Trait evolution rates shape continental patterns of species richness in North America's most diverse angiosperm genus (Carex,Cyperaceae)

Ecological opportunity has been associated with increases in diversification rates across the tree of life. Under an ecological diversification model, the emergence of novel environments is hypothesized to promote morpho- and ecospace evolution. Whether this model holds at the clade level within the most species-rich angiosperm genus found in North America (Carex, Cyperaceae) is yet to be tested. Recent works demonstrate a temporal coupling of climate cooling and widespread colonization of Carex in North America, implicating ecological diversification. In addition, research has consistently found asymmetric patterns of lineage-level diversification in the genus. Why does variation in clade sizes exist in the genus? Is ecological diversification involved? In this study, we tested whether rates of morphological and ecological trait evolution are correlated with clade-level species richness in Carex of North America north of Mexico. We constructed a phylogeny of 477 species—an almost complete regional sample. We estimated rates of evolution of morphological traits, habitat, and climatic niche and assessed whether differences in rates of evolution correlate with species richness differences in replicate non-nested sister clades. Our work demonstrates significant positive correlations between climatic niche rates, habitat and reproductive morphological evolution, and species richness. This coupling of trait and niche evolution and species richness in a diverse, continental clade sample strongly suggests that the ability of clades to explore niche and functional space has shaped disparities in richness and functional diversity across the North American flora region. Our findings highlight the importance of the evolutionary history of trait and niche evolution in shaping continental and regional floras.     

Niche versus neutrality in structuring the beta diversity of damselfly assemblages

1. Differences among communities in taxonomic composition – beta diversity – are frequently expected to result from taxon‐specific responses to spatial variation in ecological conditions, through niche partitioning. Such process‐derived patterns are in sharp contrast to arguments from neutral theory, where taxa are ecologically equivalent and beta diversity results primarily from dispersal limitation. 2. Here, we compared beta diversity among assemblages of damselflies (Odonata: Zygoptera), for which previous experiments have shown that niche differences maintain genera within a community, but patterns of relative abundance for species within each genus are shaped primarily by neutral dynamics. 3. Using null‐model and ordination‐based methods, we find that both genera and (in contrast to neutral theory) species assemblage composition vary across the landscape in a deterministic fashion, shaped by environmental and spatial factors. 4. While the observed patterns in species composition conflict with theory, we suggest that this a result of weak ecological filters acting to produce spatial variation in assemblages of ecologically similar species undergoing ecological drift within communities. Such patterns are especially likely in systems of relatively weak dispersers like damselflies.     

Morphological and niche divergence of pinyon pines

The environmental variables that define a species ecological niche should be associated with the evolutionary patterns present in the adaptations that resulted from living in these conditions. Thus, when comparing across species, we can expect to find an association between phylogenetically independent phenotypic characters and ecological niche evolution. Few studies have evaluated how organismal phenotypes might mirror patterns of niche evolution if these phenotypes reflect adaptations. Doing so could contribute on the understanding of the origin and maintenance of phenotypic diversity observed in nature. Here, we show the pattern of niche evolution of the pinyon pine lineage (Pinus subsection Cembroides); then, we suggest morphological adaptations possibly related to niche divergence, and finally, we test for correlation between ecological niche and morphology. We demonstrate that niche divergence is the general pattern within the clade and that it is positively correlated with adaptation.     

Climatic niche divergence explains angiosperm diversification across clades in China

Diversification rates are critically important for understanding patterns of species richness among clades. However, the effects of climatic niche width on plant diversification rates remain to be elucidated. Based on the phylogenetic, climatic, and distributional information of angiosperms in China, a total of 26 906 species from 182 families were included in this study. We aimed to test relationships between diversification rate and climatic niche width and climatic niche width related variables (including climatic niche divergence, climatic niche position, geographic extent, and climatic niche evolutionary rate) using phylogenetic methods. We found that climatic niche divergence had the largest unique contribution to the diversification rate, while the unique effects of climatic niche width, climatic niche position, geographic extent, and climatic niche evolutionary rate on the diversification rate were negligible. We also observed that the relationship between diversification rate and climatic niche divergence was significantly stronger than the null assumption (artefactual relationship between diversification and clade-level climatic niche width by sampling more species). Our study supports the hypothesis that wider family climatic niche widths explain faster diversification rates through a higher climatic niche divergence rather than through higher geographic extent, higher climatic niche evolutionary rate, or separated climatic niche position. Hence, the results provide a potential explanation for large-scale diversity patterns within families of plants.     

