Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Ecological niche conservatism spurs diversification in response to climate change

Lengthy debate has surrounded the theoretical and empirical science of whether climatic niche evolution is related to increased or decreased rates of biological diversification. Because species can persist for thousands to millions of years, these questions cross broad scales of time and space. Thus, short-term experiments may not provide comprehensive understanding of the system, leading to the emergence of contrasting opinions: niche evolution may increase diversity by allowing species to explore and colonize new geographic areas across which they could speciate; or, niche conservatism might augment biodiversity by supporting isolation of populations that may then undergo allopatric speciation. Here, we use a simulation approach to test how biological diversification responds to different rates and modes of niche evolution. We find that niche conservatism promotes biological diversification, whereas labile niches-whether adapting to the conditions available or changing randomly-generally led to slower diversification rates. These novel results provide a framework for understanding how Earth-life interactions produced such a diverse biota.

Accelerating local extinction associated with very recent climate change

Climate change has already caused local extinction in many plants and animals, based on surveys spanning many decades. As climate change accelerates, the pace of these extinctions may also accelerate, potentially leading to large-scale, species-level extinctions. We tested this hypothesis in a montane lizard. We resurveyed 18 mountain ranges in 2021-2022 after only ~7 years. We found rates of local extinction among the fastest ever recorded, which have tripled in the past ~7 years relative to the preceding ~42 years. Further, climate change generated local extinction in ~7 years similar to that seen in other organisms over ~70 years. Yet, contrary to expectations, populations at two of the hottest sites survived. We found that genomic data helped predict which populations survived and which went extinct. Overall, we show the increasing risk to biodiversity posed by accelerating climate change and the opportunity to study its effects over surprisingly brief timescales.

Chemical signaling glands are unlinked to species diversification in lizards

Sexual selection has long been thought to increase species diversification. Sexually selected traits, such as sexual signals that contribute to reproductive isolation, were thought to promote diversification. However, studies exploring links between sexually selected traits and species diversification have thus far primarily focused on visual or acoustic signals. Many animals often employ chemical signals (i.e., pheromones) for sexual communications, but large-scale analyses on the role of chemical communications in driving species diversification have been missing. Here, for the first time, we investigate whether traits associated with chemical communications-the presence of follicular epidermal glands-promote diversification across 6,672 lizard species. In most analyses, we found no strong association between the presence of follicular epidermal glands and species diversification rates, either across all lizard species or at lower phylogenetic scales. Previous studies suggest that follicular gland secretions act as species recognition signals that prevent hybridization during speciation in lizards. However, we show that geographic range overlap was no different in sibling species pairs with and without follicular epidermal glands. Together, these results imply that either follicular epidermal glands do not primarily function in sexual communications or sexually selected traits in general (here chemical communication) have a limited effect on species diversification. In our additional analysis accounting for sex-specific differences in glands, we again found no detectable effect of follicular epidermal glands on species diversification rates. Thus, our study challenges the general role of sexually selected traits in broad-scale species diversification patterns.

Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila

The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.

A Theory of City Biogeography and the Origin of Urban Species

Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.

Response of Iranian lizards to future climate change by poleward expansion, southern contraction, and elevation shifts

This study explores the relationships between recent Iranian lizard species distributions and the observed climate, as well as potential future distributions of species. For this purpose, an ensemble of seven algorithms was used to forecast the distributions of 30 species for the recent and future (2070) based on the averages of 14 global climate models under optimistic (RCP2.6) and pessimistic (RCP8.5) scenarios. Annual precipitation (n = 16) and annual mean temperature (n = 7) were identified as the most important variables in determining the distribution of 76.66% (23 out of 30) of the species. The consensus model predicts that the ranges of 83.33% of species (n = 25) have the potential to expand poleward at higher latitudes while preserving the majority of their recent distributions (except for four species). Furthermore, the ranges of the remaining species (n = 5) will be preserved at higher latitudes. However, they (n = 22) may contract slightly (n = 13) or excessively (n = 9) in the south of their distribution range at lower latitudes. These results indicate that species (N = 19) situated in mountainous areas such as the Zagros, Alborz, and Kopet Dagh may move or maintain their range at higher elevations as a result of future climate change. Finally, this study suggests that 30% of species (n = 9) may be threatened by future climate change and that they should be prioritized in conservation efforts.

