Adding Biotic Interactions into Paleodistribution Models: A Host-Cleptoparasite Complex of Neotropical Orchid Bees

Orchid bees compose an exclusive Neotropical pollinators group, with bright body coloration. Several of those species build their own nests, while others are reported as nest cleptoparasites. Here, the objective was to evaluate whether the inclusion of a strong biotic interaction, such as the presence of a host species, improved the ability of species distribution models (SDMs) to predict the geographic range of the cleptoparasite species. The target species were Aglae caerulea and its host species Eulaema nigrita. Additionally, since A. caerulea is more frequently found in the Amazon rather than the Cerrado areas, a secondary objective was to evaluate whether this species is increasing or decreasing its distribution given South American past and current climatic conditions. SDMs methods (Maxent and Bioclim), in addition with current and past South American climatic conditions, as well as the occurrences for A. caerulea and E. nigrita were used to generate the distribution models. The distribution of A. caerulea was generated with and without the inclusion of the distribution of E. nigrita as a predictor variable. The results indicate A. caerulea was barely affected by past climatic conditions and the populations from the Cerrado savanna could be at least 21,000 years old (the last glacial maximum), as well as the Amazonian ones. On the other hand, in this study, the inclusion of the host-cleptoparasite interaction complex did not statistically improve the quality of the produced models, which means that the geographic range of this cleptoparasite species is mainly constrained by climate and not by the presence of the host species. Nonetheless, this could also be caused by unknown complexes of other Euglossini hosts with A. caerulea, which still are still needed to be described by science.     

Conservation Value and Permeability of Neotropical Oil Palm Landscapes for Orchid Bees

The proliferation of oil palm plantations has led to dramatic changes in tropical landscapes across the globe. However, relatively little is known about the effects of oil palm expansion on biodiversity, especially in key ecosystem-service providing organisms like pollinators. Rapid land use change is exacerbated by limited knowledge of the mechanisms causing biodiversity decline in the tropics, particularly those involving landscape features. We examined these mechanisms by undertaking a survey of orchid bees, a well-known group of Neotropical pollinators, across forest and oil palm plantations in Costa Rica. We used chemical baits to survey the community in four regions: continuous forest sites, oil palm sites immediately adjacent to forest, oil palm sites 2km from forest, and oil palm sites greater than 5km from forest. We found that although orchid bees are present in all environments, orchid bee communities diverged across the gradient, and community richness, abundance, and similarity to forest declined as distance from forest increased. In addition, mean phylogenetic distance of the orchid bee community declined and was more clustered in oil palm. Community traits also differed with individuals in oil palm having shorter average tongue length and larger average geographic range size than those in the forest. Our results indicate two key features about Neotropical landscapes that contain oil palm: 1) oil palm is selectively permeable to orchid bees and 2) orchid bee communities in oil palm have distinct phylogenetic and trait structure compared to communities in forest. These results suggest that conservation and management efforts in oil palm-cultivating regions should focus on landscape features.     

The Ecological Basis for Biogeographic Classification: an Example in Orchid Bees (Apidae: Euglossini)

Biogeography has been difficult to apply as a methodological approach because organismic biology is incomplete at levels where the process of formulating comparisons and analogies is complex. The study of insect biogeography became necessary because insects possess numerous evolutionary traits and play an important role as pollinators. Among insects, the euglossine bees, or orchid bees, attract interest because the study of their biology allows us to explain important steps in the evolution of social behavior and many other adaptive tradeoffs. We analyzed the distribution of morphological characteristics in Colombian orchid bees from an ecological perspective. The aim of this study was to observe the distribution of these attributes on a regional basis. Data corresponding to Colombian euglossine species were ordered with a correspondence analysis and with subsequent hierarchical clustering. Later, and based on community proprieties, we compared the resulting hierarchical model with the collection localities to seek to identify a biogeographic classification pattern. From this analysis, we derived a model that classifies the territory of Colombia into 11 biogeographic units or natural clusters. Ecological assumptions in concordance with the derived classification levels suggest that species characteristics associated with flight performance, nectar uptake, and social behavior are the factors that served to produce the current geographical structure.     

