Diversity dynamics of post‐Palaeozoic crinoids – in quest of the factors affecting crinoid macroevolution

Following the end‐Permian biotic crisis which led to the near extinction of crinoids, this echinoderm class rebounded rapidly during the Mesozoic, resulting in forms with important morphological and behavioural novelties. However, quantitative patterns of crinoid diversity during the Mesozoic remain largely unexplored. Here, we report results of analyses of the evolutionary dynamics of post‐Palaeozoic crinoid genera spanning a time interval between 250 and 70 Myr. We show that crinoids reached their Mesozoic peak of genus‐level richness during the Late Jurassic. We also document a major reorganization of different ecological crinoid groups in the Mesozoic. More specifically, the diversity of sessile forms generally increased towards the mid‐Mesozoic but decreased significantly starting in the Cretaceous, whereas the number of motile crinoid genera increased linearly during the Mesozoic. The possible role of biotic and abiotic factors in crinoid evolution is discussed.     

An epidemiological model of host–parasite coevolution and sex

The Red Queen hypothesis posits a promising way to explain the widespread existence of sexual reproduction despite the cost of producing males. The essence of the hypothesis is that coevolutionary interactions between hosts and parasites select for the genetic diversification of offspring via cross‐fertilization. Here, I relax a common assumption of many Red Queen models that each host is exposed to one parasite. Instead, I assume that the number of propagules encountered by each host depends on the number of infected hosts in the previous generation, which leads to additional complexities. The results suggest that epidemiological feedbacks, combined with frequency‐dependent selection, could lead to the long‐term persistence of sex under biologically reasonable conditions.     

Running with the Red Queen: the role of biotic conflicts in evolution

What are the causes of natural selection? Over 40 years ago, Van Valen proposed the Red Queen hypothesis, which emphasized the primacy of biotic conflict over abiotic forces in driving selection. Species must continually evolve to survive in the face of their evolving enemies, yet on average their fitness remains unchanged. We define three modes of Red Queen coevolution to unify both fluctuating and directional selection within the Red Queen framework. Empirical evidence from natural interspecific antagonisms provides support for each of these modes of coevolution and suggests that they often operate simultaneously. We argue that understanding the evolutionary forces associated with interspecific interactions requires incorporation of a community framework, in which new interactions occur frequently. During their early phases, these newly established interactions are likely to drive fast evolution of both parties. We further argue that a more complete synthesis of Red Queen forces requires incorporation of the evolutionary conflicts within species that arise from sexual reproduction. Reciprocally, taking the Red Queen''s perspective advances our understanding of the evolution of these intraspecific conflicts.     

Independent evolution of the sexes promotes amphibian diversification

Classic ecological theory predicts that the evolution of sexual dimorphism constrains diversification by limiting morphospace available for speciation. Alternatively, sexual selection may lead to the evolution of reproductive isolation and increased diversification. We test contrasting predictions of these hypotheses by examining the relationship between sexual dimorphism and diversification in amphibians. Our analysis shows that the evolution of sexual size dimorphism (SSD) is associated with increased diversification and speciation, contrary to the ecological theory. Further, this result is unlikely to be explained by traditional sexual selection models because variation in amphibian SSD is unlikely to be driven entirely by sexual selection. We suggest that relaxing a central assumption of classic ecological models—that the sexes share a common adaptive landscape—leads to the alternative hypothesis that independent evolution of the sexes may promote diversification. Once the constraints of sexual conflict are relaxed, the sexes can explore morphospace that would otherwise be inaccessible. Consistent with this novel hypothesis, the evolution of SSD in amphibians is associated with reduced current extinction threat status, and an historical reduction in extinction rate. Our work reconciles conflicting predictions from ecological and evolutionary theory and illustrates that the ability of the sexes to evolve independently is associated with a spectacular vertebrate radiation.     

A mean field model for competition: from neutral ecology to the Red Queen

Individual species are distributed inhomogeneously over space and time, yet, within large communities of species, aggregated patterns of biodiversity seem to display nearly universal behaviour. Neutral models assume that an individual's demographic prospects are independent of its species identity. They have successfully predicted certain static, time‐independent patterns. But they have generally failed to predict temporal patterns, such as species ages or population dynamics. We construct a new, multispecies framework incorporating competitive differences between species, and assess the impact of this competition on static and dynamic patterns of biodiversity. We solve this model exactly for the special case of a Red Queen hypothesis, where fitter species are continually arising. The model predicts more realistic species ages than neutral models, without greatly changing predictions for static species abundance distributions. Our modelling approach may allow users to incorporate a broad range of ecological mechanisms.     

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earth''s history.     

Modelling the ecological-functional diversification of marine Metazoa on geological time scales

The ecological traits and functional capabilities of marine animals have changed significantly since their origin in the late Precambrian. These changes can be analysed quantitatively using multi-dimensional parameter spaces in which the ecological lifestyles of species are represented by particular combinations of parameter values. Here, we present models that describe the filling of this multi-dimensional 'ecospace' by ecological lifestyles during metazoan diversification. These models reflect varying assumptions about the processes that drove ecological diversification; they contrast diffusive expansion with driven expansion and niche conservatism with niche partitioning. Some models highlight the importance of interactions among organisms (ecosystem engineering and predator-prey escalation) in promoting new lifestyles or eliminating existing ones. These models reflect processes that were not mutually exclusive; rigorous analyses will continue to reveal their applicability to episodes in metazoan history.     

