Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis)

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population substructuring can occur as a result of survival in several isolated refugia and subsequent recolonization processes or via genetic drift following a population decline. The kea (Nestor notabilis) is an endemic parrot widely distributed in the mountains of the South Island of New Zealand that has gone through a major human‐induced population decline during the 1860s–1970s. The aims of this study were to understand the glacial and postglacial history of kea and to determine whether the recent population decline played a role in the shaping of the current genetic variation. We examined the distribution of genetic variation, differentiation and admixture in kea using 17 microsatellites and the mitochondrial control region. Mitochondrial data showed a shallow phylogeny and a genetic distinction between the North and South of the range consistent with the three genetic clusters identified with microsatellite data. Both marker types indicated an increase in genetic isolation by geographic distance. Approximate Bayesian Computation supported a scenario of postglacial divergence from a single ancestral glacial refugium, suggesting that the contemporary genetic structure has resulted from recolonization processes rather than from a recent population decline. The recent evolutionary origin of this genetic structure suggests that each genetic cluster does not need to be considered as independent conservation units.     

Unpacking the mechanisms captured by a correlative species distribution model to improve predictions of climate refugia

Climate refugia are regions that animals can retreat to, persist in and potentially then expand from under changing environmental conditions. Most forecasts of climate change refugia for species are based on correlative species distribution models (SDMs) using long‐term climate averages, projected to future climate scenarios. Limitations of such methods include the need to extrapolate into novel environments and uncertainty regarding the extent to which proximate variables included in the model capture processes driving distribution limits (and thus can be assumed to provide reliable predictions under new conditions). These limitations are well documented; however, their impact on the quality of climate refugia predictions is difficult to quantify. Here, we develop a detailed bioenergetics model for the koala. It indicates that range limits are driven by heat‐induced water stress, with the timing of rainfall and heat waves limiting the koala in the warmer parts of its range. We compare refugia predictions from the bioenergetics model with predictions from a suite of competing correlative SDMs under a range of future climate scenarios. SDMs were fitted using combinations of long‐term climate and weather extremes variables, to test how well each set of predictions captures the knowledge embedded in the bioenergetics model. Correlative models produced broadly similar predictions to the bioenergetics model across much of the species' current range – with SDMs that included weather extremes showing highest congruence. However, predictions in some regions diverged significantly when projecting to future climates due to the breakdown in correlation between climate variables. We provide unique insight into the mechanisms driving koala distribution and illustrate the importance of subtle relationships between the timing of weather events, particularly rain relative to hot‐spells, in driving species–climate relationships and distributions. By unpacking the mechanisms captured by correlative SDMs, we can increase our certainty in forecasts of climate change impacts on species.     

Hidden diversity in forest soils: Characterization and comparison of terrestrial flatworm’s communities in two national parks in Spain

Terrestrial flatworms (Platyhelminthes, Tricladida, and Geoplanidae) belong to what is known as cryptic soil fauna of humid forests and are animals not easily found or captured in traps. Nonetheless, they have been demonstrated to be good indicators of the conservation status of their habitat as well as a good model to reconstruct the recent and old events affecting biodiversity. This is mainly due to their delicate constitution, their dependence on the integrity of their habitat, and their very low dispersal capacity. At present, little is known about their communities, except for some studies performed in Brazil. In this work, we analyze for the first time in Europe terrestrial flatworm communities. We have selected two protected areas belonging to the Red Española de Parques Nacionales. Our aims include performing a first study of the species richness and community structure for European terrestrial planarian species at regional and local scale. We evaluate the effect of type of forests in the community composition and flatworms’ abundance, but also have into account the phylogenetic framework (never considered in previous studies) analyzed based on molecular data. We find differences in the species composition among parks, with an astonishingly high diversity of endemic species in the Parque Nacional de Picos de Europa and an extremely low diversity of species in the Parque Nacional de Ordesa y Monte Perdido. These divergent patterns cannot be attributed to differences in physical variables, and in addition, the analyses of their phylogenetic relationships and, for a few species, their genetic structure, point to a more probable historical explanation.     

Glacial cycles drive rapid divergence of cryptic field vole species

Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single‐nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise F_ST values of 0.45–0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status.     

Investigating past range dynamics for a weed of cultivation,Silene vulgaris

Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.     

High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end‐glacial refugia

The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An important geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyse genetic diversity and colonization history of the bank vole (Myodes glareolus) throughout Europe (>800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land‐bridge route deriving from a “Carpathian” glacial refugium and one via a north‐eastern route from an “Eastern” glacial refugium near the Ural Mountains. Clustering of genome‐wide SNPs revealed high diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red‐backed voles (Myodes rutilus) took place in Fennoscandia just after end‐glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this emerging model species.     

Explicit tests of palaeodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia)

The alteration in palaeodrainage river connections has shaped patterns of speciation, genetic diversity and the geographical distribution of the species‐rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer palaeodrainage connectivity and test alternative palaeodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that makes this clade of closely related species an ideal system to investigate the number and location of glacial refugia and compare alternative hypotheses regarding the proposed evolution of the Teays‐Mahomet palaeodrainage. This study utilized time‐calibrated mitochondrial and nuclear gene phylogenies and present‐day geographical distributions to investigate hypothesized Teays‐Mahomet River connections through time using a dispersal–extinction–cladogenesis (DEC) framework. Results of DEC ancestral area reconstructions indicate that the Teays‐Mahomet River was a key dispersal route between disjunct highland regions connecting the Mississippi River tributaries to the Old‐Ohio Drainage minimally at two separate occasions during the Pleistocene. There was a dynamic interplay between palaeodrainage connections through time and postglacial range expansion from three glacial refugia that shaped the current genetic structure and geographical distributions of the species that comprise Ceasia.     

