Taxonomy and ecological niche modeling: Implications for the conservation of wood partridges (genus Dendrortyx)

Climatic niche shifts and ecological sky-island dynamics in Mesoamerican montane birds

An ongoing challenge in evolutionary and ecological research focuses on testing biogeographic hypotheses for the understanding of both species' distributional patterns and of the factors influencing range limits. In this study, we described the climatic niches of Neotropical humid montane forest birds through the analysis of factors driving their evolution at inter- and intraspecific levels; and tested for differences among allopatric lineages within Aulacorhynchus, Chlorospingus, Cardellina, and Eupherusa. We employed ecological niche models (ENMs) along with an ordination approach with kernel smoothing to perform niche overlap analyses and test hypotheses of niche equivalence/similarity among lineages. In addition, we described the potential distributions of each lineage during the Late Pleistocene climate fluctuations, identifying historical range expansions, connectivity, and stability. Overall, we observed differences in environmental variables influencing climatic requirements and distributional patterns for our selected species. We detected the highest values of niche overlap mainly between Eupherusa and some Chlorospingus lineages. At both interspecific and intraspecific levels, sister lineages showed non-identical environmental niches. Our results offer weak support to a moist forest model, in which populations followed the expansion and contraction cycles of montane forests, leading to a lack of niche conservatism among lineages (they tend to occupy not identical climatic environments) throughout Mesoamerica. Therefore, historical climatic conditions may act as ecological barriers determining the distributional ranges of these species.

An exhaustive evaluation of modeling ecological niches above species level to predict marine biological invasions

Identifying the areas of the world with suitable environmental conditions for the establishment of invasive species represents a fundamental basis for preventing their impacts. One of the most widely used tools for this is ecological niche modeling. Nonetheless, this approach may underestimate the specie's physiological tolerances (it's potential niche) since wildlife populations of species usually do not occupy their entire environmental tolerance. Recently, it has been suggested that incorporating occurrences of phylogenetically related species improves the prediction of biological invasions. However, the reproducibility of this technique remains unclear. Here, we evaluated the generality of this protocol by assessing whether the construction of modeling units above species level improves the capacity of niche models to predict the distribution of 26 target marine invasive species. For each, we constructed supraspecific modeling units based on published phylogenies by grouping the native occurrence records of each invasive species with the records of its phylogenetically closest relative. We also considered units at species level, including only the presence of records in the native areas of the target species. We generated ecological niche models for each unit with three modeling methods (minimum volume ellipsoids - MVE, machine learning algorithms - Maxent and a presence-absence method - GLM). In addition, we grouped the 26 target species based on whether or not the species are in environmental pseudo-equilibrium (i.e., it occupies all habitats where it can disperse) and have any geographical or biological constraints. Our results suggest that the construction of supraspecific units improves the predictive capacity of correlative models to estimate the invasion area of our target species. This modeling approach consistently generated models with a higher predictive ability for species in non-environmental pseudo-equilibrium and with geographical constraints.

Dealing with disjunct populations of vascular plants: implications for assessing the effect of climate change

Species distribution models are the most widely used tool to predict species distributions for species conservation and assessment of climate change impact. However, they usually do not consider intraspecific ecological variation exhibited by many species. Overlooking the potential differentiation among groups of populations may lead to misplacing any conservation actions. This issue may be particularly relevant in species in which few populations with potential local adaptation occur, as in species with disjunct populations. Here, we used ecological niche modeling to analyze how the projections of current and future climatically suitable areas of 12 plant species can be affected using the whole taxa occurrences compared to occurrences from geographically disjunct populations. Niche analyses suggest that usually the disjunct group of populations selects the climatic conditions as similar as possible to the other according to climate availability. Integrating intraspecific variability only slightly increases models' ability to predict species occurrences. However, it results in different predictions of the magnitude of range change. In some species, integrating or not integrating intraspecific variability may lead to opposite trend in projected range change. Our results suggest that integrating intraspecific variability does not strongly improve overall models' accuracy, but it can result in considerably different conclusions about future range change. Consequently, accounting for intraspecific differentiation may enable the detection of potential local adaptations to new climate and so to design targeted conservation strategies.

