Lineage‐level distribution models lead to more realistic climate change predictions for a threatened crayfish

Shrinking suitable habitat of a sub-Arctic foundation kelp under future climate scenarios

Climate change has profound effects on the distribution of kelp forests in the Arctic and sub-Arctic. However, studies on the responses of kelps to climate change, particularly along the sub-Arctic regions of the Alaska coast, are limited. Eualaria fistulosa is a foundational kelp species in the Aleutian Islands, with an east-west distribution that extends from Japan to southern southwest Alaska. In this study, we utilized a species distribution model (SDM) to explore changes in the future habitat suitability of E. fistulosa under contrasting Shared Socioeconomic Pathway (SSP) scenarios. Our model exhibited relatively high predictive performance, validating our SDM predictions. Notably, the SDM results indicate that minimum sea surface temperature, annual range in sea surface temperatures, and annual mean current velocities are the three most important predictor variables determining E. fistulosa's distribution. Furthermore, the projected geographic distribution of Eualaria is generally consistent with its observed occurrence records. However, under high emission scenarios (SSP5-8.5), E. fistulosa is predicted to contract its distribution range by 9.0% by 2100, with widespread disappearance along the southeast Alaskan coast and limited northward migration to Kamchatka Krai in Russia and Bristol Bay in Alaska. These findings contribute valuable insights for conservation strategies via addressing climate-induced alterations in sub-Arctic kelp distribution.

Redistribution of vocal snapping shrimps under climate change

A variety of marine organisms can produce sounds that are important components of the marine soundscape and play a critical role in maintaining marine biodiversity. Climate change has greatly altered the geographical ranges of many marine species, including sound-producing organisms. However, the direction and the magnitude of the potential impact of climate change on the geographical distribution of sound-producing marine organisms in future remain largely unknown. To address this knowledge gap, we selected snapping shrimp, one of the most well-known marine sound-producing organisms, as a model species and explored their redistribution under climate change via species distribution models. We aimed to predict the redistribution of snapping shrimps under climate change and identify the influencing factors, which have important implications for marine conservation. Our models exhibited good discrimination abilities and identified maximum temperature as the most influential predictor of snapping shrimp distribution. Model predictions suggested that species richness is higher in tropical and temperate coastal waters and peaks in the Indo-Pacific region. The majority of snapping shrimp species are expected to respond to the changing climate by shifting their geographical ranges to deeper waters and higher latitudes. Our results showed that, in the future, high-latitude species were more likely to experience range expansion, whereas low-latitude species might experience range contraction. Moreover, the Central Indo-Pacific are predicted to suffer the biggest decline in species richness, whereas areas such as the coastal waters of southern Australia and northern China might serve as climate refuges for snapping shrimps in the future. In summary, this study highlights the potential effects of climate change on the distribution of sound-producing snapping shrimps, which may result in cascading effects on marine ecosystems.

Unveiling the suitable habitats and future conservation strategies of Tridacna maxima in the Indo-Pacific core area based on species distribution model

Climate change is exerting unprecedented impacts on marine habitats, and many sessile invertebrate species, such as the endangered giant clam Tridacna maxima, are particularly sensitive to climate driven changes in their environment. Understanding its spatial distribution and conservation requirements is of crucial significance in formulating effective protection strategies. However, the species has been extensively harvested and depleted in many regions, leading to its listing as endangered species by the International Union for Conservation of Nature (IUCN). While marine protected areas (MPAs) are considered effective conservation tools, it remains uncertain whether existing MPAs adequately protect these vulnerable giant clams. To enhance the management and conservation of this species, we employed a Species Distribution Models (SDMs) approach, integrating occurrence records of T. maxima with environmental variables, to predict its potential distribution based on habitat suitability and capture spatiotemporal changes. Based on geographical and genetic variations, the T. maxima in the Indo-Pacific core region is primarily divided into two populations: the East Indian Ocean-South China Sea population (EIOS) and the West Pacific-Indonesia population (WPI). We first quantified realized niche to reveal significant differences in ecological niche space among different populations. Subsequently, SDMs were constructed at both species and population levels, demonstrating that population-level SDMs provide more reliable predictions of population distributions due to differential responses to climatic predictor variables. Finally, we conducted an assessment to identify conservation gaps for T. maxima beyond the existing MPAs and proposed recommendations for future establishment of MPAs within the current framework. Based on these findings, appropriate conservation policies have been proposed to effectively protect the habitat of different geographical populations of T. maxima. Additionally, spatiotemporal predictions of habitat suitability provide crucial information for developing adaptive management strategies for T. maxima in response to climate change, including designing new protected areas and adjusting the location and extent of existing protected areas based on their geographical distribution.