Integrating Life Stages into Ecological Niche Models: A Case Study on Tiger Beetles

Detailed understanding of a species’ natural history and environmental needs across spatial scales is a primary requisite for effective conservation planning, particularly for species with complex life cycles in which different life stages occupy different niches and respond to the environment at different scales. However, niche models applied to conservation often neglect early life stages and are mostly performed at broad spatial scales. Using the endangered heath tiger beetle (Cicindela sylvatica) as a model species, we relate presence/absence and abundance data of locally dispersing adults and sedentary larvae to abiotic and biotic variables measured in a multiscale approach within the geographic extent relevant to active conservation management. At the scale of hundreds of meters, fine-grained abiotic conditions (i.e., vegetation structure) are fundamental determinants of the occurrence of both life stages, whereas the effect of biotic factors is mostly contained in the abiotic signature. The combination of dense heath vegetation and bare ground areas is thus the first requirement for the species’ preservation, provided that accessibility to the suitable habitat is ensured. At a smaller scale (centimetres), the influence of abiotic factors on larval occurrence becomes negligible, suggesting the existence of important additional variables acting within larval proximity. Sustained significant correlations between neighbouring larvae in the models provide an indication of the potential impact of neighbourhood crowding on the larval niche within a few centimetres. Since the species spends the majority of its life cycle in the larval stage, it is essential to consider the hierarchical abiotic and biotic processes affecting the larvae when designing practical conservation guidelines for the species. This underlines the necessity for a more critical evaluation of the consequences of disregarding niche variation between life stages when estimating niches and addressing effective conservation measures for species with complex life cycles.     

Honey Pollen: Using Melissopalynology to Understand Foraging Preferences of Bees in Tropical South India

The aim of the study was to use melissopalynology to delineate the foraging preferences of bees in tropical environs. This was done by comparing pollen spectra obtained from the same hives every three months for three years at four sampling locations (in two sites) within a confined landscape mosaic. If melissopalynology is highly replicable, the spatial variation of the pollen spectrum from the honey samples would be much more than the temporal (inter-annual) variations. In other words, given the three factors, Month, Year and Location, honey pollen from different Locations, in a given Year and Month, would be much less similar than samples from different Years, in a given Location and Month. We then determined how the factors, Month, Year and Location, influenced the pollen influx of honey. The pollen analyses of the 42 honey samples collected during the three years yielded 80 pollen taxa/types: 72 dicotyledonous and 8 monocotyledonous, encompassing 41 botanical families spread into seven life forms namely, trees, shrubs, epiphytes, herbs, climbers, grasses, and sedges. Our results showed that pollen spectra were equally comparable between Locations and between Months and Years; the importance of this result is that it helped to demonstrate the complexity of ecological/environmental phenomena involved in the process of foraging by bees in a heterogeneous and complex landscape.     

Plant Species Complexes as Models to Understand Speciation and Evolution: A Review of South American Studies

Identifying discontinuous entities within species complexes is a major topic in systematic and evolutionary biology. Comprehensive inventories describing and identifying species rapidly and correctly before they or their habitats disappear is especially important in megadiverse regions, such as South America continent, where a large part of the biodiversity is still unknown and remains to be discovered. Species complexes may account for a substantial number of plant groups in the South American flora, and studies investigating species boundaries in such challenging groups are needed. In this context, multidisciplinary approaches are crucial to understanding the species integrity and boundaries within species complexes. Morphometrics, cytogenetics, anatomy, crossing experiments, and molecular markers have been combined in different ways to investigate species complexes and have helped depict the mechanisms underlying the origin of South American species. Here, we review the current knowledge about plant species complexes on the hyperdiverse South American continent based on a detailed examination of the relevant literature. We discuss the main findings in light of the potential evolutionary mechanisms involved in speciation and suggest future directions in terms of integrating multispecies coalescence methods with several complementary types of morphological, ecological, and geographical data in this research field.     