The Strait of Gibraltar is an ineffective palaeogeographic barrier for some flightless darkling beetles (Coleoptera: Tenebrionidae: Pimelia)

The geographic distribution of a species is shaped by its biology and by environmental and palaeogeographic factors that interact at different spatial-temporal scales, which leads to distributions and diversification patterns observed between and within lineages. The darkling beetle genus Pimelia has been diversifying for more than 31.2 Mya showing different colonization patterns after the opening of the Gibraltar Strait 5 Mya. Three of the 14 subgenera of Pimelia have populations on both sides of the Strait. Through extensive sampling and the analysis of three molecular markers, we determine levels of intra- and interspecific genetic variation, identify evolutionary lineages in subgenera, estimate their temporal origin and distribution ranges and discuss the historical basis for the geographic and diversification patterns of Pimelia around the Strait. This single geographical feature acted both as a barrier and as a dispersal route for different Pimelia species. The Strait has represented a strong barrier for the subgenus Magrebmelia since the Middle Miocene. However, the subgenera Amblyptera and Amblypteraca share repetitive signatures of post-Messinian colonization across the Strait, possibly driven by stochastic or ‘catastrophic’ events such as tsunamis. Our demographic analyses support Wallace’s hypothesis on insect dispersal stochasticity. Some taxonomic changes, including the designation of a lectotype for Pimelia maura, are also proposed.

Evidence for ecological processes driving speciation among endemic lizards of Madagascar

Although genetic patterns produced by population isolation during speciation are well documented, the biogeographic and ecological processes that trigger speciation remain poorly understood. Alternative hypotheses for the biogeography and ecology of speciation include geographic isolation combined with niche conservation (soft allopatry) or parapatric distribution on an environmental gradient with niche divergence (ecological speciation). Here, we use species' distributions, environmental data, and two null models (the Random Translation and Rotation and the Background Similarity Test) to test these alternative hypotheses among 28 sister pairs of microendemic lizards in Madagascar. Our results demonstrate strong bimodal peaks along a niche divergence-conservation spectrum, with at least 25 out of 28 sister pairs exhibiting either niche conservation or divergence, and the remaining pairs showing weak ecological signals. Yet despite these significant results, we do not find strong associations of niche conservation with allopatric distributions or niche divergence with parapatric distributions. Our findings thus provide strong evidence of a role for ecological processes driving speciation, rather than the classic expectation of speciation through geographic isolation, but demonstrate that the link between ecological speciation and parapatry is complex and requires further analysis of a broader taxonomic sample to fully resolve.

Identifying regional environmental factors driving differences in climatic niche overlap in Peromyscus mice

Different groups of taxa exhibit varying degree of climatic niche conservatism or divergence due to evolutionary constraints imposed on taxa and distributional relationships among them. Herein, we explore to what extent regional environmental conditions that taxa occupy affect climatic niche overlap between pairs of congeneric species of Peromyscus mice exhibiting allopatric, parapatric, or sympatric distributions. We used Bayesian generalized linear mixed models to identify environmental variables that best explain differences in climatic niche overlap between species. Our results suggest that regional environmental conditions explain 13–44% of variation in climatic niche overlap. Specifically, allopatric and parapatric species pairs are more likely to occupy similar climatic niches in areas that are topographically less complex but with more complex habitats. Sympatric species are more likely to occupy similar climatic niches in areas that promote local niche partitioning (topographically less complex, warmer winter temperatures, higher precipitation, and higher habitat complexity on a local scale). By understanding the relationship between regional environmental conditions and niche overlap, we highlight how differences in geography can contribute to shaping niches of congeneric species.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini)

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.

