Species Distribution Modeling Analysis Research Articles

What explains the high island endemicity of Philippine Rafflesia? A species distribution modeling analysis of three threatened parasitic plant species and their hosts.

Rafflesia are rare holoparasitic plants. In the Philippines, all but one species are found only on single islands. This study aimed to better understand the factors contributing to this distributional pattern. Specifically, we sought to determine whether narrow environmental tolerances of host and/or parasite species might explain their island endemicity. We used Maxent species distribution modeling to identify areas with suitable habitat for R. lagascae, R. lobata, and R. speciosa and their Tetrastigma host species. These analyses were carried out for current climate conditions and two future climate change scenarios. Although species distribution models indicated suitable environmental conditions for the Tetrastigma host species in many parts of the Philippines, considerably fewer areas were inferred to have suitable conditions for the three Rafflesia species. Some of these areas are on islands from which they have not been reported. All three species will face significant threats as a result of climate change. Our results suggest that limited inter-island dispersibility and/or specific environmental requirements are likely responsible for the current pattern of island endemicity of the three Rafflesia species, rather than environmental requirements of their Tetrastigma host species.

An Endemic Vascular Plant Species for Türkiye, Ferulago Humilis Boiss., and Its Potential Distribution Areas

Turkey is expected to be affected considerably in future adverse climatic conditions. Plant species are one of the most vulnerable to these climatic changes. In this study, we aimed to investigate current and future potential distribution areas of Ferulago humilis Boiss., which is an endemic vascular plant species for Turkey, using CMIP5 projected to year 2070. For this purpose, we obtained occurence data (presence-only) from Global Biodiversity Information Facility (GBIF). Regarding bioclimatic data we used WorldClim dataset with 10 km2 resolution. Using both plant occurrence and bioclimatic data, we performed species distribution modelling analysis. We used two methods namely Boosted Regression Trees (BRT) and Random Forest (RF). Additionally, we used bootstrapping method as partitioning resampling for all analysis. Our analysis has showed that potential distribution areas of the species has slightly changed for the future projection. The species movement is towards slightly upwards as higher latitudes. We believe that our study shows the importance and relevance of the endemic species in the scope of species distribution models for plant conservation topics.

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species.

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927. Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the 'odd man out' pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER, here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.

Phylogeographical Analyses of a Relict Fern of Palaeotropical Flora (Vandenboschia speciosa): Distribution and Diversity Model in Relation to the Geological and Climate Events of the Late Miocene and Early Pliocene.

Fern phylogeographic studies have mostly focused on the influence of the Pleistocene climate on fern distributions and the prevalence of long-distance dispersal. The effect of pre-Pleistocene events on the distributions of fern species is largely unexplored. Here, we elucidate a hypothetical scenario for the evolutionary history of Vandenboschia speciosa, hypothesised to be of Tertiary palaeotropical flora with a peculiar perennial gametophyte. We sequenced 40 populations across the species range in one plastid region and two variants of the nuclear gapCp gene and conducted time-calibrated phylogenetic, phylogeographical, and species distribution modelling analyses. Vandenboschia speciosa is an allopolyploid and had a Tertiary origin. Late Miocene aridification possibly caused the long persistence in independent refugia on the Eurosiberian Atlantic and Mediterranean coasts, with the independent evolution of gene pools resulting in two evolutionary units. The Cantabrian Cornice, a major refugium, could also be a secondary contact zone during Quaternary glacial cycles. Central European populations resulted from multiple post-glacial, long-distance dispersals. Vandenboschia speciosa reached Macaronesia during the Pliocene–Pleistocene, with a phylogeographical link between the Canary Islands, Madeira, and southern Iberia, and between the Azores and northwestern Europe. Our results support the idea that the geological and climate events of the Late Miocene/Early Pliocene shifted Tertiary fern distribution patterns in Europe.

Molecular phylogeography and species distribution modelling evidence of \u2018oceanic\u2019 adaptation for Actinidia eriantha with a refugium along the oceanic\u2013continental gradient in a biodiversity hotspot

BackgroundRefugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic–continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic–continental gradient and ‘oceanic’ adaptation.ResultsThe phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic–continental gradient of the species and fit the ‘refugia in refugia’ pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to ‘oceanic’ adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods.ConclusionsOverall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic–continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to ‘oceanic’ adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.

