ABSTRACT Aim Accurate identification underpins effective conservation, shaping our understanding of species distributions and conservation. Yet for many taxa, diagnostic criteria remain poorly resolved, creating an ‘identification gap’ that limits the capacity of scientists and environmental managers to study, monitor, and protect them. We examined the identification of the White‐faced Storm Petrel Pelagodroma marina complex in the Southwest Pacific as a case study to develop a systematic, trait‐based approach for distinguishing closely related taxa and to apply these criteria to determine their distributions. Location Marine and island ecosystems across the Southwest Pacific. Methods Using nine categorically scored phenotypic traits for 1011 individuals from citizen science photographs, museum specimens, and available literature and online resources, we applied a polytomous variable latent class analysis to identify combinations of traits that distinguished among individuals, irrespective of their distributions. Results The optimal model incorporated four traits ( rump colour , rump extent , collar, and tail shape ) of which only rump colour and tail shape were required to distinguish three latent classes which aligned broadly with the distributions of the three recognised subspecies present in the study region. These results revealed records of the ‘Nationally Critical’ and poorly‐known Kermadec Storm Petrel P. m. albiclunis from south‐eastern Australia, far beyond their core distribution and showed that Australian and Aotearoa/New Zealand taxa often make cross‐Tasman movements, offering novel and management‐relevant insights into their at‐sea distributions. Main Conclusions Our approach quantitatively validated field identification features and demonstrates how citizen science photographs and museum collections can be used to bridge the ‘identification gap’. Publicly available datasets from which traits can be quantified offer an opportunity to robustly address this gap. Our objective, trait‐based framework offers a generalisable and scalable approach for resolving identification challenges in hard‐to‐identify, threatened, and cryptic taxa globally.

ABSTRACT Aim Protecting phylogenetic diversity (PD) has been advocated as a basis for spatial conservation planning. However, phylogenetic branch lengths can vary substantially depending on methodological choices made during the inference of phylogeny and divergence times, and little is known about the sensitivity of spatial patterns of PD to these choices. We aimed to test the variability of spatial PD patterns, including the size and locations of ‘hotspots’ of evolutionary history, under alternative phylogenetic methods. We then aimed to test the downstream effects for conservation priority areas selected using Systematic Conservation Planning methods. Location Australia. Methods Using phylogenomic and fossil data for the plant clade Grevilleoideae (663 species), we inferred divergence times under 26 combinations of methods relating to topology and divergence time estimation, choice of fossil calibration, calibration constraints, and evolutionary model parameterization. We compared spatial patterns of PD and conservation priority areas selected using a reserve selection algorithm across the resulting 26 phylogeny treatments. Results Continent‐wide, there was substantial incongruence in spatial PD patterns among treatments, with large areas identified as PD hotspots or priority areas under fewer than 26 treatments. Areas of incongruence in priority areas amounted to approximately 30% of the land budget allocated to expansion of the protected area network in our simulations (~8% of Australia's land area). Spatial patterns were especially sensitive to the choice of Bayesian (MCMCtree) vs. fast rate‐smoothing (RelTime) methods of divergence dating. Main Conclusions Spatial patterns of PD and choice of priority areas for conservation of PD can vary substantially under alternative, routine, methodological choices in phylogenetics. This introduces uncertainty into conservation planning that aims to maximize protection of evolutionary history. Uncritical use of phylogenetic information in conservation may lead to wasted resources or poor conservation outcomes.

