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

Scale-dependent influences of environmental, historical, and spatial processes on taxonomic and functional beta diversity of Japanese bat assemblages

This study investigated the relative influences of environmental, spatial, and historical factors, including the island-specific history of land connectivity, on bat assemblages in the Japanese Archipelago. We collected bat distribution data from 1408 studies and assigned them to Japan's First Standard Grid (approximately 6400 km2). Japanese bat assemblages were analyzed at two scales: the entire Japanese Archipelago comprised 16 islands and exclusively the four main islands. At first, we calculated taxonomic and functional total beta diversity (β total) by Jaccard pairwise dissimilarity and then divided this into turnover (β repl) and richness-difference (β rich) components. We conducted hierarchical clustering of taxonomic beta diversity to examine the influence of the two representative sea straits, Tsugaru and Tokara, which are considered biogeographical borders. Variation partitioning was conducted to evaluate the relative effects of the three factors on the beta diversity. Clustering revealed that the Tokara Strait bordered the two major clades; however, the Tsugaru Strait did not act as a biogeographical border for bats. In the variation partitioning, shared fraction between spatial and historical factors significantly explained taxonomic and functional β total and taxonomic β repl at the entire archipelago scale, but not at the four main islands scale extending only Tsugaru Strait but not Tokara Strait. Pure environmental factors significantly explained functional β total at both scales and taxonomic β total only at the four main islands scale. These results suggest that spatial and historical factors are more pronounced in biogeographical borders, primarily structuring assemblage composition at the entire archipelago scale, especially in taxonomic dimension. However, current environmental factors primarily shape the assemblage composition of Japanese bats at the main island scale. The difference in results between the two scales highlights that the primary processes governing assemblages of both dimensions depend on the quality of the dispersal barriers between terrestrial and aquatic barriers for bats.

Area, isolation and climate explain the diversity of mammals on islands worldwide

Insular biodiversity is expected to be regulated differently than continental biota, but their determinants remain to be quantified at a global scale. We evaluated the importance of physical, environmental and historical factors on mammal richness and endemism across 5592 islands worldwide. We fitted generalized linear and mixed models to accommodate variation among biogeographic realms and performed analyses separately for bats and non-volants. Richness on islands ranged from one to 234 species, with up to 177 single island endemics. Diversity patterns were most consistently influenced by the islands' physical characteristics. Area positively affected mammal diversity, in particular the number of non-volant endemics. Island isolation, both current and past, was associated with lower richness but greater endemism. Flight capacity modified the relative importance of past versus current isolation, with bats responding more strongly to current and non-volant mammals to past isolation. Biodiversity relationships with environmental factors were idiosyncratic, with a tendency for greater effects sizes with endemism than richness. The historical climatic change was positively associated with endemism. In line with theory, we found that area and isolation were among the strongest drivers of mammalian biodiversity. Our results support the importance of past conditions on current patterns, particularly of non-volant species.

A comprehensive phylogeography of the widespread pond snail genus Radix revealed restricted colonization due to niche conservatism

To clarify the effect of niche conservatism on evolutionary history, we focused on freshwater snails, which have different ecological and phylogenetic properties from previously tested taxa. We conducted a phylogenetic analysis using 750 lymnaeid individuals from 357 sites of eleven Radix species. Then, we estimated the ancestral distribution using the geographic coordinates and colonization routes. In addition, a statistical test of the colonization distances in the latitudinal and longitudinal directions was performed. We also conducted ecological niche modeling for two widely distributed species using climatic data. Ancestral geographic reconstruction estimated the origin of the genus to be around the Indian subcontinental region and showed that latitudinal immigration distances were shorter than longitudinal immigration distances in the diversification process. Ecological niche models suggested that the current distribution was restricted by climate, with annual mean temperature and precipitation of the driest month as particularly strong factors. Niche conservatism to the climate can affect the diversification of freshwater snails.