Medicinal plants in peril due to climate change in the Himalaya

Climate change is causing many irreversible changes in the Himalayan ecosystems. In this study, an attempt was made to understand the ecological response of medicinal plant species to changing climate conditions in the Sikkim Himalaya, a part of the Eastern Himalayan biodiversity hotspot. Maximum Entropy Species Distribution Modelling (SDM) approach was used to analyze the potential habitat distribution of 163 medicinal plant species in current and future climates (2050, 2070). An attempt was also made to identify the most suitable areas for conservation and test the effectiveness of the existing Protected Area (PA) network in conserving medicinal plant species in current and future climate scenarios through the Habitat Suitability and Overlap Analyses. SDM analyses revealed that the majority of the medicinal plant species are found in the tropical and sub-tropical regions in the Sikkim Himalaya (300–2000 m) at present. In future climates, however, most of the species are likely to show an upward and northward shift in their distributions. Maximum species-rich regions are likely to shift by 200 m and 400 m in 2050 and 2070, respectively. A total of 13–16% of medicinal plant species currently found in the region are likely to lose their existing potential habitats by 2050 and 2070. The results highlight that species that are restricted to specific localities and have a narrow elevational distribution are the most vulnerable species and likely to go extinct due to climate change in the Himalaya. Habitat suitability analyses indicated that elevations ranging from 860 to 2937 m serve as highly suitable habitats for medicinal plant species in Sikkim Himalaya. Consequently, these areas can be focused for conservation actions in order to mitigate the effect of climate change. The results of Overlap Analysis indicated that out of 8 PAs in Sikkim Himalaya, only 5 PAs are effective in the conservation of medicinal plant species in current and future climates. The boundaries of existing PAs need to be expanded in order to accommodate the upward shifts in the spatial distribution of species, especially in the case of those PAs that are located in the lower elevations or tropical regions. This study provides a novel integrated framework for use of ecological informatics in assessing the species vulnerability to climate change and planning conservation priorities.

Lateral Transmission of Yeast Symbionts Among Lucanid Beetle Taxa.

To deepen understanding the evolutionary process of lucanid–yeast association, the lateral transmission process of yeast symbionts among stag beetle genera Platycerus and Prismognathus around the border between Japan and South Korea was estimated based on molecular analyses and species distribution modelings. Phylogenetic analyses were based on yeast ITS and IGS sequences and beetle COI sequences using Prismognathus dauricus from the Tsushima Islands and Pr. angularis from Kyushu, Japan, as well as other sequence data from our previous studies. The range overlap based on the species distribution model (SDM) and differentiation in ecological space were analyzed. Based on the IGS sequences, Clade II yeast symbionts were shared by Platycerus hongwonpyoi and Pr. dauricus in South Korea and the Tsushima Islands, and Platycerus viridicuprus in Japan. Clade III yeasts were shared by Pr. dauricus from the Tsushima Islands and Pr. angularis in Japan. During the Last Interglacial period when the land bridge between Japan and the Korean Peninsula existed, range overlap was predicted to occur between Pl. viridicuprus and Pr. dauricus in Kyushu and between Pr. dauricus and Pr. angularis in Kyushu and the Tsushima Islands. The ecological space of Pl. hongwonpyoi was differentiated from that of Pl. viridicuprus and Pr. angularis. We demonstrated the paleogeographical lateral transmission process of Scheffersomyces yeast symbionts among lucanid genera and species: putative transmission of yeasts from Pr. dauricus to Pl. viridicuprus in Kyushu and from Pr. angularis to Pr. dauricus in Kyushu or the Tsushima Islands. We also found that the yeast symbionts are likely being replaced in Pr. dauricus on the Tsushima Islands. We present novel estimates of the lateral transmission process of microbial symbionts based on phylogenetic, SDM and environmental analyses among lucanid beetles.

Historical Dynamics of Semi-Humid Evergreen Forests in the Southeast Himalaya Biodiversity Hotspot: A Case Study of the Quercus franchetii Complex (Fagaceae).

