Phylogenetic niche conservatism and the evolutionary basis of ecological speciation

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species‐richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population‐genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well‐defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.     

Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.     

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake ( Lampropeltis getula ), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b . We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.     

The importance (or lack thereof) of niche divergence to the maintenance of a northern species complex: the case of the long‐toed salamander (Ambystoma macrodactylum Baird)

The relative importance of ecological vs. nonecological factors for the origin and maintenance of species is an open question in evolutionary biology. Young lineages – such as the distinct genetic groups that make up the ranges of many northern species – represent an opportunity to study the importance of ecological divergence during the early stages of diversification. Yet, few studies have examined the extent of niche divergence between lineages in previously glaciated regions and the role of ecology in maintaining the contact zones between them. In this study, we used tests of niche overlap in combination with ecological niche models to explore the extent of niche divergence between lineages of the long‐toed salamander (Ambystoma macrodactylum Baird) species complex and to determine whether contact zones correspond to (divergent) niche limits. We found limited evidence for niche divergence between the different long‐toed salamander lineages, substantial overlap in the predicted distribution of suitable climatic space for all lineages and range limits that are independent of niche limits. These results raise questions as to the importance of ecological divergence to the development of this widespread species complex and highlight the potential for non‐ecological factors to play a more important role in the maintenance of northern taxa.     

Hidden patterns of phylogenetic non‐stationarity overwhelm comparative analyses of niche conservatism and divergence

Aim Despite the importance of the niche concept in ecological and evolutionary theory, there are still many discussions about its definition and operational evaluation, especially when dealing with niche divergence and conservatism in an explicit phylogenetic context. Here we evaluate patterns of niche evolution in 67 New World Carnivora species, measured using Hellinger distances based on MAXENT models of species distribution. We show how inferences on niche conservatism or divergence depend on the way phylogenetic patterns are analysed using matrix comparison techniques. Innovation Initially we used the simplest approach of Mantel tests to compare Hellinger distances ( N ) derived from MAXENT and phylogenetic distances ( P ) among species. Then we extended the Mantel test to generate a multivariate correlogram, in which phylogenetic patterns are analysed at multiple levels in the phylogeny and can reveal nonlinearity in the relationship between divergence and time. Finally, we proposed a new approach to generate ‘local’ (or ‘specific’) leverages of components for Mantel correlation, evaluating the non‐stationarity in the relationship between N and P for each species. This new approach was used to show if some lineages are more prone to niche shift or conservatism than others. Main conclusions Standard Mantel tests indicated a poor correspondence between N and P matrices, discarding the idea of niche conservatism for Carnivora, but the correlogram supports that closely related species tend to be more similar than expected by chance. Moreover, the variance among Hellinger distances between pairs of closely phylogenetically related species is much larger than for the entire clade. Phylogenetic non‐stationarity analysis shows that in some Carnivora families the niche tends to divergence (Mustelidae and Canidae), whereas in others it tends to conservatism (Procyonidae and Mustelidae) at short phylogenetic distances. Our analyses clearly show that misleading results may appear if niche divergence is analysed only by simple matrix correlations not taking into account complex patterns of phylogenetic nonlinearity and non‐stationarity.     

Northwestward range expansion of the bumblebee Bombus haematurus into Central Europe is associated with warmer winters and niche conservatism

Species range expansions are crucial for understanding niche formation and the interaction with the environment. Here, we studied the bumblebee Bombus haematurus Kriechbaumer, 1870, a species historically distributed from northern Serbia through northern Iran which has very recently started expanding northwestward into Central Europe without human-mediated dispersal (i.e., it is a natural spread). After updating the global distribution of this species, we investigated if niche shifts took place during this range expansion between newly colonized and historical areas. In addition, we have explored which climatic factors may have favored the natural range expansion of the species. Our results indicated that Bombus haematurus has colonized large territories in 7 European countries outside the historical area in the period from the 1980s to 2018, a natural expansion over an area that equals 20% of the historical distribution. In addition, this bumblebee performs generalism in flower visitation and it occurs in different habitats, although a preference for forested areas clearly emerges. The land-use associated with the species in the colonized areas is similar to the historical distribution, indicating that no major niche shifts occurred during the spread. Furthermore, in recently colonized localities, the range expansion was associated with warming temperatures during the winter and also during both queen overwintering and emergence phases. These findings document a case of natural range expansion due to environmental change rather than due to niche shifts, and specifically they suggest that warmer winters could be linked to the process of natural colonization of new areas.     

