Inferring speciation rates from phylogenies

Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.     

Inferring speciation times under an episodic molecular clock

We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birth-death process with species sampling. The prior for lineage-specific substitution rates is specified using either a model with autocorrelated rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent rates among lineages specified by a log-normal probability distribution. We develop an infinite-sites theory, which predicts that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior mean of divergence times form a perfect linear relationship, with the slope indicating uncertainties in time estimates that cannot be reduced by sequence data alone. Simulations are used to study the influence of among-lineage rate variation and the number of loci sampled on the uncertainty of divergence time estimates. The analysis suggests that posterior time estimates typically involve considerable uncertainties even with an infinite amount of sequence data, and that the reliability and precision of fossil calibrations are critically important to divergence time estimation. We apply our new algorithms to two empirical data sets and compare the results with those obtained in previous Bayesian and likelihood analyses. The results demonstrate the utility of our new algorithms.     

Comparing the rates of speciation and extinction between phylogenetic trees

Over the past decade or so it has become increasingly popular to use reconstructed evolutionary trees to investigate questions about the rates of speciation and extinction. Although the methodology of this field has grown substantially in its sophistication in recent years, here I will take a step back to present a very simple model that is designed to investigate the relatively straightforward question of whether the tempo of diversification (speciation and extinction) differs between two or more phylogenetic trees, without attempting to attribute a causal basis to this difference. It is a likelihood method, and I demonstrate that it generally shows type I error that is close to the nominal level. I also demonstrate that parameter estimates obtained with this approach are largely unbiased. As this method can be used to compare trees of unknown relationship, it will be particularly well‐suited to problems in which a difference in diversification rate between clades is suspected, but in which these clades are not particularly closely related. As diversification methods can easily take into account an incomplete sampling fraction, but missing lineages are assumed to be missing at random, this method is also appropriate for cases in which we have hypothesized a difference in the process of diversification between two or more focal clades, but in which many unsampled groups separate the few of interest. The method of this study is by no means an attempt to replace more sophisticated models in which, for instance, diversification depends on the state of an observed or unobserved discrete or continuous trait. Rather, my intention is to provide a complementary approach for circumstances in which a simpler hypothesis is warranted and of biological interest.     

不同生境毁坏速度下的物种灭绝机制

已有似Levins的多物种模型,在研究生境毁坏的影响时,一方面主要集中在对瞬间毁坏影响的研究,另一方面主要研究生境毁坏对强物种影响的研究。在Tilman的多物种竞争共存模型的基础上,同时考虑了生境毁坏直接效应和生境毁坏时间异质性,提出了全新的普适的多物种竞争共存的非自治动力模式。通过模拟物种灭绝对不同速度的生境毁坏时间异质性的响应发现：（1）物种灭绝既存在强物种由强到弱的灭绝,也存在弱物种由弱到强的灭绝。同时,弱物种灭绝机制进一步分为弱物种瞬间集体灭绝,以及较长时间由弱到强的灭绝。（2）生境毁坏速度越快,物种灭绝的时间越短,弱物种灭绝的越多,因此,生境毁坏速度越慢,越有利于弱物种的长期续存。（3）最强物种的多度越大,强-强物种抵御生境毁坏的能力越强,而弱-弱物种抵御生境毁坏的能力越弱,集体灭绝的弱-弱物种就越多。最强物种的多度大的群落（如温带森林）,主要发生的是弱-弱物种灭绝,而最强物种多度小的群落（如热带雨林）同时发生强-强和弱-弱物种的灭绝。因此,争对不同结构的集合种群,不同的保护对象,应采取不同的管理策略。     

Inferring speciation modes in a clade of Iberian chafers from rates of morphological evolution in different character systems

Background  

Studies of speciation mode based on phylogenies usually test the predicted effect on diversification patterns or on geographical distribution of closely related species. Here we outline an approach to infer the prevalent speciation mode in Iberian Hymenoplia chafers through the comparison of the evolutionary rates of morphological character systems likely to be related to sexual or ecological selection. Assuming that mitochondrial evolution is neutral and not related to measured phenotypic differences among the species, we contrast hypothetic outcomes of three speciation modes: 1) geographic isolation with subsequent random morphological divergence, resulting in overall change proportional to the mtDNA rate; 2) sexual selection on size and shape of the male intromittent organs, resulting in an evolutionary rate decoupled to that of the mtDNA; and 3) ecological segregation, reflected in character systems presumably related to ecological or biological adaptations, with rates decoupled from that of the mtDNA.     

Molecular evolutionary rates predict both extinction and speciation in temperate angiosperm lineages

Background  

A positive relationship between diversification (i.e., speciation) and nucleotide substitution rates is commonly reported for angiosperm clades. However, the underlying cause of this relationship is often unknown because multiple intrinsic and extrinsic factors can affect the relationship, and these have confounded previous attempts infer causation. Determining which factor drives this oft-reported correlation can lend insight into the macroevolutionary process.     

Inferring extinction in a declining population

This note describes a test for extinction in a declining population based on a record of sightings. The test assumes that, prior to extinction, the sightings follow a Poisson process with decreasing rate function. An application to a sighting record of the black-footed ferret is presented.     

Inferring extinction from a sighting record

The extinctions of plant and animal species are almost never observed directly, but must be inferred from sighting records. This paper reviews some methods for statistical inference about the extinction of a single species based on a record of its sightings.     

Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions

If we are to plan conservation strategies that minimize the loss of evolutionary history through human-caused extinctions, we must understand how this loss is related to phylogenetic patterns in current extinction risks and past speciation rates. Nee & May (1997, Science 278, 692-694) showed that for a randomly evolving clade (i) a single round of random extinction removed relatively little evolutionary history, and (ii) extinction management (choosing which taxa to sacrifice) offered only marginal improvement. However, both speciation rates and extinction risks vary across lineages within real clades. We simulated evolutionary trees with phylogenetically patterned speciation rates and extinction risks (closely related lineages having similar rates and risks) and then subjected them to several biologically informed models of extinction. Increasing speciation rate variation increases the extinction-management pay-off. When extinction risks vary among lineages but are uncorrelated with speciation rates, extinction removes more history (compared with random trees), but the difference is small. When extinction risks vary and are correlated with speciation rates, history loss can dramatically increase (negative correlation) or decrease (positive correlation) with speciation rate variation. The loss of evolutionary history via human-caused extinctions may therefore be more severe, yet more manageable, than first suggested.     

不同样本方案下遗传元胞自动机的土地利用模拟及景观评价

利用元胞自动机(cellular automata,CA)模拟土地利用情景,有助于理解其变化机理,并为土地资源持续利用提供空间决策支持.本文基于生物进化过程的遗传算法(genetic algo-rithm,GA)将CA参数编码成为染色体,在模拟结果与真实结果差异值的引导下,通过选择、杂交和变异算子使最优的染色体得以遗传和保留,从而建立智能优化的元胞自动机模型.以浙江省嘉兴市1992-2008年土地利用变化为例,分别利用6%(66个·km-2)和3%(33个·km-2)两种样本方案构建遗传CA模型进行土地利用变化模拟,并通过混淆矩阵、Kappa系数和景观指数对模拟结果进行评估.结果表明:遗传CA模拟结果能在数量、位置和景观格局上以超过80%的水平接近真实分类,且大样本量构建的遗传CA的模拟精度更高;2008年的模拟精度和景观综合指数低于2001年,表明遗传CA的模拟精度和景观综合指数随模拟时间而衰减.     

Recovering speciation and extinction dynamics based on phylogenies

Phylogenetic trees of only extant species contain information about the underlying speciation and extinction pattern. In this review, I provide an overview over the different methodologies that recover the speciation and extinction dynamics from phylogenetic trees. Broadly, the methods can be divided into two classes: (i) methods using the phylogenetic tree shapes (i.e. trees without branch length information) allowing us to test for speciation rate variation and (ii) methods using the phylogenetic trees with branch length information allowing us to quantify speciation and extinction rates. I end the article with an overview on limitations, open questions and challenges of the reviewed methodology.     

Re-assessing current extinction rates

There is a widespread belief that we are experiencing a mass extinction event similar in severity to previous mass extinction events in the last 600 million years where up to 95% of species disappeared. This paper reviews evidence for current extinctions and different methods of assessing extinction rates including species–area relationships and loss of tropical forests, changing threat status of species, co-extinction rates and modelling the impact of climate change. For 30 years some have suggested that extinctions through tropical forest loss are occurring at a rate of up to 100 species a day and yet less than 1,200 extinctions have been recorded in the last 400 years. Reasons for low number of identified global extinctions are suggested here and include success in protecting many endangered species, poor monitoring of most of the rest of species and their level of threat, extinction debt where forests have been lost but species still survive, that regrowth forests may be important in retaining ‘old growth’ species, fewer co-extinctions of species than expected, and large differences in the vulnerability of different taxa to extinction threats. More recently, others have suggested similar rates of extinction to earlier estimates but with the key cause of extinction being climate change, and in particular rising temperatures, rather than deforestation alone. Here I suggest that climate change, rather than deforestation is likely to bring about such high levels of extinction since the impacts of climate change are local to global and that climate change is acting synergistically with a range of other threats to biodiversity including deforestation.     

The extinction time under mutational meltdown driven by high mutation rates

Mutational meltdown describes an eco‐evolutionary process in which the accumulation of deleterious mutations causes a fitness decline that eventually leads to the extinction of a population. Possible applications of this concept include medical treatment of RNA virus infections based on mutagenic drugs that increase the mutation rate of the pathogen. To determine the usefulness and expected success of such an antiviral treatment, estimates of the expected time to mutational meltdown are necessary. Here, we compute the extinction time of a population under high mutation rates, using both analytical approaches and stochastic simulations. Extinction is the result of three consecutive processes: (a) initial accumulation of deleterious mutations due to the increased mutation pressure; (b) consecutive loss of the fittest haplotype due to Muller''s ratchet; (c) rapid population decline toward extinction. We find accurate analytical results for the mean extinction time, which show that the deleterious mutation rate has the strongest effect on the extinction time. We confirm that intermediate‐sized deleterious selection coefficients minimize the extinction time. Finally, our simulations show that the variation in extinction time, given a set of parameters, is surprisingly small.     

Patterns of species ranges, speciation, and extinction

The exact nature of the relationship among species range sizes, speciation, and extinction events is not well understood. The factors that promote larger ranges, such as broad niche widths and high dispersal abilities, could increase the likelihood of encountering new habitats but also prevent local adaptation due to high gene flow. Similarly, low dispersal abilities or narrower niche widths could cause populations to be isolated, but such populations may lack advantageous mutations due to low population sizes. Here we present a large-scale, spatially explicit, individual-based model addressing the relationships between species ranges, speciation, and extinction. We followed the evolutionary dynamics of hundreds of thousands of diploid individuals for 200,000 generations. Individuals adapted to multiple resources and formed ecological species in a multidimensional trait space. These species varied in niche widths, and we observed the coexistence of generalists and specialists on a few resources. Our model shows that species ranges correlate with dispersal abilities but do not change with the strength of fitness trade-offs; however, high dispersal abilities and low resource utilization costs, which favored broad niche widths, have a strong negative effect on speciation rates. An unexpected result of our model is the strong effect of underlying resource distributions on speciation: in highly fragmented landscapes, speciation rates are reduced.