Annual precipitation predicts the phylogenetic signal in bat-fruit interaction networks across the Neotropics

Closely related species tend to be more similar than randomly selected species from the same phylogenetic tree. This pattern, known as a phylogenetic signal, has been extensively studied for intrinsic (e.g. morphology), as well as extrinsic (e.g. climatic preferences), properties but less so for ecological interactions. Phylogenetic signals of species interactions (i.e. resource use) can vary across time and space, but the causes behind such variations across broader spatial extents remain elusive. Here, we evaluated how current and historical climates influence phylogenetic signals of bat-fruit interaction networks across the Neotropics. We performed a model selection relating the phylogenetic signals of each trophic level (bats and plants) with a set of current and historical climatic factors deemed ecologically important in shaping biotic interactions. Bat and plant phylogenetic signals in bat-fruit interaction networks varied little with climatic factors, although bat phylogenetic signals positively covaried with annual precipitation. These findings indicated that water availability could increase resource availability, favouring higher niche partitioning of trophic resources among bat species and hence bat phylogenetic signals across bat-fruit interaction networks. Overall, our study advances our understanding of the spatial dynamics of bat-fruit interactions by highlighting the association of current climatic factors with phylogenetic patterns of biotic interactions.

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.

Evolutionary time drives global tetrapod diversity

Global variation in species richness is widely recognized, but the explanation for what drives it continues to be debated. Previous efforts have focused on a subset of potential drivers, including evolutionary rate, evolutionary time (maximum clade age of species restricted to a region), dispersal (migration from one region to another), ecological factors and climatic stability. However, no study has evaluated these competing hypotheses simultaneously at a broad spatial scale. Here, we examine their relative contribution in determining the richness of the most comprehensive dataset of tetrapods to our knowledge (84% of the described species), distinguishing between the direct influences of evolutionary rate, evolutionary time and dispersal, and the indirect influences of ecological factors and climatic stability through their effect on direct factors. We found that evolutionary time exerted a primary influence on species richness, with evolutionary rate being of secondary importance. By contrast, dispersal did not significantly affect richness patterns. Ecological and climatic stability factors influenced species richness indirectly by modifying evolutionary time (i.e. persistence time) and rate. Overall, our findings suggest that global heterogeneity in tetrapod richness is explained primarily by the length of time species have had to diversify.

A synthesis of ecological and evolutionary determinants of bat diversity across spatial scales

Background

Diversity patterns result from ecological to evolutionary processes operating at different spatial and temporal scales. Species trait variation determine the spatial scales at which organisms perceive the environment. Despite this knowledge, the coupling of all these factors to understand how diversity is structured is still deficient. Here, we review the role of ecological and evolutionary processes operating across different hierarchically spatial scales to shape diversity patterns of bats—the second largest mammal order and the only mammals with real flight capability.

Main body

We observed that flight development and its provision of increased dispersal ability influenced the diversification, life history, geographic distribution, and local interspecific interactions of bats, differently across multiple spatial scales. Niche packing combined with different flight, foraging and echolocation strategies and differential use of air space allowed the coexistence among bats as well as for an increased diversity supported by the environment. Considering distinct bat species distributions across space due to their functional characteristics, we assert that understanding such characteristics in Chiroptera improves the knowledge on ecological processes at different scales. We also point two main knowledge gaps that limit progress on the knowledge on scale-dependence of ecological and evolutionary processes in bats: a geographical bias, showing that research on bats is mainly done in the New World; and the lack of studies addressing the mesoscale (i.e. landscape and metacommunity scales).

Conclusions

We propose that it is essential to couple spatial scales and different zoogeographical regions along with their functional traits, to address bat diversity patterns and understand how they are distributed across the environment. Understanding how bats perceive space is a complex task: all bats can fly, but their perception of space varies with their biological traits.

Electronic supplementary material

The online version of this article (10.1186/s12898-018-0174-z) contains supplementary material, which is available to authorized users.