Niche width impacts vertebrate diversification

Aim The size of the climatic niche of a species is a major factor determining its distribution and evolution. In particular, it has been proposed that niche width should be associated with the rate of species diversification. Here, we test whether species niche width affects the speciation and extinction rates of three main clades of vertebrates: amphibians, mammals and birds. Location Global. Methods We obtained the time‐calibrated phylogenies, IUCN conservation status, species distribution maps and climatic data for 2340 species of amphibians, 4563 species of mammals and 9823 species of birds. We computed the niche width for each species as the mean annual temperature across the species range. We estimated speciation, extinction and transition rates associated with lineages with either narrow (specialist) or wide (generalist) niches using phylogeny‐based birth–death models. We also tested if current conservation status was correlated with the niche width of species. Results We found higher net diversification rates in specialist species than in generalist species. This result was explained by both higher speciation rates (for the three taxonomic groups) and lower extinction rates (for mammals and birds only) in specialist than in generalist species. In contrast, current specialist species tended to be more threatened than generalist species. Main conclusions Our diversification analysis shows that the width of the climatic niche is strongly associated with diversification rates and may thus be a crucial factor for understanding the emergence of diversity patterns in vertebrates. The striking difference between our diversification results and current conservation status suggests that the current extinction process may be different from extinction rates estimated from the whole history of the group.     

Genetic diversity and ecological niche modelling of the restricted Recordia reitzii (Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 332–348.     

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.     

What causes latitudinal gradients in species diversity? Evolutionary processes and ecological constraints on swallowtail biodiversity

The latitudinal diversity gradient (LDG) is one of the most striking ecological patterns on our planet. Determining the evolutionary causes of this pattern remains a challenging task. To address this issue, previous LDG studies have usually relied on correlations between environmental variables and species richness, only considering evolutionary processes indirectly. Instead, we use a phylogenetically integrated approach to investigate the ecological and evolutionary processes responsible for the global LDG observed in swallowtail butterflies (Papilionidae). We find evidence for the 'diversification rate hypothesis' with different diversification rates between two similarly aged tropical and temperate clades. We conclude that the LDG is caused by (1) climatically driven changes in both clades based on evidence of responses to cooling and warming events, and (2) distinct biogeographical histories constrained by tropical niche conservatism and niche evolution. This multidisciplinary approach provides new findings that allow better understanding of the factors that shape LDGs.     

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.     

洲际入侵植物生态位稳定性研究进展

人类活动引起的大规模洲际物种交换与生物入侵, 改变了当地生态系统结构与功能, 使生物多样性受到日益严重的威胁。本文通过综合分析主要国家和地区入侵植物的地理起源, 发现洲际入侵主要包括东亚—北美、东亚—南美、欧洲—南非、欧洲—北美、欧洲—东亚、北美—大洋洲等, 这些洲际入侵造成的后果往往比陆内入侵更为严重。利用物种分布模型(SDMs)预测入侵物种潜在分布范围是有效管理和提早预防生物入侵的重要依据, 但这些模型的一个关键假定是: 入侵物种的生态位在空间和时间上是保守的、稳定的。然而, 对于远离原产地种群并能快速适应新生境的洲际入侵植物来说, 生态位可能发生显著的变化。入侵种能否在入侵地保持原有的生态位, 取决于制约其生态分布的限制因素和生态过程在不同地区间是否发生变化。本文中作者总结了洲际入侵与陆内入侵的生态与进化过程的异同点, 认为这些限制物种原产地分布的因素如扩散限制、种间互作、适应性进化、生态可塑性和种群遗传特性等均可能导致入侵物种生态位的改变。建议下一步的研究应该重视: (1)对生态位属性进行多尺度的研究, 包括时间、空间、环境或系统发育等几个方面; (2)对比生态位稳定与发生偏移的物种特性, 确定什么样的入侵物种更容易改变原有的生态位; (3)进行生态位时间动态格局研究, 探讨生态位变化的倾向、历史速率和偏移程度, 以便判定生态位变化趋势。这些研究结果将会进一步提高物种分布模型的预测能力, 有助于更为准确地揭示气候变化和物种入侵对生物多样性的影响。     

