Past, present and future distributions of an Iberian Endemic, Lepus granatensis: ecological and evolutionary clues from species distribution models

The dimensionality reductions of environmental variables have a significant effect on the performance of species distribution models

How to effectively obtain species-related low-dimensional data from massive environmental variables has become an urgent problem for species distribution models (SDMs). In this study, we will explore whether dimensionality reduction on environmental variables can improve the predictive performance of SDMs. We first used two linear (i.e., principal component analysis (PCA) and independent components analysis) and two nonlinear (i.e., kernel principal component analysis (KPCA) and uniform manifold approximation and projection) dimensionality reduction techniques (DRTs) to reduce the dimensionality of high-dimensional environmental data. Then, we established five SDMs based on the environmental variables of dimensionality reduction for 23 real plant species and nine virtual species, and compared the predictive performance of those with the SDMs based on the selected environmental variables through Pearson's correlation coefficient (PCC). In addition, we studied the effects of DRTs, model complexity, and sample size on the predictive performance of SDMs. The predictive performance of SDMs under DRTs other than KPCA is better than using PCC. And the predictive performance of SDMs using linear DRTs is better than using nonlinear DRTs. In addition, using DRTs to deal with environmental variables has no less impact on the predictive performance of SDMs than model complexity and sample size. When the model complexity is at the complex level, PCA can improve the predictive performance of SDMs the most by 2.55% compared with PCC. At the middle level of sample size, the PCA improved the predictive performance of SDMs by 2.68% compared with the PCC. Our study demonstrates that DRTs have a significant effect on the predictive performance of SDMs. Specifically, linear DRTs, especially PCA, are more effective at improving model predictive performance under relatively complex model complexity or large sample sizes.

Past, present, and future predictions on the suitable habitat of the Slender racer (Orientocoluber spinalis) using species distribution models

Species distribution models (SDMs) across past, present, and future timelines provide insights into the current distribution of these species and their reaction to climate change. Specifically, if a species is threatened or not well-known, the information may be critical to understand that species. In this study, we computed SDMs for Orientocoluber spinalis, a monotypic snake genus found in central and northeast Asia, across the past (last interglacial, last glacial maximum, and mid-Holocene), present, and future (2070s). The goal of the study was to understand the shifts in distribution across time, and the climatic factors primarily affecting the distribution of the species. We found the suitable habitat of O. spinalis to be persistently located in cold-dry winter and hot summer climatic areas where annual mean temperature, isothermality, and annual mean precipitation were important for suitable habitat conditions. Since the last glacial maximum, the suitable habitat of the species has consistently shifted northward. Despite the increase in suitable habitat, the rapid alterations in weather regimes because of climate change in the near future are likely to greatly threaten the southern populations of O. spinalis, especially in South Korea and China. To cope with such potential future threats, understanding the ecological requirements of the species and developing conservation plans are urgently needed.

Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae)

Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot.

Range expansion underlies historical introgressive hybridization in the Iberian hare

Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria (“mitonuc” genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.

Determining the distribution loss of brown eared-pheasant (Crossoptilon mantchuricum) using historical data and potential distribution estimates

We analyzed the synchronous relationship between forest cover and species distribution to explain the contraction in the distribution range of the brown eared-pheasant (Crossoptilon mantchuricum) in China. Historical resources can provide effective records for reconstructing long-term distribution dynamics. The brown eared-pheasant's historical distribution from 25 to 1947 CE, which included the three provinces of Shaanxi, Shanxi, and Hebei based on this species' habitat selection criteria, the history of the forests, ancient climate change records, and fossil data. The current species distribution covers Shaanxi, Shanxi, and Hebei provinces, as well as Beijing city, while Shanxi remains the center of the distribution area. MaxEnt model indicated that the suitable conditions of the brown eared-pheasant had retreated to the western regions of Shanxi and that the historical distribution area had reduced synchronously with the disappearance of local forest cover in Shanxi. We built a correlative relationship between the presence/absence of brown eared-pheasants and forest coverage and found that forest coverage in the north, northeast, central, and southeast areas of the Shanxi province were all less than 10% in 1911. Wild brown eared-pheasants are stable in the Luliang Mountains, where forest coverage reached 13.2% in 2000. Consequently, we concluded that the distribution of this species is primarily determined by vegetation conditions and that forest cover was the most significant determining factor.

Evolutionary responses to climate change in parasitic systems

Species may respond to climate change in many ecological and evolutionary ways. In this simulation study, we focus on the concurrent evolution of three traits in response to climate change, namely dispersal probability, temperature tolerance (or niche width), and temperature preference (optimal habitat). More specifically, we consider evolutionary responses in host species involved in different types of interaction, that is parasitism or commensalism, and for low or high costs of a temperature tolerance-fertility trade-off (cost of generalization). We find that host species potentially evolve all three traits simultaneously in response to increasing temperature but that the evolutionary response interacts and may be compensatory depending on the conditions. The evolutionary adjustment of temperature preference is slower in the parasitism than in commensalism scenario. Parasitism, in turn, selects for higher temperature tolerance and increased dispersal. High costs for temperature tolerance (i.e. generalization) restrict evolution of tolerance and thus lead to a faster response in temperature preference than that observed under low costs. These results emphasize the possible role of biotic interactions and the importance of 'multidimensional' evolutionary responses to climate change.

Molecular data and ecological niche modeling reveal population dynamics of widespread shrub Forsythia suspensa (Oleaceae) in China's warm-temperate zone in response to climate change during the Pleistocene

Background

Despite its high number of endemic deciduous broad-leaved species in China’s warm-temperate zone, far less attention has been paid to phylogeographic studies in this region. In this work, the phylogeographic history of Forsythia suspensa endemic to China’s warm-temperate zone was investigated to explore the effect of climate change during the Pleistocene on the distribution of this deciduous broad-leaved species in China.

Results

The cpDNA data revealed seven phylogeographical groups corresponding to geographical regions. By contrast, the nrDNA data supported the samples clustered into three groups, which was inconsistent with separate geographical regions supported by cpDNA data. Ecological niche modeling showed that the climatically suitable area during the cold period was larger than that during the warm period.

Conclusions

Both molecular data and ecological niche modeling indicated that F. suspensa expanded to nearby low-elevation plains in the glacial periods, and retreated to mountaintops during interglacial warmer stages. This study thus supported that F. suspensa persisted in situ during the glacial of the Pleistocene with enlarged distribution area, contrary to the hypothesis of long distance southward migration or large-scale range contraction.

Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.