J. David Aguirre

Macroalgal forests dominate many rocky reef ecosystems across Aotearoa New Zealand, spanning a broad latitudinal gradient from subtropical‐to‐subantarctic waters. These habitats are characterised by high diversity and structural complexity, supporting productive coastal food webs that provide for numerous culturally and economically important species, while delivering essential ecosystem services within the coastal environment. Despite their ecological and socioeconomic importance, increasing evidence indicates that macroalgal forests in Aotearoa are declining in extent and condition. Drivers of decline vary regionally but commonly include sedimentation from land‐use change, overgrazing linked to trophic imbalances, ocean warming, marine heatwaves and invasive species. This manuscript reviews the current status and future direction of macroalgal forest restoration in Aotearoa, synthesising findings from 15 restoration research projects undertaken between 2019 and 2024 across northern, central and southern regions. These projects have trialled a range of approaches including sea urchin removal, reseeding, transplantation and invasive species control. Results indicate that while some techniques, particularly sea urchin removal, can lead to rapid recovery of macroalgae under suitable conditions, most restoration efforts remain small‐scale and experimental. Advancing restoration requires an improved understanding and amelioration of the drivers of decline, sustained funding, stronger legislative support and collaborative approaches involving mana whenua, communities, government and industry.

Biogeography has traditionally relied on species-based measures of biodiversity, partially reflecting the processes shaping spatial patterns. Incorporating the evolutionary relationships among taxa can provide a greater understanding of how distinct processes define different regional patterns over time. Here, we describe the biogeography of marine ray-finned fishes (Actinopterygii) in Aotearoa New Zealand and adjacent areas of the Southwest Pacific using phylogenetic measures of richness and endemism. Defining a geographic area of 30° latitude by 20° longitude that encompasses New Zealand’s main and offshore islands, we compiled distributional maps for 313 taxa occurring in 0–500 m waters using AquaMaps, a web-based tool that generates occurrence probability maps based on environmental and occurrence data. We describe spatial patterns of biodiversity with species and phylogenetic metrics of richness and endemism, including phylogenetic diversity and phylogenetic endemism, using a comprehensive molecular phylogeny of New Zealand’s marine fishes. To identify endemism centres, we employ the “categorical analysis of neo- and paleoendemism” (CANAPE) method which distinguishes locations with an over-representation of spatially rare short phylogenetic branches (neoendemism) and spatially rare long phylogenetic branches (paleoendemism). Latitudinal patterns of richness and endemism differ, with richness peaking at 35°S along the North Island, while endemism reaches maximum values in the northernmost oceanic islands where neoendemism dominates. Significant paleoendemism clusters around two coastal areas of mainland New Zealand. Our study shows that richness and endemism hotspots are geographically distinct for New Zealand’s marine fishes, likely the result of distinct acting processes. The richness maximum appears to be the result of a range overlap between distantly related tropical taxa shifting towards high latitudes and a lower number of older temperate taxa. Neoendemism is likely driven by the isolation of young volcanic islands, and coastal paleoendemism might be the legacy of locally stable environmental conditions that served as a refuge for relict lineages over time. We identify areas where evolutionary processes have left a signal unnoticed by species richness alone. Northern subtropical marine fish assemblages are composed of a heterogeneous mixture of distantly related taxa. Southern temperate and subantarctic areas are characterized by the presence of a low number of old lineages as well as the absence of extremely young and old taxa. We generate a phylogenetic landscape from which future biogeographic research can test hypotheses to unveil underlying evolutionary and ecological processes.

In highly dispersive taxa, gene flow can homogenise genetic variation over broad spatial and temporal scales. However, phenotypic differentiation can still arise when heritable genetic variation is available to selection and (or) when organisms exhibit plasticity. Disentangling heritable versus non-heritable components of variation is possible using genomic animal models, but this approach has been underused in wild organisms. We investigated head shape variation in the marine cryptobenthic fish Bathygobius cocosensis, a highly dispersive species occupying heterogeneous environments. Head shape, a diet-related trait, is spatially structured in Australian populations. We curated a unique dataset comprising genotypic, phenotypic, and environmental variation to: (1) contrast the scales over which genetic and phenotypic variation are structured; and (2) quantify heritable versus non-heritable contributions to head shape variation using genomic animal models and comparisons between FST, PST, and QST. At macrogeographic scales (hundreds of kilometres) and over time (2 years), phenotypic differentiation (0.0001 ≤ PST ≤ 0.47) exceeded both genomic and additive genetic differentiation (0.001 ≤ FST ≤ 0.004 and 0.00001 ≤ QST ≤ 0.004, respectively). This suggests head shape variation may primarily reflect (non-heritable) plastic responses, rather than (heritable) adaptive genetic changes in mean head shape. At microgeographic scales, associations between head shape and tide pool variables were temporally variable, indicating that local environmental conditions may structure phenotypes within populations. Overall, this study highlights the value of genomic animal models for disentangling heritable and non-heritable components of phenotypic variation in dispersive marine taxa. It provides an integrative analysis linking genetic, phenotypic, and environmental variation in a cryptobenthic fish, highlighting how phenotypic divergence can emerge without strong genetic differentiation, and challenging the common assumption that phenotypic divergence necessarily implies adaptation.

Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change. For wild populations to persist, they must adapt. Knowledge shortfalls about corals' complex ecological and evolutionary dynamics, however, stymie predictions about potential adaptation to future conditions. Here, we review adaptation through the lens of quantitative genetics. We argue that coral adaptation studies can benefit greatly from “wild” quantitative genetic methods, where traits are studied in wild populations undergoing natural selection, genomic relationship matrices can replace breeding experiments, and analyses can be extended to examine genetic constraints among traits. In addition, individuals with advantageous genotypes for anticipated future conditions can be identified. Finally, genomic genotyping supports simultaneous consideration of how genetic diversity is arrayed across geographic and environmental distances, providing greater context for predictions of phenotypic evolution at a metapopulation scale.

Aim: Lineages colonizing subtropical oceanic islands often have to overcome geographical isolation and novel climate stressors to found new populations. Historical and ecological factors influence the success of colonization and subsequent diversification, leaving a signal in the genetic constitution of the diverged, range‐restricted taxa. Here, we examined the historical biogeography of endemic marine fishes to quantify the role of geographical proximity and climate differences in determining colonization, and the underlying mechanisms of speciation.Location: Subtropical islands of the Southwest Pacific.Taxa: Thirty endemic marine ray‐finned fishes from 17 genera.Methods: Using parametric biogeographical history models, we estimated the ancestral geographical ranges for 144 species based on time‐calibrated phylogenies that included endemic species and their closest sister taxa, linking terminal nodes with geographical distribution classified into 14 biogeographical areas.Results: Ancestral range estimations revealed most species originated in Australia (66%), while only 10% and 7% originated in northern tropical Pacific locations and the East Pacific respectively, with 17% of species‐range estimations being inconclusive. Vicariant events alone were identified as the most likely process shaping range evolution in 57% of the 14 best‐fitting models, dispersal alone was favoured for 14% of species and both processes had a role for the remaining 29% of species. Across all phylogenies, likelihood‐ratio tests confirmed that geographical distance and climatic differences constrained dispersal in 73% and 33% of species, respectively.Main Conclusions: Marine fishes endemic to subtropical islands of the Southwest Pacific originated by vicariant and jump‐dispersal events mainly from ancestral populations in mainland Australia. Geographical distance and climatic differences are significant taxon‐specific factors influencing the dispersal of marine fishes in the region.

The Greenshell™ mussel, Perna canaliculus, is the most lucrative aquaculture species in New Zealand; however, losses of commercial juvenile mussels (spat) are common and can drastically reduce the yield of adults. Modification of seeding density is a potential method to manage loss of spat (~ 1–20-mm shell length), by reducing biofouling and intraspecific competition. Understanding the stress responses of spat in production systems during the early stages of aquaculture is a high priority for mussel farmers who aim to manage and optimise mussel production. Here, the effects of seeding density (low: 257, mid: 515, and high: 1030 mussels 10 cm⁻¹ of culture rope), space (depth, site), and time (December 2019 and February 2020) on oxidative stress responses (total antioxidant capacity [TAC] and lipid peroxidation [LP] biomarkers) in spat and their viability (freshwater immersion test) were assessed in the Marlborough Sounds, New Zealand. The effect of seeding density on TAC was variable among depths, sites, and times, whereas seeding density had no impact on LP. In late summer (February 2020), oxidative stress appeared to be higher compared to early summer (December 2019). This indicates that mussels were exposed to more stressful conditions later in summer, although this did not reduce their short-term viability. This research found that seeding density had no major impact on oxidative stress biomarkers and suggests that stress responses and viability of Greenshell™ mussel spat during the summer months are not affected by the seeding density levels measured in this study.

Global environmental change is happening at unprecedented rates. Coral reefs are among the ecosystems most threatened by global change and for wild populations to persist, they must adapt. However, little is known about corals’ complex ecological and evolutionary dynamics making prediction about potential adaptation to future conditions precarious. Here, we review the process of adaptation through the lens of quantitative genetics and make suggestions about how incorporating genomic tools can help to both understand and predict adaptive potential in corals. In many cases, small changes in experimental design may provide large increases in the power, precision, and accuracy of information produced for predicting corals’ adaptation to environmental changes. We also outline where quantitative genetic principles may be incorporated into current research programs that aim to bolster coral tolerance to future warming conditions.