Tracking niche change through time: simultaneous inference of ecological niche evolution and estimation of contemporary niches

Abstract

The environmental niche of a species is often studied from two different perspectives. Niche modelling correlates a species’ niche to known observations from contemporary species distribution. Niche evolution applies phylogenetic methods on summary statistics of species distribution to infer the patterns of changing niche over time. Even though the two areas of research are fundamentally linked and are typically both based on the same species distribution data, modelling the contemporary niche and inferring niche history are never combined in the same analytical framework. Here we provide a new way to combine both niche modelling and niche evolution, using distribution data and phylogenies. Doing so allows us to simultaneously infer the history of niche evolution and estimate the environmental niche of each tip species on the phylogeny. It also avoids some limitations of the separate methods, such as the failure of environmental niche models to account for the role of history in shaping current species distribution, and the use of unrealistic models of change in phylogenetic comparative methods. The novelty of our method is that it explicitly models three fundamental processes of niche evolution − adaptation, speciation, and dispersal − applying a reversible jump algorithm to infer the occurrences of these processes on phylogeny. Simulations demonstrate high accuracy of our method for estimating the environmental niche of tip species and reasonable power to identify the occurrences of the three processes on phylogeny. We also prove the efficacy of our approach using real-world data. We show that our method of combining niche modelling with niche evolution is far more effective at predicting salt tolerance in Australian Acacia species than using environmental niche modelling alone. We also show that we can correctly infer periods of evolutionary change in response to changing climate: our method identified two peak times in drought adaptation events in the evolutionary history of Australian Acacia, which correspond to the two drying periods in Australia during the Cenozoic. Therefore, we believe our method provides a promising approach to integrate different research areas in understanding species distribution.

Macroevolutionary and macroecological approaches to understanding the evolution of stress tolerance in plants

“…But we can improve our prediction of species tolerance to environmental stress if we incorporate evolutionary history into our SDMs. Incorporating phylogeny into SDMs allows us to model the impact of evolutionary processes on current distribution and leads to better prediction of salt-tolerant species (Hua, Cardillo, & Bromham, 2019).…”

“…We have applied this approach to studying the evolution of salt tolerance in Australian Acacia species (Hua et al, 2019). The approach not only better predicts known Acacia halophytes than using SDMs alone, but also paints a picture of the history of salt tolerance in Australian Acacia species over time and space.…”

“…Joint modelling of lineage evolution, dispersal and adaptation to environmental differences provides a method for comparing the relative degree of past evolutionary change in lineages in response to changes in environmental stress. The lineage-specific patterns of "evolvability" in response to stress might then provide a basis for predicting a lineage's likely adaptability to increasing environmental stress (Hua et al, 2019), on the assumption that a lineage that has demonstrated evolutionary lability in the past may continue to do so in future. However, continued adaptation to increasing environmental stress may not be possible if the lineage has already reached the limit of available variation in that trait.…”

Adapting to extremes: reconstructing evolution in response to changing climate over time and space in the diverse Australian plant genus Acacia

“…Here, we infer the history of adaptation to extreme environments by applying a recently developed method, the Niche Evolution Model (NEMo), that combines Environmental Niche Modelling (ENM) and reconstruction of the evolutionary history of fundamental niche in a single statistical framework (Hua et al 2021). This method uses species distribution data to characterise the realised niches of each contemporary species at the tips of a phylogeny, and reconstructs evolution of the fundamental niche and the associated changes in the realised niche by modelling key driving processes: (1) shift in areas of tolerable conditions and adaptation of lineages to changing conditions (hereafter referred to as an "adaptation event"); (2) dispersal away from areas that are no longer suitable and into accessible areas of suitable habitat; (3) speciation and divergence along lineages' environmental tolerances (hereafter "speciation event").…”

Climatic effects on niche evolution in a passerine bird clade depend on paleoclimate reconstruction method

“…2015; Hua et al. 2019). However, in direct contrast, other studies have found no evidence for a relationship between climatic conditions and climatic niche changes (e.g., Schnitzler et al.…”