Quaternary Climate Change was Not an Engine of Diversification in New World Bats (Chiroptera)

Quaternary climate change has been hypothesized to have played a significant role in driving diversification rates in a variety of taxa. We test the hypothesis of increased rates of diversification during the Quaternary in nine groups of New World bats (Chiroptera). The fit of six models of diversification was determined for each group. None experienced an increase in net diversification, rejecting the Quaternary hypothesis. Instead, four groups experienced constant net diversification rates, suggesting no Quaternary climate change impact. Five groups are evolving under a density-dependent model of diversification, suggesting climate cycles may have reduced rates initiated during the Pliocene or late Miocene. The distribution of divergences between sister taxa is consistent with results obtained from avian lineages experiencing declining rates of Quaternary diversification, further discrediting this often invoked hypothesis. Our results suggest that Quaternary climate change did not increase diversification rates in New World bats.     

FOSSILS AND A LARGE MOLECULAR PHYLOGENY SHOW THAT THE EVOLUTION OF SPECIES RICHNESS,GENERIC DIVERSITY,AND TURNOVER RATES ARE DISCONNECTED

The magnitude and extent of global change during the Cenozoic is remarkable, yet the impacts of these global changes on the biodiversity and evolutionary dynamics of species diversification remain poorly understood. To investigate this question, we combine paleontological and neontological data for the angiosperm order Fagales, an ecologically important clade of about 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates for Fagales. Generic diversity evolved rapidly since the Late Cretaceous and peaked during the Eocene or Oligocene. Turnover rates were high during periods of extreme global climate change, but relatively low when the climate remained stable. Species richness accumulated gradually throughout the Cenozoic, possibly at an accelerated pace after the Middle Miocene. Species diversification occurred in new environments: Quercoids radiating in Oligocene subtropical seasonally arid habitats, Casuarinaceae in Australian pyrophytic biomes, and Betula in Late Neogene holarctic habitats. These radiations were counterbalanced by regional extinctions in Late Neogene mesic warm‐temperate forests. Thus, the overall diversification at species level is linked to regional radiations of clades with appropriate ecologies exploiting newly available habitats.     

Environmental energy and evolutionary rates in flowering plants

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.     

EXPLOSIVE RADIATION OR CRYPTIC MASS EXTINCTION? INTERPRETING SIGNATURES IN MOLECULAR PHYLOGENIES

How biodiversity is generated and maintained underlies many major questions in evolutionary biology, particularly relating to the tempo and pattern of diversification through time. Molecular phylogenies and new analytical methods provide additional tools to help interpret evolutionary processes. Evolutionary rates in lineages sometimes appear punctuated, and such "explosive" radiations are commonly interpreted as adaptive, leading to causative key innovations being sought. Here we argue that an alternative process might explain apparently rapid radiations ("broom-and-handle" or "stemmy" patterns seen in many phylogenies) with no need to invoke dramatic increase in the rate of diversification. We use simulations to show that mass extinction events can produce the same phylogenetic pattern as that currently being interpreted as due to an adaptive radiation. By comparing simulated and empirical phylogenies of Australian and southern African legumes, we find evidence for coincident mass extinctions in multiple lineages that could have resulted from global climate change at the end of the Eocene.     

Both temperature fluctuations and East Asian monsoons have driven plant diversification in the karst ecosystems from southern China

Karst ecosystems in southern China are species‐rich and have high levels of endemism, yet little is known regarding the evolutionary processes responsible for the origin and diversification of karst biodiversity. The genus Primulina (Gesneriaceae) comprises ca. 170 species endemic to southern China with high levels of ecological (edaphic) specialization, providing an exceptional model to study the plant diversification in karsts. We used molecular data from nine chloroplast and 11 nuclear regions and macroevolutionary analyses to assess the origin and cause of species diversification due to palaeoenvironmental changes and edaphic specialization in Primulina. We found that speciation was positively associated with changes in past temperatures and East Asian monsoons through the evolutionary history of Primulina. Climatic change around the mid‐Miocene triggered an early burst followed by a slowdown of diversification rate towards the present with the climate cooling. We detected different speciation rates among edaphic types, and transitions among soil types were infrequently and did not impact the overall speciation rate. Our findings suggest that both global temperature changes and East Asian monsoons have played crucial roles in floristic diversification within the karst ecosystems in southern China, such that speciation was higher when climate was warmer and wetter. This is the first study to directly demonstrate that past monsoon activity is positively correlated with speciation rate in East Asia. This case study could motivate further investigations to assess the impacts of past environmental changes on the origin and diversification of biodiversity in global karst ecosystems, most of which are under threat.     

