Major disturbance events can profoundly influence biodiversity patterns, although the extent to which such shifts are predictable remains poorly understood. We used environmental DNA (eDNA) to compare forested versus recently deforested stream insect communities across disjunct regions of New Zealand, to test for parallel shifts in response to widescale disturbance. Although eDNA analyses revealed highly distinct species pools across regions, they detected concordant functional diversity shifts linked to recent deforestation, including parallel decreases in the diversity of grazing taxa. The finding that taxonomically distinct freshwater biotas have experienced broadly concordant functional shifts in the wake of deforestation indicates that disturbance can drive deterministic ecological change. By contrast, the finding that some closely related species within functional groups show discordant responses to deforestation suggests that ecological differentiation among cryptic taxa may contribute to idiosyncratic shifts. These findings highlight the potential of eDNA for resolving subtle species-level differences among anthropogenically impacted ecological assemblages.

The Southern Ocean is warming more rapidly than other parts of our planet. How this region's endemic biodiversity will respond to such changes can be illuminated by studying past events through genetic analyses of time-series data sets, including historic and fossil remains. Archaeological and subfossil remains show that the southern elephant seal (Mirounga leonina) was common along the coasts of Australia and New Zealand in the recent past. This species is now mostly confined to sub-Antarctic islands and the southern tip of South America. We analyzed ancient seal samples from Australia (Tasmania), New Zealand and the Antarctic mainland to examine how southern elephant seals have responded to a changing climate and anthropogenic pressures during the Holocene. Our analyses show that these seals formed part of a broader Australasian lineage, comprising seals from all sampled locations from the south Pacific sector of the Southern Ocean. Our study demonstrates that southern elephant seal populations have dynamically altered both range and population sizes under climatic and human pressures over surprisingly short evolutionary timeframes for such a large, long-lived mammal.

Biological dispersal – the movement of individuals and species – is an ecologically and evolutionarily important process shaping global biodiversity patterns. Species assemblages of oceanic islands are particularly contingent on overwater dispersal events. Biological dispersal ability is often highly predictable based on ecological and life history data, and dispersal directions and distances are potentially predictable based on a range of factors including oceanographic connectivity patterns, storm tracks, and bird migrations. Recent genetic studies provide striking examples of long-distance range-expansions and colonization events facilitated by transoceanic dispersal.

Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer the potential to efficiently document the distributions of endangered species, but to date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA to assess the geographic distribution of the Maungatua stonefly, Zelandoperla maungatuaensis, a flightless insect previously known from only a handful of streams draining a 4-km section of the Maungatua mountain range in southern New Zealand. We analyzed freshwater eDNA from 12 stream localities across the Maungatua range. Screening with commercial eDNA COI primers failed to detect the focal species Z. maungatuaensis. However, newly designed species-specific primers detected this taxon from four adjacent east-flowing streams known to contain Z. maungatuaensis, and two streams from which it had not previously been detected. Subsequent manual surveys confirmed the presence of two newly discovered Z. maungatuaensis populations, with COI barcoding revealing that they together represent a previously unknown, genetically divergent subclade. Our results illustrate the potential of eDNA metabarcoding to help delineate the geographic ranges of rare taxa, and highlight the importance of primer specificity when screening for rare taxa. These findings also have considerable implications for commercial companies offering biodiversity and stream health eDNA services targeting invertebrates.

Widespread deforestation has impacted biodiversity patterns globally, but the potential for forest plantations to restore biodiversity remains unclear. Here we used environmental DNA (eDNA) analysis to compare freshwater insect assemblages between native and exotic forests in New Zealand, a region that has experienced heavy deforestation over recent centuries. Our analysis of mayfly, stonefly, and caddisfly (Ephemeroptera, Plecoptera, and Trichoptera [EPT]) eDNA assemblages from 15 native forest and 15 exotic plantation streams in southern New Zealand yielded 85 taxa, most of which were shared across these habitat types. Assemblages were structured primarily by region rather than habitat type. Although the taxonomic diversity of EPT eDNA assemblages was lower in exotic plantation relative to native forest, most exotic plantation streams yielded assemblages highly similar to those of native forest streams. These findings suggest that exotic plantations can broadly restore previously deforested aquatic communities to resemble those of native forest.

Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high-dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.

