Comparative phyloclimatic analysis and evolution of ecological niches in the scimitar babblers (Aves: Timaliidae: Pomatorhinus)

Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia

BACKGROUND

Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models.

RESULTS

There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures).

CONCLUSION

Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density, but this has largely not been tested. Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide, we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species. We assessed phylogenetic signal in different taxonomic (e.g., angiosperms and gymnosperms) and ecological (e.g., tropical, temperate, and boreal) groups of tree species, explored the biogeographical and phylogenetic patterns of wood density, and quantified the relative importance of current environmental factors (e.g., climatic and soil variables) and evolutionary history (i.e., phylogenetic relatedness among species and lineages) in driving global wood density variation. We found that wood density displayed a significant phylogenetic signal. Wood density differed among different biomes and climatic zones, with higher mean values of wood density in relatively drier regions (highest in subtropical desert). Our study revealed that at a global scale, for angiosperms and gymnosperms combined, phylogeny and species (representing the variance explained by taxonomy and not direct explained by long-term evolution process) explained 84.3% and 7.7% of total wood density variation, respectively, whereas current environment explained 2.7% of total wood density variation when phylogeny and species were taken into account. When angiosperms and gymnosperms were considered separately, the three proportions of explained variation are, respectively, 84.2%, 7.5% and 6.7% for angiosperms, and 45.7%, 21.3% and 18.6% for gymnosperms. Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions

Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package.

CJ, Peterson AT. Acknowledging uncertainty in evolutionary reconstructions of ecological niches

Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods may infer the history of ecological niche evolution inaccurately because (a) species' niches are often poorly characterized; and (b) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species' environmental tolerances. Here, we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty introduced by incomplete niche characterization. Then, we modify existing ancestral state inference methods to leverage full estimates of environmental tolerances. We provide a worked empirical example of our method, investigating ecological niche evolution in the New World orioles (Aves: Passeriformes: Icterus spp.). Temperature and precipitation tolerances were generally broad and conserved among orioles, with niche reduction and specialization limited to a few terminal branches. Tools for performing these reconstructions are available in a new R package called nichevol.

The combined role of dispersal and niche evolution in the diversification of Neotropical lizards

Ecological requirements and environmental conditions can influence diversification across temporal and spatial scales. Understanding the role of ecological niche evolution under phylogenetic contexts provides insights on speciation mechanisms and possible responses to future climatic change. Large-scale phyloclimatic studies on the megadiverse Neotropics, where biomes with contrasting vegetation types occur in narrow contact, are rare. We integrate ecological and biogeographic data with phylogenetic comparative methods, to investigate the relative roles of biogeographic events and niche divergence and conservatism on the diversification of the lizard genus Kentropyx Spix, 1825 (Squamata: Teiidae), distributed in South American rainforests and savannas. Using five molecular markers, we estimated a dated species tree, which recovered three clades coincident with previously proposed species groups diverging during the mid-Miocene. Biogeography reconstruction indicates a role of successive dispersal events from an ancestral range in the Brazilian Shield and western Amazonia. Ancestral reconstruction of climatic tolerances and niche overlap metrics indicates a trend of conservatism during the diversification of groups from the Amazon Basin and Guiana Shield, and a strong signal of niche divergence in the Brazilian Shield savannas. Our results suggest that climatic-driven divergence at dynamic forest-savanna borders might have resulted in adaptation to new environmental niches, promoting habitat shifts and shaping speciation patterns of Neotropical lizards. Dispersal and ecological divergence could have a more important role in Neotropical diversification than previously thought.

Contrasting drivers of diversification rates on islands and continents across three passerine families

Diversification rates vary greatly among taxa. Understanding how species-specific traits influence speciation rates will help elucidate mechanisms driving biodiversity over broad spatio-temporal scales. Ecological specialization and range size are two hypothesized drivers of speciation rates, yet each mechanism predicts both increases and decreases in speciation. We constructed a continuous index of specialization using avian bill morphology to determine the relative effect of specialization and range size and shape on speciation rates across 559 species within the Emberizoidea superfamily, a morphologically diverse New World clade. We found a significant positive correlation between specialization and speciation rate and a negative correlation with range size. Only the effect of specialization persisted after removing island endemics, however, suggesting that ecological specialization is an important driver of diversity across large macroevolutionary scales, and the relative importance of specific drivers may differ between islands and continents.