气候变化对野生植物的影响及保护对策

以温室气体浓度持续上升、全球气候变暖为主要特征的全球气候变化对野生植物及生物多样性造成的潜在影响, 已经引起了国际学者的高度关注。本文总结了全球气候变化的现状与未来趋势, 概述了中国野生植物的保护及管理现状, 从不同侧面综述了国内外关于全球气候变暖对野生植物影响的研究进展和动态, 包括气候带北移、两极冰山退缩、高海拔山地变暖、海平面上升、早春温度提前升高、荒漠草原土壤增温、旱涝急转弯等对野生植物造成的影响以及气候变暖对种间关系和敏感植物类群的影响, 并从气候变化背景下全球生态系统敏感度、植物多样性、物种迁移与气候槽(sink areas)、物种适应与灭绝以及物候节律5个方面分析了未来全球变暖影响野生植物的总体趋势。在以后的野生植物保护与管理中, 应确定全球气候变化的植物多样性敏感区, 重点关注对气候变化敏感的植物类群以及气候要素改变植物-动物互作关系中的野生植物, 自然保护区的建设要重点考虑全球气候变化的影响, 通过在全球范围内对野生植物分布和种群变化进行长期、系统的追踪监测, 建立有效的数据库, 发展野生植物迁地保护的保育技术及信息网络, 发展有关野生植物对全球气候变化响应的量化指标及相应的模型。最后提出应将全球气候变化下野生植物保护与管理列入相关基金会的研究重点。     

Historical species losses in bumblebee evolution

Investigating how species coped with past environmental changes informs how modern species might face human-induced global changes, notably via the study of historical extinction, a dominant feature that has shaped current biodiversity patterns. The genus Bombus, which comprises 250 mostly cold-adapted species, is an iconic insect group sensitive to current global changes. Through a combination of habitat loss, pathogens and climate change, bumblebees have experienced major population declines, and several species are threatened with extinction. Using a time-calibrated tree of Bombus, we analyse their diversification dynamics and test hypotheses about the role of extinction during major environmental changes in their evolutionary history. These analyses support a history of fluctuating species dynamics with two periods of historical species loss in bumblebees. Dating estimates gauge that one of these events started after the middle Miocene climatic optimum and one during the early Pliocene. Both periods are coincident with global climate change that may have extirpated Bombus species. Interestingly, bumblebees experienced high diversification rates during the Plio-Pleistocene glaciations. We also found evidence for a major species loss in the past one million years that may be continuing today.     

Climate and host‐plant associations shaped the evolution of ceutorhynch weevils throughout the Cenozoic

Using molecular phylogenetic data and methods we inferred divergence times and diversification patterns for the weevil subfamily Ceutorhynchinae in the context of host‐plant associations and global climate over evolutionary time. We detected four major diversification shifts that correlate with both host shifts and major climate events. Ceutorhynchinae experienced an increase in diversification rate at ～53 Ma, during the Early Eocene Climate Optimum, coincident with a host shift to Lamiaceae. A second major diversification phase occurred at the end of the Eocene (～34 Ma). This contrasts with the overall deterioration in climate equability at the Eocene‐Oligocene boundary, but tracks the diversification of important host plant clades in temperate (higher) latitudes, leading to increased diversification rates in the weevil clades infesting temperate hosts. A third major phase of diversification is correlated with the rising temperatures of the Late Oligocene Warming Event (～26.5 Ma); diversification rates then declined shortly after the Middle Miocene Climate Transition (～14.9 Ma). Our results indicate that biotic and abiotic factors together explain the evolution of Ceutorhynchinae better than each of these drivers viewed in isolation.     

