The Protected Area Paradox and refugee species: The giant panda and baselines shifted towards conserving species in marginal habitats

Linking diet switching to reproductive performance across populations of two critically endangered mammalian herbivores

Optimal foraging theory predicts that animals maximise energy intake by consuming the most valuable foods available. When resources are limited, they may include lower-quality fallback foods in their diets. As seasonal herbivore diet switching is understudied, we evaluate its extent and effects across three Kenyan reserves each for Critically Endangered eastern black rhino (Diceros bicornis michaeli) and Grevy's zebra (Equus grevyi), and its associations with habitat quality, microbiome variation, and reproductive performance. Black rhino diet breadth increases with vegetation productivity (NDVI), whereas zebra diet breadth peaks at intermediate NDVI. Black rhino diets associated with higher vegetation productivity have less acacia (Fabaceae: Vachellia and Senegalia spp.) and more grass suggesting that acacia are fallback foods, upending conventional assumptions. Larger dietary shifts are associated with longer calving intervals. Grevy's zebra diets in high rainfall areas are consistently grass-dominated, whereas in arid areas they primarily consume legumes during low vegetation productivity periods. Whilst microbiome composition between individuals is affected by the environment, and diet composition in black rhino, seasonal dietary shifts do not drive commensurate microbiome shifts. Documenting diet shifts across ecological gradients can increase the effectiveness of conservation by informing habitat suitability models and improving understanding of responses to resource limitation.

A grazer's niche edge is associated with increasing diet diversity and poor population performance

The core-periphery hypothesis predicts niche cores should be associated with greater survivorship, reproductive output and population performance rates than marginal habitats at niche edges. However, there is very little empirical evidence of whether niche centrality influences population trends in animals. Using the Cape mountain zebra (Equus zebra zebra) as a model system, we evaluated whether niche centrality is associated with population trends, resource availability and diet across a core-periphery gradient. Population growth rates and density progressively declined towards niche peripheries. Niche peripheries were resource-poor and Cape mountain zebra consumed more phylogenetically diverse diets dominated by non-grass families. In core habitats they consumed grass-rich diets and female reproductive success was higher. This combination of spatial niche modelling and functional ecology provides a novel evaluation of how bottom-up resource limitation can shape species distributions, population resilience and range change and can guide conservation management.

Contrasting ecological information content in whaling archives with modern cetacean surveys for conservation planning and identification of historical distribution changes

Many species are restricted to a marginal or suboptimal fraction of their historical range due to anthropogenic impacts, making it hard to interpret their ecological preferences from modern-day data alone. However, inferring past ecological states is limited by the availability of robust data and biases in historical archives, posing a challenge for policy makers . To highlight how historical records can be used to understand the ecological requirements of threatened species and inform conservation, we investigated sperm whale (Physeter macrocephalus) distribution in the Western Indian Ocean. We assessed differences in information content and habitat suitability predictions based on whale occurrence data from Yankee whaling logs (1792-1912) and from modern cetacean surveys (1995-2020). We built maximum entropy habitat suitability models containing static (bathymetry-derived) variables to compare models comprising historical-only and modern-only data. Using both historical and modern habitat suitability predictions  we assessed marine protected area (MPA) placement by contrasting suitability in- and outside MPAs. The historical model predicted high habitat suitability in shelf and coastal regions near continents and islands, whereas the modern model predicted a less coastal distribution with high habitat suitability more restricted to areas of steep topography. The proportion of high habitat suitability inside versus outside MPAs was higher when applying the historical predictions than the modern predictions, suggesting that different marine spatial planning optimums can be reached from either data sources. Moreover, differences in relative habitat suitability predictions between eras were consistent with the historical depletion of sperm whales from coastal regions, which were easily accessed and targeted by whalers, resulting in a modern distribution limited more to steep continental margins and remote oceanic ridges. The use of historical data can provide important new insights and, through cautious interpretation, inform conservation planning and policy, for example, by identifying refugee species and regions of anticipated population recovery.

Anthropogenic predictors of varying Holocene occurrence for Europe's large mammal fauna

Understanding how species respond to different anthropogenic pressures is essential for conservation planning. The archaeological record has great potential to inform extinction risk assessment by providing evidence on past human-caused biodiversity loss, but identifying specific drivers of past declines from environmental archives has proved challenging. We used 17 684 Holocene zooarchaeological records for 15 European large mammal species together with data on past environmental conditions and anthropogenic activities across Europe, to assess the ability of environmental archives to determine the relative importance of different human pressures in shaping faunal distributions through time. Site occupancy probability showed differing significant relationships with environmental covariates for all species, and nine species also showed significant relationships with anthropogenic covariates (human population density, % cropland, % grazing land). Across-species differences in negative relationships with covariates provide ecological insights for understanding extinction dynamics: some mammals (red deer, aurochs, wolf, wildcat, lynx, pine marten and beech marten) were more vulnerable to past human-environmental interactions, and differing single and synergistic anthropogenic factors influenced likelihood of past occurrence across species. Our results provide new evidence for pre-industrial population fragmentation and depletion in European mammals, and demonstrate the usefulness of historical baselines for understanding species' varying long-term sensitivity to multiple threats.