Will climate change cause Sargassum beds in temperate waters to expand or contract? Evidence from the range shift pattern of Sargassum

Understanding the range shift patterns of foundation species (e.g., macroalgae) under future climatic conditions is critical for biodiversity conservation in coastal ecosystems. These predictions are typically made using species distribution models (SDMs), and severe habitat loss has been predicted for most brown algal forests. Nevertheless, some models showed that local adaptation within species can reduce range loss projections. In this study, we used the brown algae Sargassum fusiforme and Sargassum thunbergii, which are distributed in the Northwest Pacific, to determine whether climate change will cause the Sargassum beds in Northwest Pacific temperate waters to expand or contract. We divided S. fusiforme and S. thunbergii into northern and southern lineages, considering the temperature gradients and phylogeographic structures. We quantified the realized niches of the two lineages using an n-dimensional hypervolume. Significant niche differentiation was detected between lineages for both species, suggesting the existence of local adaptation. Based on these results, lineage-level SDMs were constructed for both species. The prediction results showed the different responses of different lineages to climate change. The suitable distribution area for both species was predicted to move northward, retaining part of the suitable habitat at low latitudes (along the East China Sea). Unfortunately, this expansion could not compensate for losing middle-low latitude areas. Our results have important implications for the future management and protection of macroalgae and emphasize the importance of incorporating intraspecific variation into species distribution predictions.

The use of an integrated framework combining eco-evolutionary data and species distribution models to predict range shifts of species under changing climates

Species distribution models (SDMs) are powerful tools that can predict potential distributions of species under climate change. However, traditional SDMs that rely on current species occurrences may underestimate their climatic tolerances and potential distributions. To address this limitation, we developed an integrated framework that incorporates eco-evolutionary data into SDMs. In our approach, the fundamental niches of species are constructed by their realized niches in different periods, and those fundamental niches are used to predict potential distributions of species. Our framework includes multiple phylogenetic analyses, such as niche evolution rate estimation and ancestral area reconstruction. These analyses provide deeper insights into the responses of species to climate change. We applied our approach to the Chrysanthemum zawadskii species complex to evaluate its efficacy through comprehensive performance evaluations and validation tests. Our framework can be applied broadly to species with available phylogenetic data and occurrence records, making it a valuable tool for understanding species adaptation in a rapidly changing world.•Integrating the niches of species in different periods estimates more complete climatic envelopes for them.•Combining eco-evolutionary data with SDMs predicts more comprehensive potential distributions of species under climate change.•Our framework provides a general procedure for species with phylogenetic data and occurrence records.

Incorporating physiological knowledge into correlative species distribution models minimizes bias introduced by the choice of calibration area

