Intraspecific differentiation: Implications for niche and distribution modelling

Abstract

Aim Mounting evidence suggests that failure of species distribution models to integrate local adaptation hinders our ability to predict distribution ranges, raising the question of whether modelling should be performed at the level of species (clade models) or intraspecific lineages (subclade models), characterized by the restricted availability of occurrence points. While Ensembles of Small Models (ESMs) offer an attractive framework for small datasets, their evaluation remains critical. We address these issues in the case of very small datasets inherent to subclade models and discuss which modelling strategy should be applied based on niche overlap among lineages. Location Sweden. Taxon Mosses. Methods Ensembles of Small Models were evaluated by null models built from randomly sampled presence points. We compared the extent of suitable area predicted by the projections of clade and subclade models. Niche overlap was quantified using Schoener's D and Hellinger'sImetrics, and the significance of these metrics in terms of niche conservatism or divergence was assessed by similarity tests. Results We introduced a simple procedure for evaluating ESMs based on the pooling of the statistics used to assess model accuracy from the replicates. Despite fairly high AUC and TSS values, 2 of the 23 subclade models did not perform better than null models and should be discarded. Combined predictions from subclade models contributed, on average, five times more than clade models to the total suitable area predicted by the combination of subclade and clade models. The D and I metrics averaged 0.45 and 0.71, with evidence for niche conservatism in half of the species and no signal for niche divergence. Main conclusions In addition to the assessment of ESM accuracy based on the simple procedure described here, we recommend that ESMs should be systematically evaluated against null models. Lumping or splitting occurrence data at the intraspecific level substantially impacted model projections. Given the poor performance of models based on small datasets, even when employing ESMs, we pragmatically suggest that, in the absence of evidence for niche divergence during diversification of closely related intraspecific lineages, SDMs should be based on all available occurrence data at the species level.

Niche overlap and divergence times support niche conservatism in eastern Asia–eastern North America disjunct plants

“…The performance (or accuracy) of ENMs has previously been found to be influenced by the number of occurrence records, especially small sample sizes (Collart et al., 2021; van Proosdij et al., 2016). Given this concern would also exist with our ensemble ENMs of focal species within the EAS–ENA disjunct plants, we used a sample size of > 20 occurrence records.…”

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

“…How different plant species can adapt to a changing climate represents a crucial ecological and evolutionary question. As widely distributed species often possess many genetic lineages or subspecies (Van Rossum et al., 2018 ), revealing their population structure may help to predict their response to different environmental conditions at present and under future conditions (Collart et al., 2021 ). In many European plant species, a phylogeographic pattern can be found that resulted from the survival in different refugia during the last glacial maximum (LGM) (Bagnoli et al., 2016 ; Beatty & Provan, 2011 ; Krebs et al., 2019 ; Listl et al., 2017 ; Roces‐Díaz et al., 2018 ; Schwarzer & Joshi, 2019 ; Sebasky et al., 2016 ; Taberlet et al., 2012 ).…”

“…If we are interested in how species can adapt to these habitat changes, their genetic background has to be considered (Anderson et al., 2011 ; Bowles & Whelan, 1996 ; Corlett, 2017 ; McMahon et al., 2014 ; Vandergast et al., 2008 ). The inclusion of intraspecifc lineages is of strong importance here as it has been proven to substantially impact analyses on ecological niche modeling (Collart et al., 2021 ). Therefore, we included the phylogenetic data to investigate possible response differences in S .…”

“…help to predict their response to different environmental conditions at present and under future conditions (Collart et al, 2021). In many European plant species, a phylogeographic pattern can be found that resulted from the survival in different refugia during the last glacial maximum (LGM) (Bagnoli et al, 2016;Beatty & Provan, 2011;Krebs et al, 2019;Listl et al, 2017;Roces-Díaz et al, 2018;Schwarzer & Joshi, 2019;Sebasky et al, 2016;Taberlet et al, 2012).…”

The influence of climate and palaeoclimate on distributions of global conifer clades depends on geographical range size

“…Nevertheless, we have tried to overcome the limitations of any one approach by combining multiple methods and constructing ensemble species distribution models with multiple algorithms, and their results are largely congruent. Recent studies have also recommended null models as a means of exploring the robustness of species distribution models (Collart et al, 2021); for example, a null model could conceivably test if range-restricted conifer taxa (located anywhere on the globe) always lead to high percent relative contributions of palaeoclimates in species distribution models. However, range-restricted conifer taxa can show low contributions from palaeoclimate variables to their current distributions and widespread taxa can show high contributions, as seen in species distributions models from the LGM (Figure S1).…”