Integrating datasets from herbarium specimens and images to treat a Neotropical myrtle species complex.

BACKGROUND AND AIMS: Herbaria are the most important source of information for plant taxonomic work. Resources and technologies available today, such as digitised collections and herbarium DNA sequencing, can help accelerate taxonomic decisions in challenging plant groups. Here we employ an integrative methodology relying exclusively on herbarium specimens to investigate species boundaries in the Neotropical Myrcia neoobscura complex (Myrtaceae). METHODS: We collected morphometric data from high-resolution images of herbarium sheets and analysed it using hierarchical clustering. We posteriorly tested the obtained morpho-groups with phylogenomics using the Angiosperms353 probe kit. We also gathered phenological and geographic information from specimen labels and built phenological histograms and ecological niche models to investigate ecological differences amongst taxa. KEY RESULTS: Current circumscriptions of Myrcia arenaria, Myrcia neoglabra and Myrcia neoregeliana are confirmed in this study. Conversely, the four pieces of evidence together support Calyptranthes langsdorffii var. grandiflora, Marlierea regeliana var. parviflora and Marlierea warmingiana as separate from Myrcia marliereana, Myrcia neoriedeliana and Myrcia neoobscura, respectively, contrary to arrangements proposed by previous authors. Integrated analyses also support separation between Myrcia excoriata and two similar, undescribed taxa. CONCLUSIONS: Our data reveal the need for major changes in the systematics of the group, with recognition of 12 species. The successful delivery of our study aims was possible due to obtaining robust, high-quality data from museum specimens. We emphasise the importance of maintaining botanical collections physically and digitally available for taxonomic work and advocate their use to accelerate holistic taxonomic solutions of tropical species complexes. This is urgent, given the paucity of funds for fieldwork and unprecedented rates of habitat loss in the tropics.

Evidence of introgression, ecological divergence and adaptation in Asterias sea stars.

Hybrid zones are important windows into the evolutionary dynamics of populations, revealing how processes like introgression and adaptation structure population genomic variation. Importantly, they are useful for understanding speciation and how species respond to their environments. Here, we investigate two closely related sea star species, Asterias rubens and A. forbesi, distributed along rocky European and North American coastlines of the North Atlantic, and use genome-wide molecular markers to infer the distribution of genomic variation within and between species in this group. Using genomic data and environmental niche modelling, we document hybridization occurring between northern New England and the southern Canadian Maritimes. We investigate the factors that maintain this hybrid zone, as well as the environmental variables that putatively drive selection within and between species. We find that the two species differ in their environmental niche breadth; Asterias forbesi displays a relatively narrow environmental niche while conversely, A. rubens has a wider niche breadth. Species distribution models accurately predict hybrids to occur within environmental niche overlap, thereby suggesting environmental selection plays an important role in the maintenance of the hybrid zone. Our results imply that the distribution of genomic variation in North Atlantic sea stars is influenced by the environment, which will be crucial to consider as the climate changes.

The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia.

Wide-ranging species are seldom considered conservation priorities, yet they have the potential to harbour genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decline, as they may comprise a set of even more endangered lineages or species with small distributions. However, studies of wide-ranging species, particularly when they cross political borders, are extremely challenging. One approach to overcoming these challenges is to conduct detailed local analyses in combination with less detailed, range-wide studies. We used this approach with the red-footed tortoise (Chelonoidis carbonarius), a threatened species likely to contain cryptic diversity given its vast range and the distinctive ecoregions that it inhabits. Previous single-gene molecular studies indicated the presence of at least five lineages, two of which occur in different ecoregions separated by the Andes within Colombia. We used a comprehensive genomic analysis to test the hypothesis of cryptic diversity within the single jurisdiction of Colombia. We used a combination of restriction-site-associated DNA sequencing and environmental niche modelling to provide three independent lines of evidence that support the presence of important cryptic diversity that may deserve taxonomic recognition: allopatric reproductive isolation, local adaptation and ecological divergence. We also provide a fine-scale genetic map with the distribution of conservation units in Colombia. As we complete ongoing range-wide analyses and make taxonomic adjustments, we recommend that the two lineages in Colombia be treated as separate units for conservation purposes.

