Using data from related species to overcome spatial sampling bias and associated limitations in ecological niche modelling

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 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.

A new species of small-eared shrew (Soricidae,Cryptotis) from El Triunfo Biosphere Reserve, Chiapas, Mexico

The Cryptotis goodwini species group of small-eared shrews (Eulipotyphla, Soricidae) includes at least 12 species discontinuously distributed in the cloud forests from southern Mexico to Honduras. Its taxonomy is still under study, with several species described only in the last decade. Previous genetic studies have highlighted that a population from El Triunfo Biosphere Reserve in Chiapas, Mexico, previously assigned to C. goodwini, is evolutionarily divergent from the other known species. However, the available specimens from this region have not been examined rigorously. Herein, I use morphological and biogeographic analyses to evaluate the taxonomic status of this population. The results confirm that it is an independent lineage, which I describe here as a new species endemic to Mexico. Overall, this is the largest shrew within the C. goodwini group. Its morphological and genetic distinction is probably due to long-term geographic isolation in the mountains of El Triunfo. I present what is now the first and only record of C. goodwini (sensu stricto) for Mexico. Finally, I identify some priority regions to direct field surveys on the C. goodwini species group to better understand its richness and distribution.

Dealing with disjunct populations of vascular plants: implications for assessing the effect of climate change

Species distribution models are the most widely used tool to predict species distributions for species conservation and assessment of climate change impact. However, they usually do not consider intraspecific ecological variation exhibited by many species. Overlooking the potential differentiation among groups of populations may lead to misplacing any conservation actions. This issue may be particularly relevant in species in which few populations with potential local adaptation occur, as in species with disjunct populations. Here, we used ecological niche modeling to analyze how the projections of current and future climatically suitable areas of 12 plant species can be affected using the whole taxa occurrences compared to occurrences from geographically disjunct populations. Niche analyses suggest that usually the disjunct group of populations selects the climatic conditions as similar as possible to the other according to climate availability. Integrating intraspecific variability only slightly increases models' ability to predict species occurrences. However, it results in different predictions of the magnitude of range change. In some species, integrating or not integrating intraspecific variability may lead to opposite trend in projected range change. Our results suggest that integrating intraspecific variability does not strongly improve overall models' accuracy, but it can result in considerably different conclusions about future range change. Consequently, accounting for intraspecific differentiation may enable the detection of potential local adaptations to new climate and so to design targeted conservation strategies.

Mountain frog species losing out to climate change around the Sichuan Basin

Amphibians are particularly vulnerable to climate changes that are expected to cause habitat fragmentation and loss and, ultimately, local extirpations. However, little is known about how the interaction between climate change and fragmentation may impede the ability of amphibians to adapt to climate change. Here, we used the iconic mountain frog Quasipaa boulengeri as an indicator species to extrapolate climate-driven shifts in its habitat availability and connectivity in central and southern China according to the minimum and maximum representative concentration pathways. The models projected an average habitat loss of 36%-71% and the in situ and ex situ climate-change refugia to be 29%-64% and 5%-18% of the present-day suitable habitats, respectively. An increase in habitat fragmentation was reflected in a 51% decrease in core patch size, a 9% increase in the mean least-cost path (LCP) length, and a 19% increase in the cost-weighted distance. These climate-driven shifts varied spatially around the Sichuan Basin, with those in the southeast of the Basin being the most pronounced habitat and connectivity losses and those along the Basin being relatively optimistic. The effectiveness of refugia may only be maintained through a narrow passageway along the southern Sichuan Basin because of the presence of LCPs over time. Our results emphasize the need to understand how climate change and connectivity will jointly affect the distribution of mountain amphibians and to accordingly adopt conservation strategies. Further, our findings highlight the importance of identifying and preserving climate-change refugia and habitat connectivity for species persistence and conservation planning.

