Find research datasets worth reusing

Data from: Phylogenetic measures of biodiversity and neo- and paleo-endemism

Understanding spatial patterns of biodiversity is critical for conservation planning, particularly given rapid habitat loss and human-induced climatic change. Diversity and endemism are typically assessed by comparing species ranges across regions. However, investigation of patterns of species diversity alone misses out on the full richness of patterns that can be inferred using a phylogenetic approach. Here, using Australian Acacia as an example, we show that the application of phylogenetic methods, particularly two new measures, relative phylogenetic diversity and relative phylogenetic endemism, greatly enhances our knowledge of biodiversity across both space and time. We found that areas of high species richness and species endemism are not necessarily areas of high phylogenetic diversity or phylogenetic endemism. We propose a new method called categorical analysis of neo- and paleo-endemism (CANAPE) that allows, for the first time, a clear, quantitative distinction between centres of neo- and paleo-endemism, useful to the conservation decision-making process.

Data from: Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae

Both historical and contemporary processes influence the genetic structure of species, but the relative roles of such processes are still difficult to access. Population genetic studies of species with recent evolutionary histories such as the New Zealand endemic scallop Pecten novaezelandiae (<1 Ma) permit testing of the effects of recent processes affecting gene flow and shaping genetic structure. In addition, studies encompassing the entire distributional range of species can provide insight into colonization processes. Analyses of genetic variation in P. novaezelandiae (952 individuals from 14 locations, genotyped at 10 microsatellite loci) revealed a weak but significant regional structure across the distributional range of the species, as well as latitudinal gradients of genetic diversity and differentiation: estimates of migration rates supported these patterns. Our results suggest that the observed genetic structure and latitudinal gradients reflect a stepping-stone model of colonization (north to south) and emerging divergence of populations as a result of ongoing limitations to gene flow and insufficient time to reach migration–drift equilibrium. The low levels of interpopulation and interregional genetic differentiation detected over hundreds of kilometres reflect the recent evolutionary history of P. novaezelandiae and stand in contrast to patterns reported for other evolutionary older species at the same spatial scale. The outcomes of this study contribute to a better understanding of evolutionary processes influencing the genetic variation of species and provide vital information on the genetic structure of P. novaezelandiae.

Data from: Taking the discovery approach in integrative taxonomy: decrypting a complex of narrow-endemic Alpine harvestmen (Opiliones: Phalangiidae: Megabunus)

Species delimitation is fundamental for biological studies, yet precise delimitation is not an easy task, and every involved approach has an inherent failure rate. Integrative taxonomy, a method that merges multiple lines of evidence, can profoundly contribute to reliable alpha taxonomy and shed light on the processes behind speciation. In this study, we explored and validated species limits in a group of closely related Megabunus harvestmen (Eupnoi, Phalangiidae) endemic to the European Alps. Without a priori species hypotheses, we used multiple sources of inference, including mitochondrial and multilocus nuclear DNA, morphometrics, and chemistry. The results of these discovery approaches revealed morphological crypsis and multiple new species within two of the five hitherto known species. Based on our analyses, we discussed the most plausible evolutionary scenarios, invoked the most reasonable species hypotheses, and validated the new species limits. Building upon the achieved rigour, three new species, M. cryptobergomas Muster & Wachter sp. nov., M. coelodonta Muster & Steiner sp. nov., and M. lentipes Muster & Komposch sp. nov., are formally described. In addition, we provide a dichotomous morphological key to the Megabunus species of the Alps. Our work demonstrates the suitability of integrative, discovery-based approaches in combination with validation approaches to precisely characterise species and enabled us to implement nomenclatural consequences for this genus.