Applying Landscape-Scale Habitat-Potential Models to Understand Deer Spatial Structure and Movement Patterns

Abstract: Ecologically based management must incorporate components that consider how individuals associate temporally and spatially to environments that provide specific habitat requirements. Recent research has assessed how environments could be classified based on potential to provide deer (Odocoileus virginianus) habitat components. If habitat potential (HP; i.e., capability of habitat types to provide annual life requisites) classifications can be correlated to deer spatial structure and seasonal movement patterns, managers could better understand how spatial distribution of habitat components influences deer distribution. We analyzed home-range distribution and seasonal movement patterns from 45 adult (≥2 yr old) female deer radiocollared between 1999-2002, and deer habitat characteristics in northeastern Lower Peninsula, Michigan, USA, to investigate whether we can predict deer seasonal movement patterns based on the distribution of HP. We constructed logistic regression models that calculated the probability of deer migration given specific HP within seasonal home ranges of migratory and nonmigratory deer. Our results suggested that the probability of seasonal deer migrations relates to the juxtaposition (arrangement) of different habitat types that collectively provide all annual life requisites. We demonstrated that use of habitat-type classifications and HP models can track and predict deer movement patterns, which can facilitate establishment of management units and ecologically based deer management practices.     

Cuticular Hydrocarbons of Orchid Bees Males: Interspecific and Chemotaxonomy Variation

Recent studies have investigated the composition of compounds that cover the cuticle in social insects, but few studies have focused on solitary bees. Cuticular hydrocarbons may provide a tool for chemotaxonomy, and perhaps they can be used as a complement to morphology and genetic characters in phylogenetic studies. Orchid bees (Tribe Euglossini) are a highly diverse group of Neotropical bees with more than 200 species. Here, the cuticular hydrocarbons of 17 species were identified and statistical analysis revealed 108 compounds, which allowed for the taxonomic classification according to the genera. The most significant compounds discriminating the four genera were (Z)-9-pentacosene, (Z,Z)-pentatriacontene-3, (Z)-9-tricosene, and (Z)-9-heptacosene. The analyses demonstrated the potential use of CHCs to identify different species.     

Niche Divergence in a Brown Lemur (<Emphasis Type="Italic">Eulemur</Emphasis> spp.) Hybrid Zone: Using Ecological Niche Models to Test Models of Stability

Endogenous selection is often implicated in the maintenance of stability of natural hybrid zones. Environmental conditions often vary across these zones, suggesting that local adaptation to ecological conditions could also play a role in this process. We used niche modeling to investigate these alternatives in a hybrid zone between two species of brown lemur (Eulemur rufifrons and E. cinereiceps) in southeastern Madagascar. We produced ecological niche models (ENMs) for parental and hybrid populations and compared values of niche overlap to null expectations using identity and background tests. All three taxonomic groups had nonequivalent ENMs with limited spatial overlap, supporting a role for niche divergence and local adaptation in the maintenance of this zone. However, values of niche overlap between ENMs were not greater than null expectations controlling for background environmental differences. These results could suggest that taxa in this hybrid zone inhabit portions of their environments that are more similar to their backgrounds, i.e., niche conservatism. Nevertheless, we did find evidence of niche divergence when using background tests that examined environmental variables separately. Although we could not rule out models indicating selection against hybrids, most lines of evidence were consistent with predictions for the bounded superiority model of hybrid zone stability. This study thus provides support that exogenous, environmental selection may be responsible for maintaining the hybrid zone, and may be implicated in the evolutionary divergence of these taxa.     