Climatic Niche Shift during Azolla filiculoides Invasion and Its Potential Distribution under Future Scenarios

In order to prevent future biological invasions, it is crucial to know non-native species distributions. We evaluated the potential global distribution of Azolla filiculoides, a free-floating macrophyte native to the Americas by using species distribution models and niche equivalency tests to analyze the degree of niche overlap between the native and invaded ranges of the species. The models were projected under two future emission scenarios, three global circulation models and two time periods. Our results indicate a possible niche shift between the distribution ranges of the species, indicating that A. filiculoides can adapt to novel environmental conditions derived from climatic differences during the invasion process. Our models also show that the future potential distribution of A. filiculoides will decrease globally, although the species could colonize new vulnerable regions where it is currently absent. We highlight that species occurrence records in the invaded area are necessary to generate accurate models, which will, in turn, improve our ability to predict potential invasion risk areas.

Climatic niche evolution in the viviparous Sceloporus torquatus group (Squamata: Phrynosomatidae)

The cold-climate hypothesis maintains that viviparity arose as a means to prevent increased egg mortality in nests owing to low temperatures, and this hypothesis represents the primary and most strongly supported explanation for the evolution of viviparity in reptiles. In this regard, certain authors have stated that viviparous species will exhibit speciation via climatic niche conservatism, with similar climatic niches being observed in allopatric sister species. However, this prediction remains to be tested with bioclimatic variables relevant to each viviparous group. In the present study, we examined climatic niche evolution in a group of North American viviparous lizards to determine whether their diversification is linked to phylogenetic niche conservatism (PNC). We evaluated the phylogenetic signal and trait evolution of individual bioclimatic variables and principal component (PC) scores of a PC analysis, along with reconstructions of ancestral climate tolerances. The results suggest that diversification of the Sceloporus torquatus group species is associated with both niche differentiation and PNC. Furthermore, we did not observe PNC across nearly all bioclimatic variables and in PC2 and PC3. However, in Precipitation Seasonality (Bio15), in Precipitation of Coldest Quarter (Bio19) and in PC1 (weakly associated with variability of temperature), we did observe PNC. Additionally, variation of the scores along the phylogeny and Pagel's delta (δ) >1 of PC3 suggests a fast, recent evolution to dry conditions in the clade that sustains S. serrifer.

Reconstructing Ecological Niche Evolution When Niches Are Incompletely Characterized

Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches often produce incomplete characterizations, as they are inferred from present-day distributions that may be limited in full expression of the fundamental ecological niche by biotic interactions, dispersal limitations, and the existing set of environmental conditions. Here, we test whether incomplete niche characterizations inherent in most estimates of species' niches bias phylogenetic reconstructions of niche evolution, using simulations of virtual species with known niches. Results establish that incompletely characterized niches inflate estimates of evolutionary change and lead to error in ancestral state reconstructions. Our analyses also provide a potential mechanism to explain the frequent observation that maximum thermal tolerances are more conserved than minimum thermal tolerances: populations and species experience more spatial variation in minimum temperature than in maximum temperature across their distributions and, consequently, may experience stronger diversifying selection for cold tolerance.

The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938)

One of the most contentious theories in current ecology is the ecological niche conservatism, which is defined as conservatism among closely related species; however, the ecological niche can also be shifted, as documented in several cases. Genetic drift and ecological divergent selection may cause ecological niche divergence. The current study aims to test whether the ecological niche is conserved or divergent and to determine the main factor that drives ecological niche divergence or conservation. We analyzed the phylogenetic relationship, ecological niche model (ENM) and demographic history of Eared Pheasants in the genus Crossoptilon (Galliformes: Phasianidae) to test niche conservatism with respect to different geographically distributed patterns. The phylogenetic relationship was reconstructed using ∗BEAST with mitochondrial cytochrome b (cyt b) and 44 unlinked autosomal exonic loci, and ENMs were reconstructed in MAXENT using an average of 41 occurrence sites in each species and 22 bioclimatic variables. A background similarity test was used to detect whether the ecological niche is conserved. Demographic history was estimated using the isolation with migration (IM) model. We found that there was asymmetric gene flow between the allopatric sister species Crossoptilon mantchuricum and C. auritum and the parapatric sister species C. harmani and C. crossoptilon. We found that ecological niches were divergent, not conserved, between C. mantchuricum and C. auritum, which began to diverge at approximately 0.3 million years ago. However, the ecological niches were conserved between C. crossoptilon and C. harmani, which gradually diverged approximately half a million years ago. Ecological niches can be either conserved or divergent, and ecological divergent selection for local adaptation is probably an important factor that promotes and maintains niche divergence in the face of gene flow. This study provides a better understanding of the role that divergent selection has in the initial speciation process. The platform combined demographic processes and ecological niches to offer new insights into the mechanism of biogeography patterns.