The Oligocene and Miocene are key periods in the formation of the modern topography and flora of East Asian and Indo-China. However, it is unclear how geological and climatic factors contributed to the high endemism and species richness of this region. The Quercus franchetii complex is widespread in the southeast Himalaya fringe and northern Indo-China with a long evolutionary history. It provides a unique proxy for studying the diversity pattern of evergreen woody lineages in this region since the Oligocene. In this study, we combined chloroplast (cpDNA) sequences, nuclear microsatellite loci (nSSRs), and species distribution modeling (SDM) to investigate the impacts of geological events on genetic diversity of the Q. franchetii complex. The results showed that the initial cpDNA haplotype divergence was estimated to occur during the middle Oligocene (30.7 Ma), which might have been raised by the tectonic activity at this episode to the Miocene. The nSSR results revealed two major groups of populations, the central Yunnan-Guizhou plateau (YGP) group and the peripheral distribution group when K = 2, in responding to the rapid YGP uplift during the late Miocene, which restricted gene flow between the populations in core and marginal areas. SDM analysis indicated that the distribution ranges of the Q. franchetii complex expanded northwards after the last glacial maximum, but the core distribution range in YGP was stable. Our results showed that the divergence of Q. franchetii complex is rooted in the mid-Oligocene. The early geological events during the Oligocene, and the late Miocene may play key roles to restrict seed-mediated gene flow among regions, but the pollen-mediated gene flow was less impacted. The uplifts of the YGP and the climate since LGM subsequently boosted the divergence of the populations in core and marginal areas.

Macaronesia Acts as a Museum of Genetic Diversity of Relict Ferns: The Case of Diplazium caudatum (Athyriaceae).

Macaronesia has been considered a refuge region of the formerly widespread subtropical lauroid flora that lived in Southern Europe during the Tertiary. The study of relict angiosperms has shown that Macaronesian relict taxa preserve genetic variation and revealed general patterns of colonization and dispersal. However, information on the conservation of genetic diversity and range dynamics rapidly diminishes when referring to pteridophytes, despite their dominance of the herbaceous stratum in the European tropical palaeoflora. Here we aim to elucidate the pattern of genetic diversity and phylogeography of Diplazium caudatum, a hypothesized species of the Tertiary Palaeotropical flora and currently with its populations restricted across Macaronesia and disjunctly in the Sierras de Algeciras (Andalusia, southern Iberian Peninsula). We analysed 12 populations across the species range using eight microsatellite loci, sequences of a region of plastid DNA, and carry out species-distribution modelling analyses. Our dating results confirm the Tertiary origin of this species. The Macaronesian archipelagos served as a refuge during at least the Quaternary glacial cycles, where populations of D. caudatum preserved higher levels of genetic variation than mainland populations. Our data suggest the disappearance of the species in the continent and the subsequent recolonization from Macaronesia. The results of the AMOVA analysis and the indices of clonal diversity and linkage disequilibrium suggest that D. caudatum is a species in which inter-gametophytic outcrossing predominates, and that in the Andalusian populations there was a shift in mating system toward increased inbreeding and/or clonality. The model that best explains the genetic diversity distribution pattern observed in Macaronesia is, the initial and recurrent colonization between islands and archipelagos and the relatively recent diversification of restricted area lineages, probably due to the decrease of favorable habitats and competition with lineages previously established. This study extends to ferns the concept of Macaronesia archipelagos as refugia for genetic variation.

Ethno-ornithological notes and neglected references on the Harpy Eagle Harpia harpyja in western Venezuela

Harpy Eagle Harpia harpyja has been documented only recently (2004) in the Lake Maracaibo basin of western Venezuela, specifically in the central Sierra de Perijá, at 1,100 m. Observations in the southern plains of the basin are reported from heretofore neglected sources published in 1599, 1889 and 1893. Two overlooked photographs of dead birds dating from 1947–51 (Perijá Mountains) and 1959 (Santa Bárbara del Zulia) are reproduced. Several other records are established (in 1974, the 1980s, 1994/95, 2002 and 2006), based on empirical observations and material evidence collected by anthropologists who have visited the still heavily forested area inhabited by the Barí people since the early 1960s. Circumstantial evidence of the use of Harpy Eagle bones and feathers by the indigenous Barí provides additional ethno-ornithological information. Although Harpy Eagle is currently categorised as Vulnerable in Venezuela, the cumulative historical evidence coupled with Species Distribution Modelling analysis predictions of suitable habitat locally available to the species suggests it might still be frequent in the western and southern Lake Maracaibo basin, where considerable expanses of tropical forest are conserved within four major protected areas and an indigenous reserve.