Using Networks To Understand Medical Data: The Case of Class III Malocclusions

A system of elements that interact or regulate each other can be represented by a mathematical object called a network. While network analysis has been successfully applied to high-throughput biological systems, less has been done regarding their application in more applied fields of medicine; here we show an application based on standard medical diagnostic data. We apply network analysis to Class III malocclusion, one of the most difficult to understand and treat orofacial anomaly. We hypothesize that different interactions of the skeletal components can contribute to pathological disequilibrium; in order to test this hypothesis, we apply network analysis to 532 Class III young female patients. The topology of the Class III malocclusion obtained by network analysis shows a strong co-occurrence of abnormal skeletal features. The pattern of these occurrences influences the vertical and horizontal balance of disharmony in skeletal form and position. Patients with more unbalanced orthodontic phenotypes show preponderance of the pathological skeletal nodes and minor relevance of adaptive dentoalveolar equilibrating nodes. Furthermore, by applying Power Graphs analysis we identify some functional modules among orthodontic nodes. These modules correspond to groups of tightly inter-related features and presumably constitute the key regulators of plasticity and the sites of unbalance of the growing dentofacial Class III system. The data of the present study show that, in their most basic abstraction level, the orofacial characteristics can be represented as graphs using nodes to represent orthodontic characteristics, and edges to represent their various types of interactions. The applications of this mathematical model could improve the interpretation of the quantitative, patient-specific information, and help to better targeting therapy. Last but not least, the methodology we have applied in analyzing orthodontic features can be applied easily to other fields of the medical science.     

Using Phylogenetic,Functional and Trait Diversity to Understand Patterns of Plant Community Productivity

Background

Two decades of research showing that increasing plant diversity results in greater community productivity has been predicated on greater functional diversity allowing access to more of the total available resources. Thus, understanding phenotypic attributes that allow species to partition resources is fundamentally important to explaining diversity-productivity relationships.

Methodology/Principal Findings

Here we use data from a long-term experiment (Cedar Creek, MN) and compare the extent to which productivity is explained by seven types of community metrics of functional variation: 1) species richness, 2) variation in 10 individual traits, 3) functional group richness, 4) a distance-based measure of functional diversity, 5) a hierarchical multivariate clustering method, 6) a nonmetric multidimensional scaling approach, and 7) a phylogenetic diversity measure, summing phylogenetic branch lengths connecting community members together and may be a surrogate for ecological differences. Although most of these diversity measures provided significant explanations of variation in productivity, the presence of a nitrogen fixer and phylogenetic diversity were the two best explanatory variables. Further, a statistical model that included the presence of a nitrogen fixer, seed weight and phylogenetic diversity was a better explanation of community productivity than other models.

Conclusions

Evolutionary relationships among species appear to explain patterns of grassland productivity. Further, these results reveal that functional differences among species involve a complex suite of traits and that perhaps phylogenetic relationships provide a better measure of the diversity among species that contributes to productivity than individual or small groups of traits.     

Ecological Niche Models using MaxEnt in Google Earth Engine: Evaluation,guidelines and recommendations

Google Earth Engine (GEE) has revolutionized geospatial analyses by fast-processing formerly demanding analyses from multiple research areas. Recently, maximum entropy (MaxEnt), the most commonly used method in ecological niche models (ENMs), was integrated into GEE. This integration can significantly enhance modeling efficiency and encourage multidisciplinary approaches of ENMs, but an evaluation assessment of MaxEnt in GEE is lacking. Herein, we present the first MaxEnt models in GEE, as well as its first statistical and spatial evaluation. We also identify the limitations of the approach, providing guidelines and recommendations for its easier applicability in GEE.We tested MaxEnt in GEE using 11 case studies. For each case, we used species of different taxa (insects, amphibians, reptiles, birds and mammals) distributed across global and regional extents. Each species occupied habitats with distinct environmental characteristics (nine terrestrial and two marine species) and within divergent ecoregions across five continents. The models were performed in GEE and Maxent software, and both approaches were contrasted for their model discrimination performance (assessed by eight evaluation metrics) and spatial consistency (correlation analyses and two measures of niche overlap/equivalency).MaxEnt in GEE allows setting several parameters, but important analyses and outputs are unavailable, such as automatic selection of background data, model replicates, and analyses of variable importance (concretely, jackknife analyses and response curves). GEE provided MaxEnt models with high discrimination performance (area under the curve mean between all species models of 0.90) and with spatial equivalency in relation to Maxent software outputs (Hellinger's I mean between all species models >0.90).Our work demonstrates the first application and assessment of MaxEnt in GEE at global and regional scales. We conclude that the GEE modeling method provides ENMs with high performance and reliable spatial predictions, comparable to the widely used Maxent software. We also acknowledge important limitations that should be integrated into GEE in the future, particularly those related to the assessment of variable importance. We expect that our guidelines, recommendations and potential solutions to surpass the identified limitations could help researchers easily apply MaxEnt in GEE across different research fields.     