Differentiation and speciation in mountain streams: a case study in the caddisfly Rhyacophila aquitanica (Trichoptera)

Few studies have analysed the biogeography of mountain aquatic organisms, although this habitat provides stable conditions in which many species survived Pleistocene climatic oscillations, usually in the geographical vicinity of their present distribution ranges. The mountain caddisfly Rhyacophila aquitanica was selected as a model organism for this habitat type. Morphological measurements of genitalia and external characters of male individuals were obtained from almost the entire range of distribution of the species. Morphometric results were analysed by cluster analysis and multivariate statistics. Important differences were discovered among three population groups of R. aquitanica inhabiting different European mountain ranges: (i) mountain ranges north‐west of the Alps (Massif Central, Vosges, Schwarzwald and Fribourg); (ii) the southern Alps (Lombardia and Carinthia); and (iii) the western part of the southern Carpathians. This divergence suggests a long‐term isolation among these groups, which presumably took place long before the last Pleistocene glaciation, with no secondary contact among these populations. The differentiation centres of the southern Alps and Carpathian groups may have been mostly homotopic to their actual ranges, whereas the western group must have been distributed in the areas west or north‐west of the Alps with secondary expansions and disjunctions.     

Increased genetic structuring of isolated Salamandra salamandra populations (Caudata: Salamandridae) at the margins of the Carpathian Mountains

The traditional southern Pleistocene refugia hypothesis in Europe has lately been challenged for several animal and plant species. The Carpathian Basin, especially at the marginal regions, is one of the recently recognized biodiversity hotspots in Europe. Marginal populations are prone to have lower genetic diversity and higher genetic differentiation than central populations. Here, we examined one mitochondrial DNA fragment (D‐loop) and nine nuclear (microsatellite) loci to describe the genetic diversity and phylogeographical pattern of fire salamander (Salamandra salamandra) populations in the Carpathian Basin with focusing on the southern margins of the Western Carpathians, where isolated populations of this species are present. Analyses of microsatellites indicated reduced genetic diversity for most of the isolated populations. Based on the mitochondrial DNA, only two haplotypes were found, whereas the analyses with the nuclear markers revealed a more recent genetic split between Western (Alpine) and Eastern (Carpathian) populations, and separated the Apuseni Mountains population (part of the Western Carpathians). Using approximate Bayesian computation analyses, we identified the most probable colonization scenario for the isolated North Hungarian Carpathian Basin populations. The split between isolated salamander populations from the central populations in the Carpathian Mountains dates back to the beginning of the Late Pleistocene, while the split between most of the Hungarian populations can be associated with the Last Glacial Maximum. We found evidence for long‐time isolation between the marginal Carpathian Basin and central populations. Our results also show that S. salamandra survived glacial periods in the temperate forests of north‐east Pannonia (North Hungarian Mountains), confirming that the Carpathian Basin served as important northerly refugia during the Pleistocene climatic oscillations.     

A new species in the genus Dioon (Zamiaceae) from north-central Oaxaca, Mexico

Dioon argenteum sp. nov. (Zamiaceae) is described from northern Oaxaca, México. Flat leaves, and persistently tomentose, slightly imbricate leaflets with marginal prickles characterize this species. The specific epithet argenteum was chosen to describe the silver appearance of the persistent tomentum covering the new leaves. D. argenteum appears to have affinities with D. purpusii and D. califanoi.   © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 471–476.     

Aggregated recruitment patterns under adult crowns in Photinia glabra,a bird‐dispersed tree species

To clarify recruitment patterns of Photinia glabra, which is an evergreen, broad‐leaved, bird‐dispersed tree species, we analyzed spatial distribution in P. glabra recruits at each growth stage and demography of current‐year seedlings with respect to distributions of adults in a warm‐temperate secondary forest, western Japan. Although individuals ≥ 5 cm diameter at breast height (DBH) that had nearly produced fruits showed a random distribution, seedlings (≥ 1 year old, < 10‐cm stem length [SL]), small saplings (10 ≤ SL < 30 cm) and large saplings (≥ 30‐cm SL, < 5‐cm DBH) were clumped and associated with reproductive adults at approximately 2–3‐m scales, nearly equal to their average crown radius. Based on monitoring the demography of current‐year seedlings, emerged seedling density profoundly decreased, and no seedlings survived at longer than an adult's crown scales, with distance‐dependent mortality as a result of disease and herbivory not greatly affecting the current‐year seedling mortality. Thus, aggregated seed dispersal under the crown of adult P. glabra would directly influence the distribution of recruits for P. glabra in this forest. Of the bird‐dispersed tree species in this forest, P. glabra produced the highest amount of fruits during large crop years, and their fruits ripened during the late seasonal period (early January), suggesting that birds might be strongly attracted to these species, in turn leading to seeds being deposited mostly under the tree crowns. We propose that dispersal limitation would occur, even in a bird‐dispersed tree species such as P. glabra, owing to plant–bird interactions in the forest.