Frequent but asymmetric niche shifts in Bulbophyllum orchids support environmental and climatic instability in Madagascar over Quaternary time scales

BACKGROUND

Species or clades may retain or shift their environmental niche space over evolutionary time. Understanding these processes offers insights into the environmental processes fuelling lineage diversification and might also provide information on past range dynamics of ecosystems. However, little is known about the relative contributions of niche conservatism versus niche divergence to species diversification in the tropics. Here, we examined broad-scale patterns of niche evolution within a Pliocene-Pleistocene clade of epiphytic Bulbophyllum orchids (30 spp.) whose collective distribution covers the northwest and eastern forest ecosystems of Madagascar.

RESULTS

Using species occurrence data, ecological niche models, and multivariate analyses of contributing variables, we identified a three-state niche distribution character for the entire clade, coinciding with three major forest biomes viz. phytogeographical provinces in Madagascar: A, Northwest 'Sambirano'; B, 'Eastern Lowlands'; and C, 'Central Highlands'. A time-calibrated phylogeny and Bayesian models of niche evolution were then used to detect general trends in the direction of niche change over the clade's history (≤5.3 Ma). We found highest transitions rates between lowlands (A and B) and (mostly from B) into the highland (C), with extremely low rates out of the latter. Lowland-to-highland transitions occurred frequently during the Quaternary, suggesting that climate-induced vegetational shifts promoted niche transitions and ecological speciation at this time.

CONCLUSIONS

Our results reveal that niche transitions occurred frequently and asymmetrically within this Madagascan orchid clade, and in particular over Quaternary time scales. Intrinsic features germane to Bulbophyllum (e.g., high dispersal ability, drought tolerance, multiple photosynthetic pathways) as well as extrinsic factors (ecological, historical) likely interacted to generate the niche transition patterns observed. In sum, our results support the emerging idea of dramatic environmental and climatic fluctuations in Madagascar during the recent geological past, which overturns the long-held paradigm of long-term stability in tropical forest settings. The generality of the patterns and timings reported here awaits the availability of additional comparative studies in other Madagascan endemics.

Untangling taxonomic confusion and diversification patterns of the Streak-breasted Scimitar Babblers (Timaliidae: Pomatorhinus ruficollis complex) in southern Asia

Biodiversity patterns in Asia are poorly understood due to inferences drawn from incorrect taxonomy and limited survey effort. The Streak-breasted Scimitar Babblers (Pomatorhinus ruficollis complex) have a wide distribution across southern Asia and exhibit a high degree of plumage variability within and among populations. Continued use of traditional subspecies designations over revised species-limits based on plumage and DNA sequence data furthers confusion in this group and obscures complex biogeographic patterns. In this study, we combined previously published DNA sequences with newly sampled populations to produce a comprehensive dataset for the ruficollis complex. Phylogenetic analysis of these data confirms that traditional subspecies based on plumage alone are paraphyletic and therefore not good descriptors of evolutionary history. With increased sampling, our study supported previous delimitations of phylogenetic species as distinct units, refined the range limits of two taxa - P. reconditus (throughout central China) and P. nigrostellatus (Hainan, Guangxi, N Vietnam), showed two additional clades that may be distinct species, and uncovered a 'suture' zone where populations of multiple species occur in the same localities. Diversification within the ruficollis complex indicates a clade of Sino-Himalayan and SE Asian species sister to a clade distributed in central and southern China species. The 'suture' zone where different ruficollis species are in contact coincides with the meeting of these four major geographic areas in a highly geomorphologically complex region.