The Geography of Speciation: Case Studies from Birds

Our understanding of the origin of species, or speciation, is sometimes viewed as incomplete, a ??mystery of mysteries.?? We in fact know a lot about speciation, especially when we consider its two basic components, the geography of speciation and the biology of speciation (changes in phenotype and genotype that occur during the process). Our understanding of the geography of speciation is quite clear. The process involves the separation of a once-continuous range into two or more geographically isolated, or allopatric parts, which over time accrue genetic changes that result in new daughter species. Current distributions show that recently evolved species are currently allopatric, supporting the role of allopatry in speciation. However, many species originated in the early- to mid-Pleistocene, meaning that they persisted through the environmental perturbations of multiple glacial cycles. It has been assumed that species maintained allopatric distributions during these episodes of glacial advance and retreat. I used Grinnelian niche models to estimate species distributions at the Last Glacial Maximum and the Last Interglacial. For a pair of recently isolated warbler species, and a pair of relatively old sister species of gnatcatchers, allopatry was observed at all time periods. Thus, there is no mystery about the geography of speciation: at least in birds, allopatry predominates. The sentiment that speciation is mysterious comes, I argue, from the biological species concept, which requires populations to be reproductively isolated before recognizing them as species. Reproductive isolation is a complicated process that rarely occurs the same way twice, and I argue that this lack of generality has been misinterpreted as a mystery.     

Ecological Patterns and Biological Invasions: Using Regional Species Inventories in Macroecology

Macroecology depends heavily on a comparative methodology in order to identify large-scale patterns and to test alternative hypotheses that might generate such patterns. With the advent and accessibility of large electronic databases of species and their life history and ecological attributes, ecologists have begun seeking generalities, and examining large-scale ecological hypotheses involving core themes of range, abundance and diversity. For example, combinations of ecological, life history and phylogenetic data have been analysed using large species sets to test hypotheses in invasion biology. Analysis of regional species inventories can contribute cogently to our understanding of invasions. Here we examine several ways in which database analysis is effective. We review 19 studies of comparative invasions biology, each using >100 species of plants in their analyses, and show that invader success is linked to seven correlates: short life cycle, abiotic (mostly wind) dispersal, large native range size, non-random taxonomic patterns (emphasizing certain families or orders), presence of clonal organs, occupying disturbed habitats, and earlier time of introduction. These phylogenetically influenced, comparative analyses using regional species inventories are only just beginning and have much potential.     

Climate Change and Risk of Leishmaniasis in North America: Predictions from Ecological Niche Models of Vector and Reservoir Species

Background

Climate change is increasingly being implicated in species'' range shifts throughout the world, including those of important vector and reservoir species for infectious diseases. In North America (México, United States, and Canada), leishmaniasis is a vector-borne disease that is autochthonous in México and Texas and has begun to expand its range northward. Further expansion to the north may be facilitated by climate change as more habitat becomes suitable for vector and reservoir species for leishmaniasis.