Las especies con distribuciones amplias rara vez son consideradas prioridades de conservación, sin embargo, tienen el potencial de albergar unidades genéticamente diferenciadas que en algunos casos justifican reconocimiento taxonómico. Documentar dicha diversidad genética críptica es especialmente importante para las especies de rangos amplios que ya están en peligro de extinción, pues pueden comprender un conjunto de linajes o especies aún más amenazadas y con distribuciones más pequeñas. Sin embargo, los estudios de especies de rangos amplios, particularmente cuando cruzan fronteras políticas, son extremadamente desafiantes. Un enfoque para superar estos desafíos es realizar análisis locales detallados en combinación con estudios en todo el rango de distribución menos detallados. Nosotros usamos este enfoque con la tortuga de patas rojas (Chelonoidis carbonarius), una especie amenazada que probablemente contiene diversidad genética críptica dada su amplia distribución y las distintas ecorregiones en las que habita. Estudios moleculares previos de un solo gen indicaron la presencia de al menos cinco linajes, dos de los cuales ocurren en diferentes ecorregiones separadas por los Andes en Colombia. En este estudio utilizamos una combinación de secuenciación de ADN asociada a sitios de restricción (RADseq) y modelamiento de nicho ecológico para proporcionar tres líneas independientes de evidencia que respaldan la presencia de diversidad críptica importante que puede merecer reconocimiento taxonómico: aislamiento reproductivo alopátrico, adaptación local y divergencia ecológica. También proporcionamos un mapa genético a escala fina con la distribución de unidades de conservación en Colombia. Mientras completamos análisis genómicos en todo el rango de distribución y hacemos ajustes taxonómicos, recomendamos que los dos linajes en Colombia se traten como unidades independientes para fines de conservación.

Historical biogeography and local adaptation explain population genetic structure in a widespread terrestrial orchid.

BACKGROUND AND AIMS: Historical changes in environmental conditions and colonization-extinction dynamics have a direct impact on the genetic structure of plant populations. However, understanding how past environmental conditions influenced the evolution of species with high gene flow is challenging when signals for genetic isolation and adaptation are swamped by gene flow. We investigated the spatial distribution and genetic structure of the widespread terrestrial orchid Epipactis helleborine to identify glacial refugia, characterize postglacial population dynamics and assess its adaptive potential. METHODS: Ecological niche modelling was used to locate possible glacial refugia and postglacial recolonization opportunities of E. helleborine. A large single-nucleotide polymorphism (SNP) dataset obtained through genotyping by sequencing was used to define population genetic diversity and structure and to identify sources of postglacial gene flow. Outlier analyses were used to elucidate how adaptation to the local environment contributed to population divergence. KEY RESULTS: The distribution of climatically suitable areas was restricted during the Last Glacial Maximum to the Mediterranean, south-western Europe and small areas in the Alps and Carpathians. Within-population genetic diversity was high in E. helleborine (mean expected heterozygosity, 0.373 ± 0.006; observed heterozygosity, 0.571 ± 0.012; allelic richness, 1.387 ± 0.007). Italy and central Europe are likely to have acted as important genetic sources during postglacial recolonization. Adaptive SNPs were associated with temperature, elevation and precipitation. CONCLUSIONS: Forests in the Mediterranean and Carpathians are likely to have acted as glacial refugia for Epipactis helleborine. Postglacial migration northwards and to higher elevations resulted in the dispersal and diversification of E. helleborine in central Europe and Italy, and to geographical isolation and divergent adaptation in Greek and Italian populations. Distinguishing adaptive from neutral genetic diversity allowed us to conclude that E. helleborine has a high adaptive potential to climate change and demonstrates that signals of adaptation and historical isolation can be identified even in species with high gene flow.

Forest degradation limits the complementarity and quality of animal seed dispersal.