Ancient and modern scats record broken ecological interactions and a decline in dietary breadth of the critically endangered kākāpō parrot (Strigops habroptilus)

Threatened animal taxa are often absent from most of their original habitats, meaning their ecological niche cannot be fully captured by contemporary data alone. Although DNA metabarcoding of scats and coprolites (palaeofaeces) can identify the past and present species interactions of their depositors, the usefulness of coprolites in conservation biology is untested as few endangered taxa have known coprolite records. Here, we perform multilocus metabarcoding sequencing and palynological analysis of dietary plants of >100 coprolites (estimated to date from c. 400–1900 A.D.) and > 100 frozen scats (dating c. 1950 A.D. to present) of the critically endangered, flightless, herbivorous kākāpō (Strigops habroptilus), a species that disappeared from its natural range in Aotearoa-New Zealand (NZ) after the 13th C. A.D. We identify 24 orders, 56 families and 67 native plant genera unrecorded in modern kākāpō diets (increases of 69, 108 and 75% respectively). We found that southern beeches (Nothofagaceae), which are important canopy-forming trees and not an important kākāpō food today, dominated kākāpō diets in upland (c. >900 m elevation) habitats. We also found that kākāpō frequently consumed hemiparasitic mistletoes (Loranthaceae) and the holoparasitic wood rose (Dactylanthus taylorii), taxa which are nutrient rich, and now threatened by mammalian herbivory and a paucity of dispersers and pollinators. No single dataset or gene identified all taxa in our dataset, demonstrating the value of multiproxy or multigene datasets in studies of animal diets. Our results highlight how contemporary data may considerably underestimate the full dietary breadth of threatened species and demonstrate the potential value of coprolite analysis in conservation biology.

Territory and population attributes affect Florida scrub-jay fecundity in fire-adapted ecosystems

Fecundity, the number of young produced by a breeding pair during a breeding season, is a primary component in evolutionary and ecological theory and applications. Fecundity can be influenced by many environmental factors and requires long-term study due to the range of variation in ecosystem dynamics. Fecundity data often include a large proportion of zeros when many pairs fail to produce any young during a breeding season due to nest failure or when all young die independently after fledging. We conducted color banding and monthly censuses of Florida scrub-jays (Aphelocoma coerulescens) across 31 years, 15 populations, and 761 territories along central Florida's Atlantic coast. We quantified how fecundity (juveniles/pair-year) was influenced by habitat quality, presence/absence of nonbreeders, population density, breeder experience, and rainfall, with a zero-inflated Bayesian hierarchical model including both a Bernoulli (e.g., brood success) and a Poisson (counts of young) submodel, and random effects for year, population, and territory. The results identified the importance of increasing "strong" quality habitat, which was a mid-successional state related to fire frequency and extent, because strong territories, and the proportion of strong territories in the overall population, influenced fecundity of breeding pairs. Populations subject to supplementary feeding also had greater fecundity. Territory size, population density, breeder experience, and rainfall surprisingly had no or small effects. Different mechanisms appeared to cause annual variation in fecundity, as estimates of random effects were not correlated between the success and count submodels. The increased fecundity for pairs with nonbreeders, compared to pairs without, identified empirical research needed to understand how the proportion of low-quality habitats influences population recovery and sustainability, because dispersal into low-quality habitats can drain nonbreeders from strong territories and decrease overall fecundity. We also describe how long-term study resulted in reversals in our understanding because of complications involving habitat quality, sociobiology, and population density.

J. Desbiez A, Díaz‐Muñoz SL, Fennessy J, Fichtel C, Fischer C, Fisher JT, Fischhoff I, Ford AT, Fryxell JM, Gehr B, Goheen JR, Hauptfleisch M, Hewison AJM, Hering R, Heurich M, Isbell LA, Janssen R, Jeltsch F, Kaczensky P, Kappeler PM, Krofel M, LaPoint S, Latham ADM, Linnell JDC, Markham AC, Mattisson J, Medici EP, de Miranda Mourão G, Van Moorter B, Morato RG, Morellet N, Mysterud A, Mwiu S, Odden J, Olson KA, Ornicāns A, Pagon N, Panzacchi M, Persson J, Petroelje T, Rolandsen CM, Roshier D, Rubenstein DI, Saïd S, Salemgareyev AR, Sawyer H, Schmidt NM, Selva N, Sergiel A, Stabach J, Stacy‐Dawes J, Stewart FEC, Stiegler J, Strand O, Sundaresan S, Svoboda NJ, Ullmann W, Voigt U, Wall J, Wikelski M, Wilmers CC, Zięba F, Zwijacz‐Kozica T, Schipper AM, Tucker MA. Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data

Aim

Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species.