Data from: The world's biogeographical regions revisited: global patterns of endemism in Tipulidae (Diptera)

This paper explores the distributional data of 4,224 Tipulidae (Insecta: Diptera) species to search for endemism patterns in a worldwide scale and to test the extent to which the global patterns of endemism of the group fit into previously proposed regionalization schemes, particularly Wallace's system and recent revisions of it. Large scale areas of endemism are assessed using the grid-based method implemented in VNDM. VNDM depends on the prior definition of the grid size for analysis, but a criterion for choosing beforehand a particular grid size is not clear. The same holds for the choice of the level of similarity in species composition selected for the calculation of consensus areas. In our study, we developed a methodological approach that helped defining objective criteria for choosing suitable values for these critical variables. Large-scale areas of endemism around the globe are identified and ranked according to endemicity levels: 1—West Palaearctic, 2—Nearctic, 3—East Palaearctic-Oriental, 4—West North America, 5—Australia, 6—Neotropical, 7—Sub-Saharan Africa, 8—Palaearctic, and 9—Middle East. Our main conclusion is that there are still some limitations in applying biogeographical classifications proposed mostly on the basis of vertebrate distribution to other taxonomic groups, such as the Tipulidae. While there is a general congruence of the broad-scale areas of endemism of tipulids with previously proposed regionalization schemes, for some areas, the sharpness of boundaries between traditional regions is not so acute, due to a great level of overlap of part of its biotic elements.

Data from: Recent speciation and secondary contact in endemic ants

Gene flow is the main force opposing divergent selection, and its effects are greater in populations in close proximity. Thus, complete reproductive isolation between parapatric populations is not expected, particularly in the absence of ecological adaptation and sharp environmental differences. Here, we explore the biogeographical patterns of an endemic ant species, Cataglyphis floricola, for which two colour morphs (black and bicolour) coexist in parapatry throughout continuous sandy habitat in southern Spain. Discriminant analyses of six biometric measurements of male genitalia and 27 cuticular hydrocarbons reveal high differentiation between morphs. Furthermore, the low number of shared alleles derived from nuclear markers (microsatellites) between the morphs at their contact zone suggests the absence of recent gene flow. Mitochondrial DNA (COI) phylogenetic analysis and median-joining networks show that the black morph is basal to the bicolour morph, with unique haplotypes recovered for each morph. Mismatch distribution analysis and Bayesian skyline plots suggest that they are undergoing different demographic changes, with the bicolour and black morphs at demographic equilibrium and expansion, respectively. Thus, our results show complete reproductive isolation between the two colour morphs as evidenced from genetic, chemical and morphological data. We suggest that these divergence events could be explained by historical vicariance during the Pleistocene, in which reproductive traits experienced strong divergent selection between the morphs initiating or culminating speciation.

opencc-zeroDec 2010View details →

Data from: A tight balance between natural selection and gene flow in a southern African arid-zone endemic bird

Gene flow is traditionally thought to be antagonistic to population differentiation and local adaptation. However, recent studies have demonstrated that local adaptation can proceed provided that selection is greater than the homogenising effects of gene flow. We extend these initial studies by combining ecology (climate), phenotype (body size), physiological genetics (oxidative phosphorylation genes) and neutral loci (nuclear microsatellites and introns) to test whether selection can counter-balance gene flow and hence promote local adaptation in a bird whose distribution spans an aridity gradient. Our results show that the Karoo scrub-robin's climatic niche is spatially structured, providing the potential for local adaptation to develop. We found remarkably discordant patterns of divergence among mtDNA, morphology and neutral loci. For the mitochondrial genes, two amino acid replacements, strong population structure and reduced gene flow were associated with the environmental gradient separating western coastal sites from the interior of southern Africa. In contrast, morphology and the neutral loci exhibited variation independent of environmental variables, and revealed extensive levels of gene flow across the aridity gradient, 50 times larger than the estimates for mitochondrial genes. Together, our results suggest that selective pressures on physiology, mediated by the mitochondrial genome, may well be a common mechanism for facilitating local adaptation to new climatic conditions.

Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Data from: Endemic chronic wasting disease causes mule deer population decline in Wyoming

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting white-tailed deer (Odocoileus virginianus), mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces shirasi) in North America. In southeastern Wyoming average annual CWD prevalence in mule deer exceeds 20% and appears to contribute to regional population declines. We determined the effect of CWD on mule deer demography using age-specific, female-only, CWD transition matrix models to estimate the population growth rate (λ). Mule deer were captured from 2010–2014 in southern Converse County Wyoming, USA. Captured adult (≥ 1.5 years old) deer were tested ante-mortem for CWD using tonsil biopsies and monitored using radio telemetry. Mean annual survival rates of CWD-negative and CWD-positive deer were 0.76 and 0.32, respectively. Pregnancy and fawn recruitment were not observed to be influenced by CWD. We estimated λ = 0.79, indicating an annual population decline of 21% under current CWD prevalence levels. A model derived from the demography of only CWD-negative individuals yielded; λ = 1.00, indicating a stable population if CWD were absent. These findings support CWD as a significant contributor to mule deer population decline. Chronic wasting disease is difficult or impossible to eradicate with current tools, given significant environmental contamination, and at present our best recommendation for control of this disease is to minimize spread to new areas and naïve cervid populations.

Data from: Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the eastern Mediterranean

At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low-copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid-Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin.

Data from: The importance of naming cryptic species and the conservation of endemic subterranean amphipods

Molecular taxonomy often uncovers cryptic species, reminding us that taxonomic incompleteness is even more severe than previous thought. The importance of cryptic species for conservation is poorly understood. Although some cryptic species may be seriously threatened or otherwise important, they are rarely included in conservation programs as most of them remain undescribed. We analysed the importance of cryptic species in conservation by scrutinizing the South European cryptic complex of the subterranean amphipod Niphargus stygius sensu lato. Using uni- and multilocus delineation methods we show that it consists of 15 parapatric and sympatric species, which we describe using molecular diagnoses. The new species are not mere "taxonomic inflation" as they originate from several distinct branches within the genus and coexist with no evidence of lineage sharing. They are as evolutionarily distinct as average nominal species of the same genus. Ignoring these cryptic species will underestimate the number of subterranean endemics in Slovenia by 12 and in Croatia by four species, although alpha diversity of single caves remains unchanged. The new taxonomy renders national Red Lists largely obsolete, as they list mostly large-ranged species but omit critically endangered single-site endemics. Formal naming of cryptic species is critical for them to be included in conservation policies and faunal listings.

Data from: Ecological explanations to island gigantism: dietary niche divergence, predation and size in an endemic lizard

Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.

Data from: Punctuated changes in the morphology of an endemic diatom from Lake Titicaca

High levels of biodiversity and endemism in ancient lakes have motivated research on evolutionary processes in these systems. Drill core records from Lake Titicaca (Bolivia, Peru), an ancient lake in the high-elevation Altiplano, record the history of climate, landscape dynamics, and diatom evolution. That record was used to examine the patterns and drivers of morphological evolution of an endemic species complex of diatoms in the lake, the Cyclostephanos andinus complex. In an attempt to delineate species within the complex based on morphology, no discernible evidence was found for species separation based on an ordination analysis of multiple characters, but multiple populations were detected based on the distribution of valve size in individual samples. Likelihood modeling of phyletic evolution showed that size evolved through punctuated change. Correlation of size trends with other environmental variables indicates that C. andinus size responded to regional environmental change driven by global processes that influenced Lake Titicaca by affecting lake level and thermal stratification.

opencc-zeroDec 2017View details →

Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers

Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. eDNA concentration and individual counts both gradually increased from May–July, then both decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.

opencc-zeroDec 2015View details →

Data from: Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen

The Pleistocene climatic fluctuations had a huge impact on all life-forms, and various hypotheses regarding the survival of organisms during glacial periods have been postulated. In the European Alps, evidence has been found in support of refugia outside the ice shield (massifs de refuge) acting as sources for postglacial recolonisation of inner-Alpine areas. In contrast, evidence for survival on nunataks, ice-free areas above the glacier, remains scarce. Here, we combine multivariate genetic analyses with ecological niche models (ENMs) through multiple timescales to elucidate the history of alpine Megabunus harvestmen throughout the ice ages, a genus that comprises eight high altitude endemics. ENMs suggest two types of refugia throughout the Last Glacial Maximum, inner-Alpine survival on nunataks for four species and peripheral refugia for further four species. In some geographic regions, the patterns of genetic variation are consistent with long-distance dispersal out of massifs de refuge, repeatedly coupled with geographic parthenogenesis. In other regions, long-term persistence in nunataks may dominate the patterns of genetic divergence. Overall, our results suggest that glacial cycles contributed to allopatric diversification in Alpine Megabunus, both within and at the margins of the ice shield. These findings exemplify the power of ENM projections coupled with genetic analyses to identify hypotheses about the position and number of glacial refugia and thus to evaluate the role of Pleistocene glaciations in driving species-specific responses of recolonisation or persistence that may have contributed to observed patterns of biodiversity.