Forest degradation changes the structural heterogeneity of forests and species communities, with potential consequences for ecosystem functions including seed dispersal by frugivorous animals. While the quantity of seed dispersal may be robust towards forest degradation, changes in the effectiveness of seed dispersal through qualitative changes are poorly understood. Here, we carried out extensive field sampling on the structure of forest microhabitats, seed deposition sites and plant recruitment along three characteristics of forest microhabitats (canopy cover, ground vegetation and deadwood) in Europe's last lowland primeval forest (Bialowieza, Poland). We then applied niche modelling to study forest degradation effects on multi-dimensional seed deposition by frugivores and recruitment of fleshy-fruited plants. Forest degradation was shown to (i) reduce the niche volume of forest microhabitat characteristics by half, (ii) homogenize the spatial seed deposition within and among frugivore species, and (iii) limit the regeneration of plants via changes in seed deposition and recruitment. Our study shows that the loss of frugivores in degraded forests is accompanied by a reduction in the complementarity and quality of seed dispersal by remaining frugivores. By contrast, structure-rich habitats, such as old-growth forests, safeguard the diversity of species interactions, forming the basis for high-quality ecosystem functions.

Ancient volcanos as species pumps: A case study of freshwater amphipods in Northeast Asia.

Volcano-tectonic processes have been viewed as primary drivers in the formation of present-day diversity. Volcanos associated with mountain uplifts drive allopatric speciation through vicariance and may impact the surrounding areas like species pump or species attractor. However, the application of these hypotheses to aquatic fauna has rarely been tested explicitly. We tested these hypotheses in the Changbai Mountains (Mts), which are one of the most typical, active volcanic ranges in Northeast (NE) Asia with a long and turbulent geological history. The Gammarus nekkensis species complex of amphipod crustaceans, widely distributed throughout NE Asia with poor dispersal abilities and a long evolutionary history, is a suitable model for testing hypotheses of species pump or species attractor. Phylogenetic and ancestral range reconstructions demonstrated that the studied amphipod originated from the Changbai Mts ~27 Ma and diverged into eastern (Clade I) and western (Clade II) clades, which corresponds well with the initial volcanic eruption of the Changbai Mts in the Late Oligocene. The subsequent diversifications of subclades CI-3, CII-1a and CII-2a were probably driven by second and third eruptions of the Changbai Mts during the Miocene. In particular, the Changbai lineages had spread to the Russian Far East multiple times since the Early Miocene, and widely colonized the region during the Pleistocene. Our discoveries suggest that the ancient volcanos of the Changbai Mts act as species pumps in NE Asia, resulted in burst of diversification around the Changbai Mts and subsequent dispersals into adjacent regions.

Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation.

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes (Ne) and current genomic variability (H), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that Ne and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

Volcanism and palaeoclimate change drive diversification of the world's largest whip spider (Amblypygi).

The tropics contain many of the most biodiverse regions on Earth but the processes responsible for generating this diversity remain poorly understood. This study investigated the drivers of diversification in arthropods with stenotopic ecological requirements and limited dispersal capability using as a model the monotypic whip spider (Amblypygi) genus Acanthophrynus, widespread in the tropical deciduous forests of Mexico. We hypothesized that for these organisms, the tropical deciduous forests serve as a conduit for dispersal, with their disappearance imposing barriers. Given that these forests are located in a region of complex geological history and that they fluctuated in extent during the Pliocene-Pleistocene glacial/interglacial cycles we combine molecular divergence dating, palaeoclimatic niche modelling and ancestral area reconstruction to test if and when habitat fragmentation promoted diversification in Acanthophrynus. Concomitant with the expected role of landscape change, we demonstrate that orogeny of the Trans-Mexican Volcanic Belt, in the Late Miocene or Early Pliocene (6.95-5.21 million years ago), drove the earliest divergence of Acanthophrynus by vicariance. Similarly, as expected, the later onset of glaciations strongly impacted diversification. Whereas a more stable climate in the southern part of the distribution enabled further diversification, a marked loss of suitable habitat during the glaciations only allowed dispersal and diversification in the north to occur later, resulting in a lower overall diversity in this region. Barriers and diversification patterns identified in Acanthophrynus are reflected in the phylogeography of codistributed vertebrates and arthropods, emphasizing the profound impact of Trans-Mexican Volcanic Belt orogeny and glacial/interglacial cycles as drivers of diversification in the Mexican Neotropics.