From surviving to thriving, the assembly processes of microbial communities in stone biodeterioration: A case study of the West Lake UNESCO World Heritage area in China

Serious concerns regarding stone biodeterioration have been raised due to the loss of aesthetic value and hidden dangers in stone cultural heritages and buildings. Stone biodeterioration involves a complex ecological interplay among organisms, however, the ecological mechanisms (deterministic or stochastic processes) that determine the microbial community on stone remain poorly understood. Here, using both amplicon and shotgun metagenomic sequencing approaches, we comprehensively investigated the biodiversity, assembly, and function of communities (including prokaryotes, fungi, microfauna, and plants) on various types of deteriorating limestone across different habitats in Feilaifeng. By generalizing classic ecological models to stone habitats, we further uncovered and quantified the mechanisms underlying microbial community assembly processes and microbial interactions within the biodeteriorated limestone. Community profiling revealed stable ecosystem functional potential despite high taxonomic variation across different biodeterioration types, suggesting non-random community assembly. Increased niche differentiation occurred in prokaryotes and fungi but not in microfauna and plant during biodeterioration. Certain microbial groups such as nitrifying archaea and bacteria showed wider niche breadth and likely contributing to the initiation, succession and expansion of stone biodeterioration. Consistently, prokaryotes were more strongly structured by selection-based deterministic processes, while micro-eukaryotes were more influenced by dispersal and drift-based stochastic processes. Importantly, microbial coexistence maintains network robustness within stone microbiotas, highlighting mutual cooperation among functional microorganisms. These results provide new insights into microbial community assembly mechanisms in stone ecosystems and may aid in the sustainable conservation of stone materials of interest.

Supraspecific units in correlative niche modeling improves the prediction of geographic potential of biological invasions

BACKGROUND

Biological invasions rank among the most significant threats to biodiversity and ecosystems. Correlative ecological niche modeling is among the most frequently used tools with which to estimate potential distributions of invasive species. However, when areas accessible to the species across its native distribution do not represent the full spectrum of environmental conditions that the species can tolerate, correlative studies often underestimate fundamental niches.

METHODS

Here, we explore the utility of supraspecific modeling units to improve the predictive ability of models focused on biological invasions. Taking into account phylogenetic relationships in correlative ecological niche models, we studied the invasion patterns of three species (Aedes aegypti, Pterois volitans and Oreochromis mossambicus).

RESULTS

Use of supraspecific modeling units improved the predictive ability of correlative niche models in anticipating potential distributions of three invasive species. We demonstrated that integrating data on closely related species allowed a more complete characterization of fundamental niches. This approach could be used to model species with invasive potential but that have not yet invaded new regions.

Altitudinal, latitudinal and longitudinal responses of cloud forest species to Quaternary glaciations in the northern Neotropics

The glaciations of the Quaternary caused changes in the geographical distributions of species associated with tropical montane cloud forests. The most obvious effect of the glacial conditions was the downward displacement of cloud forest species, thus giving opportunities for population connectivity in the lowlands. Considerable attention has been paid to these altitudinal changes, but latitudinal and longitudinal movements remain poorly understood in the northern Neotropics. Here, I use ecological niche modelling to generate palaeodistributions of small-eared shrews (Mammalia: Soricidae) closely associated with cloud forests in the mountain systems of Mexico and then retrodict their range shifts during the Last Glacial Maximum (LGM), one of the coldest periods of the Quaternary. The results suggest that cloud forest species not only migrated downwards in response to global cooling and dryness but also migrated latitudinally and longitudinally onto those slopes that maintained moist conditions (other slopes remained unsuitable during the LGM), thus revealing a hitherto unknown route for postglacial colonization of cloud forest species. This scenario of past distributional change probably had genetic and demographic implications and has repercussions for the identification of areas of refugia and postglacial colonization routes of cloud forest species.

Genetic, phenotypic and ecological differentiation suggests incipient speciation in two Charadrius plovers along the Chinese coast

Background

Speciation with gene flow is an alternative to the nascence of new taxa in strict allopatric separation. Indeed, many taxa have parapatric distributions at present. It is often unclear if these are secondary contacts, e.g. caused by past glaciation cycles or the manifestation of speciation with gene flow, which hampers our understanding of how different forces drive diversification. Here we studied genetic, phenotypic and ecological aspects of divergence in a pair of incipient shorebird species, the Kentish (Charadrius alexandrinus) and the White-faced Plovers (C. dealbatus), shorebirds with parapatric breeding ranges along the Chinese coast. We assessed divergence based on molecular markers with different modes of inheritance and quantified phenotypic and ecological divergence in aspects of morphometric, dietary and climatic niches.

Results

Our integrative analyses revealed small to moderate levels of genetic and phenotypic distinctiveness with symmetric gene flow across the contact area at the Chinese coast. The two species diverged approximately half a million years ago in dynamic isolation with secondary contact occurring due to cycling sea level changes between the Eastern and Southern China Sea in the mid-late Pleistocene. We found evidence of character displacement and ecological niche differentiation between the two species, invoking the role of selection in facilitating divergence despite gene flow.