Correlative species distribution models (SDMs) are important tools to estimate species' geographic distribution across space and time, but their reliability heavily relies on the availability and quality of occurrence data. Estimations can be biased when occurrences do not fully represent the environmental requirement of a species. We tested to what extent species' physiological knowledge might influence SDM estimations. Focusing on the Japanese sea cucumber Apostichopus japonicus within the coastal ocean of East Asia, we compiled a comprehensive dataset of occurrence records. We then explored the importance of incorporating physiological knowledge into SDMs by calibrating two types of correlative SDMs: a naïve model that solely depends on environmental correlates, and a physiologically informed model that further incorporates physiological information as priors. We further tested the models' sensitivity to calibration area choices by fitting them with different buffered areas around known presences. Compared with naïve models, the physiologically informed models successfully captured the negative influence of high temperature on A. japonicus and were less sensitive to the choice of calibration area. The naïve models resulted in more optimistic prediction of the changes of potential distributions under climate change (i.e., larger range expansion and less contraction) than the physiologically informed models. Our findings highlight benefits from incorporating physiological information into correlative SDMs, namely mitigating the uncertainties associated with the choice of calibration area. Given these promising features, we encourage future SDM studies to consider species physiological information where available.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00226-0.

Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria

Investigating spatial pattern of adaptive variation and its underlying processes can inform the adaptive potential distributed within species ranges, which is increasingly important in the context of a changing climate. A correct interpretation of adaptive variation pattern requires that population history and the ensuing population genetic structure are taken into account. Here we carried out such a study by integrating population genomic analyses, demographic model testing and species distribution modeling to investigate patterns and causes of adaptive differentiation in a widespread mantis shrimp, Oratosquilla oratoria, along a replicated, broad-scale temperature gradient in the northwestern Pacific (NWP). Our results supported a strong hierarchical ecogeographic structure dominated by habitat-linked divergence among O. oratoria populations accompanied with introgressive hybridization. A combined FST outlier and environmental correlation analyses revealed remarkable temperature-associated clines in allele frequency across paired North-South populations on Chinese and Japanese coasts, and identified a suite of loci associated with temperature adaptation. Further demographic model testing revealed the observed clinal variation derived partly from Pleistocene divergence followed by recent secondary contact. More importantly, the likelihood of hybridization is predicted to increase as climate change progresses, which would break barriers to gene flow and enable the spread of adaptive genetic variation. These results support that not only is temperature-driven adaptive differentiation occurs in O. oratoria but that such pattern is likely attributed to ancient adaptive variation, sustained by contemporary ocean conditions and a semi-permeable barrier to gene flow maintained by selection. They moreover provide genomic insights into the distribution of adaptive potential across O. oratoria' s species range. This work can serve as a case study to characterize adaptive diversity of marine species in the NWP by integrating environmental and genetic data at temporal and spatial scales in a population genomic framework, which would improve management and conservation actions under climate change.

Incorporating adaptive genomic variation into predictive models for invasion risk assessment

Global climate change is expected to accelerate biological invasions, necessitating accurate risk forecasting and management strategies. However, current invasion risk assessments often overlook adaptive genomic variation, which plays a significant role in the persistence and expansion of invasive populations. Here we used Molgula manhattensis, a highly invasive ascidian, as a model to assess its invasion risks along Chinese coasts under climate change. Through population genomics analyses, we identified two genetic clusters, the north and south clusters, based on geographic distributions. To predict invasion risks, we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability, respectively. These approaches yielded distinct predictions: the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster (i.e., lower invasion risks), while the species distribution model indicated higher future habitat suitability for the same cluster (i.e, higher invasion risks). By integrating these models, we found that the south cluster exhibited minor genome-niche disruptions in the future, indicating higher invasion risks. Our study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate change. Moreover, incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.

Incorporating eco-evolutionary information into species distribution models provides comprehensive predictions of species range shifts under climate change