Systematics and phylogeography of bats of the genus Rhynchonycteris (Chiroptera: Emballonuridae): Integrating molecular phylogenetics, ecological niche modeling and morphometric data

Rhynchonycteris is a monotypic genus of Embalonurid bats, whose geographic distribution extends from southern Mexico to tropical regions of the South American continent, including Trinidad and Tobago. Although species that have a wide geographic distribution are frequently revealed to be polytypic, to date, no study has evaluated the taxonomic status of populations of Rhynchonycteris naso. Thus, the aim of this study is to address the patterns of phylogeographic structure and taxonomic subdivision of R. naso using molecular phylogenetics, morphometric data and ecological niche modeling. Phylogenetic results recovered using the genes COI, Cytb, Chd1, Dby, and Usp9x, supported the monophyly of the genus Rhynchonycteris, in addition, a deep phylogeographic structure was revealed by the mitochondrial gene COI for the populations of Belize and Panama in comparison to those of South America. The PCA, and the linear morphometry indicated an apparent differentiation between the cis-Andean and trans-Andean populations. Furthermore, according to the skull morphology, at least two morphotypes were identified. Ecological niche modeling projections in the present have shown that the Andean cordillera acts as a climatic barrier between these two populations, with the depression of Yaracuy (Northwest Venezuela) being the only putative climatically suitable path that could communicate these two populations. On the other hand, projections for the last glacial maximum showed a drastic decrease in climatically suitable areas for the species, suggesting that cycles of lower temperatures played an important role in the separation of these populations.

Global assessment of three Rumex species reveals inconsistent climatic niche shifts across multiple introduced ranges

Climatic niche shifts occur when species occupy different climates in the introduced range than in their native range. Climatic niche shifts are known to occur across a range of taxa, however we do not currently understand whether climatic niche shifts can consistently be predicted across multiple introduced ranges. Using three congeneric weed species, we investigate whether climatic niche shifts in one introduced range are consistent in other ranges where the species has been introduced. We compared the climatic conditions occupied by Rumex conglomeratus, R. crispus, and R. obtusifolius between their native range (Eurasia) and three different introduced ranges (North America, Australia, New Zealand). We considered metrics of niche overlap, expansion, unfilling, pioneering, and similarity to determine whether climatic niche shifts were consistent across ranges and congeners. We found that the presence and direction of climatic niche shifts was inconsistent between introduced ranges for each species. Within an introduced range, however, niche shifts were qualitatively similar among species. North America and New Zealand experienced diverging niche expansion into drier and wetter climates respectively, whilst the niche was conserved in Australia. This work highlights how unique characteristics of an introduced range and local introduction history can drive different niche shifts, and that comparisons between only the native and one introduced range may misrepresent a species’ capacity for niche shifts. However, predictions of climatic niche shifts could be improved by comparing related species in the introduced range rather than relying on the occupied environments of the native range.

The need for multidisciplinary conservation: a case study of Ceratozamia (Zamiaceae, Cycadales) in eastern Mexico

As an evolutionary lineage cycads are rare, and the extinction risk is high for many species. The genus Ceratozamia, one of the most diverse in Mexico, is experiencing drastic reductions of its habitat. Ceratozamia is widely distributed along the Sierra Madre Oriental, a complex mountain range, in a region characterized by high ecological and cultural diversity. Since 1990, various conservation and management strategies have been applied to this taxon in Mexico but evidence for the effectiveness of these measures is lacking. Ceratozamia in the Mexican Sierra Madre Oriental is highly diverse and endemic, offering a model for analysing geographical distribution patterns with ecological niche modelling. It also presents an opportunity for assessing the success of conservation and management strategies that have been implemented in this area. Here, we examined three aspects that are considered fundamental for the development and evaluation of conservation strategies: (1) taxonomy, (2) ecology and (3) sociocultural anthropology. Our findings suggest a pessimistic outlook for the long-term survival of Ceratozamia species in their natural environment, indicating the need to review the current IUCN Cycad Action Plan for the genus. To improve the protection of Ceratozamia and other taxonomic and/or ecological assemblages, we encourage a multidisciplinary approach, with increased collaboration between natural and social scientists.