Spatiotemporally explicit demographic modelling supports a joint effect of historical barriers to dispersal and contemporary landscape composition on structuring genomic variation in a red-listed grasshopper.

Inferring the processes underlying spatial patterns of genomic variation is fundamental to understand how organisms interact with landscape heterogeneity and to identify the factors determining species distributional shifts. Here, we use genomic data (restriction site-associated DNA sequencing) to test biologically informed models representing historical and contemporary demographic scenarios of population connectivity for the Iberian cross-backed grasshopper Dociostaurus hispanicus, a species with a narrow distribution that currently forms highly fragmented populations. All models incorporated biological aspects of the focal taxon that could hypothetically impact its geographical patterns of genomic variation, including (a) spatial configuration of impassable barriers to dispersal defined by topographic landscapes not occupied by the species; (b) distributional shifts resulting from the interaction between the species bioclimatic envelope and Pleistocene glacial cycles; and (c) contemporary distribution of suitable habitats after extensive land clearing for agriculture. Spatiotemporally explicit simulations under different scenarios considering these aspects and statistical evaluation of competing models within an Approximate Bayesian Computation framework supported spatial configuration of topographic barriers to dispersal and human-driven habitat fragmentation as the main factors explaining the geographical distribution of genomic variation in the species, with no apparent impact of hypothetical distributional shifts linked to Pleistocene climatic oscillations. Collectively, this study supports that both historical (i.e., topographic barriers) and contemporary (i.e., anthropogenic habitat fragmentation) aspects of landscape composition have shaped major axes of genomic variation in the studied species and emphasizes the potential of model-based approaches to gain insights into the temporal scale at which different processes impact the demography of natural populations.

Distribution of euptyctimous mite Phthiracarus longulus (Acari: Oribatida) under future climate change in the Palearctic.

The aim of this paper is to prepare, describe and discuss the models of the current and future distribution of Phthiracarus longulus (Koch, 1841) (Acari: Oribatida: Euptyctima), the oribatid mite species widely distributed within the Palearctic. We used the maximum entropy (MAXENT) method to predict its current and future (until the year 2100) distribution based on macroclimatic bio-variables. To our best knowledge, this is the first-ever prediction of distribution in mite species using environmental niche modelling. The main thermal variables that shape the current distribution of P. longulus are the temperature annual range, mean temperature of the coldest quarter and the annual mean temperature, while for precipitation variables the most important is precipitation of the driest quarter. Regardless of the climatic change scenario (SSP1-2.6, SSP2-4.5, SSP5-8.5) our models show generally the northward shift of species range, and in Southern Europe the loss of most habitats with parallel upslope shift. According to our current model, the most of suitable habitats for P. longulus are located in the European part of Palearctic. In general, the species range is mostly affected in Europe. The most stable areas of P. longulus distribution were the Jutland with surrounding southern coasts of Scandinavia, islands of the Danish Straits and the region of Trondheim Fjord.

Locustamigratoria (L.) (Orthoptera) in a warming world: unravelling the ecological consequences of climate change using GIS.

The migratory locust, Locustamigratoria (L.), a significant grasshopper species known for its ability to form large swarms and cause extensive damage to crops and vegetation, is subject to the influence of climate change. This research paper employs geographic information system (GIS) and MaxEnt ecological modelling techniques to assess the impact of climate change on the distribution patterns of L.migratoria. Occurrence data and environmental variables are collected and analysed to create predictive models for the current and future distribution of the species. The study highlights the crucial role of climate factors, particularly temperature and precipitation, in determining the locust's distribution. The MaxEnt models exhibit high-performance indicators, accurately predicting the potential habitat suitability of L.migratoria. Additionally, specific bioclimatic variables, such as mean temperature and annual precipitation, are identified as significant factors influencing the species' presence. The generated future maps indicate how this species will invade new regions especially in Europe. Such results predict the risk of this destructive species for many agriculture communities as a direct result of a warming world. The research provides valuable insights into the complex relationship between locust distribution and environmental factors, enabling the development of effective strategies for locust management and early warning systems to mitigate the impact on agriculture and ecosystems.

Spatial prioritization of dugong habitats in India can contribute towards achieving the 30 × 30 global biodiversity target.