opencc-zeroDec 2011View details →

Data from: Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)

Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (HE: 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults RS: 3.91; juveniles RS: 2.83) and observed heterozygosity than adult trees (adults HO: 0.62; juveniles HO: 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to mis-management of genetic resources and population fragmentation.

Data from: Islands within islands: two montane paleo-endemic birds impacted by recent anthropogenic fragmentation

Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky-island-endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (DPS) was higher relative to historic differentiation (FST) in anthropogenic fragments, despite the species' ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high DPS/FST values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky-island systems.

Data from: An integrative approach to understanding the evolution and diversity of Copiapoa (Cactaceae), a threatened endemic Chilean genus from the Atacama Desert

PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. METHODS: Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively. KEY RESULTS: Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas. CONCLUSIONS: Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity.

opencc-zeroDec 2015View details →

Data from: Genome-wide SNP discovery in the annual herb, Lasthenia fremontii (Asteraceae): genetic resources for the conservation and restoration of a California vernal pool endemic

California vernal pool (VP) ecosystems support a diverse community of endemic plants that are threatened by multiple anthropogenic pressures, generating a need for molecular tools to quantify the extent and distribution of genetic variation in native populations. Here, we used RADseq to discover single nucleotide polymorphisms (SNPs) for a widespread VP endemic plant species, Lasthenia fremontii. We discovered nuclear-based SNPs using a RAD-tag library of 12 individuals from different VP complexes using SbfI, a restriction enzyme that does not cleave the chloroplast genome in Lasthenia. A total of 316,106 catalog loci were obtained across all twelve individuals in the library. Of these, 713 loci were polymorphic, yielding 3918 candidate SNPs. Next, we genotyped an additional 285 additional plants to validate and characterize 71 of the candidate SNPs. Of these, 44 were polymorphic among VP complexes. A preliminary analysis of the distribution of genetic variation using these loci revealed significant isolation-by-distance across the species' geographic range. Weaker, but in some cases significant, genetic differentiation was detected among subpopulations from different pools within a single VP complex. Thus, in this study, RADseq allowed the discovery of SNP markers that can characterize patterns of genetic variation at multiple spatial scales in L. fremontii, which can be used to inform the conservation and mitigation of VP populations.

Data from: Latitudinal environmental niches and riverine barriers shaped the phylogeography of the central Chilean endemic Dioscorea humilis (Dioscoreaceae)

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.

Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

1. To prevent the invasion of exotic species causing a decline in an endangered endemic species, it is important to determine the distribution of both species at an early stage, when the density of the exotic species is still low, and to manage the invasion immediately. However, distinguishing between closely related species is difficult because they share similar characteristics. 2. The identification of DNA fragments sampled from a body of water (environmental DNA) has become a popular technique for rapidly determining the distribution of a target species. In this study, we analysed environmental DNA in water samples from 37 sites across the Katsura River basin in Japan. We used TaqMan real-time PCR to distinguish the Japanese giant salamander Andrias japonicus from the closely related Chinese giant salamander Andrias davidianus, which is known to invade Japanese rivers and hybridize with the Japanese species. 3. In environmental samples, we detected mtDNA of the endemic species at 25 sites and mtDNA of the exotic species at nine sites. The DNA detection sites were concentrated in the upstream region. The exotic species DNA was found beyond the limits of an earlier capturing survey. 4. Synthesis and applications. Using environmental DNA to monitor the two salamander species requires less time and effort than traditional surveys, so a wide-ranging survey can be conducted rapidly. Our results showed that performing three environmental DNA surveys for each site between autumn and winter is desirable for giant salamanders. Further collection of environmental DNA, in combination with conventional population surveys, will provide valuable information that can help protect rare endemic species in a variety of aquatic ecosystems and can help monitor the invasion of exotic species.