台州玉环北部沿岸海域主要游泳动物生态位和种间联结性

基于2016年11月(秋季)和2017年4月(春季)在玉环北部沿岸海域渔业调查所获的数据资料,运用相对重要性指数(IRI)、生态位宽度、生态位重叠、方差比率法、X² 检验、联结系数(AC)、Jaccard指数(JI)、点相关系数(Φ)和Spearman秩相关系数等方法对主要游泳动物物种间的生态位和种间联结性进行研究.结果表明: 三疣梭子蟹的生态位宽度值最大,占绝对竞争优势;重要经济种类刀鲚与长蛸的生态位宽度值最小,处于弱势竞争地位.该海域主要游泳动物生态位重叠程度不均匀,可能是由于生活环境多样化所致.总体联结性分析表明,本海域物种之间呈不显著负关联. X²检验、AC、JI结果均与总体联结性的结果一致且物种之间趋于独立.Φ和Spearman秩相关系数的结果显示,正联结的种对多于负联结的种对,可能是由于所捕获的大个体海鳗对其他物种产生空间排斥,使得其余14个物种组成的种对间多呈现正联结所致.根据Spearman秩相关系数计算结果,采用聚类分析方法将15个物种分为5个生态种组:同一生态种组内,各物种对生境具有相似的生态适应性要求;不同生态种组的物种之间则具有不同的生活习性和不同的生态要求.     

Stable isotope analyses reveal dense trophic species packing and clear niche differentiation in a malagasy primate community

Understanding the mechanisms maintaining local species richness is a major topic in tropical ecology. In ecological communities of Madagascar, primates represent a major part of mammalian diversity and, thus, are a suitable taxon to study these mechanisms. Previous research suggested that ecological niche differentiation facilitates the coexistence of lemurs. However, detailed data on all species making up diverse local primate assemblages is rarely available, hampering community‐wide tests of niche differentiation among Malagasy mammals. Here, we took an indirect approach and used stable isotopes as long‐term indicators of individuals' diets to answer the question of whether trophic patterns and food‐related mechanisms stabilize coexistence in a species‐rich lemur community. We analyzed stable carbon and nitrogen isotopes in hair collected from eight syntopic lemurs in Kirindy Forest. We found that lemur species were well separated into trophic niches and ranged over two trophic levels. Furthermore, species were densely packed in isotopic space suggesting that past competitive interactions between species are a major structuring force of this dry forest lemur community. Results of other comparative studies on primates and our findings underline that—in contrast to communities worldwide—the structure and composition of lemur communities follow predictions of ecological niche theory. Patterns of competitive interactions might be more clearly revealed in Malagasy primate communities than elsewhere because lemurs represent a large fraction of ecologically interacting species in these communities. The pronounced trophic niche differentiation among lemurs is most likely due to intense competition in the past as is characteristic for adaptive radiations. Am J Phys Anthropol 153:249–259, 2014. © 2013 Wiley Periodicals, Inc.     

Shifts in Climate Foster Exceptional Opportunities for Species Radiation: The Case of South African Geraniums

Climate change is often assumed to be a major driver of biodiversity loss. However, it can also set the stage for novel diversification in lineages with the evolutionary ability to colonize new environments. Here we tested if the extraordinary evolutionary success of the genus Pelargonium was related to the ability of its species to capitalize on the climate niche variation produced by the historical changes in southern Africa. We evaluated the relationship between rates of climate niche evolution and diversification rates in the main Pelargonium lineages and disentangled the roles of deep and recent historical events in the modification of species niches. Pelargonium clades exhibiting higher ecological differentiation along summer precipitation (SPP) gradients also experienced higher diversification rates. Faster rates of niche differentiation in spatially structured variables, along with lower levels of niche overlap among closely related species, suggest recent modification in species niches (e.g. dispersal or range shift) and niche lability. We suggest that highly structured SPP gradients established during the aridification process within southern Africa, in concert with niche lability and low niche overlap, contributed to species divergence. These factors are likely to be responsible for the extensive diversification of other lineages in this diversity hot spot.     

Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage‐specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range‐wide statistical phylogeographic analysis on restriction site‐associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.     

Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter‐ and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.     

The latitudinal gradient in dispersal constraints: ecological specialisation drives diversification in tropical birds

Physiological and behavioural constraints arising from ecological specialisation are proposed to limit gene flow and promote diversification in tropical lineages. In this study, we use phylogenetic analyses to test this idea in 739 Amazonian bird species. We show that patterns of species and subspecies richness are best predicted by a suite of avian specialisms common in tropical avifaunas but rare in the temperate zone. However, this only applied to niche traits associated with dispersal limitation rather than vagility. These findings are consistent with the view that diversity is promoted by more finely partitioned niches, although not simply by coevolutionary adaptation and niche packing as is often assumed. Instead, they suggest that diversification is driven by dispersal constraints, and that niches characterised by these constraints are biased towards tropical systems. We conclude that specialised tropical niches reduce the likelihood of dispersal across barriers, thereby increasing allopatric diversification and contributing to the latitudinal diversity gradient.     