Niche conservatism promotes speciation in cycads: the case of Dioon merolae (Zamiaceae) in Mexico

Niche conservatism is the tendency of lineages to retain the same niche as their ancestors. It constrains biological groups and prevents ecological divergence. However, theory predicts that niche conservatism can hinder gene flow, strengthen drift and increase local adaptation: does it mean that it also can facilitate speciation? Why does this happen? We aim to answer these questions. We examined the variation of chloroplast DNA, genome-wide single nucleotide polymorphisms, morphological traits and environmental variables across the Dioon merolae cycad populations. We tested geographical structure, scenarios of demographic history, and niche conservatism between population groups. Lineage divergence is associated with the presence of a geographical barrier consisting of unsuitable habitats for cycads. There is a clear genetic and morphological distinction between the geographical groups, suggesting allopatric divergence. However, even in contrasting available environmental conditions, groups retain their ancestral niche, supporting niche conservatism. Niche conservatism is a process that can promote speciation. In D. merolae, lineage divergence occurred because unsuitable habitats represented a barrier against gene flow, incurring populations to experience isolated demographic histories and disparate environmental conditions. This study explains why cycads, despite their ancient lineage origin and biological stasis, have been able to diversify into modern ecosystems worldwide.

Higher temperatures lower rates of physiological and niche evolution

Understanding rates and patterns of change in physiological and climatic-niche variables is of urgent importance as many species are increasingly threatened by rising global temperatures. Here, we broadly test several fundamental hypotheses about physiological and niche evolution for the first time (with appropriate phylogenetic methods), using published data from 2059 vertebrate species. Our main results show that: (i) physiological tolerances to heat evolve more slowly than those to cold, (ii) the hottest climatic-niche temperatures change more slowly than the coldest climatic-niche temperatures, and (iii) physiological tolerances to heat and cold evolve more slowly than the corresponding climatic-niche variables. Physiological tolerances are significantly and positively related to the corresponding climatic-niche variables, but species often occur in climates outside the range of these tolerances. However, mismatches between climate and physiology do not necessarily mean that the climatic-niche data are misleading. Instead, some standard physiological variables used in vertebrates (i.e. critical thermal maxima and minima) may reflect when species are active (daily, seasonally) and their local-scale microhabitats (sun versus shade), rather than their large-scale climatic distributions.

Climatic-niche evolution follows similar rules in plants and animals

Climatic niches are essential in determining where species can occur and how they will respond to climate change. However, it remains unclear if climatic-niche evolution is similar in plants and animals or is intrinsically different. For example, previous authors have proposed that plants have broader environmental tolerances than animals but are more sensitive to climate change. Here, we test ten predictions about climatic-niche evolution in plants and animals, using phylogenetic and climatic data for 19 plant clades and 17 vertebrate clades (2,087 species total). Surprisingly, we find that for all ten predictions, plants and animals show similar patterns. For example, in both groups, climatic niches change at similar mean rates and species have similar mean niche breadths, and niche breadths show similar relationships with latitude across groups. Our results suggest that there are general 'rules' of climatic-niche evolution that span plants and animals, despite the fundamental differences in their biology. These results may help to explain why plants and animals have similar responses to climate change and why they often have shared species richness patterns, biogeographic regions, biomes and biodiversity hotspots.

Shifts to multiple optima underlie climatic niche evolution in New World phyllostomid bats

Climate underlies species distribution patterns, especially in species where climate limits distributions, such as the phyllostomid bats, which are mostly restricted to the New World tropics. The evolutionary dynamics that shaped phyllostomid climatic niches remain unclear, and a broad phylogenetic perspective is required to uncover their patterns. We used geographical distributions and evolutionary relationships of 130 species, climate data and phylogenetic comparative methods to uncover dynamics of phyllostomid climatic niche evolution. Diversification of climatic niches began early in phyllostomid evolution (~34 Mya), with most changes taking place ~20 Mya. Although most of these bats were found in tropical regions, shifts towards different evolutionary optima were common. Shifts were mostly towards temperate climates, reflecting complexities in phyllostomid evolution highlighted by the probable role of species-specific adaptations to cope with these climates, the influence of palaeoclimatic events, and biogeographical effects related to the evolution and dispersal of clades in the New World. Our results broaden our understanding of the relationships between phyllostomid bats and climate, filling an important gap in knowledge and suggesting a complex evolution in their occupation of the climatic niche space.

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.