Methods and Findings

The analysis began with the construction of ecological niche models using a maximum entropy algorithm for the distribution of two sand fly vector species (Lutzomyia anthophora and L. diabolica), three confirmed rodent reservoir species (Neotoma albigula, N. floridana, and N. micropus), and one potential rodent reservoir species (N. mexicana) for leishmaniasis in northern México and the United States. As input, these models used species'' occurrence records with topographic and climatic parameters as explanatory variables. Models were tested for their ability to predict correctly both a specified fraction of occurrence points set aside for this purpose and occurrence points from an independently derived data set. These models were refined to obtain predicted species'' geographical distributions under increasingly strict assumptions about the ability of a species to disperse to suitable habitat and to persist in it, as modulated by its ecological suitability. Models successful at predictions were fitted to the extreme A2 and relatively conservative B2 projected climate scenarios for 2020, 2050, and 2080 using publicly available interpolated climate data from the Third Intergovernmental Panel on Climate Change Assessment Report. Further analyses included estimation of the projected human population that could potentially be exposed to leishmaniasis in 2020, 2050, and 2080 under the A2 and B2 scenarios. All confirmed vector and reservoir species will see an expansion of their potential range towards the north. Thus, leishmaniasis has the potential to expand northwards from México and the southern United States. In the eastern United States its spread is predicted to be limited by the range of L. diabolica; further west, L. anthophora may play the same role. In the east it may even reach the southern boundary of Canada. The risk of spread is greater for the A2 scenario than for the B2 scenario. Even in the latter case, with restrictive (contiguous) models for dispersal of vector and reservoir species, and limiting vector and reservoir species occupancy to only the top 10% of their potential suitable habitat, the expected number of human individuals exposed to leishmaniasis by 2080 will at least double its present value.

Conclusions

These models predict that climate change will exacerbate the ecological risk of human exposure to leishmaniasis in areas outside its present range in the United States and, possibly, in parts of southern Canada. This prediction suggests the adoption of measures such as surveillance for leishmaniasis north of Texas as disease cases spread northwards. Potential vector and reservoir control strategies—besides direct intervention in disease cases—should also be further investigated.     

Comparative Development of Anurans: Using Phylogeny to Understand Ontogeny

Hypotheses of relationships are critical to describing and understandingpatterns of evolution within groups of organisms. But rarelyhas a comparative, historical approach been employed to studydevelopmental change, particularly among anurans. A recent resurgenceof interest in collecting basic ontogenetic information providesus with the opportunity to compare ontogenetic trajectoriesin a phylogenetic framework. Larval skeletons and osteologicaldevelopment were examined for 22 taxa and compared to two hypothesesof relationships—that of Cannatella, and one proposedherein based on 41 morphological characters from larvae and62 from adults. Larval characters were mapped on the alternatecladograms using the ACCTRAN optimization criterion. Severallarval features are highly conserved among some anurans, suggestingthat there is some level of canalization of morphology earlyin ontogeny. In contrast, a number of morphologies vary amonggroups, supporting the fact that there have been major evolutionarymodifications to anuran larval morphologies early in ontogenyand in the early evolutionary history of anurans.     

Niche Divergence versus Neutral Processes: Combined Environmental and Genetic Analyses Identify Contrasting Patterns of Differentiation in Recently Diverged Pine Species

Background and Aims

Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis.

Methods

Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species.

Key Results and Conclusion

Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.     

Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae)

Rapid diversification may be caused by ecological adaptive radiation via niche divergence. In this model, speciation is coupled with niche divergence and lineage diversification is predicted to be correlated with rates of niche evolution. Studies of the role of niche evolution in diversification have generally focused on ecomorphological diversification but climatic‐niche evolution may also be important. We tested these alternatives using a phylogeny of 298 species of ovenbirds (Aves: Furnariidae). We found that within Furnariidae, variation in species richness and diversification rates of subclades were best predicted by rate of climatic‐niche evolution than ecomorphological evolution. Although both are clearly important, univariate regression and multivariate model averaging more consistently supported the climatic‐niche as the best predictor of lineage diversification. Our study adds to the growing body of evidence, suggesting that climatic‐niche divergence may be an important driver of rapid diversification in addition to ecomorphological evolution. However, this pattern may depend on the phylogenetic scale at which rate heterogeneity is examined.