We integrate multidisciplinary observations to provide a regional-scale synthesis of river drainage reconfiguration in Southland (New Zealand) between the Miocene and the Holocene. Distributions of sedimentary clasts, including alluvial gold, garnets and chromite, are combined with freshwater fish genetics, surface geomorphology, and basement geology to constrain river drainage directions and interconnections through time. River evolution in much of the South Island has been dominated by localised tectonic uplift linked to distant Alpine Fault tectonism. In the southeast, the rise of ranges between Central Otago and Southland severed initial long-distance southward drainage and gold transport and isolated fish species. Plio-Pleistocene range uplift caused the recycling of older alluvial gold deposits into the new Southland river systems. The most significant Southland drainage reorientations have occurred through the Pleistocene, in parallel with similar processes in Central Otago. In particular, the Pomahaka River has evolved geomorphologically from a Southland-linked catchment to become a major tributary of the Clutha catchment, with associated biological evolution of distinctive endemic freshwater fish.

Large‐scale disturbance events provide ideal opportunities to directly study recolonisation processes in natural environments, via the removal of competitors and the formation of newly vacant habitat. A high magnitude earthquake in central New Zealand in 2016 created major ecological disturbance, with coastal tectonic uplift of up to ~ 6 m extirpating vast swathes of intertidal organisms. One of the affected species was Durvillaea antarctica (rimurapa or southern bull kelp), which is an important habitat‐forming intertidal macroalga capable of long‐distance dispersal. Across the complex fault system with varying amounts of uplift, the species was either locally extirpated or heavily reduced in abundance. We hypothesised that neutral priority effects and chance dispersal from other populations would influence which lineages would establish. We sampled individuals of D. antarctica across the uplift zone immediately after the earthquake in 2016 and then repeatedly sampled new recruits in the same areas between 2017 and 2020, using genotyping‐by‐sequencing to provide ‘before' and ‘after' genomic comparisons. Our results revealed strong geographic clustering but little evidence of new lineages establishing at disturbed sites, although populations at uplifted sites remain at remarkably low densities. We infer that recolonisation has thus far primarily originated from refugial, remnant patches within the uplift zone. To complement the phylogeographic analysis, we estimated oceanographic connectivity among the uplift zone sample locations. The connectivity modelling estimated that northbound dispersal of D. antarctica was more likely, but we have not yet detected southern genotypes in the recolonised populations. As the ongoing recolonisation process transitions from an ecological to an evolutionary timescale, change remains possible. This study provides the first genomic ‘snapshots' of a natural recolonisation process following a large‐scale ecological disturbance event, and ongoing research has the potential to reveal important insight into both micro‐ and macroevolutionary processes.

Understanding the landscape factors governing population connectivity in riverine ecosystems represents an ongoing challenge for freshwater biologists. We used DNA sequence analysis to test the hypothesis that major geomorphological features underpin freshwater-limited fish diversity in a tectonically dynamic region of New Zealand. Phylogeographic analysis of 101 Galaxias depressiceps cytochrome b sequences, incorporating 55 localities from southern New Zealand, revealed 26 haplotypes, with only one shared among rivers. We detect strong hierarchical genetic differentiation both among and within river systems. Genetic structuring is particularly pronounced across the Taieri River system (63 individuals from 35 sites, 18 haplotypes), with 92% of variation partitioned among locations. Distinctive within-river genetic clusters are invariably associated with major subcatchment units, typically isolated by substantial gorges. The anomalous distribution of a single lineage across a major drainage divide is consistent with local, tectonically driven headwater capture. We conclude that major landscape features such as gorges can strongly partition riverine fish diversity and constrain freshwater biodiversity.

Deforestation is considered a major threat to biodiversity across many parts of the globe, but the biological impacts of this dramatic ecosystem disturbance often remain incompletely understood. In New Zealand - the world's last major landmass to be colonised by humans - widespread deforestation over recent centuries has left a highly fragmented suite of relict forest stands, ideal for assessing anthropogenic biological change. We hypothesise that this widespread environmental disturbance has underpinned repeated and predictable ecological shifts across distinct rivers and regions. Here we use freshwater environmental DNA (eDNA) data (113 samples across 38 locations; 89 insect taxa) to test for concordant biological shifts linked to this deforestation. eDNA analyses highlight consistent compositional and functional differentiation between forested versus deforested assemblages, including turnover of 'cryptic' congeneric taxa that are morphologically similar yet ecologically and genetically distinct. These dramatic biological shifts are evident even over fine spatial scales within streams, emphasising the widespread emergence of a novel 'deforested' assemblage. Our results illustrate that environmental change can drive predictable biological shifts across broad geographic regions, and highlight the power of eDNA for assessing anthropogenic ecosystem change over large geographic scales.

