The role of frugivory in the diversification of bats in the Neotropics

Aim Ecological interactions are among the most important biotic factors influencing the processes of speciation and extinction. Our aim was to test whether diversification rates of New World Noctilionoidea bats are associated with specialization for frugivory, and how this pattern differs between the mainland and the West Indies. Location The New World. Methods We reconstructed a time‐calibrated molecular phylogenetic hypothesis for the New World genera of the superfamily Noctilionoidea. We compiled data on diet, morphology, geographical distribution and number of ecoregions in which each genus occurs. Then, using the phylogenetic tree constructed, we tested whether diversification was driven by diet (animalivorous and sanguinivorous versus nectarivorous and frugivorous) and specialization for frugivory. Afterwards, we conducted phylogenetic comparative analyses to identify correlates of species richness and net diversification rates. Results The diversification rate was higher in mutualistic than in antagonistic clades in mainland and Antillean biogeographical scenarios, but only strictly frugivorous clades showed a markedly higher diversification rate than the rest of the genera. Geographical range and number of ecoregions were positively associated with species richness and diversification rate in continental and insular lineages. Lower body mass, lower forearm length and specialization for frugivory were significantly positively correlated with higher diversification rates in continental lineages, whereas these parameters were negatively correlated in Antillean lineages. Main conclusions The direction of the relationship of intrinsic factors (specialization for frugivory and body size) with diversification of noctilionoid bats depends on the biogeographical context, whereas the direction of the relationship of extrinsic factors (geographical range and number of ecoregions) with diversification is consistent in both mainland and the West Indian lineages.     

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.     

Exploring the tempo of species diversification in legumes

Whatever criteria are used to measure evolutionary success – species numbers, geographic range, ecological abundance, ecological and life history diversity, background diversification rates, or the presence of rapidly evolving clades – the legume family is one of the most successful lineages of flowering plants. Despite this, we still know rather little about the dynamics of lineage and species diversification across the family through the Cenozoic, or about the underlying drivers of diversification. There have been few attempts to estimate net species diversification rates or underlying speciation and extinction rates for legume clades, to test whether among-lineage variation in diversification rates deviates from null expectations, or to locate species diversification rate shifts on specific branches of the legume phylogenetic tree. In this study, time-calibrated phylogenetic trees for a set of species-rich legume clades – Calliandra, Indigofereae, Lupinus, Mimosa and Robinieae – and for the legume family as a whole, are used to explore how we might approach these questions. These clades are analysed using recently developed maximum likelihood and Bayesian methods to detect species diversification rate shifts and test for among-lineage variation in speciation, extinction and net diversification rates. Possible explanations for rate shifts in terms of extrinsic factors and/or intrinsic trait evolution are discussed. In addition, several methodological issues and limitations associated with these analyses are highlighted emphasizing the potential to improve our understanding of the evolutionary dynamics of legume diversification by using much more densely sampled phylogenetic trees that integrate information across broad taxonomic, geographical and temporal levels.     

Factors influencing diversification in angiosperms: at the crossroads of intrinsic and extrinsic traits

Recent studies indicate that both key innovations and available area influence species richness in angiosperms. Available area has been observed to have the greatest effect, however, and appears to alter the "carrying capacity" of a lineage rather than alter diversification rates. Here, we review and weigh the evidence of predictors of angiosperm diversification and further dissect how area can place ecological limits on diversification of angiosperms, specifically addressing the following: (1) theoretical mechanisms by which particular intrinsic and extrinsic traits may affect diversification in angiosperm families; (2) evidence that the amount of available area determines the ecological limits on lineages; and (3) geographical distribution of diversification hotspots in angiosperms, concentrating on the effects of zygomorphy, noncontiguous area, and latitude. While we found that dispersal to numerous noncontiguous areas is most important in spurring diversification, diversification of tropical and zygomorphic families appears to be elevated by the generation of more species per given area.     