Phylogeography and systematics of Algyroides (Sauria: Lacertidae) of the Balkan Peninsula

AbstractThe area of the south‐western Balkans hosts a remarkably high species richness and has been considered a biodiversity hotspot. The significance of the Balkan Peninsula as a biodiversity refugium during the Quaternary climatic fluctuations has been repeatedly pointed out in literature, yet the area remains quite understudied in terms of phylogeography. Contributing to the biogeography and phylogeography of the Balkan area, we herein present the phylogeographic relationships within the lizards of the genus Algyroides, focusing on the two species that occur in the Balkans (namely, A. nigropunctatus and A. moreoticus), including representatives of Dinarolacerta and Lacerta lizards as outgroups. We combined phylogenetic, phylogeographic and species distribution modelling analyses, using both mitochondrial and nuclear DNA data, in order to uncover the phylogeographic history of the genus and evaluate the validity of the extant taxonomy. Our results reveal three major clades within Algyroides in southern Balkans; one corresponds to A. moreoticus, having sister group relationships with the genus Dinarolacerta, and the other two to A. nigropunctatus, each corresponding to one of the morphological subspecies, which seem to be monophyletic, allopatric and reproductively isolated. These results expose an unprecedented phylogeographic pattern in the area of western Greece where the two major clades of A. nigropunctatus meet, and can contribute to a taxonomic re‐evaluation of the species. Moreover, questions are raised on the validity of Dinarolacerta as a genus due to it clustering within the genus Algyroides.

Predicting disease occurrence of cabbage Verticillium wilt in monoculture using species distribution modeling.

BackgroundAlthough integrated pest management (IPM) is essential for conservation agriculture, this method can be inadequate for severely infected fields. The ability to predict the potential occurrence of severe infestation of soil-borne disease would enable farmers to adopt suitable methods for high-risk areas, such as soil disinfestation, and apply other options for lower risk areas. Recently, researchers have used species distribution modeling (SDM) to predict the occurrence of target plant and animal species based on various environmental variables. In this study, we applied this technique to predict and map the occurrence probability of a soil-borne disease, Verticillium wilt, using cabbage as a case study.MethodsA disease survey assessing the distribution of Verticillium wilt in cabbage fields in Tsumagoi village (central Honshu, Japan) was conducted two or three times annually from 1997 to 2013. Road density, elevation and topographic wetness index (TWI) were selected as explanatory variables for disease occurrence potential. A model of occurrence probability of Verticillium wilt was constructed using the MaxEnt software for SDM analysis. As the disease survey was mainly conducted in an agricultural area, the area was weighted as “Bias Grid” and area except for the agricultural area was set as background.ResultsGrids with disease occurrence showed a high degree of coincidence with those with a high probability occurrence. The highest contribution to the prediction of disease occurrence was the variable road density at 97.1%, followed by TWI at 2.3%, and elevation at 0.5%. The highest permutation importance was road density at 93.0%, followed by TWI at 7.0%, while the variable elevation at 0.0%. This method of predicting disease probability occurrence can help with disease monitoring in areas with high probability occurrence and inform farmers about the selection of control measures.

The role of environment, local adaptation, and past climate fluctuation on the amount and distribution of genetic diversity in two subspecies of Mexican wild Zea mays.

Past climate fluctuations during the Holocene and Pleistocene shaped the distribution of several plant species in temperate areas over the world. Wild maize, commonly known as teosinte, is a good system to evaluate the effects of historical climate fluctuations on genetic diversity due to its wide distribution in Mexico with contrasting environmental conditions. We explored the influence of contemporary factors and historical environmental shifts on genetic diversity, including present and three historical periods using neutral markers. We used 22 nuclear microsatellite loci to examine the genetic diversity of 14 populations of Zea mays subsp. parviglumis and 15 populations of Zea mays subsp. mexicana (527 individuals total). We implemented genetic structure analyses to evaluate genetic differentiation between and within subspecies. We applied coalescent-based demographic analysis and species distribution modeling to evaluate the effects of historical environmental shifts. We found 355 alleles in total for the two subspecies and variable levels of diversity in each (Z. mays subsp. parviglumis expected heterozygosity HE = 0.3646-0.7699; Z. mays subsp. mexicana HE = 0.5885-0.7671). We detected significant genetic structure among populations (DEST = 0.4332) with significant heterozygote deficiency (FIS = 0.1796), and variable selfing rates (sg2 = 0.0-0.3090). The Bayesian assignment analysis differentiated four genetic groups. Demographic and species distribution modeling analysis suggested that environmental shifts were influential in the amount of genetic diversity. Our analyses suggest that the current genetic diversity in teosinte is shaped by factors such as local adaptation and genetic isolation, along with historical environmental fluctuations.