Morphological disparity opposes latitudinal diversity gradient in lacertid lizards

While global variation in taxonomic diversity is strongly linked to latitude, the extent to which morphological disparity follows geographical gradients is less well known. We estimated patterns of lineage diversification, morphological disparity and rates of phenotypic evolution in the Old World lizard family Lacertidae, which displays a nearly inverse latitudinal diversity gradient with decreasing species richness towards the tropics. We found that lacertids exhibit relatively constant rates of lineage accumulation over time, although the majority of morphological variation appears to have originated during recent divergence events, resulting in increased partitioning of disparity within subclades. Among subclades, tropical arboreal taxa exhibited the fastest rates of shape change while temperate European taxa were the slowest, resulting in an inverse relationship between latitudinal diversity and rates of phenotypic evolution. This pattern demonstrates a compelling counterexample to the ecological opportunity theory of diversification, suggesting an uncoupling of the processes generating species diversity and morphological differentiation across spatial scales.     

Climatic Variability Leads to Later Seasonal Flowering of Floridian Plants

Understanding species responses to global change will help predict shifts in species distributions as well as aid in conservation. Changes in the timing of seasonal activities of organisms over time may be the most responsive and easily observable indicator of environmental changes associated with global climate change. It is unknown how global climate change will affect species distributions and developmental events in subtropical ecosystems or if climate change will differentially favor nonnative species. Contrary to previously observed trends for earlier flowering onset of plant species with increasing spring temperatures from mid and higher latitudes, we document a trend for delayed seasonal flowering among plants in Florida. Additionally, there were few differences in reproductive responses by native and nonnative species to climatic changes. We argue that plants in Florida have different reproductive cues than those from more northern climates. With global change, minimum temperatures have become more variable within the temperate-subtropical zone that occurs across the peninsula and this variation is strongly associated with delayed flowering among Florida plants. Our data suggest that climate change varies by region and season and is not a simple case of species responding to consistently increasing temperatures across the region. Research on climate change impacts need to be extended outside of the heavily studied higher latitudes to include subtropical and tropical systems in order to properly understand the complexity of regional and seasonal differences of climate change on species responses.     

Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on geno...     

Correlated evolution between climate and suites of traits along a fast–slow continuum in the radiation of Protea

Evolutionary radiations are responsible for much of Earth's diversity, yet the causes of these radiations are often elusive. Determining the relative roles of adaptation and geographic isolation in diversification is vital to understanding the causes of any radiation, and whether a radiation may be labeled as “adaptive” or not. Across many groups of plants, trait–climate relationships suggest that traits are an important indicator of how plants adapt to different climates. In particular, analyses of plant functional traits in global databases suggest that there is an “economics spectrum” along which combinations of functional traits covary along a fast–slow continuum. We examine evolutionary associations among traits and between trait and climate variables on a strongly supported phylogeny in the iconic plant genus Protea to identify correlated evolution of functional traits and the climatic‐niches that species occupy. Results indicate that trait diversification in Protea has climate associations along two axes of variation: correlated evolution of plant size with temperature and leaf investment with rainfall. Evidence suggests that traits and climatic‐niches evolve in similar ways, although some of these associations are inconsistent with global patterns on a broader phylogenetic scale. When combined with previous experimental work suggesting that trait–climate associations are adaptive in Protea, the results presented here suggest that trait diversification in this radiation is adaptive.     