ABSTRACT Aim Orchids make up 8% of Madagascar's vascular plant species richness and are typically associated with the island's forests. Yet most of the island is covered by open ecosystems, long dismissed as degraded. This perception has contributed to their neglect, limiting our understanding of species ecology and hindering conservation action in this global biodiversity hotspot. Using orchids, we provide a novel understanding of plant diversity patterns across Madagascar's ecosystems. Location Madagascar. Methods We assessed the ecosystem attribution of the 884 orchid species of Madagascar among closed (forest) and open (grassy, marsh, rocky outcrop, scrub) ecosystems. We analysed the taxonomic composition, richness, environmental niche, geographic patterns, phenology, and collection patterns of orchids using a mix of herbarium, publication, and iNaturalist data. Results We find that 31% of Madagascar's orchid species occur in open ecosystems, with 17% restricted to them. These species match closed‐ecosystem species in degree of endemism to Madagascar (~85%) but are associated with higher elevations, fire, and pronounced precipitation seasonality, and are distributed particularly in the grassy Central Highlands, a region historically undervalued ecologically compared to humid forests. Temporally, open‐ecosystem specialist orchids exhibit strongly synchronous, brief wet‐season flowering, unlike the more diffuse flowering observed throughout the year in forests. Conclusions We reveal a distinct component of Madagascar's orchid flora, demonstrating that open‐ecosystem species represent high endemism and ecological specialisation, with implications for understanding biogeography and conservation planning across tropical landscapes. These results provide an evidence base for open ecosystem conservation and suggest that other taxa may also be under‐represented in our understanding of Madagascar's open‐ecosystem biodiversity. Re‐evaluating open ecosystems can uncover overlooked dimensions of species diversity and ecological function, informing more balanced conservation strategies across contrasting ecosystems.

ABSTRACT Aim Spatiotemporal data gaps in fishery‐independent surveys—arising from offshore wind development, marine protected areas or spatially uneven sampling effort—pose challenges to the consistency and reliability of abundance indices that inform stock assessments. This study evaluates how survey preclusion affects the spatial and temporal behaviour of abundance indices, using offshore wind survey exclusion in key NOAA fisheries surveys in the Mid‐Atlantic as a case study to assess impacts on temporal trends, deviations over space and uncertainty for four iconic stocks. Location Mid‐Atlantic Ocean, US. Methods Using four species as case studies, we compared design‐based abundance indices derived from a Full dataset (without offshore wind) and a wind energy excluded (WEE) dataset that hypothetically removed all survey tows within wind energy areas (WEAs) across the full time series. Model‐based approaches, including statistical models, machine learning methods and vector autoregressive spatial–temporal model (VAST), were then applied to reconstruct tow‐level survey data using the WEE dataset and derive spatial and temporal abundance indices. Model‐based indices were evaluated in terms of deviations in spatial abundance indices, changes in relative precision, and consistency of temporal trends relative to design‐based indices. Results Design‐based indices retained consistent temporal trends despite emerging errors in absolute abundance estimates and increased variance. Model‐based reconstruction partially recovered spatial information within WEAs, but reconstructed spatial abundance indices exhibited greater variability in deviations inside WEAs than outside, whereas changes in relative precision were generally small. Temporal trends in model‐based indices were generally consistent with design‐based indices, though sensitivity varied by species and time series. Differences among modelling approaches were species‐dependent, reflecting contrasts in mobility, spatial aggregation and life history traits. Main Conclusions This offshore wind case study demonstrates that survey preclusion primarily affects the spatial representation and magnitude of abundance indices, whereas temporal trend signals can remain robust under moderate data loss. No single modelling approach was consistently robust to survey preclusion across species and index dimensions, reflecting trade‐offs between spatial reconstruction behaviour, uncertainty propagation and temporal stability. Species life history traits played a role in model performance: mobile species with stronger spatial autocorrelation were generally less sensitive to spatial preclusion than sessile species with patchy distribution. These general patterns highlight the need for dimension‐specific, life‐history‐informed modelling approaches when addressing spatiotemporal data gaps arising from marine development and other forms of conflicting marine use.