Intestinal microflora and diversification of the rabbit antibody repertoire

The rabbit establishes its primary Ab repertoire by somatically diversifying an initial repertoire that is limited by restricted VH gene segment usage during VDJ gene rearrangement. Somatic diversification occurs in gut-associated lymphoid tissue (GALT), and by about 1-2 mo of age nearly all Ig VDJ genes are somatically diversified. In other species that are known to establish their primary Ab repertoire by somatic diversification, such as chicken, sheep, and cattle, diversification appears to be developmentally regulated: it begins before birth and occurs independent of exogenous factors. Because somatic diversification in rabbit occurs well after birth in GALT, the diversification process may not be developmentally regulated, but may require interaction with exogenous factors derived from the gut. To test this hypothesis, we examined Ab repertoire diversification in rabbits in which the appendix was ligated shortly after birth to prevent microbial colonization and all other organized GALT was surgically removed. We found that by 12 wk of age nearly 90% of the Ig VDJ genes in PBL were undiversified, indicating that intestinal microflora are required for somatically diversifying the Ab repertoire. We also examined repertoire diversification in sterilely derived remote colony rabbits that were hand raised away from contact with conventional rabbits and thereby acquired a different gut microflora. In these remote colony rabbits, GALT was underdeveloped, and 70% of the Ig VDJ genes in PBL were undiversified. We conclude that specific, currently unidentified intestinal microflora are required for Ab repertoire diversification.     

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.     

Diversification of the climatic niche drove the recent processes of speciation in Sigmodontinae (Rodentia,Cricetidae)

Evolutionary radiations are among the most intriguing natural phenomena. Sigmodontine rodents form a megadiverse group for which doubts exist about the adaptive or non‐adaptive nature of its radiation. We analysed whether or not the rates of diversification of species of Sigmodontinae are related to the rates of diversification of the climatic niches occupied by the species. Our results show a clear association between niche diversification and speciation processes. However, this association is linked to recent and independent processes of diversification in sigmodontines, as opposed to an early link that would indicate a niche‐filling consistent with an adaptive radiation of the subfamily.     

Models for the diversification of life

The diversification of life through geological time a rise from presumably one species to many millions today. The diversification of marine families in the past 600 million years (Myr) appears to have followed two or three logistic curves, with equilibrium levels that lasted for up to 200 Myr. In contrast, continental organisms clearly show an exponential pattern of diversification, and although it is not clear whether the empirical diversification patterns are real or are artefacts of a poor fossil record, the latter explanation seems unlikely. Perhaps marine and continental organisms diversified in different ways, or perhaps the appearance of equilibrium patterns for marine organisms is an artefact of taxonomic structures.     

Evolutionary diversification of reef corals: a comparison of the molecular and fossil records

Understanding historical patterns of diversity dynamics is of paramount importance for many evolutionary questions. The fossil record has long been the only source of information on patterns of diversification, but the molecular record, derived from time-calibrated phylogenies, is becoming an important additional resource. Both fossil and molecular approaches have shortcomings and biases. These have been well studied for fossil data but much less so for molecular data and empirical comparisons between approaches are lacking. Here, we compare the patterns of diversification derived from fossil and molecular data in scleractinian reef coral species. We also assess the robustness of molecular diversification rates to poor taxon sampling. We find that the temporal pattern of molecular diversification rates is robust to incomplete sampling when rates are calculated per interval. The major obstacle of molecular methods is that rate estimates are distorted because diversification rates can never be negative, whereas the fossil record suffers from incomplete preservation and inconsistent taxonomy. Nevertheless, the molecular pattern of diversification is comparable to the pattern we observe in the fossil record, with the timing of major diversification pulses coinciding in each dataset. For example, both agree that the end-Triassic coral extinction was a catastrophic bottleneck in scleractinian evolution.     