Indian coastal waters are critical for dugong populations in the western Indian Ocean. Systematic spatial planning of dugong habitats can help to achieve biodiversity conservation and area-based protection targets in the region. In this study, we employed environmental niche modelling to predict suitable dugong habitats and identify influencing factors along its entire distribution range in Indian waters. We examined data on fishing pressures collected through systematic interview surveys, citizen-science data, and field surveys to demarcate dugong habitats with varying risks. Seagrass presence was the primary factor in determining dugong habitat suitability across the study sites. Other variables such as depth, bathymetric slope, and Euclidean distance from the shore were significant factors, particularly in predicting seasonal suitability. Predicted suitable habitats showed a remarkable shift from pre-monsoon in Palk Bay to post-monsoon in the Gulf of Mannar, indicating the potential of seasonal dugong movement. The entire coastline along the Palk Bay-Gulf of Mannar region was observed to be at high to moderate risk, including the Gulf of Mannar Marine National Park, a high-risk area. The Andaman Islands exhibited high suitability during pre- and post-monsoon season, whereas the Nicobar Islands were highly suitable for monsoon season. Risk assessment of modelled suitable areas revealed that < 15% of high-risk areas across Andaman and Nicobar Islands and Palk Bay and Gulf of Mannar, Tamil Nadu, fall within the existing protected areas. A few offshore reef islands are identified under high-risk zones in the Gulf of Kutch, Gujarat. We highlight the utility of citizen science and secondary data in performing large-scale spatial ecological analysis. Overall, identifying synoptic scale 'Critical Dugong Habitats' has positive implications for the country's progress towards achieving the global 30 × 30 target through systematic conservation planning.

The role of reservoir species in mediating plague's dynamic response to climate.

The distribution and transmission of Yersinia pestis, the bacterial agent of plague, responds dynamically to climate, both within wildlife reservoirs and human populations. The exact mechanisms mediating plague's response to climate are still poorly understood, particularly across large environmentally heterogeneous regions encompassing several reservoir species. A heterogeneous response to precipitation was observed in plague intensity across northern and southern China during the Third Pandemic. This has been attributed to the response of reservoir species in each region. We use environmental niche modelling and hindcasting methods to test the response of a broad range of reservoir species to precipitation. We find little support for the hypothesis that the response of reservoir species to precipitation mediated the impact of precipitation on plague intensity. We instead observed that precipitation variables were of limited importance in defining species niches and rarely showed the expected response to precipitation across northern and southern China. These findings do not suggest that precipitation-reservoir species dynamics never influence plague intensity but that instead, the response of reservoir species to precipitation across a single biome cannot be assumed and that limited numbers of reservoir species may have a disproportional impact upon plague intensity.

Fragility of nocturnal interactions: Pollination intensity increases with distance to light pollution sources but decreases with increasing environmental suitability.

Light pollution represents a widespread long-established human-made disturbance and an important threat to nocturnal pollination. Distance from the niche centroid where optimal environmental conditions join may be related to species sensitivity to habitat change. We estimated the environmental suitability of the plant species Erythrostemon gilliesii and of its guild of hawkmoth pollinators. We considered the overlap of suitability maps of both partners as the environmental suitability of the interaction. We used a three-year record of ten E. gilliesii populations to calculate pollination intensity as the number of individuals that received pollen per population. In addition, for each population, we measured the distance to the high light pollution source around a buffer of 15 km radius. Finally, we predicted pollination intensity values for environmental suitability ranging from 0 to 1, and distance to high light pollution sources ranging from 0 to 56 Km. Pollination intensity decreased along an axis of increasing environmental suitability and increased with distance to sources of light pollution. The highest values of pollination intensity were observed at greatest distances to sources of light pollution and where environmental suitability of the interaction was lowest. The prediction model evidenced that, when environmental suitability was lowest, pollination intensity increased with distance to sources of high light pollution. However, when environmental suitability was intermediate or high, pollination intensity decreased away and until 28 km from the sources of high light pollution. Beyond 28 km from the sources of high light pollution, pollination intensity remained low and constant. Populations under conditions of low environmental suitability might be more likely to respond to disturbances that affect pollinators than populations under conditions of high environmental suitability.