Integrating intraspecific variation in species distribution models by quantifying niche differentiation

Intraspecific variation provides insight into heterogeneous demography and adaptive history across distribution ranges of organisms. Most species distribution models assume that species respond to the environment as a single undifferentiated entity across their entire distribution. However, populations occupying different niches might differ in their ability to cope with climate change. Here, we assessed potential climatic niche differentiation at the species and subspecies levels and identified the palaeoclimatic range of three cold-adapted, low-dispersal beetle species: Carabus irregularis, Platycerus albisomni and Platycerus takakuwai. Our results showed that: (1) MaxEnt models incorporating information derived from intraspecific variation outperformed the species-level models; (2) tests of niche similarity revealed niche conservatism in most subspecies, except for two subspecies of C. irregularis, C. i. irregularis and C. i. bucephalus; and (3) historical predictions suggested substantial shifts within species ranges, with multiple glacial refugia during the Last Glacial Maximum. In conclusion, we recommend closer examination of intraspecific variation when predicting species distributions, in order to obtain more accurate generalizations regarding range shifts under climate change.

Community science validates climate suitability projections from ecological niche modeling

Climate change poses an intensifying threat to many bird species and projections of future climate suitability provide insight into how species may shift their distributions in response. Climate suitability is characterized using ecological niche models (ENMs), which correlate species occurrence data with current environmental covariates and project future distributions using the modeled relationships together with climate predictions. Despite their widespread adoption, ENMs rely on several assumptions that are rarely validated in situ and can be highly sensitive to modeling decisions, precluding their reliability in conservation decision-making. Using data from a novel, large-scale community science program, we developed dynamic occupancy models to validate near-term climate suitability projections for bluebirds and nuthatches in summer and winter. We estimated occupancy, colonization, and extinction dynamics across species' ranges in the United States in relation to projected climate suitability in the 2020s, and used a Gibbs variable selection approach to quantify evidence of species-climate relationships. We also included a Bird Conservation Region strata-level random effect to examine among-strata variation in occupancy that may be attributable to land-use and ecoregional differences. Across species and seasons, we found strong evidence that initial occupancy and colonization were positively related to 2020 climate suitability, illustrating an independent validation of projections from ENMs across a large geographic area. Random strata effects revealed that occupancy probabilities were generally higher than average in core areas and lower than average in peripheral areas of species' ranges, and served as a first step in identifying spatial patterns of occupancy from these community science data. Our findings lend much-needed support to the use of ENM projections for addressing questions about potential climate-induced changes in species' occupancy dynamics. More broadly, our work highlights the value of community scientist observations for ground-truthing projections from statistical models and for refining our understanding of the processes shaping species' distributions under a changing climate.

Influence of climate change on the predicted distributions of the genus Tympanoctomys (Rodentia, Hystricomorpha, Octodontidae), and their conservation implications

Viscacha rats (genus Tympanoctomys Yepes, 1942) are ecologically, physiologically, and behaviorally unusual octodontid rodents endemic to the Monte and Patagonian desert biomes of Argentina. The geographic ranges of the different species of Tympanoctomys have been described in general terms but have not been associated with spatial and climate data. Within species, populations are patchily distributed and genetically distinct. We investigated the predicted distribution of Tympanoctomys and the influence of climate fluctuations on their geographic range in historical, current, and future, scenarios. Our objectives were to characterize the environmental niche of the genus, propose a paleoclimatic context for the oldest fossils, characterize the environmental niches for T. barrerae and T. kirchnerorum, and forecast potential future distributions for these taxa. Ecological niche models were constructed using occurrence records from 1941 to the present wherein we identified several precipitation and temperature variables as important predictors of the geographic distributions of the genus, and the species T. barrerae and T. kirchnerorum. Based on our models’ results, we hypothesize that the distribution of Tympanoctomys has contracted from historical to modern times. At the species level, T. kirchnerorum likely experienced the most dramatic change, suffering a large contraction of its historical distribution resulting in its limited present distribution. Given these findings, projected future climate fluctuations and global warming are expected to affect the distributions and persistence of these species.