Dynamics of clade diversification on the morphological hypercube

Understanding the relationship between taxonomic and morphological changes is important in identifying the reasons for accelerated morphological diversification early in the history of animal phyla. Here, a simple general model describing the joint dynamics of taxonomic diversity and morphological disparity is presented and applied to the data on the diversification of blastozoans. I show that the observed patterns of deceleration in clade diversification can be explicable in terms of the geometric structure of the morphospace and the effects of extinction and speciation on morphological disparity without invoking major declines in the size of morphological transitions or taxonomic turnover rates. The model allows testing of hypotheses about patterns of diversification and estimation of rates of morphological evolution. In the case of blastozoans, I find no evidence that major changes in evolutionary rates and mechanisms are responsible for the deceleration of morphological diversification seen during the period of this clade''s expansion. At the same time, there is evidence for a moderate decline in overall rates of morphological diversification concordant with a major change (from positive to negative values) in the clade''s growth rate.     

Sources and sinks of diversification and conservation priorities for the Mexican tropical dry forest

Elucidating the geographical history of diversification is critical for inferring where future diversification may occur and thus could be a valuable aid in determining conservation priorities. However, it has been difficult to recognize areas with a higher likelihood of promoting diversification. We reconstructed centres of origin of lineages and identified areas in the Mexican tropical dry forest that have been important centres of diversification (sources) and areas where species are maintained but where diversification is less likely to occur (diversity sinks). We used a molecular phylogeny of the genus Bursera, a dominant member of the forest, along with information on current species distributions. Results indicate that vast areas of the forest have historically functioned as diversity sinks, generating few or no extant Bursera lineages. Only a few areas have functioned as major engines of diversification. Long-term preservation of biodiversity may be promoted by incorporation of such knowledge in decision-making.     

Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations

We explore patterns of diversification in the plant clades Adoxaceae and Valerianaceae (within Dipsacales), evaluating correlations between biogeographic change (i.e., movements into new areas), morphological change (e.g., the origin of putative key innovations associated with vegetative and reproductive characters), and shifts in rates of diversification. Our findings indicate that rates of diversification in these plants tend to be less tightly correlated with the evolution of morphological innovations but instead exhibit a pronounced correlation with movement into new geographic areas, particularly the dispersal of lineages into new mountainous regions. The interdependence among apparent novelties (arising from their nested phylogenetic distribution) and the correlation between morphological and biogeographic change suggests a complex history of diversification in Dipsacales. Overall, these findings highlight the importance of incorporating biogeographic history in studies of diversification rates and in the study of geographic gradients in species richness. Furthermore, these results argue against a simple deterministic relationship between dispersal and diversification: like other factors that may influence the probability of speciation and/or extinction, the impact of dispersal on diversification rates depends on being in the right place at the right time.     

Diversification rate shifts in the Cape Floristic Region: The right traits in the right place at the right time

Species diversity patterns are the product of diversification rate variation, but the factors influencing changes in diversification rates are poorly known. Radiation is thought to be the result of ecological opportunity: the right traits in the right environment at the right time. We test this in the Cape Floristic Region (CFR) of South Africa, in which pyrophytic heathland (fynbos) and non-pyrophytic Afromontane forest occur interdigitated. We infer transitions from forest to fynbos in three Cape clades (Penaeaceae, Phyliceae and Diosmeae) and test if they are associated with diversification rate shifts and the evolution of functional traits linked to fire, high insolation and seasonal drought. We estimate diversification rate shifts using maximum likelihood and use phylogenetic comparative methods to show that forest to fynbos shifts were associated with decreases in leaf area and specific leaf area and preceded or coincided with increases in diversification rates. Furthermore, we show that Penaeaceae, Phyliceae and Diosmeae species are typical members of their vegetation types in terms of their traits. The diversification rate shifts of Penaeaceae and Phyliceae are dated to the Miocene, when postulated aridification-driven changes in the CFR fire regimes may have triggered expansion of the fynbos at the cost of forest, providing an ecological opportunity for the diversification of fynbos lineages.     