Location

Worldwide.

Time period

1998-2021.

Major taxa studied

Forty-nine terrestrial mammal species.

Methods

Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types.

Results

IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively.

Main conclusions

We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.

The effect of past defaunation on ranges, niches, and future biodiversity forecasts

Humans have reshaped the distribution of biodiversity across the globe, extirpating species from regions otherwise suitable and restricting populations to a subset of their original ranges. Here, we ask if anthropogenic range contractions since the Late Pleistocene led to an under-representation of the realized niches for megafauna, an emblematic group of taxa often targeted for restoration actions. Using reconstructions of past geographic distributions (i.e., natural ranges) for 146 extant terrestrial large-bodied (>44 kg) mammals, we estimate their climatic niches as if they had retained their original distributions and evaluate their observed niche dynamics. We found that range contractions led to a sizeable under-representation of the realized niches of several species (i.e., niche unfilling). For 29 species, more than 10% of the environmental space once seen in their natural ranges has been lost due to anthropogenic activity, with at least 12 species undergoing reductions of more than 50% of their realized niches. Eighteen species may now be confined to low-suitability locations, where fitness and abundance are likely diminished; we consider these taxa 'climatic refugees'. For those species, conservation strategies supported by current ranges risk being misguided if current, suboptimal habitats are considered baseline for future restoration actions. Because most climate-based biodiversity forecasts rely exclusively on current occurrence records, we went on to test the effect of neglecting historical information on estimates of species' potential distribution - as a proxy of sensitivity to climate change. We found that niche unfilling driven by past range contraction leads to an overestimation of sensitivity to future climatic change, resulting in 50% higher rates of global extinction, and underestimating the potential for megafauna conservation and restoration under future climate change. In conclusion, range contractions since the Late Pleistocene have also left imprints on megafauna realized climatic niches. Therefore, niche truncation driven by defaunation can directly affect climate and habitat-based conservation strategies.

Loss of Migratory Traditions Makes the Endangered Patagonian Huemul Deer a Year-Round Refugee in Its Summer Habitat

The huemul (Hippocamelus bisulcus) is endangered, with 1500 deer split into >100 subpopulations along 2000 km of Andes. Currently occupied areas are claimed-erroneously, to be critical prime habitats. We analyzed historical spatiotemporal behavior since current patterns represent only a fraction of pre-Columbian ones. Given the limited knowledge, the first group (n = 6) in Argentina was radio-marked to examine spatial behavior. Historically, huemul resided year-round in winter ranges, while some migrated seasonally, some using grasslands >200 km east of their current presence, reaching the Atlantic. Moreover, huemul anatomy is adapted to open unforested habitats, also corroborated by spotless fawns. Extreme naivety towards humans resulted in early extirpation on many winter ranges—preferentially occupied by humans, resulting in refugee huemul on surrounding mountain summer ranges. Radio-marked huemul remained in small ranges with minimal altitudinal movements, as known from other subpopulations. However, these resident areas documented here are typical summer ranges as evidenced by past migrations, and current usage for livestock. The huemul is the only cervid known to use mountain summer ranges year-round in reaction to anthropogenic activities. Losing migratory traditions is a major threat, and may explain their presently prevalent skeletal diseases, reduced longevity, and lacking recolonizations for most remaining huemul subpopulations.

Novel Conditions in Conservation Translocations: A Conservative-Extrapolative Strategic Framework

In response to anthropogenic threats, conservation translocations are increasingly used to combat species' population and range declines. However, moving animals outside of their current distribution can mean introducing them to novel conditions, even in the case of reintroductions to formerly inhabited areas due to ecosystem changes following extirpation. This exposure to novel conditions introduces uncertainty that can undermine decision making for species conservation. Here we propose two strategies, which we define as conservative and extrapolative, for approaching and managing novelty and the resulting uncertainty in conservation translocations. Conservative strategies are characterised by the avoidance and removal of novel conditions as much as possible, whereas extrapolative strategies are more experimental, allowing exposure to novel conditions and monitoring outcomes to increase understanding of a species' ecology. As each strategy carries specific risks and opportunities, they will be applicable in different scenarios. Extrapolative strategies suit species in recovery which can afford some experimental management, or species facing novel and emerging threats which require less traditional translocations, such as assisted colonisations. We provide examples, applying our framework to two endemic New Zealand species with long histories of translocation management: tuatara (Sphenodon punctatus), a reptile and takahē (Porphyrio hochstetteri), a flightless bird.