The impact of environmental change on host-parasite coevolutionary dynamics

Environmental factors are known to affect the strength and the specificity of interactions between hosts and parasites. However, how this shapes patterns of coevolutionary dynamics is not clear. Here, we construct a simple mathematical model to study the effect of environmental change on host-parasite coevolutionary outcome when interactions are of the matching-alleles or the gene-for-gene type. Environmental changes may effectively alter the selective pressure and the level of specialism in the population. Our results suggest that environmental change altering the specificity of selection in antagonistic interactions can produce alternating time windows of cyclical allele-frequency dynamics and cessation thereof. This type of environmental impact can also explain the maintenance of polymorphism in gene-for-gene interactions without costs. Overall, our study points to the potential consequences of environmental variation in coevolution, and thus the importance of characterizing genotype-by-genotype-by-environment interactions in natural host-parasite systems, especially those that change the direction of selection acting between the two species.     

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...     

The Ratchet and the Red Queen: the maintenance of sex in parasites

The adaptive significance of sexual reproduction remains as an unsolved problem in evolutionary biology. One promising hypothesis is that frequency‐dependent selection by parasites selects for sexual reproduction in hosts, but it is unclear whether such selection on hosts would feed back to select for sexual reproduction in parasites. Here we used individual‐based computer simulations to explore this possibility. Specifically, we tracked the dynamics of asexual parasites following their introduction into sexual parasite populations for different combinations of parasite virulence and transmission. Our results suggest that coevolutionary interactions with hosts would generally lead to a stable coexistence between sexual parasites and a single parasite clone. However, if multiple mutations to asexual reproduction were allowed, we found that the interaction led to the accumulation of clonal diversity in the asexual parasite population, which led to the eventual extinction of the sexual parasites. Thus, coevolution with sexual hosts may not be generally sufficient to select for sex in parasites. We then allowed for the stochastic accumulation of mutations in the finite parasite populations (Muller's Ratchet). We found that, for higher levels of parasite virulence and transmission, the population bottlenecks resulting from host–parasite coevolution led to the rapid accumulation of mutations in the clonal parasites and their elimination from the population. This result may explain the observation that sexual reproduction is more common in parasitic animals than in their free‐living relatives.     

Coinfecting parasites can modify fluctuating selection dynamics in host–parasite coevolution

Genetically specific interactions between hosts and parasites can lead to coevolutionary fluctuations in their genotype frequencies over time. Such fluctuating selection dynamics are, however, expected to occur only under specific circumstances (e.g., high fitness costs of infection to the hosts). The outcomes of host–parasite interactions are typically affected by environmental/ecological factors, which could modify coevolutionary dynamics. For instance, individual hosts are often infected with more than one parasite species and interactions between them can alter host and parasite performance. We examined the potential effects of coinfections by genetically specific (i.e., coevolving) and nonspecific (i.e., generalist) parasite species on fluctuating selection dynamics using numerical simulations. We modeled coevolution (a) when hosts are exposed to a single parasite species that must genetically match the host to infect, (b) when hosts are also exposed to a generalist parasite that increases fitness costs to the hosts, and (c) when coinfecting parasites compete for the shared host resources. Our results show that coinfections can enhance fluctuating selection dynamics when they increase fitness costs to the hosts. Under resource competition, coinfections can either enhance or suppress fluctuating selection dynamics, depending on the characteristics (i.e., fecundity, fitness costs induced to the hosts) of the interacting parasites.     

Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts

Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro‐evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several articles have concluded that estimates of net diversification rates from the method‐of‐moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts.     

Speciation dynamics during the global radiation of extant bats

Species richness varies widely across extant clades, but the causes of this variation remain poorly understood. We investigate the role of diversification rate heterogeneity in shaping patterns of diversity across families of extant bats. To provide a robust framework for macroevolutionary inference, we assemble a time‐calibrated, species‐level phylogeny using a supermatrix of mitochondrial and nuclear sequence data. We analyze the phylogeny using a Bayesian method for modeling complex evolutionary dynamics. Surprisingly, we find that variation in family richness can largely be explained without invoking heterogeneous diversification dynamics. We document only a single well‐supported shift in diversification dynamics across bats, occurring at the base of the subfamily Stenodermatinae. Bat diversity is phylogenetically imbalanced, but—contrary to previous hypotheses—this pattern is unexplained by any simple patterns of diversification rate heterogeneity. This discordance may indicate that diversification dynamics are more complex than can be captured using the statistical tools available for modeling data at this scale. We infer that bats as a whole are almost entirely united into one macroevolutionary cohort, with decelerating speciation through time. There is also a significant relationship between clade age and richness, suggesting that global bat diversity may still be expanding.     

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.     