Exposed and isolated alpine ecosystems present evolutionary challenges for flying species worldwide. Many insects have undergone dramatic wing reduction in response to these harsh conditions, losing the ability to fly. By contrast, some taxa have countered alpine conditions by evolving larger wings to improve flight ability. In this study, we investigated how two independent clades of Zelandoperla fenestrata stoneflies respond to upland environments. Our results revealed strikingly different adaptations to elevation across the two closely related clades. In Clade 1 (southern South Island), wing length decreases sharply with increasing elevation. In contrast, wing length in the geographically adjacent Clade 2 (northern South Island, and North Island) increases with elevation. These contrasting strategies highlight the diverse adaptive pathways that may exist even for closely related lineages encountering similar environmental challenges.

Rapid adaptation is thought to be critical for the survival of species under global change, but our understanding of human-induced evolution in the wild remains limited. We show that widespread deforestation has underpinned repeated color shifts in wild insect populations. Specifically, loss of forest has led to color changes across lineages that mimic the warning coloration of a toxic forest stonefly. Predation experiments suggest that the relative fitness of color phenotypes varies between forested and deforested habitats. Genomic and coloration analyses of 1200 specimens show repeated selection at the ebony locus controlling color polymorphism across lineages. These findings represent an example of human-driven evolution linked to altered species interactions, highlighting the possibility for populations to adapt rapidly in the wake of sudden environmental change.

Wing reduction is a common feature of upland insect communities. This phenomenon is thought to be primarily driven by selection against flight, which is typically unfavourable in upland environments due to high winds and cold temperatures. In some insect taxa, wing reduction has been directly linked to increased fecundity. However, few studies have directly tested for shifts in fecundity linked to flight musculature. Here, we test for dispersal-fecundity trade-offs in the widespread subalpine stonefly Zelandoperla fenestrata. Our analysis of 450 stoneflies across 81 localities reveals significant dispersal-fecundity trade-offs. Specifically, we identify a positive association between the size of their flight muscles and the length of their wings, and a negative association between wing length and ovarian mass. Furthermore, we found a significant negative relationship between flight musculature and ovary mass. These results represent a rare example of a dispersal-fecundity trade-off in the wild and illustrate that such trade-offs can potentially involve corresponding reductions in both flight musculature and wing development. Our findings suggest that widespread taxa subject to variable environmental conditions may benefit from flexible allocation of energetic resources.

Freshwater-limited fish populations are often tightly constrained by river drainage boundaries. As a case in point, the distribution of lineages within New Zealand's diverse Galaxias vulgaris complex is broadly structured by geographic barriers, reflecting tectonic processes. However, several drainages of the Central Otago region have been locally modified by past gold-mining activities, with artificial water races connecting formerly isolated headwaters of distinct river drainage systems. Here we synthesise published genetic data to highlight the role of anthropogenic catchment modification in redistributing fish diversity. These data show that several local phylogeographic anomalies for stream-resident Galaxias fishes are closely linked to anthropogenic connections across major drainage divides. While these anthropogenic translocations may parallel natural geologically-driven mixing events that occur on deeper time scales, they nevertheless have potential conservation implications given the increasing fragmentation of native fish populations. Our review also highlights the role of sub-catchment units in shaping the hierarchical structure of intraspecific biodiversity.

