Estimating alpha, beta, and gamma diversity through deep learning

The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsampled areas deemed suitable by environmental niche models. Here we present a deep learning approach that directly estimates species richness, skipping the step of estimating individual species ranges. We train a neural network model based on species lists from inventory plots, which provide ground truthing for supervised machine learning. The model learns to predict species richness based on spatially associated variables, including climatic and geographic predictors, as well as counts of available species records from online databases. We assess the empirical utility of our approach by producing independently verifiable maps of alpha, beta, and gamma plant diversity at high spatial resolutions for Australia, a continent with highly contrasting diversity patterns. Our deep learning framework provides a powerful and flexible new approach for estimating biodiversity patterns.

Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophilic lizard genus Acanthodactylus

Climate has a large impact on diversity and evolution of the world’s biota. The Eocene–Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene–Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them—and especially A. guineensis—as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene–Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.

RELICT HUMID TROPICAL FOREST IN MEXICO PROMOTES DIFFERENTIATION IN BARRED WOODCREEPERS Dendrocolaptes (AVES: FURNARIIDAE)

Humid tropical forests in Mesoamerica are distributed along the Atlantic slope and, in scattered locations, along the Mexican Pacific slope. These poorly explored Mexican forests include microendemic bird species. Two species in the genus Dendrocolaptes occur in lowland and foothill humid tropical forests of Mesoamerica. One of these, D. sanctithomae, is comprised of four subspecies, of which the two that occur in Mexico, D. s. sanctithomae and D. s. sheffleri, are distinctly different morphologically, and the latter is a poorly known microendemic taxon of the Mexican Pacific humid tropical forest in the Sierra Madre del Sur. We used both nuclear (nDNA) and mitochondrial DNA (mtDNA) to evaluate the genetic variation of D. sanctithomae in Mexico, and complemented this with a quantitative analysis of phenotypic traits. We also conducted analyses of environmental niche models to test the hypothesis of niche differentiation of D. s. sheffleri from other taxa of D. sanctithomae. Our phylogenetic reconstructions of mtDNA consistently recovered D. s. sheffleri and D. s. sanctithomae as reciprocally monophyletic, while they shared alleles of nDNA. These mtDNA differences are comparable with differences reported between other Dendrocolaptes sister-taxa pairs. Our analysis of phenotypic traits also indicated that the taxa differ in measurements of hallux and feather barring. In contrast, niche differentiation tests suggest that the niches of both taxa are more similar than expected by chance. Our evidence leads us to propose species status for D. sheffleri. This is an additional example of recent speciation in Mexico that indicates active and peripatric evolutionary differentiation in the northern Neotropics.

Using Remote Sensing for Modeling and Monitoring Species Distributions

Interpolated climate surfaces have been widely used to predict species distributions and develop environmental niche models. However, the spatial coverage and density of meteorological sites used to develop these surfaces vary among countries and regions, such that the most biodiverse regions often have the most sparsely sampled climatic data. We explore the potential of satellite remote sensing (S-RS) products—which have consistently high spatial and temporal resolution and nearly global coverage—to quantify species-environment relationships that predict species distributions. We propose several new environmental metrics that take advantage of high temporal resolution in S-RS data and compare these approaches to classic climate-only approaches using the live oaks (Quercus section Virentes) as a case study. We show that models perform similarly but for some species, particularly in understudied regions, show less precision in predicting spatial distribution. These results provide evidence supporting efforts to enhance environmental niche models and species distribution models (ENMs/SDMs) with S-RS data and, when combined with other approaches for species detection, will likely enhance our ability to monitor biodiversity globally.

Invasive in the North: New latitudinal record for Argentine ants in Europe

Environmental niche models predict the presence of the invasive Argentine ant in north-western Europe, especially along all the French Atlantic coast. Yet, the species has never been observed North from the 45th parallel in Europe, suggesting either that current models are wrong or that Argentine ants are already spreading north inconspicuously. Here, we report a three-hectare wide colony of Argentine ants, detected in 2016 in Nantes, France, which is 300 km north of the former northern-most outdoor population of this species in Europe. COI sequencing revealed that the haplotype of this new colony is the same as the one found in the so-called Catalonian supercolony, which is distinct from the haplotype found over most of the species range in Europe. Our discovery confirms models’ predictions that Argentine ants can colonize north-western Europe and suggests that they might have already reached several other locations along the French Atlantic coast. Detection surveys should be conducted in order to assess Argentine ants’ invasion patterns in Western France, particularly in high introduction risk areas such as major cities and maritime ports.

Predictions of Future Geographical Distribution of Two Vectors of American Trypanosomiasis: Implications for Endemic Chagas disease in Texas, USA

It is known that climate has a direct effect on vectorborne and zoonotic diseases, and in the face of climate change, understanding this link has become more urgent. Many such vector-borne diseases primarily afflict impoverished populations and have therefore been previously understudied. One major focus of our research is to understand the influence that climate has on the distribution of disease causing microorganisms and their vectors, especially those in relation to American trypanosomiasis (Chagas disease). Chagas disease is caused by the hemoflagellate protozoan parasite, Trypanosoma cruzi. For this study, we hypothesized that the increasing prevalence Chagas in the state of Texas is due to expanding distributions of vectors. To test this hypothesis, historical data on vector distribution and climate was used to determine the probable locations of prevalent vectors in Texas. Predictions for the future distributions were made using environmental niche models for bioclimatic variables with a maximum entropy algorithm. Of the two Triatominae species studied, the range and concentration of both decreased under a global warming scenario, a finding that is consistent with the current research of risk of Chagas disease in Venezuela. In future, this same procedure will be used on more Chagas vectors to better understand if there is a northward shift for vectors, or if Texas is becoming more inhospitable to all vectors of Chagas.

Niche characteristics and potential distribution of Thelocactus species, a Mexican genus of globular cacti

AimAlthough Mexican Cactaceae are a significative component of Mexican flora and have a relevant economic and ornamental value, the knowledge of the environmental factors characterising their niche is still quite incomplete. This study was aimed at defining the potential distribution and ecological niche of Thelocactus species.MethodsClimatic and environmental variables constraining the distribution of Thelocactus species were identified by means of environmental niche models (ENM) and ordination techniques, and used to generate potential distribution maps. The constructed ENMs were compared to assess the similarities of the ecological niche of Thelocactus species and to know if they share the same ecological niche space.ResultsThe distribution of Thelocactus species was mostly limited by a combination of two environmental factors, isothermality and precipitation of wettest quarter. The null hypothesis of the niche equivalency test was rejected for all paired comparisons between all Thelocactus species except between the pair Thelocactus leucacanthus-Thelocactus hastifer. The results of the niche similarity tests were quite varied, for some species pairs the niche similarities were higher than expected by chance, for others the null hypothesis was rejected, while in other species pairs niches were more similar than expected by chance, but only in one direction.Main conclusionsThe differences in habitat requirements were well documented by the significative differences in the niche ecological space as shown by the equivalency test, while the high percentage of niches that were more similar than expected by chance suggest a high degree of niche conservatism among Thelocactus species. The spatial predictions could serve to improve field design sampling to discover new populations, while niche characteristics could be relevant for improving preservation actions and guiding reintroduction programs for a better conservation of Thelocactus species.