Genetic and ecological processes promoting early diversification in the lowland Mesoamerican bat Sturnira parvidens (Chiroptera: Phyllostomidae)

With 22 species, Sturnira is the most speciose genus of frugivorous Neotropical bats. Sturnira parvidens inhabits lowland tropical areas from Mexico to Central America. The elevation of this taxon to species level was recent, and discrepancies with respect to its geographic limits and phylogenetic position continue to exist. In order to identify genetic and ecological processes likely involved in the diversification and current distribution of S. parvidens, we evaluated relationships, researched phylogeographic and demographic history, and tested the divergence/conservatism of the climatic niche of this bat. We used data from mitochondrial loci (cytochrome b and the hypervariable D-loop region I) and the nuclear recombination activating gene 1, in 173 samples of S. parvidens and 77 samples of related species. We performed Bayesian analyses to infer phylogenetic relationships and analyzed phylogeographic structure, genetic diversity, divergence times and historical demography. Sturnira bakeri is the sister group of S. parvidens, and inhabits Western Ecuador. The two species diverged c. 1.84Ma, and their distributions are disjunct and separated by Sturnira luisi. Within S. parvidens there are two haplogroups with nearly allopatric distributions that are limited to the Sierra Madre del Sur, on the Mexican Pacific Slope. The divergence time between haplogroups was c. 0.423Ma and we detected signals of demographic expansion. We also analyzed 526 occurrence data of S. parvidens to test for changes in environmental niche of this species. We detected signals of divergence of climatic niche, mainly in temperature and seasonality variables. Likely, both genetic and ecological processes have shaped the evolutionary history of S. parvidens. Despite many climatic fluctuations during the Pleistocene, only the most intense oscillations had an impact on these bats. In addition, ecological differentiation prevents admixture of genetic lineages that are in contact and lack apparent geographical barriers at the southern Sierra Madre del Sur. We concluded that speciation in Sturnira was promoted by this taxon's ability to colonize new geographical and environmental spaces and form genetically structured groups when populations become isolated.

Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales

Numerous processes influence community structure. The relative importance of these processes is thought to vary with spatial, temporal and taxonomic scales: density-dependent interactions are thought to be most important at small scales; at intermediate scales, environmental conditions may be the most influential factor; and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat filtering, whereas communities experiencing more favourable conditions will be structured predominantly by density-dependent interactions such as competition. The aim of this study was to investigate the influence of environmental factors on phylogenetic community structure (PCS) of North American desert bats at multiple spatial and taxonomic scales. We also examined whether the stress-dominance hypothesis is upheld in desert bats across an environmental gradient. Phylogenetic community structure metrics were calculated using species pools that differed in spatial (from all deserts to individual deserts) and taxonomic (all bat taxa, a single family and a single genus) scales. We calculated mean temperature, precipitation and seasonality for each site to determine whether environmental gradients were related to degree of community structure. At the largest spatial and taxonomic scales, communities were significantly phylogenetically clustered while degree of clustering decreased at the smallest spatial and taxonomic scales. Climatic data, particularly mean temperature and temperature seasonality, were important predictors of PCS at larger scales and under harsher conditions, but at smaller scales and in less stressful conditions there was a weaker relationship between PCS and climate. This suggests that North American deserts, while harsh, are not uniform in the challenges they present to the faunas residing in them. Overall, the relationship between PCS and climatic data at large spatial and taxonomic scales, and in harsher conditions, suggests the influence of habitat filtering has been important in North American desert bat community assembly and that other processes have been important at smaller scales.