Conclusion

These findings imply that ecology can indeed counter gene flow through divergent selection and thus contributes to incipient speciation in these plovers. Furthermore, our study highlights the importance of using integrative datasets to reveal the evolutionary history and assist the inference of mechanisms of speciation.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1449-5) contains supplementary material, which is available to authorized users.

Genetic diversity in frogs linked to past and future climate changes on the roof of the world

Mountains, representing storehouses of biodiversity, endemism and threatened species, are biodiversity hotspots of great conservation importance. However, increasing evidence indicates that mountain species throughout the world are responding to climate change, past or contemporary, by shifting their geographic distributions and patterns of genetic diversity, potentially affecting their adaptive capacity and increasing risk of extinction. Using the iconic high-elevation frog Nanorana parkeri as indicator, we showed how spatial analyses of climatic stability combined with genetic data allow unravelling amphibian responses to past and future climate changes on 'the roof of the world'-the Qinghai-Tibetan Plateau. We found that areas along the Yarlung Tsangpo Valley were climatically more stable relative to other regions, apparently serving as a large climatic refugium during Quaternary glaciations, but that these areas will likely be affected by future climate change. As populations closer to Quaternary refugia usually had higher genetic diversity, current genetic diversity can be explained in the largest part by distance to historically stable areas, outweighing other historical and contemporary factors. Along with the dynamics of suitable range, a fluctuating habitat fragmentation supported the pattern of historical changes in genetic diversity (N_e ) over time. Our results emphasize strong relationships between amphibian genetic diversity, past range dynamics and where to preserve suitable habitats in the face of future climate changes. More generally, our findings highlighted a central role of refugia during Quaternary climatic fluctuations, and how isolation from refugia may have modulated amphibian genetic diversity across the Qinghai-Tibetan Plateau.

New records of a critically endangered shrew from Mexican cloud forests (Soricidae, Cryptotis nelsoni) and prospects for future field research

The Nelson´s small-eared shrew, Cryptotisnelsoni (Merriam, 1895), is a critically endangered species, endemic to cloud forests in Los Tuxtlas, a mountain range along the Gulf of Mexico coast. This species is only known from the type locality and its surroundings. Here we present new records that extend its distribution approximately 7 km southeast of the type locality and report more specimens near to the type locality. We also identified climatically suitable areas for C.nelsoni using ecological niche modelling and investigated the sampling bias to identify poorly sampled areas in Los Tuxtlas. We suggest that the scarcity of records in other areas with suitable climatic conditions throughout Los Tuxtlas is a consequence of incomplete surveys. We strongly highlight the importance of continuing surveying this critically endangered shrew using more efficient sampling techniques to better understand its current distribution and conservation status. Despite all known localities occurring inside Los Tuxtlas Biosphere Reserve, deforestation and climate change still pose current and future threats to this species.

Examining the interglacial high-elevation refugia scenario in East Asian subtropical mountain systems with the frog species Leptobrachium liui

The effects of Quaternary climatic oscillations on the distributions of organisms in different parts of the world are not equally well understood, limiting the ability to understand the determinants of biodiversity. Compared with the mountain regions in southern Europe and southwestern North America, such effects on high-elevation species in the East Asian subtropical mountain systems located in southern and southeastern China have seldom been addressed. In this study, using Leptobrachium liui (Megophryidae), we made one of the earliest attempts to examine the interglacial high-elevation refugia scenario in these Asian mountains. Based on our current understanding of the study system, we formulated a hypothesis that these frogs of western origin were distributed more widely and continuously during glacial phases, allowing eastward dispersal, and that they are currently isolated in interglacial refugia at higher elevations. Microsatellite data and mitochondrial and nuclear sequence data were obtained with extensive sampling followed by the synthesis of phylogeographic and population genetic analyses and modeling of the species distribution. The analyses revealed a sequential eastward divergence of microsatellite clusters and gene lineages accompanied by a decline in genetic diversity. Molecular dating estimates revealed divergence events in the Pleistocene, and a reduction in local populations was inferred to have occurred at a time comparable to the end of the last glacial. Strong genetic isolation by distance reflecting a more continuous historical distribution was detected. Furthermore, environmental niche models inferred a wide planar distribution during the last glacial maximum, providing further support for the hypothesis.

Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data

Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.