Patterns of host plant utilization and diversification in the brush‐footed butterflies

Herbivorous insects represent one of the most successful animal radiations known. They occupy a wide range of niches, feed on a great variety of plants, and are species rich; yet the factors that influence their diversification are poorly understood. Host breadth is often cited as a major factor influencing diversification, and, according to the Oscillation Hypothesis, shifts from generalist to specialist feeding states increase the diversification rate for a clade. We explored the relationship between host breadth and diversification within the Nymphalidae (Lepidoptera) and explicitly tested predictions of the Oscillation Hypothesis. We found strong evidence of diversification rate heterogeneity, but no difference in host breadth between clades with a higher diversification rate compared to their sisters. We also found some clades exhibited phylogenetic nonindependence in host breadth and these clades had lower host plant turnover than expected by chance, suggesting host breadth is evolutionarily constrained. Finally, we found that transitions among host breadth categories varied, but the likelihood of reductions in host breadth was greater than that of increases. Our results indicate host breadth is decoupled from diversification rate within the Nymphalidae, and that constraints on diet breadth might play an important role in the evolution of herbivorous insects.     

Deep under the sea: unraveling the evolutionary history of the deep-sea squat lobster Paramunida (Decapoda, Munididae)

The diversification of Indo-Pacific marine fauna has long captivated the attention of evolutionary biologists. Previous studies have mainly focused on coral reef or shallow water-associated taxa. Here, we present the first attempt to reconstruct the evolutionary history--phylogeny, diversification, and biogeography--of a deep-water lineage. We sequenced the molecular markers 16S, COI, ND1, 18S, and 28S for nearly 80% of the nominal species of the squat lobster genus Paramunida. Analyses of the molecular phylogeny revealed an accelerated diversification in the late Oligocene-Miocene followed by a slowdown in the rate of lineage accumulation over time. A parametric biogeographical reconstruction showed the importance of the southwest Pacific area, specifically the island arc of Fiji, Tonga, Vanuatu, Wallis, and Futuna, for diversification of squat lobsters, probably associated with the global warming, high tectonic activity, and changes in oceanic currents that took place in this region during the Oligocene-Miocene period. These results add strong evidence to the hypothesis that the Neogene was a period of major diversification for marine organisms in both shallow and deep waters.     

Untangling the ecological signal in the dental morphology in the bat superfamily Noctilionoidea

Journal of Mammalian Evolution - Diet has been linked to the diversification of the bat superfamily Noctilionoidea, a group that underwent an impressive ecological diversification within Mammalia....     

Key innovations and island colonization as engines of evolutionary diversification: a comparative test with the Australasian diplodactyloid geckos

The acquisition of key innovations and the invasion of new areas constitute two major processes that facilitate ecological opportunity and subsequent evolutionary diversification. Using a major lizard radiation as a model, the Australasian diplodactyloid geckos, we explored the effects of two key innovations (adhesive toepads and a snake‐like phenotype) and the invasion of new environments (island colonization) in promoting the evolution of phenotypic and species diversity. We found no evidence that toepads had significantly increased evolutionary diversification, which challenges the common assumption that the evolution of toepads has been responsible for the extensive radiation of geckos. In contrast, a snakelike phenotype was associated with increased rates of body size evolution and, to a lesser extent, species diversification. However, the clearest impact on evolutionary diversification has been the colonization of New Zealand and New Caledonia, which were associated with increased rates of both body size evolution and species diversification. This highlights that colonizing new environments can drive adaptive diversification in conjunction or independently of the evolution of a key innovation. Studies wishing to confirm the putative link between a key innovation and subsequent evolutionary diversification must therefore show that it has been the acquisition of an innovation specifically, not the colonization of new areas more generally, that has prompted diversification.     