Radical pluralism, classificatory norms and the legitimacy of species classifications

Moderate pluralism is a popular position in contemporary philosophy of biology. Despite its popularity, various authors have argued that it tends to slide off into a radical form of pluralism that is both normatively and descriptively unacceptable. This paper looks at the case of biological species classification, and evaluates a popular way of avoiding radical pluralism by relying on the shared aims and norms of a discipline. The main contention is that while these aims and norms may play an important role in the legitimacy of species classifications, they fail to fend off radical pluralism. It follows from this that the legitimacy of species classifications is also determined by local decisions about the aims of research and how to operationalize and balance these. This is important, I argue, because it means that any acceptable view on the legitimacy of classification should be able to account for these local decisions.

Crumble analysis of the historic sympatric distribution between Dendrortyx macroura and D. barbatus (Aves: Galliformes)

In Mexico, the Long-tailed Wood-Partridge (Dendrortyx macroura) is distributed in the mountains of the Trans-Mexican Volcanic Belt, Sierra Madre del Sur and Sierra Norte de Oaxaca; while the Bearded Wood-Partridge (D. barbatus) is distributed in the Sierra Madre Oriental (SMO). There is a controversial overlap in distribution (sympatry) between these two species (on the Cofre de Perote and Pico de Orizaba volcanoes, SMO and Sierra Norte de Oaxaca), based on the ambiguity and current lack of information regarding the distribution of these two species. In order to disentangle the possible presence of both species in the area of sympatry, we conducted a crumble analysis of the historic knowledge regarding the geographic distribution of both species, based on a review of scientific literature, database records, the specimen examination (in ornithological collections), field work and a reconstruction of the distribution range based on Ecological Niche Modeling. Our results support the presence of only one of these two species in the overlapping area, rejecting the existence of such an area of sympatry between the two species. We discuss alternative hypotheses that could explain the historically reported distribution pattern: 1) an error in the single existing historical record; 2) a possible local extinction of the species and 3) the past existence of interspecific competition that has since been resolved under the principle of competitive exclusion. We propose that the Santo Domingo River in northern Oaxaca and western slope of the Sierra Madre Oriental, mark the distribution limits between these species.

Potential distribution of mosquito vector species in a primary malaria endemic region of Colombia

Rapid transformation of natural ecosystems changes ecological conditions for important human disease vector species; therefore, an essential task is to identify and understand the variables that shape distributions of these species to optimize efforts toward control and mitigation. Ecological niche modeling was used to estimate the potential distribution and to assess hypotheses of niche similarity among the three main malaria vector species in northern Colombia: Anopheles nuneztovari, An. albimanus, and An. darlingi. Georeferenced point collection data and remotely sensed, fine-resolution satellite imagery were integrated across the Urabá -Bajo Cauca-Alto Sinú malaria endemic area using a maximum entropy algorithm. Results showed that An. nuneztovari has the widest geographic distribution, occupying almost the entire study region; this niche breadth is probably related to the ability of this species to colonize both, natural and disturbed environments. The model for An. darlingi showed that most suitable localities for this species in Bajo Cauca were along the Cauca and Nechí river. The riparian ecosystems in this region and the potential for rapid adaptation by this species to novel environments, may favor the establishment of populations of this species. Apparently, the three main Colombian Anopheles vector species in this endemic area do not occupy environments either with high seasonality, or with low seasonality and high NDVI values. Estimated overlap in geographic space between An. nuneztovari and An. albimanus indicated broad spatial and environmental similarity between these species. An. nuneztovari has a broader niche and potential distribution. Dispersal ability of these species and their ability to occupy diverse environmental situations may facilitate sympatry across many environmental and geographic contexts. These model results may be useful for the design and implementation of malaria species-specific vector control interventions optimized for this important malaria region.