can be used to search for the causal mechanisms associated with these patterns. In this paper, we analyzed Rapoport effect using a null model to evaluate how phylogenetic structure and geometric constraints simultaneously affect latitudinal extents of 40 species of South American terrestrial Carnivora. The latitudinal extents of Carnivora tended to decrease toward Southern latitudes, in the opposite direction expected under a simple Rapoport effect, but in accordance to geometric expectations of position of midpoints in the continent. Using 5000 simulations, it was possible to show that the null regression coefficients of latitudinal extents against midpoints are positively biased, reflecting the geometric constraints in the latitudinal extents. The results were equivalent in phylogenetic and non-phylogenetic analyses. The observed regression coefficient was significantly smaller (line is less inclined) than expected by chance alone, demonstrating that the geometric constraints in the latitudinal extents exist even after controlling for phylogenetic structure in data using eigenvector regressions. This suggests that the "spirit" of Rapoport effect (sensu Lyons & Willig, 1997) could be maintained, i.e., that latitudinal extents in Southern region of the continent are relatively larger than those in Northern regions, even after controlling for phylogenetic effects.