Relative effects of time for speciation and tropical niche conservatism on the latitudinal diversity gradient of phyllostomid bats

Determinants of contemporary patterns of diversity, particularly those spanning extensive latitudinal gradients, are some of the most intensely debated issues in ecology. Recently, focus has shifted from a contemporary environmental perspective to a historical one in an attempt to better understand the construction of latitudinal gradients. Although the vast majority of research on historical mechanisms has focused on tropical niche conservatism (TNC), other historical scenarios could produce similar latitudinal gradients. Herein, I formalize predictions to distinguish between two such historical processes--namely time for speciation (TFS) and TNC--and test relative support based on diversity gradients of New World bats. TFS and TNC are distinctly spatial and environmental mechanisms, respectively. Nonetheless, because of the way that environmental characteristics vary spatially, these two mechanisms are hard to distinguish. Evidence provided herein suggests that TNC has had a more important effect than TFS in determining diversity gradients of New World bats. Indeed, relative effects of different historical mechanisms, as well as relative effects of historical and contemporary environmental determinants, are probably context-dependent. Future research should move away from attempting to identify the mechanism with primacy and instead attempt to understand the particular contexts in which different mechanisms have greater influence on diversity gradients.     

Broad‐scale environmental response and niche conservatism in lacustrine diatom communities

Aim (1) To resolve theoretical debates regarding the role of environment versus dispersal limitation, the conservatism of niches across distances and the prevalence of environmental specialists in diatom communities. (2) To provide guidance on the use of diatom communities and other microbial analogues to analyse ecological response to environmental change. Location Eight hundred and ninety‐one lakes in five regional datasets from north‐western Europe and four regional datasets from north‐eastern North America. Methods Lacustrine diatom communities were analysed at three scales: inter‐continental, intra‐continental and regional. Nested partial redundancy analyses (RDAs) were used to determine spatial versus environmental components of community variation. Weighted‐averaging (WA) regression and calibration, as well as logistic and quadratic regressions, were used to detect niche conservatism and the prevalence of environmental specialists. Results Community patterns indicate that dispersal limitation acts predominantly at the inter‐continental scale, while at the regional (less than c. 1,000,000 km²) scale, a single environmental variable (pH) explains more than five times the community variation as spatial (dispersal‐related) variables. In addition, pH niche components appear to be conserved at the inter‐continental scale, and environmental specialization does not impose relative rarity, as specialists apparently readily disperse to suitable environments. Main conclusions Analysis at multiple scales is clearly important in determining the influences of community variation. For diatom communities, dispersal limitation acts most strongly at the broadest scales, giving way to environment at the scales considered by most analyses. The availability of a wide variety of propagules with consistent niches across regions indicates that diatom communities reflect the succession of taxa according to local environmental conditions, rather than disequilibrium with the environment or adaptation of local populations. While multi‐scale analyses must be undertaken for other groups to resolve debates over community drivers and determine appropriate scales for prediction, for diatoms (and probably other microbial communities), responses to environmental change can be inferred using analogue datasets from large geographic areas.     

Environmental niche conservatism explains the accumulation of species richness in Mediterranean‐hotspot plant genera

The causes of exceptionally high plant diversity in Mediterranean‐climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of “hotspot niche conservatism” whereby the accumulation of plant diversity in Mediterranean‐type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches.     

