The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA‐like gene that underwent selection during domestication on 15^th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB‐ARC domain‐containing gene was found to strongly affect anthocyanin accumulation using a genome‐wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.

Mountains create steep environmental gradients that are sensitive barometers of climate change. We calibrated 10 statistical models to formulate ensemble ecological niche models for 12 predominantly alpine, flightless grasshopper species in Aotearoa New Zealand, using their current distributions and current conditions. Niche models were then projected for two future global climate scenarios: representative concentration pathway (RCP) 2.6 (1.0°C rise) and RCP8.5 (3.7°C rise). Results were species specific, with two-thirds of our models suggesting a reduction in potential range for nine species by 2070, but surprisingly, for six species, we predict an increase in potential suitable habitat under mild (+1.0°C) or severe global warming (+3.7°C). However, when the limited dispersal ability of these flightless grasshoppers is taken into account, all 12 species studied are predicted to suffer extreme reductions in range, with a quarter likely to go extinct due to a 96–100% reduction in suitable habitat. Habitat loss is associated with habitat fragmentation that is likely to escalate stochastic vulnerability of remaining populations. Here, we present the predicted outcomes for an endemic radiation of alpine taxa as an exemplar of the challenges that alpine species, both in New Zealand and internationally, are subject to by anthropogenic climate change.

Aim: Species living on steep environmental gradients are expected to be especially sensitive to global climate change, but little is known about the factors influencing their responses to contemporary warming. Here, we investigate the influence of climate on the biogeography of three alpine species with overlapping ranges.Location: Te Waipounamu (South Island) Aotearoa–New Zealand.Taxon: Endemic alpine adapted Catantopinae grasshoppers.Methods: We used niche modelling to estimate and project the potential niche of three focal species under past and future climate scenarios. Vulnerability assessments were performed using niche factor analyses. Demographic trends and phylogeographic structure were investigated using samples from 15 mountain tops to generate mitochondrial DNA haplotype networks and population genetic statistics.Results: Niche models and genetic data suggest suitable habitat for all three alpine species was more widespread and contiguous in the past than today. Demographic analyses indicate in situ survival rather than post‐Pleistocene colonisation of current habitat. Population structuring and genetic divergence suggest that mountain uplift during the Pliocene and environmental barriers during Pleistocene glacial and interglacial stages shaped contemporary population structure of each species. Although geographically overlapping, niche analyses suggest these alpine species are not ecologically identical, each showing distinct responses to environmental change, but all will lose intraspecific diversity through population extinction.Main Conclusions: Climatic, biological and geophysical factors controlled population structuring of three cold‐adapted species during the Pleistocene with a legacy of spatially separate intraspecific lineages. Ecological niche models for each species emphasise distinct combinations of environmental proxies, but all are expected to experience severe habitat reduction during climate warming. Increased global temperatures drive available habitat to higher elevation resulting in population contractions, range shifts, habitat fragmentation, local extinctions and genetic impoverishment. Despite alpine species not being ecologically identical, we predict all mountain biota will lose significant genetic diversity due to global warming.