Spatiotemporal monitoring of the rare northern dragonhead (Dracocephalum ruyschiana, Lamiaceae) - SNP genotyping and environmental niche modeling herbarium specimens.

The species we have studied the spatiotemporal genetic change in the northern dragonhead, a plant species that has experienced a drastic population decline and habitat loss in Europe. We have added a temporal perspective to the monitoring of northern dragonhead in Norway by genotyping herbarium specimens up to 200 years old. We have also assessed whether northern dragonhead has achieved its potential distribution in Norway. To obtain the genotype data from 130 herbarium specimens collected from 1820 to 2008, mainly from Norway (83) but also beyond (47), we applied a microfluidic array consisting of 96 SNP markers. To assess temporal genetic change, we compared our new genotype data with existing data from modern samples. We used sample metadata and observational records to model the species' environmental niche and potential distribution in Norway. Our results show that the SNP array successfully genotyped all included herbarium specimens. Hence, with the appropriate design procedures, the SNP array technology appears highly promising for genotyping old herbarium specimens. The captured genetic diversity correlates negatively with distance from Norway. The historical-modern comparisons reveal similar genetic structure and diversity across space and limited genetic change through time in Norway, providing no signs of any regional bottleneck (i.e., spatiotemporal stasis). The regional areas in Norway have remained genetically divergent, however, both from each other and more so from populations outside of Norway, rendering continued protection of the species in Norway relevant. The ENM results suggest that northern dragonhead has not fully achieved its potential distribution in Norway and corroborate that the species is anchored in warmer and drier habitats.

Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic.

Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man's fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951-2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081-2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.

Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifolius.

The Balkan Peninsula represents one of the three southern European glacial refugia where biodiversity persisted throughout the climatically unstable Quaternary. This study considered the 'refugia within refugia' model, which assumes the environmental heterogeneity over time and space in larger refugia. To better understand patterns shaped during the Quaternary climatic oscillations, the present and last glacial maximum (LGM) environmental conditions and current morphological variability of Edraianthus tenuifolius, an endemic plant of the western Balkans with a well-known therphical structure, were considered. Potential present and LGM distributions were studied through environmental niche modelling using 161 data of occurrences and six bioclimatic variables, hindcasting the model to LGM conditions using three different global circulation models. To test the geographical variability of the reproductive region, 41 characters of 667 inflorescences from 35 populations within the distribution range were measured. Geographical patterns, using geostatistics together with univariate and multivariate statistical approaches, were analysed. The environmental niche model suggested the current potential distribution in correspondence to its known occurrences. The hindcast to LGM conditions suggested two separate areas of environmental suitability, one in the present-day northern Adriatic coast of Croatia (Istrian Peninsula, Kvarner) and another on the present-day south-eastern Adriatic coast (southern Dalmatia, Montenegro and northern Albania). Morphological variability showed a similar pattern, where southern populations separated from northern populations according to a major split in the central part of its distribution range (central Dalmatia). On other levels, stronger barriers were predicted to separate northern populations from the eastern Istrian Peninsula and the Kvarner area. The results suggested congruent biogeographical patterns to the already known phylogeographical structure. Both environmental niche modelling and the geographical variability of morphological characters suggested spatial partitioning, indicating the potential presence of two separate refugia during the LGM.

MaxEnt's parameter configuration and small samples: are we paying attention to recommendations? A systematic review.