Explaining disparities in species richness between Mediterranean floristic regions: a case study in Gladiolus (Iridaceae)

Aim The causes of geographical variation in species richness in clades that do not follow the latitudinal diversity gradient have rarely been investigated. Here, we examine spatial asymmetries of diversity in Gladiolus (Iridaceae), a large genus (> 260 species) that is present in two mediterranean climate biomes: the Cape of southern Africa (106 species) and the Mediterranean Basin (7 species). Despite convergence of climatic conditions between the two regions, the species density of Gladiolus is over one order of magnitude higher in the Cape than in the Mediterranean Basin. We investigate whether the diversity disparities observed in the genus are better explained by recent colonization of species‐poor areas (temporal hypothesis) or by differential rates of diversification (evolutionary hypothesis). Location Africa, Madagascar and Eurasia Methods We employ a recently developed Bayesian method for the estimation of diversification rates and a biogeographical optimization approach within a phylogenetic framework. Results In Gladiolus, the ‘diversity anomaly’ between the two Mediterranean climate regions cannot be explained solely by the time available for speciation in the Cape, but is also due to locally reduced rates of diversification in the Mediterranean Basin. Furthermore, high overall diversity in southern Africa stems from an ancient origin in the Cape allied with high rates of diversification in the summer‐rainfall region of the subcontinent. Main conclusions Both evolutionary and temporal hypotheses must be taken into account in order to explain the diversity anomaly between the Mediterranean Basin and the Cape. Our results suggest that regions at comparable latitudes and/or with similar climate may not converge in diversity levels due to heterogeneity of diversification rates and contrasting biogeographical histories.     

Macroevolutionary patterns in the diversification of parrots: effects of climate change,geological events and key innovations

Aim Parrots are thought to have originated on Gondwana during the Cretaceous. The initial split within crown group parrots separated the New Zealand taxa from the remaining extant species and was considered to coincide with the separation of New Zealand from Gondwana 82–85 Ma, assuming that the diversification of parrots was mainly shaped by vicariance. However, the distribution patterns of several extant parrot groups cannot be explained without invoking transoceanic dispersal, challenging this assumption. Here, we present a temporal and spatial framework for the diversification of parrots using external avian fossils as calibration points in order to evaluate the relative importance of the influences of past climate change, plate tectonics and ecological opportunity. Location Australasian, African, Indo‐Malayan and Neotropical regions. Methods Phylogenetic relationships were investigated using partial sequences of the nuclear genes c‐mos, RAG‐1 and Zenk of 75 parrot and 21 other avian taxa. Divergence dates and confidence intervals were estimated using a Bayesian relaxed molecular clock approach. Biogeographic patterns were evaluated taking temporal connectivity between areas into account. We tested whether diversification remained constant over time and if some parrot groups were more species‐rich than expected given their age. Results Crown group diversification of parrots started only about 58 Ma, in the Palaeogene, significantly later than previously thought. The Australasian lories and possibly also the Neotropical Arini were found to be unexpectedly species‐rich. Diversification rates probably increased around the Eocene/Oligocene boundary and in the middle Miocene, during two periods of major global climatic aberrations characterized by global cooling. Main conclusions The diversification of parrots was shaped by climatic and geological events as well as by key innovations. Initial vicariance events caused by continental break‐up were followed by transoceanic dispersal and local radiations. Habitat shifts caused by climate change and mountain orogenesis may have acted as a catalyst to the diversification by providing new ecological opportunities and challenges as well as by causing isolation as a result of habitat fragmentation. The lories constitute the only highly nectarivorous parrot clade, and their diet shift, associated with morphological innovation, may have acted as an evolutionary key innovation, allowing them to explore underutilized niches and promoting their diversification.     

Relative sea‐level change regulates organic carbon accumulation in coastal habitats

Because coastal habitats store large amounts of organic carbon (C_org), the conservation and restoration of these habitats are considered to be important measures for mitigating global climate change. Although future sea‐level rise is predicted to change the characteristics of these habitats, its impact on their rate of C_org sequestration is highly uncertain. Here we used historical depositional records to show that relative sea‐level (RSL) changes regulated C_org accumulation rates in boreal contiguous seagrass–saltmarsh habitats. Age–depth modeling and geological and biogeochemical approaches indicated that C_org accumulation rates varied as a function of changes in depositional environments and habitat relocations. In particular, C_org accumulation rates were enhanced in subtidal seagrass meadows during times of RSL rise, which were caused by postseismic land subsidence and climate change. Our findings identify historical analogs for the future impact of RSL rise driven by global climate change on rates of C_org sequestration in coastal habitats.     

