Aim: Species responses to global warming will depend on intraspecific diversity, yet studies of factors governing biogeographic patterns of variability are scarce. Here, we investigate the evolutionary processes underlying genetic and phenotypic diversity in the flightless and cold-adapted grasshopper Sigaus piliferus, and project its suitable space in time. Location: Te Ika-a-Māui Aotearoa—North Island of New Zealand. Methods: We used mitochondrial sequences to investigate population connectivity and demographic trends using phylogeographic tools and neutrality statistics. Metric data were used to document phenotypic variation using naïve clustering. We used niche metrics to assess intraspecific niche variation, and niche modelling to investigate suitability under past and future scenarios. Multiple matrix regressions with randomization explored the processes contributing to phenotypic differentiation among grasshopper populations. Results: Niche models and demographic analyses suggest suitable space for this grasshopper was more restricted during glacial than interglacial stages. Genealogical relationships among ND2 haplotypes revealed a deep north-south split partly concordant with phenotypic and niche variation, suggesting two ecotypes that have mixed during recolonisation of the central volcanic region. Multiple matrix regressions with randomization indicate a link between climate and phenotypic differentiation inferred from leg and pronotum dimensions but not pronotum shape. Niche projections predict severe habitat reduction due to climate warming. Main conclusions: The current distribution and intraspecific diversity of S. piliferus reflect complex biogeographical scenarios consistent with Quaternary climates and volcanism. Phenotypic divergence appears adaptive. Current levels of genetic and phenotypic variation suggest adaptive potential, yet the pace of anthropogenic warming over the next 50 years could result in small populations that may collapse before adapting. Differences in niche features between diverging intraspecific lineages suggest distinct responses to climate change, and this has implications for prioritising conservation actions and management strategies.

Aim: Species living on steep environmental gradients are expected to be especially sensitive to global climate change. Here, we combined genetic, ecological niche modelling and climatic niche comparisons to 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 Cataontopinae 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. Though geographically overlapping, niche analyses suggest these alpine species are not ecologically identical, and each shows similar but 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.

The physiological demands of flight exert strong selection pressure on avian morphology and so it is to be expected that the evolutionary loss of flight capacity would involve profound changes in traits. Here we investigate morphological consequences of flightlessness in a bird family where the condition has evolved repeatedly. The Rallidae include more than 130 recognised species of which over 30 are flightless. Morphological and molecular phylogenetic data were used here to compare species with and without the ability to fly in order to determine major phenotypic effects of the transition from flighted to flightless. We find statistical support for similar morphological response among unrelated flightless lineages, characterised by a shift in energy allocation from the forelimbs to the hindlimbs. Indeed flightless birds exhibit smaller sterna and wings than flighted taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests demonstrate that those differences are independent of phylogeny and instead demonstrate convergent morphological adaptation associated with a walking ecology. We found too that morphological variation was greater among flightless rails than flighted ones, suggesting that relaxation of physiological demands during the transition to flightlessness frees morphological traits to evolve in response to more varied ecological opportunities.

It has recently been suggested that a ‘living fossil’ can be identified because it is both morphologically conservative and exhibits a significantly slower rate of morphological evolution compared to related lineages (Herrera-Flores et al. 2017). As an exemplar, variation among known rhynchocephalians was investigated, and it was concluded that the New Zealand tuatara Sphenodon punctatus Gray, 1831 is a living fossil species (Herrera-Flores et al. 2017). In addition to the dubious biological meaning and basis of describing a ‘living fossil’ (Grandcolas et al. 2014; Grandcolas and Trewick 2016), we find major flaws in the methods used to investigate morphological conservatism among rhynchocephalians. To assist future studies of dentary shape variation among rhynchocephalians and morphological conservatism, we provide a geometric morphometric dataset for tuatara.

Variation in snail shell shape has provided evolutionary biologists with excellent material for the study of local adaptation to local environments. However, assuming shell shape variation is evidence of distinct lineages (species) may have led to taxonomic inflation within some gastropod lineages. Here we compare shell shape variation and genetic structure of two independent lineages of New Zealand rocky shore whelks in order to understand the process that lead to an unusual disjunct distribution. We examined the Buccinulum vittatum complex (three subspecies plus B. colensoi) using mitochondrial DNA sequences, 849 single nucleotide polymorphisms, and geometric morphometric data on shell shape. Specimens within the range of Buccinulum colensoi shared nuclear markers and mtDNA haplotypes with the southern subspecies B. vittatum littorinoides, while the northern samples (B. v. vittatum) had distinct genotypes. We infer that gene flow between B. colensoi and B. v. littorinoides is greater than between either of these taxa and B. v. vittatum. The distinctive shell sculpturing of B. colensoi is maintained despite gene flow, suggesting a role for selection. Although the shell form of B. colensoi appears to be an adaptation to local conditions we did not observe convergent evolution in the sympatric whelk species Cominella maculosa.

Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an exemplar to distinguish among competing hypotheses. Within our sample of tree wētā (Hemideina crassidens; Orthoptera), we found multiple mtDNA haplotypes for a protein-coding region (cytb/ND1) that differed by a maximum of 7.9%. From sequencing the whole mitochondrial genome of two representative individuals, we found evidence of constraining selection. Heterozygotes were as common as expected under random mating at five nuclear loci. Morphological traits and nuclear markers did not resolve the mtDNA groupings of individuals. We concluded that the large differences found among our sample of mtDNA sequences were simply owing to a large population size over an extended period of time allowing an equilibrium between mutation and drift to retain a great deal of genetic diversity within a single species.

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β-fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide-ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.

Hypotheses of hybrid origin are common. Here we use next generation sequencing to test a hybrid hypothesis for a non-model insect with a large genome. We compared a putative hybrid triploid stick insect species (Acanthoxyla geisovii) with its putative paternal diploid taxon (Clitarchus hookeri), a relationship that provides clear predictions for the relative genetic diversity within each genome. The parental taxon is expected to have comparatively low allelic diversity that is nested within the diversity of the hybrid daughter genome. The scale of genome sequencing required was conveniently achieved by extracting mRNA and sequencing cDNA to examine expressed allelic diversity. This allowed us to test hybrid-progenitor relationships among non-model organisms with large genomes and different ploidy levels. Examination of thousands of independent loci avoids potential problems produced by the silencing of parts of one or other of the parental genomes, a phenomenon sometimes associated with the process of stabilisation of a hybrid genome. Transcript assembles were assessed for evidence of paralogs and/or alternative splice variants before proceeding. Comparison of transcript assemblies was not an appropriate measure of genetic variability, but by mapping reads back to clusters derived from each species we determined levels of allelic diversity. We found greater cDNA sequence diversity among alleles in the putative hybrid species (Acanthoxyla geisovii) than the non-hybrid. The allelic diversity within the putative paternal species (Clitachus hookeri) nested within the hybrid-daughter genome, supports the current view of a hybrid-progenitor relationship for these stick insect species. Next generation sequencing technology provides opportunities for testing evolutionary hypotheses with non-model organisms, including, as here, genomes that are large due to polyploidy