Pliocene–Pleistocene ecological niche evolution shapes the phylogeography of a Mediterranean plant group

Estimating species ability to adapt to environmental changes is crucial to understand their past and future response to climate change. The Mediterranean Basin has experienced remarkable climatic changes since the Miocene, which have greatly influenced the evolution of the Mediterranean flora. Here, we examine the evolutionary history and biogeographic patterns of two sedge sister species (Carex, Cyperaceae) restricted to the western Mediterranean Basin, but with Pliocene fossil record in central Europe. In particular, we estimated the evolution of climatic niches through time and its influence in lineage differentiation. We carried out a dated phylogenetic–phylogeographic study based on seven DNA regions (nDNA and ptDNA) and fingerprinting data (AFLPs), and modelled ecological niches and species distributions for the Pliocene, Pleistocene and present. Phylogenetic and divergence time analyses revealed that both species form a monophyletic lineage originated in the late Pliocene–early Pleistocene. We detected clear genetic differentiation between both species with distinct genetic clusters in disjunct areas, indicating the predominant role of geographic barriers limiting gene flow. We found a remarkable shift in the climatic requirements between Pliocene and extant populations, although the niche seems to have been relatively conserved since the Pleistocene split of both species. This study highlights how an integrative approach combining different data sources and analyses, including fossils, allows solid and robust inferences about the evolutionary history of a plant group since the Pliocene.     

Speciation and ecology revisited: phylogenetic niche conservatism and the origin of species

Evolutionary biologists have often suggested that ecology is important in speciation, in that natural selection may drive adaptive divergence between lineages that inhabit different environments. I suggest that it is the tendency of lineages to maintain their ancestral ecological niche (phylogenetic niche conservatism) and their failure to adapt to new environments which frequently isolates incipient species and begins the process of speciation. Niche conservatism may be an important and widespread component of allopatric speciation but is largely unstudied. The perspective outlined here suggests roles for key microevolutionary processes (i.e., natural selection, adaptation) that are strikingly different from those proposed in previous literature on ecology and speciation. Yet, this perspective is complementary to the traditional view because it focuses on a different temporal stage of the speciation process.     

Niche conservatism and phylogenetic clustering in a tribe of arid‐adapted marsupial mice,the Sminthopsini

The progressive expansion of the Australian arid zone during the last 20 Ma appears to have spurred the diversification of several families of plants, vertebrates and invertebrates, yet such taxonomic groups appear to show limited niche radiation. Here, we test whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence in a tribe of marsupial mice (Sminthopsini; 23 taxa) that includes the most speciose genus of living dasyurids, the sminthopsins. To that end, we integrated phylogenetic data with ecological niche modelling, to enable us to reconstruct the evolution of climatic suitability within Sminthopsini. Niche overlap among species was low‐moderate (but generally higher than expected given environmental background similarity), and the degree of phylogenetic clustering increased with aridity. Climatic niche reconstruction illustrates that there has been little apparent evolution of climatic tolerance within clades. Accordingly, climatic disparity tends to be accumulated among clades, suggesting considerable niche conservatism. Our results also indicate that evolution of climatic tolerances has been heterogeneous across different dimensions of climate (temperature vs. precipitation) and across phylogenetic clusters (Sminthopsis murina group vs. other groups). Although some results point to the existence of shifts in climatic niches during the speciation of sminthopsins, our study provides evidence for substantial phylogenetic niche conservatism in the group. We conclude that niche diversification had a low impact on the speciation of this tribe of small, but highly mobile marsupials.     

Latitudinal gradients in climatic‐niche evolution accelerate trait evolution at high latitudes

Despite the importance of divergent selection to the speed of evolution, it remains poorly understood if divergent selection is more prevalent in the tropics (where species richness is highest), or at high latitudes (where paleoclimate change has been most intense). We tested whether the rate of climatic‐niche evolution – one proxy for divergent selection – varies with latitude for 111 pairs of bird species. Using Brownian motion and Ornsetin–Ulhenbeck models, we show that evolutionary rates along two important axes of the climatic‐niche – temperature and seasonality – have been faster at higher latitudes. We then tested whether divergence of the climatic‐niche was associated with evolution in traits important in ecological differentiation (body mass) and reproductive isolation (song), and found that climatic divergence is associated with faster rates in both measures. These results highlight the importance of climate‐mediated divergent selection pressures in driving evolutionary divergence and reproductive isolation at high latitudes.