Detached buoyant kelp can disperse thousands of kilometres at sea and can colonize newly available shores in the wake of disturbances that wipe out competitors. Localized earthquake uplift can cause extirpation of intertidal kelp populations followed by recolonization. Sources of recolonizing kelp can be detectable in genomic structure of contemporary populations. Our field observations combined with LiDAR mapping identified a previously unrecognized zone of uplifted rocky coastline in a region that is slowly subsiding. Intertidal kelp (Durvillaea antarctica) on the uplifted section of coast is genetically distinctive from nearby populations, with genomic signatures most similar to that of kelp 300 km to the south. Genetic divergence between these locations suggests reproductive isolation for thousands of years. Combined geological and genetic data suggest that this uplift event occurred during one of four major earthquakes between 6000 and 2000 years ago, with one of the younger events most likely. Extirpation of the pre-existing kelp required sudden uplift of approximately 2 metres, precluding several small incremental uplift events. Our results show the power of integrating biological (genomic) analyses with geological data to understand ancient geological processes and their ecological impacts.

Aim Genotyping-by-sequencing (GBS) and similar reduced-representation sequencing methods, such as restriction site-associated DNA sequencing (RADseq), have been revolutionary for genetic analyses in biogeography. However, navigating the many different methodological and analytical approaches and numerous sources of potential error can be overwhelming. We provide an overview of key considerations for biogeographical research using GBS, from sample design through data filtering to the sharing of data, which should particularly assist new users. Taxon All taxa. Location Worldwide. Methods We review recent advances for GBS and compare differences among GBS methods and analytical approaches. We highlight the concerns most relevant for biogeographical research, and emphasise practical limitations for studies on non-model organisms. Results GBS methods vary substantially and recent literature demonstrates the need for careful study design and data filtering relevant to the study organism and hypothesis under investigation. Biogeographical research using non-model organisms or long-term sampling are likely to face some practical limitations compared to ideal GBS study designs. The methodological information recorded in published manuscripts often varies. We outline a general framework for planning and undertaking biogeographical research using GBS. Main conclusions GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow-across sampling, library preparation and sequencing, identifying and filtering samples and loci, biogeographical analyses, and sharing data-is crucial for improving scientific reproducibility and compatibility among GBS datasets. This review outlines ways to improve and simplify GBS research, thereby enhancing our capacity to use genomic data to address broad-scale biogeographical questions.

Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time-calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.

Freshwater ecosystems frequently house diverse assemblages of closely related fish taxa, which can be particularly prone to hybridization and introgression. While extensive introgression may be expected among biogeographically proximate lineages, recent analyses imply that contemporary distributions do not always accurately predict hybridization history. Here, we use the ABBA-BABA approach to test biogeographic hypotheses regarding the extent of hybridization in the recent evolution of New Zealand's species-rich freshwater Galaxias vulgaris fish complex. Genome-wide comparisons reveal significant increases in introgression associated with increasing geographic overlap of taxa. The estimator DP, which assesses the net proportion of a genome originating from introgression, shows a particularly strong relationship with biogeographic overlap (R2 = .43; p = .005). Our analyses nevertheless reveal surprisingly substantial signatures of introgression among taxa that currently have disjunct distributions within drainages (e.g., separate subcatchments). These "anomalies" imply that current biogeography is not always an accurate predictor of introgression history. Our study suggests that both modern and ancient biogeographic shifts, including recent anthropogenic range fragmentation and tectonically driven riven capture events, have influenced introgression histories in this dynamic freshwater fish radiation.

Landlocking is a process whereby a population of normally diadromous fish becomes limited to freshwater, potentially leading to behavioural, morphological, and genetic changes, and occasionally speciation. The study of recently landlocked populations can shed light on how populations adapt to environmental change, and how such life-history shifts affect population-genetic structure. Kōaro (Galaxias brevipinnis) is a facultatively diadromous Southern Hemisphere galaxiid fish that frequently becomes landlocked in inland lakes. This study compares seven landlocked kōaro populations to diadromous populations from main and offshore islands of New Zealand. Genotyping-by-sequencing was used to obtain genotypes at 18,813 single nucleotide polymorphism sites for each population. Analyses of population structure revealed that most landlocked populations were genetically highly distinct from one another, as well as from diadromous populations. A few particularly isolated island and lake populations were particularly strongly genetically differentiated. Landscape characteristics were measured to test whether lake elevation, size, or distance from the sea predicted genetic diversity or differentiation from diadromous kōaro. While there were no significant relationships indicating isolation-by-distance or isolation-by-environment, we detected a trend toward lower genetic diversity in lakes at higher elevations. Our findings illustrate the critical role that landlocking can play in the structure of intraspecific genetic diversity within and between populations.