Methodologies for testing a pluralist idea for the maintenance of sex

The paradox of sex, despite decades of attention, remains unresolved. Recent efforts to gain insight into the nature of the mechanisms underlying the maintenance of sex have led to an emphasis on a pluralist approach, with a particular focus on interaction between multiple mechanisms. However, few empirical tests of pluralist models exist, perhaps due to the widely held assumption that major complications inevitably accompany such tests. Here, we address this issue by providing an overview of how testing of a pluralist idea for the maintenance of sex could be achieved. We also suggest a more specific methodology designed to test for interactive effects between Muller's ratchet and Red Queen dynamics, two models that are widely seen as providing potentially general explanations for the maintenance of sex.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 605–613.     

Cultural and climatic changes shape the evolutionary history of the Uralic languages

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both ‘biotic’ interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed‐clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno‐Ugric, Finnic and Saami languages. Some of the divergences co‐occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both ‘biotic’ and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution.     

The potential role of chromosome telomere resetting consequent upon sex in the population dynamics of aphids: an hypothesis

Models of population structure have emphasized the importance of sex in maintaining lineages. This is because, despite the well known ‘two‐fold cost of sex’ compared with asex, it is considered that recombination rids the genome of accumulated mutations and increases its potential for adaptive variation. However, asexual lineages of eukaryotic organisms can also rapidly gain genetic variance directly by various mutational processes, thereby proving that so‐called ‘clones’ do not have strict genetic fidelity ( Lushai & Loxdale, 2002 ; Loxdale & Lushai, 2003a ), whereas the variation so produced may well have adaptive advantage during the evolutionary process. This being so, obligated asexuals or cyclical parthenogens that occasionally indulge in sexual recombination (‘rare sex’) cannot be deemed as ‘evolutionary dead‐ends’( Lushai, Loxdale & Allen, 2003a ). In addition, the persistence of asexual lineages (i.e. lineage longevity) may also involve the integrity of the telomere region, the physical end of the chromosomes ( Loxdale & Lushai, 2003b ). In this earlier study on this topic, we argued that the persistence and ultimate senescence of eukaryotic cell lineages (based upon the frequency of ‘capped’ and ‘uncapped’ chromosomes related to telomere functionality; Blackburn, 2000 ) may directly relate to the survival and persistence of lineages of whole asexual organisms. Aphids are a good model system to test this hypothesis because they show a variety of sexual/asexual reproductive strategies, whereas their mode of asexual reproduction is of the mitotic (= apomictic) type. We also suggested that many aphid lineages require occasional or even rare sexual recombination to re‐set telomere length to allow lineages to persist. Ample empirical evidence from diverse taxa, lineages, and different developmental stages now reveals that the telomere states are indeed re‐set by recombination (homologous or meiotic), thereby rejuvenating the lineage in question. The generational clock element of telomeric functionality has also been successfully described in artificially‐induced mammalian clonal systems. It thus appears that telomere function is a central molecular mechanism instigating and promoting lineage continuity per se. By contrast, we hypothesized that other long‐lived asexuals, or the rare category of ancient asexuals such as bdelloid rotifers, have compensatory mechanisms for maintaining chromosome functional integrity, which are somewhat different from conventional telomeric repeats. In the present study, we carry the analogy between eukaryotic cell functionality and aphid lineages a stage further. Here, we hypothesize that the changing frequency of capped and uncapped telomeres, progressing to senescence in a stochastic manner, may be an underlying factor that significantly contributes to population dynamics in asexual lineage evolution. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 90 , 719–728.     

Impact of density and disease on frequency-dependent selection and genetic polymorphism: experiments with stripe rust and wheat

Frequency-dependent disease impacts may contribute to the maintenance of genetic diversity and sexual reproduction in plant populations. In earlier work with experimental wheat (Triticum aestivum) populations at a single density, we found that stripe rust (caused by Puccinia striiformis) created frequency-dependent selection on its host but competitive interactions between host genotypes reduced the potential for disease to maintain genetic polymorphisms in this highly self-pollinated species; the weaker competitor actually exhibited positive disease-mediated frequency-dependent selection. Based on these results we predicted that at low density, where the overall level of competition is lower, disease would have a stronger impact relative to competition and thus be more likely to maintain genetic polymorphisms; at low densities the greatest effect of disease for negative frequency-dependent selection should be seen in the weak competitor. Here we report on results with wheat stripe rust in which we altered both the frequency and density of host genotypes in factorial combinations of two-way mixtures where each host genotype was attacked by its own specialized race of rust. Within each density disease levels increased with genotype frequencies, creating frequency-dependent disease attack at all densities. Similarly, disease created negative frequency-dependent selection on its host at all densities, as a genotype’s fitness was often greater at low than high frequency when disease was present. Disease levels increased with plant density in 1997 but decreased in 1998. While increasing plant density reduced absolute fitness, presumably as a result of increased competition, a genetic polymorphism was not more likely to be maintained at low than high density as we had predicted. Within each density, the impact of disease was insufficient to reverse the slope of the relationship between absolute fitness and planted frequency from positive to negative for the less competitive host genotype, thus preventing the maintenance of a genetic polymorphism.