ABSTRACT Aim Climate change is driving species to either shift their ranges or face extinction. While its effects on taxonomic diversity (TD) are relatively well understood, the impacts on functional diversity (FD) and phylogenetic diversity (PD) remain less explored. Among the biological metrics considered in protected area (PA) selection, TD is the most common, yet its effectiveness in also capturing high FD and PD under future climate scenarios is uncertain. Here, we assess the implications of future climate scenarios for the conservation of TD, FD and PD of forest birds. Location Central Corridor of the Atlantic Forest (CCAF), Brazil. Methods We used ecological niche models to project the species distributions of 292 forest birds for baseline and future (2050 and 2070) scenarios. We generated binary maps of suitable areas for each species and calculated alpha and beta diversities for TD, FD and PD. We also evaluated spatial overlaps between highly diverse areas and the current PA network. Results Most species are projected to experience range contractions, leading to declines in TD, FD, and PD. The western CCAF, a subregion with low diversity, is expected to face the greatest losses, while coastal areas show greater resilience with fewer declines. FD and PD exhibit distinct spatial patterns, including functional type replacements in the northwestern CCAF and variations in phylogenetic lineages in the central‐eastern subregion. Northeastern PAs may retain higher diversity in the future, while the southern CCAF remains underrepresented in the current PA network. The eastern CCAF is identified as a subregion of community stability across TD, FD and PD. Main Conclusions Incorporating multiple facets of diversity offers a comprehensive framework for conservation strategies. Beta diversity highlights critical stable areas connecting highly diverse subregions of the CCAF. Therefore, a better understanding of these patterns can guide the preservation of species, their ecological roles and evolutionary heritage in a changing world.

ABSTRACT Aim Knowledge of the main drivers of population differentiation is crucial for understanding evolutionary processes and preserving biodiversity. While primarily studied in terrestrial habitats, the mechanisms operating in the marine realm are less well understood. This study reconstructed the phylogeographic history of a tropical seabird to identify relevant marine barriers promoting intraspecific diversity in the Western Indian Ocean. Location Western Indian Ocean. Taxon Three subspecies of tropical shearwater : Puffinus bailloni bailloni , P. b. nicolae, P. b. colstoni. Methods We used restriction site‐associated DNA sequencing and applied population genomics to birds from six breeding colonies to assess intraspecific diversity, population genetic structure and connectivity in the tropical shearwater. Results were complemented with data from six oceanographic variables and effective migration surfaces to evaluate the role of oceanographic factors in driving population differentiation. Results All analyses consistently separated the birds from the northern colonies (subsp. nicolae and colstoni ) from those of the southern islands (subsp. bailloni ), but failed to assign the colstoni birds as a different taxon. Results revealed remarkable levels of genetic differentiation within an ocean basin in a highly vagile species and suggested higher levels of gene flow at the northern limit of the species' distribution compared to the southern range. Main Conclusions Our study suggests that ocean surfaces and sea surface temperature may constitute an important barrier to gene flow for the tropical shearwater and potentially other marine species in the region. This study does not support the colstoni form as a different subspecies, highlighting the need for further taxonomic reassessment. Ultimately, the results allowed us to identify Europa and Aldabra as the most threatened management units and propose conservation strategies directly applicable to these most at‐risk colonies.

ABSTRACT Aim Global climate projections identify tropical regions as hotspots of climate change during the 21st century. The few ground data in tropical Africa confirm significant warming and drying over the last decades, but how plant communities will tolerate these new climate conditions remains vastly uncertain. In this study, we assess the climatic vulnerability of tropical moist forests across Africa. Location Tropical Africa. Methods We mapped climate change exposure across the tropical moist forest biome, focusing on mean annual temperature (MAT), mean annual precipitation (MAP) and climatological water deficit (CWD) using climate projections for 2085 from five regional models under RCP4.5 and RCP8.5. Using occurrence records for 3,536 tree and shrub species, we estimated species' climatic limits and safety margins, then averaged these margins at the community level. Finally, we combined exposure and safety margins to assess species‐ and community‐level risk by 2085. Results Under RCP4.5, corresponding to an average warming of 2.4°C by 2085, 92% of species (3,256) could be at risk in at least one community where they occur. This rate increases to 96% (3,405 species) under RCP8.5, with an average warming of 4.3°C. In all scenarios, the most at‐risk communities are concentrated in low‐elevation regions, where species have few opportunities to migrate if their climatic limits are exceeded. The high risk across the forest biome results from the combination of significant and widespread temperature increases and the relatively narrow safety margins of the species. Specifically, 50% of species have an average safety margin below 1.6°C above baseline temperatures, suggesting they are already near their observed climatic limits. Main Conclusions Beyond refining our understanding of the vulnerability of tropical moist forests across Africa, our results have far‐reaching implications for conservation, allowing us to target species and communities of interest for further monitoring and conservation efforts.

