1. The range of a species is controlled by biotic and abiotic factors; both could have changed recently due to human activity.2. We used environmental modelling, morphometric and genetic data to interpret ecological responses at the species boundary of a pair of New Zealand grasshoppers with very different ranges; one widespread (Phaulacridium marginale) and one restricted to semi-arid central/southern South Island (Phaulacridium otagoense).3. Climate-and habitat-based distribution models for grasshoppers in the past (last glacial maximum), present and future (2070), in concert with modelling of vegetation patterns imply range and demographic expansion of P. marginale and stability of P. otagoense.4. mtDNA sequence revealed four main lineages with pronounced differences in genetic diversity and geographical range. The widespread lineage associated with P. marginale revealed a signature of range expansion but regionally restricted lineages were geographically structured at a fine scale. Within the narrow geographical range of P. otagoense, three mtDNA lineages resulted in high diversity, more typical of large stable populations.5. Geometric analysis of pronotum shape identified individuals from a region of sympatry with mixed characteristics. Mismatch of phenotype, mtDNA lineage and nuclear DNA sequence indicates introgression between grasshopper species now in contact. This appears to be accompanied by P. otagoense range reduction through ecological competition. 6. Deforestation by people starting $ 800 years ago best explains range change and resulting hybridisation of these grasshoppers. Anthropogenic habitat modification can have indirect consequences on insect biodiversity and conservation by enabling introgression between formerly separate populations and species.

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9–12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

Cold‐adapted species are likely to have had more widespread ranges and greater population connectivity during the last glacial period than is the case today. This contrasts with the trend in many species for range and population size to increase during interglacials. We examined the pattern of genetic and morphological variation within an endemic, wingless, alpine grasshopper Sigaus australis (Orthoptera: Acrididae) in the Southern Alps of New Zealand, testing for isolation by distance using geometric morphometric and mitochondrial ND2 sequences to document variation. Presence/absence data were analysed to estimate the environmental envelope (niche) of Sigaus australis and the resulting model used to infer the extent of available habitat for the species during the last glacial maximum. Estimates of past range size were modified using models of montane ice extent during the LGM. Clinal patterns of pronotum shape variation and signatures of isolation by distance support the hypothesis of a formerly more connected species. A north/south division was observed in pronotum shape, but the phenotypic variation was not diagnostic, as one would expect within a single species. Although the current habitat area occupied by Sigaus australis is much smaller than estimates for the LGM from our climate model, we show that realised area differed less due to the extension of valley glaciers. However, the current distribution of S. australis is more fragmented than in the past. This and other flightless alpine species currently restricted to fragmented high elevation habitat demonstrate genetic lag but are subject to loss of diversity as anthropogenic climate warming proceeds.

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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.

Resistance to the pandemic strain of Austropuccinia psidii was identified in New Zealand provenance Leptospermum scoparium, Kunzea robusta, and K. linearis plants. Only 1 Metrosideros excelsa-resistant plant was found (of the 570 tested) and no resistant plants of either Lophomyrtus bullata or L. obcordata were found. Three types of resistance were identified in Leptospermum scoparium. The first two, a putative immune response and a hypersensitive response, are leaf resistance mechanisms found in other myrtaceous species while on the lateral and main stems a putative immune stem resistance was also observed. Both leaf and stem infection were found on K. robusta and K. linearis plants as well as branch tip dieback that developed on almost 50% of the plants. L. scoparium, K. robusta, and K. linearis are the first myrtaceous species where consistent infection of stems has been observed in artificial inoculation trials. This new finding and the first observation of significant branch tip dieback of plants of the two Kunzea spp. resulted in the development of two new myrtle rust disease severity assessment scales. Significant seed family and provenance effects were found in L. scoparium, K. robusta, and K. linearis: some families produced significantly more plants with leaf, stem, and (in Kunzea spp.) branch tip dieback resistance, and provenances provided different percentages of resistant families and plants. The distribution of the disease symptoms on plants from the same seed family, and between plants from different seed families, suggested that the leaf, stem, and branch tip dieback resistances were the result of independent disease resistance mechanisms.

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.

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 15th 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.