As climate changes increasingly influence species distributions, ecosystem functions, and biodiversity, the urgency to understand how species' ranges shift under those changes is great. Species distribution models (SDMs) are vital approaches that can predict species distributions under changing climates. However, SDMs based on the species' current occurrences may underestimate the species' climatic tolerances. Integrating species' realized niches at different periods, also known as multi-temporal calibration, can provide an estimation closer to its fundamental niche. Based on this, we further proposed an integrated framework that combines eco-evolutionary data and SDMs (phylogenetically-informed SDMs) to provide comprehensive predictions of species range shifts under climate change. To evaluate our approach's performance, we applied it to a group of related species, the Chrysanthemum zawadskii species complex (Anthemidae, Asteracee). First, we investigated the niche differentiation between species and intraspecific lineages of the complex and estimated their rates of niche evolution. Next, using both standard SDMs and our phylogenetically-informed SDMs, we generated predictions of suitability areas for all species and lineages and compared the results. Finally, we reconstructed the historical range dynamics for the species of this complex. Our results showed that the species and intraspecific lineages of the complex had varying degrees of niche differentiation and different rates of niche evolution. Lineage-level SDMs can provide more realistic predictions for species with intraspecific differentiation than species-level models can. The phylogenetically-informed SDMs provided more complete environmental envelopes and predicted broader potential distributions for all species than the standard SDMs did. Range dynamics varied among the species that have different rates of niche evolution. Our framework integrating eco-evolutionary data and SDMs contributes to a better understanding of the species' responses to climate change and can help to make more targeted conservation efforts for the target species under climate change, particularly for rare species.

Vulnerability of protected areas to future climate change, land use modification, and biological invasions in China

Anthropogenic climate change, land use modifications, and alien species invasions are major threats to global biodiversity. Protected areas (PAs) are regarded as the cornerstone of biodiversity conservation, however, few studies have quantified the vulnerability of PAs to these global change factors together. Here, we overlay the risks of climate change, land use change, and alien vertebrate establishment within boundaries of a total of 1020 PAs with different administrative levels in China to quantify their vulnerabilities. Our results show that 56.6% of PAs will face at least one stress factor, and 21 PAs are threatened under the highest risk with three stressors simultaneously. PAs designed for forest conservation in Southwest and South China are most sensitive to the three global change factors. In addition, wildlife and wetland PAs are predicted to mainly experience climate change and high land use anthropogenetic modifications, and many wildlife PAs can also provide suitable habitats for alien vertebrate establishment. Our study highlights the urgent need for proactive conservation and management planning of Chinese PAs by considering different global change factors together.

Estimating the Spatial Distribution and Future Conservation Requirements of the Spotted Seal in the North Pacific

Local adaptation has been increasingly involved in the designation of species conservation strategies to response to climate change. Marine mammals, as apex predators, are climatechange sensitive, and their spatial distribution and conservation requirements are critically significant for designing protection strategies. In this study, we focused on an ice-breeding marine mammal, the spotted seal (Phoca largha), which exhibits distinct morphological and genetic variations across its range. Our objectives were to quantify the ecological niches of three spotted seal populations, construct the species-level model and population-level models that represent different regions in the Bering population (BDPS), Okhotsk population (ODPS) and southern population (SDPS), and conduct a conservation gap analysis. Our findings unequivocally demonstrated a clear niche divergence among the three populations. We predicted habitat contraction for the BDPS and ODPS driven by climate change; in particular, the spotted seals inhabiting Liaodong Bay may face breeding habitat loss. However, most spotted seal habitats are not represented in existing marine protected areas. Drawing upon these outcomes, we propose appropriate conservation policies to effectively protect the habitat of the different geographical populations of spotted seals. Our research addresses the importance of incorporating local adaptation into species distribution modeling to inform conservation and management strategies.

Preferred prey reduce species realized niche shift and improve range expansion prediction

Many studies have detected realized climatic niche shifts during range changes; this is challenging the fundamental theory of the niche conservatism hypothesis (NCH) and the usefulness of the ecological niche model (ENM) for predicting the distributions of species in space and time by tracking environmental change. Biotic factors such as predatory interactions are important components of species realized niches but are generally difficult to quantify during NCH testing and ENM building. Identifying species' preferred prey may provide a unique opportunity to include trophic interactions in assessing the NCH and determine whether more precise ENM predictions are generated. In this study, we focused on a range-expanding predatory bird, the Asian openbill (Anastomus oscitans). The main prey of the Asian openbill include 136 snail species. We observed a realized climatic niche shift during the northward expansion of the Asian openbill by considering only climates; however, niche conservatism was detected after incorporating their preferred prey. ENMs including preferred snails also predicted the distributions of the Asian openbill better than climate-only models and models including nonpreferred snails or only habitat variables. The results of our study suggested the importance of incorporating preferred prey in evaluating the NCH and developing a framework for predicting the range shifts of both native and alien species in response to global climate change.