Environmental niche modeling (ENM) is commonly used to develop probabilistic maps of species distribution. Among available ENM techniques, MaxEnt has become one of the most popular tools for modeling species distribution, with hundreds of peer-reviewed articles published each year. MaxEnt's popularity is mainly due to the use of a graphical interface and automatic parameter configuration capabilities. However, recent studies have shown that using the default automatic configuration may not be always appropriate because it can produce non-optimal models; particularly when dealing with a small number of species presence points. Thus, the recommendation is to evaluate the best potential combination of parameters (feature classes and regularization multiplier) to select the most appropriate model. In this work we reviewed 244 articles published between 2013 and 2015 to assess whether researchers are following recommendations to avoid using the default parameter configuration when dealing with small sample sizes, or if they are using MaxEnt as a "black box tool." Our results show that in only 16% of analyzed articles authors evaluated best feature classes, in 6.9% evaluated best regularization multipliers, and in a meager 3.7% evaluated simultaneously both parameters before producing the definitive distribution model. We analyzed 20 articles to quantify the potential differences in resulting outputs when using software default parameters instead of the alternative best model. Results from our analysis reveal important differences between the use of default parameters and the best model approach, especially in the total area identified as suitable for the assessed species and the specific areas that are identified as suitable by both modelling approaches. These results are worrying, because publications are potentially reporting over-complex or over-simplistic models that can undermine the applicability of their results. Of particular importance are studies used to inform policy making. Therefore, researchers, practitioners, reviewers and editors need to be very judicious when dealing with MaxEnt, particularly when the modelling process is based on small sample sizes.

Anthropogenic impacts drive niche and conservation metrics of a cryptic rattlesnake on the Colorado Plateau of western North America.

Ecosystems transition quickly in the Anthropocene, whereas biodiversity adapts more slowly. Here we simulated a shifting woodland ecosystem on the Colorado Plateau of western North America by using as its proxy over space and time the fundamental niche of the Arizona black rattlesnake (Crotalus cerberus). We found an expansive (= end-of-Pleistocene) range that contracted sharply (= present), but is blocked topographically by Grand Canyon/Colorado River as it shifts predictably northwestward under moderate climate change (= 2080). Vulnerability to contemporary wildfire was quantified from available records, with forested area reduced more than 27% over 13 years. Both 'ecosystem metrics' underscore how climate and wildfire are rapidly converting the Plateau ecosystem into novel habitat. To gauge potential effects on C. cerberus, we derived a series of relevant 'conservation metrics' (i.e. genetic variability, dispersal capacity, effective population size) by sequencing 118 individuals across 846 bp of mitochondrial (mt)DNA-ATPase8/6. We identified five significantly different clades (net sequence divergence = 2.2%) isolated by drainage/topography, with low dispersal (F ST = 0.82) and small sizes (2N ef = 5.2). Our compiled metrics (i.e. small-populations, topographic-isolation, low-dispersal versus conserved-niche, vulnerable-ecosystem, dispersal barriers) underscore the susceptibility of this woodland specialist to a climate and wildfire tandem. We offer adaptive management scenarios that may counterbalance these metrics and avoid the extirpation of this and other highly specialized, relictual woodland clades.

Predicting the potential environmental suitability for Theileria orientalis transmission in New Zealand cattle using maximum entropy niche modelling.

The tick-borne haemoparasite Theileria orientalis is the most important infectious cause of anaemia in New Zealand cattle. Since 2012 a previously unrecorded type, T. orientalis type 2 (Ikeda), has been associated with disease outbreaks of anaemia, lethargy, jaundice and deaths on over 1000 New Zealand cattle farms, with most of the affected farms found in the upper North Island. The aim of this study was to model the relative environmental suitability for T. orientalis transmission throughout New Zealand, to predict the proportion of cattle farms potentially suitable for active T. orientalis infection by region, island and the whole of New Zealand and to estimate the average relative environmental suitability per farm by region, island and the whole of New Zealand. The relative environmental suitability for T. orientalis transmission was estimated using the Maxent (maximum entropy) modelling program. The Maxent model predicted that 99% of North Island cattle farms (n=36,257), 64% South Island cattle farms (n=15,542) and 89% of New Zealand cattle farms overall (n=51,799) could potentially be suitable for T. orientalis transmission. The average relative environmental suitability of T. orientalis transmission at the farm level was 0.34 in the North Island, 0.02 in the South Island and 0.24 overall. The study showed that the potential spatial distribution of T. orientalis environmental suitability was much greater than presumed in the early part of the Theileria associated bovine anaemia (TABA) epidemic. Maximum entropy offers a computer efficient method of modelling the probability of habitat suitability for an arthropod vectored disease. This model could help estimate the boundaries of the endemically stable and endemically unstable areas for T. orientalis transmission within New Zealand and be of considerable value in informing practitioner and farmer biosecurity decisions in these respective areas.