净多样化速率和进化时间对虎耳草目科间物种多样性差异的影响

不同生物类群包含的物种数目常存在巨大差异,这是生态学和生物学研究中普遍观察到的现象。然而,这一现象产生的原因仍然是未解之谜。从宏观进化的角度,进化时间假说和多样化速率假说是两个比较流行的假说。进化时间假说认为类群的演化时间越长,积累的物种丰富度越高;而多样化速率假说认为类群的净多样化速率越快,则其物种丰富度越高。为验证这两个假说,该文以一棵包含1 539个物种化石定年的虎耳草目系统发育树为基础,通过宏观进化分析获取了虎耳草目内15个科的物种形成和灭绝速率,并计算了每个科的平均多样化速率。结果表明：(1)虎耳草目的物种多样化速率有着增加的趋势,并且多样化速率的增加主要出现在温带和高山类群,如茶藨子科、景天科和芍药科等。(2)采用系统发育广义最小二乘模型(PGLS)和线性回归模型(LM)结果表明,虎耳草目15个科的物种丰富度与科的分化时间和科内物种的最近共同祖先年龄都没有显著相关关系,而与净多样化速率显著正相关(R² =0.380,P<0.05)。该研究支持了多样化速率假说,认为不同科的净多样化速率的差异是导致虎耳草目科间物种数目差异的主要原因之一。全球气候变冷...     

Effects of changing climate on species diversification in tropical forest butterflies of the genus Cymothoe (Lepidoptera: Nymphalidae)

Extant clades may differ greatly in their species richness, suggesting differential rates of species diversification. Based on phylogenetic trees, it is possible to identify potential correlates of such differences. Here, we examine species diversification in a clade of 82 tropical African forest butterfly species (Cymothoe), together with its monotypic sister genus Harma. Our aim was to test whether the diversification of the Harma–Cymothoe clade correlates with end‐Miocene global cooling and desiccation, or with Pleistocene habitat range oscillations, both postulated to have led to habitat fragmentation. We first generated a species‐level phylogenetic tree for Harma and Cymothoe, calibrated within an absolute time scale, and then identified temporal and phylogenetic shifts in species diversification. Finally, we assessed correlations between species diversification and reconstructed global temperatures. Results show that, after the divergence of Harma and Cymothoe in the Miocene (15 Mya), net species diversification was low during the first 7 Myr. Coinciding with the onset of diversification of Cymothoe around 7.5 Mya, there was a sharp and significant increase in diversification rate, suggesting a rapid radiation, and correlating with a reconstructed period of global cooling and desiccation in the late Miocene, rather than with Pleistocene oscillations. Our estimated age of 4 Myr for a clade of montane species corresponds well with the uplift of the Eastern Arc Mountains where they occur. We conclude that forest fragmentation caused by changing climate in the late Miocene as well as the Eastern Arc Mountain uplift are both likely to have promoted species diversification in the Harma–Cymothoe clade. Cymothoe colonized Madagascar much later than most other insect lineages and, consequently, had less time available for diversification on the island. We consider the diversification of Cymothoe to be a special case compared with other butterfly clades studied so far, both in terms of its abrupt diversification rate increase and its recent occurrence (7 Myr). It is clear that larval host plant shift(s) cannot explain the difference in diversification between Cymothoe and Harma; however, such a shift(s) may have triggered differential diversification rates within Cymothoe. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, ●● , ●●–●●.     

A Cladistic Analysis of the Evolutionary Relationships of the Members of the Tyrosinase Gene Family Using Sequence Data

Recently, DNA sequence data have been published on tyrosinase and tyrosinase-related proteins (TRPs) in a wide variety of vertebrates ranging from Rana to Homo. These proteins are in turn members of a larger family of binuclear copper-binding proteins, which all contain two highly conserved copper-binding domains. This gene family also includes tyrosinases from fungi and bacteria as well as arthropodan and molluscan hemocyanins. Parsimony-based alignment and tree construction algorithms (Malign, vl.85 and PAUP, 3.1.1) were used to analyze the diversification of both the evolutionarily conserved copper-binding domains i6n copper-binding proteins in general as well as the diversification of the vertebrate tyrosinase gene family more specifically. These analyses show that the diversification of the vertebrate tyrosinase gene family minimally predates the diversification of vertebrates. Vertebrate tyrosinases proper first diverged from an ancestral tyrosinase-related protein (TRP) that then subsequently diverged to form tyrosinase-related protein-Is (TRP-1s) and tyrosinase-related protein-2s (TRP-2s).