Litter stoichiometric traits of plant species of high-latitude ecosystems show high responsiveness to global change without causing strong variation in litter decomposition

? High-latitude ecosystems are important carbon accumulators, mainly as a result of low decomposition rates of litter and soil organic matter. We investigated whether global change impacts on litter decomposition rates are constrained by litter stoichiometry. ? Thereto, we investigated the interspecific natural variation in litter stoichiometric traits (LSTs) in high-latitude ecosystems, and compared it with climate change-induced LST variation measured in the Meeting of Litters (MOL) experiment. This experiment includes leaf litters originating from 33 circumpolar and high-altitude global change experiments. Two-year decomposition rates of litters from these experiments were measured earlier in two common litter beds in sub-Arctic Sweden. ? Response ratios of LSTs in plants of high-latitude ecosystems in the global change treatments showed a three-fold variation, and this was in the same range as the natural variation among species. However, response ratios of decomposition were about an order of magnitude lower than those of litter carbon/nitrogen ratios. ? This implies that litter stoichiometry does not constrain the response of plant litter decomposition to global change. We suggest that responsiveness is rather constrained by the less responsive traits of the Plant Economics Spectrum of litter decomposability, such as lignin and dry matter content and specific leaf area.     

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.     

Divergent timing and patterns of species accumulation in lowland and highland neotropical birds

Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.     

The relationship between diet breadth and geographic range size in the butterfly subfamily Nymphalinae--a study of global scale

The "oscillation hypothesis" has been proposed as a general explanation for the exceptional diversification of herbivorous insect species. The hypothesis states that speciation rates are elevated through repeated correlated changes--oscillations--in degree of host plant specificity and geographic range. The aim of this study is to test one of the predictions from the oscillation hypothesis: a positive correlation between diet breadth (number of host plants used) and geographic range size, using the globally distributed butterfly subfamily Nymphalinae. Data on diet breadth and global geographic range were collected for 182 Nymphalinae butterflies species and the size of the geographic range was measured using a GIS. We tested both diet breadth and geographic range size for phylogenetic signal to see if species are independent of each other with respect to these characters. As this test gave inconclusive results, data was analysed both using cross-species comparisons and taking phylogeny into account using generalised estimating equations as applied in the APE package in R. Irrespective of which method was used, we found a significant positive correlation between diet breadth and geographic range size. These results are consistent for two different measures of diet breadth and removal of outliers. We conclude that the global range sizes of Nymphalinae butterflies are correlated to diet breadth. That is, butterflies that feed on a large number of host plants tend to have larger geographic ranges than do butterflies that feed on fewer plants. These results lend support for an important step in the oscillation hypothesis of plant-driven diversification, in that it can provide the necessary fuel for future population fragmentation and speciation.     

LINEAGES THAT CHEAT DEATH: SURVIVING THE SQUEEZE ON RANGE SIZE

Evolutionary lineages differ greatly in their net diversification rates, implying differences in rates of extinction and speciation. Lineages with a large average range size are commonly thought to have reduced extinction risk (although linking low extinction to high diversification has proved elusive). However, climate change cycles can dramatically reduce the geographic range size of even widespread species, and so most species may be periodically reduced to a few populations in small, isolated remnants of their range. This implies a high and synchronous extinction risk for the remaining populations, and so for the species as a whole. Species will only survive through these periods if their individual populations are “threat tolerant,” somehow able to persist in spite of the high extinction risk. Threat tolerance is conceptually different from classic extinction resistance, and could theoretically have a stronger relationship with diversification rates than classic resistance. I demonstrate that relationship using primates as a model. I also show that narrowly distributed species have higher threat tolerance than widespread ones, confirming that tolerance is an unusual form of resistance. Extinction resistance may therefore operate by different rules during periods of adverse global environmental change than in more benign periods.