Distribution of Foliicolous Lichen Strigula and Genetic Structure of S. multiformis on Jeju Island, South Korea.

Strigula is a pantropic foliicolous lichen living on the leaf surfaces of evergreen broadleaf plants. In South Korea, Strigula is the only genus of foliicolous lichen recorded from Jeju Island. Several Strigula species have been recorded, but the ecology of Strigula in South Korea has been largely unexplored. This study examined the distribution and genetic structure of Strigula on Jeju Island. The distribution was surveyed and the influence of environmental factors (e.g., elevation, forest availability, and bioclimate) on the distribution was analyzed using a species distribution modeling analysis. In addition, the genetic variations and differentiation of Strigula multiformis populations were analyzed using two nuclear ribosomal regions. The distribution of Strigula was largely restricted to a small portion of forest on Jeju Island, and the forest availability was the most important factor in the prediction of potential habitats. The genetic diversity and differentiation of the S. multiformis population were found to be high and were divided according to geography. On the other hand, geographic and environmental distance did not explain the population differentiation. Distribution and population genetic analysis suggested that the available habitat and genetic exchange of Strigula on Jeju Island are limited by the lack of available forest in the lowlands.

Phylogeography and species distribution modelling of Cryptocephalusbarii (Coleoptera: Chrysomelidae): is this alpine endemic species close to extinction?

The alternation of glacial and interglacial cycles of the Quaternary period contributed in shaping the current species distribution. Cold-adapted organisms experienced range expansion and contraction in response to the temperature decrease and increase, respectively. In this study, a fragment of the mitochondrial marker COI was used to investigate the phylogeography of Cryptocephalusbarii, a cold-adapted alpine leaf beetle species endemic of Orobie Alps, northern Italy. The relationships among populations, their divergence time, and the most probable migration model were estimated and are discussed in light of the Pleistocene climate oscillations. Through a species distribution modelling analysis, the current habitat suitability was assessed and the distribution in a future global warming scenario predicted. The main divergence events that led to the actual population structure took place from ~750,000 to ~150,000 years ago, almost following the pattern of the climate oscillations that led to the increase of the connections between the populations during cold periods and the isolation on massifs in warm periods. The most supported migration model suggests that the species survived to past adverse climatic conditions within refugia inside and at the limit of the actual range. The species distribution modelling analysis showed that C.barii is extremely sensitive to air temperature variations, thus the increase of temperature caused by global warming will reduce the suitable areas within the species range, leading to its possible extinction in the next 50 years. Cryptocephalusbarii is a representative case of how cold adapted and limited distributed species have been and could be affected by climate change, that highlights the implementation of conservation actions.

Conservation strategy for aquatic plants: endangered Ottelia acuminata (Hydrocharitaceae) as a case study

Knowledge of the extent and structure of genetic diversity and a species’ ecological niche are integral to formulating management plans for the conservation of threatened species. This is particularly important for aquatic organisms, which are especially vulnerable to human-induced environmental degradation and experience rapid global decline. To develop a proper conservation strategy for a threatened aquatic plant, Ottelia acuminata (Hydrocharitaceae), we utilized species distribution modeling (SDM) to delimit its potentially suitable range, both under the current climate and the climate expected in the near future, and employed AFLP to analyze the extent and structure of genetic variation over its entire distribution range. The within-population genetic diversity (He = 0.085) was lower than in the other species of Hydrocharitaceae studied using AFLP. The structuring of the genetic variation corresponded well to the distribution of previously described phenotypic varieties. There was 100% clustering of individuals according to their population origin suggesting a lack of inter-population gene flow. Based on the results of SDM and population genetic analysis we recommend (i) collecting seeds from all extant populations for seed banking through cryopreservation and the creation of living collections; (ii) reintroductions after restoration of once-occupied habitats utilizing plants of local origin, or, if the local variety has been extirpated, utilizing the most genetically similar population representing the same phenotypic variety; and (iii) experimental introduction of the species into lakes, ponds and small rivers in protected areas within the identified suitable range utilizing either a single population or a mix of populations belonging to the same genetic or phenotypic group.

Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan.

Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of the coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.

SDMtoolbox 2.0: the next generation Python-based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses

SDMtoolbox 2.0 is a software package for spatial studies of ecology, evolution, and genetics. The release of SDMtoolbox 2.0 allows researchers to use the most current ArcGIS software and MaxEnt software, and reduces the amount of time that would be spent developing common solutions. The central aim of this software is to automate complicated and repetitive spatial analyses in an intuitive graphical user interface. One core tenant facilitates careful parameterization of species distribution models (SDMs) to maximize each model’s discriminatory ability and minimize overfitting. This includes carefully processing of occurrence data, environmental data, and model parameterization. This program directly interfaces with MaxEnt, one of the most powerful and widely used species distribution modeling software programs, although SDMtoolbox 2.0 is not limited to species distribution modeling or restricted to modeling in MaxEnt. Many of the SDM pre- and post-processing tools have ‘universal’ analogs for use with any modeling software. The current version contains a total of 79 scripts that harness the power of ArcGIS for macroecology, landscape genetics, and evolutionary studies. For example, these tools allow for biodiversity quantification (such as species richness or corrected weighted endemism), generation of least-cost paths and corridors among shared haplotypes, assessment of the significance of spatial randomizations, and enforcement of dispersal limitations of SDMs projected into future climates—to only name a few functions contained in SDMtoolbox 2.0. Lastly, dozens of generalized tools exists for batch processing and conversion of GIS data types or formats, which are broadly useful to any ArcMap user.

The zoon r package for reproducible and shareable species distribution modelling

Abstract The rapid growth of species distribution modelling (SDM) as an ecological discipline has resulted in a large and diverse set of methods and software for constructing and evaluating SDMs. The disjointed nature of the current SDM research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon r package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows. zoon modules are interoperable snippets of r code, each carrying a SDM method that zoon combines into a single analysis object. Rather than defining these modules, zoon draws modules from an open, version‐controlled online repository. zoon makes it easy for SDM researchers to contribute modules to this repository, enabling others to rapidly deploy new methods in their own workflows or to compare alternative methods. Each workflow object created by zoon is a rerunnable record of the data, code and results of an entire SDM analysis. This can then be easily shared, scrutinised, reproduced and extended by the whole SDM research community. We explain how zoon works and demonstrate how it can be used to construct a completely reproducible SDM analyses, create and share a new module, and perform a methodological comparison study.

Rapid poleward distributional shifts in the European cave‐dwelling Meta spiders under the influence of competition dynamics

AbstractAimTo describe the distribution of two congeneric species of cave‐dwelling spiders under current climatic conditions and future warming scenarios, keeping into account their bioclimatic requirements, dispersal capacity and competition dynamics.LocationEurope and North Africa.MethodsWe gathered detailed occurrence data for Meta menardi and M. bourneti (Araneae: Tetragnathidae) and modelled their distribution across their bioclimatic range. We evaluated the breadth of the bioclimatic niche of the two species and assessed the potential overlap between their multidimensional Hutchinsonian hypervolumes. We compared these results with their current distribution maps obtained by species distribution modelling (SDMs) keeping into account dispersal and competition dynamics, and we projected future trends of distribution according to different climatic scenarios.ResultsThe overall size of the niche hypervolumes of the two species was very similar and highly overlapping. However, when accounting for competition in the model, the predicted ranges of the two species showed only minor areas of overlap. On the base of SDM analysis, we predicted a significant poleward shift in the distribution of both species, with the appearance of a new contact area especially in Central Europe, southern UK, France and northern Spain.Main conclusionsInterspecific competition keeps the current ranges of the two European Meta species apart, although their fundamental bioclimatic niches are very similar. Rapid poleward shifts of the two species are likely due to the high dispersal capacity of the two spiders. The case of Meta spiders exemplifies rapid shift in range of distribution associated with global warming, which are unlikely to occur in the case of most cave‐dwelling arthropods.