The effects of intraspecific variation on forecasts of species range shifts under climate change

As global climate change is altering the distribution range of macroalgae across the globe, it is critical to assess its impact on species range shifts to inform the biodiversity conservation of macroalgae. Latitude/environmental gradients could cause intraspecific variability, which may result in distinct responses to climate change. It remains unclear whether geographical variation occurs in the response of species' populations to climate change. We tested this assumption using the brown alga Sargassum thunbergii, a habitat-forming macroalgae encompassing multiple divergent lineages along the Northwest Pacific. Previous studies revealed a distinct lineage of S. thunbergii in rear-edge populations. Given the phylogeographic structure and temperature gradients, we divided these populations into the southern and northern groups. We assessed the physiological responses of the two groups to temperature changes and estimated their niche differences using n-dimensional hypervolumes. A higher photosynthetic rate and antioxidative abilities were detected in the southern group of S. thunbergii than in the northern group. In addition, significant niche differentiation was detected between the two groups, suggesting the possibility for local adaptation. Given these results, we inferred that the southern group (rear-edge populations) may be more resilient to climate change. To examine climate-driven range shifts of S. thunbergii, we constructed species- and lineage-level species distribution models (SDMs). Predictions of both levels showed considerable distribution contracts along the Chinese coasts in the future. For the southern group, the lineage-level model predicted less habitat loss than the species-level model. Our results highlight the importance of considering intraspecific variation in climate change vulnerability assessments for coastal species.

Climate change will redefine taxonomic, functional, and phylogenetic diversity of Odonata in space and time

Climate change is rearranging the mosaic of biodiversity worldwide. These broad-scale species re-distributions affect the structure and composition of communities with a ripple effect on multiple biodiversity facets. Using European Odonata, we asked: i) how climate change will redefine taxonomic, phylogenetic, and functional diversity at European scales; ii) which traits will mediate species' response to global change; iii) whether this response will be phylogenetically conserved. Using stacked species distribution models, we forecast widespread latitudinal and altitudinal rearrangements in Odonata community composition determining broad turnovers in traits and evolutionary lineages. According to our phylogenetic regression models, only body size and flight period can be partly correlated with observed range shifts. In considering all primary facets of biodiversity, our results support the design of inclusive conservation strategies able to account for the diversity of species, the ecosystem services they provide, and the phylogenetic heritage they carry in a target ecosystem.

Aggregate population-level models informed by genetics predict more suitable habitat than traditional species-level model across the range of a widespread riparian tree

Identifying and predicting how species ranges will shift in response to climate change is paramount for conservation and restoration. Ecological niche models are the most common method used to estimate potential distributions of species; however, they traditionally omit knowledge of intraspecific variation that can allow populations to respond uniquely to change. Here, we aim to test how population X environment relationships influence predicted suitable geographic distributions by comparing aggregated population-level models with species-level model predictions of suitable habitat within population ranges and across the species’ range. We also test the effect of two variable selection methods on these predictions–both addressing the possibility of local adaptation: Models were built with (a) a common set, and number, of predictors and, (b) a unique combination and number of predictors specific to each group’s training extent. Our study addresses the overarching hypothesis that populations have unique environmental niches, and specifically that (1) species-level models predict more suitable habitat within the ranges of genetic populations than individual models built from those groups, particularly when compared models are built with the same set of environmental predictors; and (2) aggregated genetic population models predict more suitable habitat across the species’ range than the species-level model, an = d this difference will increase when models are trained with individualized predictors. We found the species models predicted more habitat within population ranges for two of three genetic groups regardless of variable selection, and that aggregated population models predicted more habitat than species’ models, but that individualized predictors increased this difference. Our study emphasizes the extent to which changes to model predictions depend on the inclusion of genetic information and on the type and selection of predictors. Results from these modeling decisions can have broad implications for predicting population-level ecological and evolutionary responses to climate change.