ABSTRACT Aim Understanding the effects of habitat degradation on biodiversity is essential for undertaking conservation initiatives, but commonly used metrics of biodiversity, like species richness and beta diversity, can miss important signals of change. Greater insights can be gained by partitioning beta diversity into nestedness, which relates to species loss, and turnover, which relates to species replacement. To obtain a more comprehensive understanding of biodiversity change with habitat degradation, we investigate how nestedness and turnover vary when comparing assemblages from the same or different habitat degradation levels, and how assemblage aggregation resolution influences this relationship. Location Sweden. Methods We used beta diversity partitioning to assess lichen, fungi and bryophyte species composition from 120 forest sites across Sweden, from three different habitat degradation levels, and at two aggregation scales (pairwise local assemblages and assemblages pooled at the habitat degradation level across our study sites). We examined how pairwise total beta diversity, nestedness and turnover varied when comparing assemblages from sites of either the same or different habitat degradation levels. In addition, we examined the relationship between total beta diversity, nestedness and turnover when assemblages pooled at the habitat degradation level were compared. Results We detected a small increase in pairwise lichen total beta diversity (Cliffs delta 0.40) and nestedness (Cliffs delta 0.19), but not in any other pairwise comparisons. In contrast, for all taxa, comparisons between assemblages pooled at the habitat degradation level showed higher values of nestedness and lower values of turnover than the corresponding pairwise comparisons, suggesting biotic homogenisation in highly degraded sites. Main Conclusions Our results highlight the importance of considering biodiversity change across multiple spatial resolutions to fully capture the effects of local species replacements in highly degraded habitats on biotic homogenisation.

ABSTRACTAimFreshwater ecosystems cover less than 3% of the Earth's surface, yet support nearly 10% of all known animal species, majorly represented by freshwater fishes and amphibians, both of which are highly threatened groups. Geographically isolated freshwater species, such as those inhabiting islands, are at high risk. Australia, with nearly 9300 islands, is home to diverse island freshwater fauna. However, the lack of published literature on their island occurrence, threats and management impedes effective conservation across islands. We aim to describe the distributional patterns of amphibians and freshwater fishes on islands and analyse the island characteristics that influence these patterns.LocationAustralia's Islands.MethodsWe compiled the first database of occurrences of amphibians and freshwater fishes across Australia's islands. Utilising the database, we used regression analysis to examine the main drivers of distributional patterns, species richness and species composition on Australia's islands.ResultsWe found that 102 amphibians and 95 freshwater fishes occur on Australia's islands. Fifty‐five fishes were obligate freshwater species, 21 were euryhaline and 19 were diadromous. Although freshwater fishes showed lower richness on islands than amphibians, potentially due to lower survey efforts, fishes had a higher proportion of threatened and alien species. Islands with more precipitation that are closer to the mainland hosted higher amphibian richness, which likely retained mainland amphibian assemblages or were more easily colonised. In contrast, larger islands hosted higher freshwater fish richness, where diverse habitats were likely to sustain more species.Main ConclusionsUsing the new database compiled, we found that occurrences of amphibians and freshwater fishes on islands were influenced by climate, island size and distance from the mainland. This provides a baseline for follow‐up studies on phylogeny and biogeography. This research contributes to future conservation of amphibians and freshwater fishes on islands by revealing islands of potential conservation concern and lays the groundwork for future spatial prioritisation work.