Niche shifts and range expansions along cordilleras drove diversification in a high‐elevation endemic plant genus in the tropical Andes

The tropical Andes represent one of the world's biodiversity hot spots, but the evolutionary drivers generating their striking species diversity still remain poorly understood. In the treeless high‐elevation Andean environments, Pleistocene glacial oscillations and niche differentiation are frequently hypothesized diversification mechanisms; however, sufficiently densely sampled population genetic data supporting this are still lacking. Here, we reconstruct the evolutionary history of Loricaria (Asteraceae), a plant genus endemic to the Andean treeless alpine zone, based on comprehensive population‐level sampling of 289 individuals from 67 populations across the entire distribution ranges of its northern Andean species. Partly incongruent AFLP and plastid DNA markers reveal that the distinct genetic structure was shaped by a complex interplay of biogeography (spread along and across the cordilleras), history (Pleistocene glacial oscillations) and local ecological conditions. While plastid variation documents an early split or colonization of the northern Andes by at least two lineages, one of which further diversified, a major split in the AFLP data correlate with altitudinal ecological differentiation. This suggests that niche shifts may be important drivers of Andean diversification not only in forest–alpine transitions, but also within the treeless alpine zone itself. The patterns of genetic differentiation at the intraspecific level reject the hypothesized separation in spatially isolated cordilleras and instead suggest extensive gene flow among populations from distinct mountain chains. Our study highlights that leveraging highly variable markers against extensive population‐level sampling is a promising approach to address mechanisms of rapid species diversifications.     

Large‐scale longitudinal gradients of genetic diversity: a meta‐analysis across six phyla in the Mediterranean basin

Biodiversity is the diversity of life at all scales, from genes to ecosystems. Predicting its patterns of variation across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. Using published data on the genetic diversity of species whose populations occur in the Mediterranean basin, we calculated a coefficient of correlation between within‐population genetic diversity indices and longitude. Using a meta‐analysis framework, we estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. Overall, genetic diversity increases from west to east in the Mediterranean basin. This correlation is significant for both animals and plants, but is not uniformly expressed for all groups. It is stronger in the southern than in the northern Mediterranean, in true Mediterranean plants than in plants found at higher elevations, in trees than in other plants, and in bi‐parentally and paternally than in maternally inherited DNA makers. Overall, this correlation between genetic diversity and longitude, and its patterns across biological and ecological traits, suggests the role of two non‐mutually exclusive major processes that shaped the genetic diversity in the Mediterranean during and after the cold periods of the Pleistocene: east‐west recolonization during the Holocene and population size contraction under local Last Glacial Maximum climate in resident western and low elevation Mediterranean populations.     

ECOLOGICAL CAUSES OF DECELERATING DIVERSIFICATION IN CARNIVORAN MAMMALS

Clade diversification is a central topic in macroevolutionary studies. Recently, it has been shown that diversification rates appear to decelerate over time in many clades. What causes this deceleration remains unclear, but it has been proposed that competition for limited resources between sympatric, ecologically similar species slows diversification. Employing carnivoran mammals as a model system, we test this hypothesis using a comprehensive time‐calibrated phylogeny. We also explore several conceptually related explanations including limited geographic area and limited rates of niche evolution. We find that diversification slowdowns are strong in carnivorans. Surprisingly, these slowdowns are independent of geographic range overlap between related species and are also decoupled from rates of niche evolution, suggesting that slowdowns are unrelated to competition and niche filling. When controlling for the effects of clade diversity, diversification slowdowns appear independent of geographic area. There is a significant effect of clade diversity on diversification slowdowns, but simulations show that this relationship may arise as a statistical artifact (i.e., greater clade diversity increases the ability of the gamma statistic to refute constant diversification). Overall, our results emphasize the need to test hypotheses about the causes of diversification slowdowns with ecological data, rather than assuming ecological processes from phylogenies alone.     

Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes

The role of ecology in phenotypic and species diversification is widely documented. Nonetheless, numerous nonadaptive processes can shape realized niches and phenotypic variation in natural populations, complicating inferences about adaptive evolution at macroevolutionary scales. We tested for evolved differences in thermal tolerances and their association with the realized thermal niche (including metrics describing diurnal and seasonal patterns of temperature extremes and variability) across a genus of tropical freshwater fishes reared in a standardized environment. There was limited evolution along the thermal niche axis associated with variation in maximum temperature and in upper thermal limits. In contrast, there was considerable diversification along the first major axis of the thermal niche associated with minimum temperatures and in lower thermal limits. Across our adaptive landscape analyses, 70% of species exhibited evidence of divergence in thermal niches. Most importantly, the first two major axes of thermal niche variation were significantly correlated with variation in lower thermal limits. Our results indicate adaptation to divergent thermal niches and adaptive evolution of related functional traits, and highlight the importance of divergence in lower thermal limits for the evolution of tropical biodiversity.