Temperate and tropical lizards are vulnerable to climate warming due to increased water loss and heat stress

Climate warming has imposed profound impacts on species globally. Understanding the vulnerabilities of species from different latitudinal regions to warming climates is critical for biological conservation. Using five species of Takydromus lizards as a study system, we quantified physiological and life-history responses and geography range change across latitudes under climate warming. Using integrated biophysical models and hybrid species distribution models, we found: (i) thermal safety margin is larger at high latitudes and is predicted to decrease under climate warming for lizards at all latitudes; (ii) climate warming will speed up embryonic development and increase annual activity time of adult lizards, but will exacerbate water loss of adults across all latitudes; and (iii) species across latitudes are predicted to experience habitat contraction under climate warming due to different limitations-tropical and subtropical species are vulnerable due to increased extremely high temperatures, whereas temperate species are vulnerable due to both extremely high temperatures and increased water loss. This study provides a comprehensive understanding of the vulnerability of species from different latitudinal regions to climate warming in ectotherms, and also highlights the importance of integrating environmental factors, behaviour, physiology and life-history responses in predicting the risk of species to climate warming.

Ecological niche modelling and climate change in two species groups of huntsman spider genus Eusparassus in the Western Palearctic

The huntsman spiders' genus Eusparassus are apex arthropod predators in desert ecosystems of the Afrotropical and Palearctic ecoregions. The Eusparassus dufouri and E. walckenaeri clades are two distinct taxonomic, phylogenetic, and geographic units concerning morphology, molecular phylogeny, and spatial data; but little is known about their ecological niche. We applied the maximum-entropy approach and modelled ecologic niches of these two phylogenetically closely related clades. Ecological niches of the two clades were compared using identity and background tests and two different metrics, the Schooner's D and Warren's I. We also predicted the impacts of climate change on the distribution of the two clades. The results of the identity test showed that the ecological niches of the two clades were different in geographic space but were similar in environmental space. While results of the background test revealed that the ecological niches of the two clades were similar in geographic and environmental space. This indicated that "niche conservatism" had an important role over the evolutionary time of allopatric diversification. However, the normalized difference vegetation index vs. topographic heterogeneity had influenced the niches of the dufouri and walckenaeri clades, respectively. The analyses recovered that the two clades' climatically suitable habitats will increase under future climate (the year 2070). However, since the two clades are characterized by the narrow range of environmental optimum and the accordingly high limits of tolerance, they are vulnerable to climate change.

Intraspecific genetic variation matters when predicting seagrass distribution under climate change

Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly in recent decades. To improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species' potential distribution under present and future climatic scenarios given species' presence data and climatic predictor variables. However, these models are typically constructed with species-level data, and thus ignore intraspecific genetic variability, which can give rise to populations with adaptations to heterogeneous climatic conditions. Here, we explore the link between intraspecific adaptation and niche differentiation in Thalassia hemprichii, a seagrass broadly distributed in the tropical Indo-Pacific Ocean and a crucial provider of habitat for numerous marine species. By retrieving and re-analysing microsatellite data from previous studies, we delimited two distinct phylogeographical lineages within the nominal species and found an intermediate level of differentiation in their multidimensional environmental niches, suggesting the possibility for local adaptation. We then compared projections of the species' habitat suitability under climate change scenarios using species-level and lineage-level SDMs. In the Central Tropical Indo-Pacific region, models for both levels predicted considerable range contraction in the future, but the lineage-level models predicted more severe habitat loss. Importantly, the two modelling approaches predicted opposite patterns of habitat change in the Western Tropical Indo-Pacific region. Our results highlight the necessity of conserving distinct populations and genetic pools to avoid regional extinction due to climate change and have important implications for guiding future management of seagrasses.