skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Paleobiogeographic insights gained from ecological niche models: progress and continued challenges
The spatial distribution of individuals within ecological assemblages and their associated traits and behaviors are key determinants of ecosystem structure and function. Consequently, determining the spatial distribution of species, and how distributions influence patterns of species richness across ecosystems today and in the past, helps us understand what factors act as fundamental controls on biodiversity. Here, we explore how ecological niche modeling has contributed to understanding the spatiotemporal distribution of past biodiversity and past ecological and evolutionary processes. We first perform a semiquantitative literature review to capture studies that applied ecological niche models (ENMs) to the past, identifying 668 studies. We coded each study according to focal taxonomic group, whether and how the study used fossil evidence, whether it relied on evidence or methods in addition to ENMs, spatial scale of the study, and temporal intervals included in the ENMs. We used trends in publication patterns across categories to anchor discussion of recent technical advances in niche modeling, focusing on paleobiogeographic ENM applications. We then explored contributions of ENMs to paleobiogeography, with a particular focus on examining patterns and associated drivers of range dynamics; phylogeography and within-lineage dynamics; macroevolutionary patterns and processes, including niche change, speciation, and extinction; drivers of community assembly; and conservation paleobiogeography. Overall, ENMs are powerful tools for elucidating paleobiogeographic patterns. ENMs are most commonly used to understand Quaternary dynamics, but an increasing number of studies use ENMs to gain important insight into both ecological and evolutionary processes in pre-Quaternary times. Deeper integration with traits and phylogenies may further extend those insights.  more » « less
Award ID(s):
2149416 1750597 2149419
PAR ID:
10597822
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
Cambridge University Press
Date Published:
Journal Name:
Paleobiology
Volume:
51
Issue:
1
ISSN:
0094-8373
Page Range / eLocation ID:
8 to 28
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Species distribution modelling (SDM), also called environmental or ecological niche modelling, has developed over the last 30 years as a widely used tool used in core areas of biogeography including historical biogeography, studies of diversity patterns, studies of species ranges, ecoregional classification, conservation assessment and projecting future global change impacts. In the 50th anniversary year of Journal of Biogeography , I reflect on developments in species distribution modelling, illustrate how embedded the methodology has become in all areas of biogeography and speculate on future directions in the field. Challenges to species distribution modelling raised in this journal in 2006 have been addressed to a significant degree. Those challenges are clarification of the niche concept; improved sample design for species occurrence data; model parameterization; predictor selection; assessing model performance and transferability; and integrating correlative and process models of species distributions. SDM is used, often in conjunction with other evidence, to understand past species range dynamics, identify patterns and drivers of biological diversity, identify drivers of species range limits, define and delineate ecoregions, estimate the distributions of biodiversity elements in relation to protected status and to prioritize conservation action, and to forecast species range shifts in response to climate change and other global change scenarios. Areas of progress in SDM that may become more widely accessible and useful tools in biogeography include genetically informed models and community distribution models. 
    more » « less
  2. Abstract Community ecology typically assumes that competitive exclusion and species coexistence are unaffected by evolution on the time scale of ecological dynamics. However, recent studies suggest that rapid evolution operating concurrently with competition may enable species coexistence. Such findings necessitate general theory that incorporates the coexistence contributions of eco‐evolutionary processes in parallel with purely ecological mechanisms and provides metrics for quantifying the role of evolution in shaping competitive outcomes in both modelling and empirical contexts. To foster the development of such theory, here we extend the interpretation of the two principal metrics of modern coexistence theory—niche and competitive ability differences—to systems where competitors evolve. We define eco‐evolutionary versions of these metrics by considering how invading and resident species adapt to conspecific and heterospecific competitors. We show that the eco‐evolutionary niche and competitive ability differences are sums of ecological and evolutionary processes, and that they accurately predict the potential for stable coexistence in previous theoretical studies of eco‐evolutionary dynamics. Finally, we show how this theory frames recent empirical assessments of rapid evolution effects on species coexistence, and how empirical work and theory on species coexistence and eco‐evolutionary dynamics can be further integrated. 
    more » « less
  3. Lozier, J (Ed.)
    Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community. 
    more » « less
  4. null (Ed.)
    Urban areas are dynamic ecological systems defined by interdependent biological, physical, and social components. The emergent structure and heterogeneity of urban landscapes drives biotic outcomes in these areas, and such spatial patterns are often attributed to the unequal stratification of wealth and power in human societies. Despite these patterns, few studies have effectively considered structural inequalities as drivers of ecological and evolutionary outcomes and have instead focused on indicator variables such as neighborhood wealth. In this analysis, we explicitly integrate ecology, evolution, and social processes to emphasize the relationships that bind social inequities—specifically racism—and biological change in urbanized landscapes. We draw on existing research to link racist practices, including residential segregation, to the heterogeneous patterns of flora and fauna observed by urban ecologists. In the future, urban ecology and evolution researchers must consider how systems of racial oppression affect the environmental factors that drive biological change in cities. Conceptual integration of the social and ecological sciences has amassed considerable scholarship in urban ecology over the past few decades, providing a solid foundation for incorporating environmental justice scholarship into urban ecological and evolutionary research. Such an undertaking is necessary to deconstruct urbanization’s biophysical patterns and processes, inform equitable and anti-racist initiatives promoting justice in urban conservation, and strengthen community resilience to global environmental change. 
    more » « less
  5. Abstract 1. Species distribution models (SDMs) are crucial tools for understanding and predicting biodiversity patterns, yet they often struggle with limited data, biased sampling, and complex species-environment relationships. Here I present NicheFlow, a novel foundation model for SDMs that leverages generative AI to address these challenges and advance our ability to model and predict species distributions across taxa and environments. 2. NicheFlow employs a two-stage generative approach, combining species embeddings with two chained generative models, one to generate a distribution in environmental space, and a second to generate a distribution in geographic space. This architecture allows for the sharing of information across species and captures complex, non-linear relationships in environmental space. I trained NicheFlow on a comprehensive dataset of reptile distributions and evaluated its performance using both standard SDM metrics and zero-shot prediction tasks. 3. NicheFlow demonstrates good predictive performance, particularly for rare and data-deficient species. The model successfully generated plausible distributions for species not seen during training, showcasing its potential for zero-shot prediction. The learned species embeddings captured meaningful ecological information, revealing patterns in niche structure across taxa, latitude and range sizes. 4. As a proof-of-principle foundation model, NicheFlow represents a significant advance in species distribution modeling, offering a powerful tool for addressing pressing questions in ecology, evolution, and conservation biology. Its ability to model joint species distributions and generate hypothetical niches opens new avenues for exploring ecological and evolutionary questions, including ancestral niche reconstruction and community assembly processes. This approach has the potential to transform our understanding of biodiversity patterns and improve our capacity to predict and manage species distributions in the face of global change. 
    more » « less