Ludovic Dutoit

Genomics can provide conservation-relevant insights into population size, genetic diversity, and connectivity with relatively little sampling effort. However, for frogs and other small vertebrates, invasive genetic sampling (e.g. toe-clipping) can impact animals’ long-term survival and welfare. Minimally-invasive genetic sampling methods may be required to facilitate robust conservation genomic studies of small vertebrates. In Aotearoa | New Zealand, previous genetic studies of the three native Leiopelma spp.

Conservation management of endangered species increasingly relies on genomic approaches to understand how long‐term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding‐related phenomena has been largely overlooked. Here, we compare the use of whole‐genome and reduced‐representation sequencing approaches in 148 individuals of the critically endangered parrot, the kākāpō ( Strigops habroptilus ), to assess inbreeding and its effects on female reproductive success. We explore how sequencing choice influences the identification of long stretches of homozygosity across the genome (runs of homozygosity, ROH), and compare the conservation implications of the results produced by each method. Both whole‐genome and reduced‐representation sequencing approaches provided comparable estimates of genome‐wide inbreeding ( F _ROH ) and revealed consistent effects on egg hatching success, suggesting that reduced‐representation sequencing is capable of detecting inbreeding depression in wild populations under certain conditions. Whole‐genome sequencing enabled chromosome‐level inbreeding analyses, which revealed no strong evidence of chromosome‐specific effects beyond the genome‐wide signal. These results suggest that inbreeding depression in kākāpō reflects small effects across many chromosomes rather than strong effects on only a few, and that the primary benefit of whole‐genome sequencing lies in improving the precision of genome‐wide inbreeding estimates rather than identifying chromosome‐specific effects. Our findings highlight the distinct benefits of each sequencing approach in conservation, particularly within the context of resource limitations.

Parasites can provide valuable insights into the ecology and health of their hosts and the state of the surrounding ecosystem. In this study, we describe the helminth parasite communities infecting penguin species in Otago, New Zealand (little blue penguin, Fiordland crested penguin, Snares crested penguin, erect crested penguin and yellow-eyed penguin). We investigate differences in parasite communities among penguin species, and changes over time for little blue penguins. In total, 19 parasite species representing 8 families (Desmidocercidae, Anisakidae, Acuariidae, Capillariidae, Tetrabothriidae, Heterophyidae, Renicolidae and Polymorphidae) were recorded from 121 penguin individuals. Parasite assemblages differed among penguin species, likely reflective of their differences in diet and feeding strategies. We also observed significant changes in the composition of parasite communities of little blue penguins using samples from a 30-year timespan (1993–2023). There was an overall increase in parasite diversity over time, including some species of potential disease concern, which could reflect a shift in prey availability of fish in the area. Our findings contribute to the understanding of penguin ecology and emphasise the use of parasites as indicators of ecological change.

Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome‐level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterise long‐term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high‐quality genomes for species of conservation concern despite less‐than‐optimal samples and/or sequencing data, demonstrating its use on Hector's and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector's dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference‐guided techniques, utilising chromosome‐level genomes of closely related species. The pipeline assembled highly contiguous chromosome‐level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores > 96.35%), despite non‐optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long‐term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector's and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high‐quality genomic resources to facilitate ongoing conservation genomics research.

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.

Escalating concern regarding the impacts of reduced genetic diversity on the conservation of endangered species has spurred efforts to obtain chromosome-level genomes through consortia such as the Vertebrate Genomes Project. However, assembling reference genomes for many threatened species remains challenging due to difficulties obtaining optimal input samples (e.g., fresh tissue, cell lines) that can characterize long-term conservation collections. Here, we present a pipeline that leverages genome synteny to construct high-quality genomes for species of conservation concern despite less-than-optimal samples and/or sequencing data, demonstrating its use on Hector’s and Māui dolphins. These endemic New Zealand dolphins are threatened by human activities due to their coastal habitat and small population sizes. Hector’s dolphins are classified as endangered by the IUCN, while the Māui dolphin is among the most critically endangered marine mammals. To assemble reference genomes for these dolphins, we created a pipeline combining de novo assembly tools with reference-guided techniques, utilizing chromosome-level genomes of closely related species. The pipeline assembled highly contiguous chromosome-level genomes (scaffold N50: 110 MB, scaffold L50: 9, miniBUSCO completeness scores >96.35%), despite non-optimal input tissue samples. We demonstrate that these genomes can provide insights relevant for conservation, including historical demography revealing long-term small population sizes, with subspecies divergence occurring ~20 kya, potentially linked to the Last Glacial Maximum. Māui dolphin heterozygosity was 40% lower than Hector’s and comparable to other cetacean species noted for reduced genetic diversity. Through these exemplar genomes, we demonstrate that our pipeline can provide high-quality genomic resources to facilitate ongoing conservation genomics research.

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.

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.

Fertility‐targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression and results from mouse knockout models. This framework identified 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other non‐drive genetic pest control technology. Further, a comparative genomics analysis demonstrates the conservation of the identified genes across several globally significant invasive mammals. In addition to providing important considerations for identifying candidate genes, our framework and the genes identified in this study may have utility in developing additional pest control tools such as wildlife contraceptives.

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 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 D_P, which assesses the net proportion of a genome originating from introgression, shows a particularly strong relationship with biogeographic overlap (R ² = 0.43; p = 0.005). 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.