Stronger tests of mechanisms underlying geographic gradients of biodiversity: insights from the dimensionality of biodiversity

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE). Species composition of 10,000-km(2) grid cells was determined by overlaying geographic range maps of 133 noctilionoid bat taxa. We determined empirical diversity gradients in the Neotropics by calculating species richness and three indices each of phylogenetic, functional and phenetic diversity for each grid cell. We also created 1,000 simulated gradients of each examined metric of biodiversity based on a MDE model to estimate patterns expected if species distributions were randomly placed within the Neotropics. For each simulation run, we regressed the observed gradient onto the MDE-expected gradient. If a MDE drives empirical gradients, then coefficients of determination from such an analysis should be high, the intercept no different from zero and the slope no different than unity. Species richness gradients predicted by the MDE fit empirical patterns. The MDE produced strong spatially structured gradients of taxonomic, phylogenetic, functional and phenetic diversity. Nonetheless, expected values generated from the MDE for most dimensions of biodiversity exhibited poor fit to most empirical patterns. The MDE cannot account for most empirical patterns of biodiversity. Fuller understanding of latitudinal gradients will come from simultaneous examination of relative effects of random, environmental and historical mechanisms to better understand distribution and abundance of the current biota.

Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north-south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales.

Is regional species diversity bounded or unbounded?

Two conflicting hypotheses have been proposed to explain large-scale species diversity patterns and dynamics. The unbounded hypothesis proposes that regional diversity depends only on time and diversification rate and increases without limit. The bounded hypothesis proposes that ecological constraints place upper limits on regional diversity and that diversity is usually close to its limit. Recent evidence from the fossil record, phylogenetic analysis, biogeography, and phenotypic disparity during lineage diversification suggests that diversity is constrained by ecological processes but that it is rarely asymptotic. Niche space is often unfilled or can be more finely subdivided and still permit coexistence, and new niche space is often created before ecological limits are reached. Damped increases in diversity over time are the prevalent pattern, suggesting the need for a new 'damped increase hypothesis'. The damped increase hypothesis predicts that diversity generally increases through time but that its rate of increase is often slowed by ecological constraints. However, slowing due to niche limitation must be distinguished from other possible mechanisms creating similar patterns. These include sampling artifacts, the inability to detect extinctions or declines in clade diversity with some methods, the distorting effects of correlated speciation-extinction dynamics, the likelihood that opportunities for allopatric speciation will vary in space and time, and the role of undetected natural enemies in reducing host ranges and thus slowing speciation rates. The taxonomic scope of regional diversity studies must be broadened to include all ecologically similar species so that ecological constraints may be accurately inferred. The damped increase hypothesis suggests that information on evolutionary processes such as time-for-speciation and intrinsic diversification rates as well as ecological factors will be required to explain why regional diversity varies among times, places and taxa.

An asymmetry in niche conservatism contributes to the latitudinal species diversity gradient in New World vertebrates

The Tropical Niche Conservatism hypothesis is a leading explanation for why biodiversity increases towards the equator. The model suggests that most lineages have tropical origins, with few dispersing into temperate regions. However, biotas are comprised of lineages with differing geographical origins, thus it is unclear whether lineages that originated on different continents will exhibit similar patterns of niche conservatism. Here, we summarised biogeographical patterns of New World vertebrates and compared species diversity patterns between families that originated in North and South America. Overall, families with southern origins exhibit niche conservatism with many lineages restricted to the Neotropics, whereas many northern-origin families are distributed across the Neotropics and the Nearctic. Consequently, northern lineages have contributed to high tropical biodiversity, but southern lineages have contributed relatively little to temperate biodiversity in North America. The asymmetry in niche conservatism between northern and southern lineages is an important contributor to the biodiversity gradient.

Quantifying phylogenetic beta diversity: distinguishing between 'true' turnover of lineages and phylogenetic diversity gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as ‘broad-sense’ measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for ‘true’ phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the ‘true’ phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.

Strong influence of regional species pools on continent-wide structuring of local communities

There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use a continent-wide dataset of local ant communities and implement ecologically explicit source pool definitions to examine the relative importance of regional species pools and local interactions for shaping community structure. Then we assess which factors underlie systematic variation in the structure of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution of climatic niches influences the phylogenetic structure of regional source pools and that the influence of regional source pools on local community structure is strong.