Climatic niche characteristics of native and invasive Lilium lancifolium

Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae)

The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.

Climatic niche convergence through space and time for a potential archaeophyte (Acacia caven) in South America

Based on the niche conservatism hypothesis, i.e. the idea that niches remain unchanged over space and time, climatic niche modelling (CNM) is a useful tool for predicting the spread of introduced taxa. Recent advances have extended such predictions deeper in time for plant species dispersed by humans before the modern era. The latest CNMs successfully evaluate niche differentiation and estimate potential source areas for intriguing taxa such as archaeophytes (i.e., species introduced before 1492 AD). Here, we performed CNMs for Acacia caven, a common Fabaceae tree in South America, considered an archaeophyte west of the Andes, in Central Chile. Accounting for the infraspecific delimitation of the species, our results showed that even when climates are different, climatic spaces used by the species overlap largely between the eastern and western ranges. Despite slight variation, results were consistent when considering one, two, or even three-environmental dimensions, and in accordance with the niche conservatism hypothesis. Specific distribution models calibrated for each region (east vs west) and projected to the past, indicate a common area of occupancy available in southern Bolivia-northwest Argentina since the late Pleistocene, which could have acted as a source-area, and this signal becomes stronger through the Holocene. Then, in accordance with a taxon introduced in the past, and comparing regional vs continental distribution models calibrated at the infraspecific or species level, the western populations showed their spread status to be mostly in equilibrium with the environment. Our study thus indicates how niche and species distribution models are useful to improve our knowledge related to taxa introduced before the modern era.

Niche divergence at the intraspecific level in an endemic rare peony (Paeonia rockii): A phylogenetic, climatic and environmental survey

Ecological factors have received increasing attention as drivers of speciation but also in the maintenance of postspeciation divergence. However, the relative significance of the responses of species to climate oscillations for driving niche divergence or conservatism in the evolution of many species that pass through diverse environments and limited geographical boundaries remains poorly understood. Paeonia rockii (one of the ancient species of Paeonia) comprising two subspecies called Paeonia rockii subsp. rockii and Paeonia rockii subsp. taibaishanica is an endemic, rare, and endangered medicinal plant in China. In this study, we integrated whole chloroplast genomes, and ecological factors to obtain insights into ecological speciation and species divergence in this endemic rare peony. RAxML analysis indicated that the topological trees recovered from three different data sets were identical, where P. rockii subsp. rockii and P. rockii subsp. taibaishanica clustered together, and molecular dating analyses suggested that the two subspecies diverged 0.83 million years ago. In addition, ecological niche modeling showed that the predicted suitable distribution areas for P. rockii subsp. rockii and P. rockii subsp. taibaishanica differed considerably, although the predicted core distribution areas were similar, where the population contracted in the last interglacial and expanded in the last glacial maximum. Under the emissions scenarios for the 2050s and 2070s, the suitable distribution areas were predicted to contract significantly, where the migration routes of the two subspecies tended to migrate toward high latitudes and elevations, thereby suggesting strong responses of the distributions of the two subspecies to climate change. These findings combined with the phylogeographic relationships provide comprehensive insights into niche variation and differentiation in this endemic rare peony, and they highlight the importance of geological and climatic changes for species divergence and changes in the population geographic patterns of rare and endangered medicinal plants in East Asia.

Genetic Differentiation and Demographic History of Three Cerris Oak Species in China Based on Nuclear Microsatellite Makers

Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous Cerris oak species (Q. acutissima, Q. variabilis and Q. chenii) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that Q. acutissima and Q. chenii were clustered in the same group, whereas Q. variabilis formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that Q. variabilis and Q. acutissima diverged from their most common ancestor around 19.84 Ma, and subsequently Q. chenii diverged from Q. acutissima at about 9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three Cerris oak species repeatedly underwent considerable ‘expansion–contraction’ during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.

Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China

Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.

Distribution modelling of an introduced species: do adaptive genetic markers affect potential range?

Biological invasions have increased in the last few decades mostly due to anthropogenic causes such as globalization of trade. Because invaders sometimes cause large economic losses and ecological disturbances, estimating their origin and potential geographical ranges is useful. Drosophila subobscura is native to the Old World but was introduced in the New World in the late 1970s and spread widely. We incorporate information on adaptive genetic markers into ecological niche modelling and then estimate the most probable geographical source of colonizers; evaluate whether the genetic bottleneck experienced by founders affects their potential distribution; and finally test whether this species has spread to all its potential suitable habitats worldwide. We find the environmental space occupied by this species in its native and introduced distributions are notably the same, although the introduced niche has shifted slightly towards higher temperature and lower precipitation. The genetic bottleneck of founding individuals was a key factor limiting the spread of this introduced species. We also find that regions in the Mediterranean and north-central Portugal show the highest probability of being the origin of the colonizers. Using genetically informed environmental niche modelling can enhance our understanding of the initial colonization and spread of invasive species, and also elucidate potential areas of future expansions worldwide.

Assessing Niche Shifts and Conservatism by Comparing the Native and Post-Invasion Niches of Major Forest Invasive Species

Invasive species experience biotic and abiotic conditions that may (or may not) resemble their native environment. We explored the methodology of determining climatic niches and compared the native and post-invasion niches of four invasive forest pests to determine if these species experienced shifts or changes in their new climatic niches. We used environmental principle components analysis (PCA-env) method to quantify climatic niche shifts, expansions, and temporal changes. Furthermore, we assessed the effect of variable selection in the delineation and comparison of niche space. We found that variable selection influenced the delineation and overlap of each niche, whereas the subset of climatic variables selected from the first two PCA-env axes explained more variance in environmental conditions than the complete set of climatic variables for all four species. Most focal species showed climatic niche shifts in their invasive range and had not yet fully occupied the available niche within the invaded range. Our species varied the proportion of niche overlap between the native and invasive ranges. By comparing native and invasive niches, we can help predict a species’ potential range expansion and invasion potential. Our results can guide monitoring and help inform management of these and other invasive species.

Modeling the Putative Ancient Distribution of Aedes togoi (Diptera: Culicidae)

The coastal rock pool mosquito, Aedes (Tanakius) togoi (Theobald) (Diptera: Culicidae), is found in coastal east Asia in climates ranging from subtropical to subarctic. However, a disjunct population in the Pacific Northwest of North America has an ambiguous heritage. Two potential models explain the presence of Ae. togoi in North America: ancient Beringian dispersal or modern anthropogenic introduction. Genetic studies have thus far proved inconclusive. Here we described the putative ancient distribution of Ae. togoi habitat in east Asia and examined the climatic feasibility of a Beringian introduction into North America using modern distribution records and ecological niche modeling of bioclimatic data from the last interglacial period (~120,000 BP), the last glacial maximum (~21,000 BP), and the mid-Holocene (~6000 BP). Our results suggest that suitable climatic conditions existed for Ae. togoi to arrive in North America through natural dispersal as well as to persist there until present times. Furthermore, we find that ancient distributions of suitable Ae. togoi habitat in east Asia may explain the genetic relationships between Ae. togoi populations identified in other studies. These findings indicate the utility of ecological niche modeling as a complementary tool for studying insect phylogeography.