Taking the pulse of the cambrian radiation

The Cambrian radiation is that key episode in the history oflife when a large number of animal phyla appeared in the fossilrecord over a geologically short period of time. Over the last20 years, scientific understanding of this radiation has increasedsignificantly. Still, fundamental questions remain about thetiming of the radiation and also the tempo of evolution. Trilobitesare an excellent group to address these questions because oftheir rich abundance and diversity. Moreover, their complexmorphology makes them readily amenable to phylogenetic analysis,and deducing the nature of macroevolutionary processes duringthe Cambrian radiation requires an understanding of evolutionarypatterns. Phylogenetic biogeographic analysis of Early Cambrianolenellid trilobites, based on a modified version of BrooksParsimony Analysis, revealed the signature of the breakup ofPannotia, a tectonic event that most evidence suggests is constrainedto the interval 600 to 550 Ma. As trilobites are derived metazoans,this suggests the phylogenetic proliferation associated withthe Cambrian radiation was underway tens of millions of yearsbefore the Early Cambrian, although not hundreds of millionsof years as some have argued. Phylogenetic information from Early Cambrian olenellid trilobiteswas also used in a stochastic approach based on two continuoustime models to test the hypothesis that rates of speciationwere unusually high during the Cambrian radiation. No statisticalevidence was found to support this hypothesis. Instead, ratesof evolution during the Cambrian radiation, at least those pertainingto speciation, were comparable to those that have occurred duringother times of adaptive or taxic radiation throughout the historyof life.     

The Cambrian radiation of bilaterians: Evolutionary origins and palaeontological emergence; earth history change and biotic factors

Evidence from a variety of research areas, including phylogenetic palaeobiogeographic studies of trilobites, indicates that there may be a fuse to the Cambrian radiation, with a duration on the order of 20–70 myr. Evolution in trilobites appears to have been powerfully influenced by the tectonic changes occurring at the end of the Neoproterozoic: especially the breakup of Pannotia. This continental fragmentation may have also elevated opportunities for vicariance and speciation in trilobites, and other metazoans, given that speciation rates at this time period were high, though not phenomenally so. This provides clear evidence that abiotic factors played an important role in motivating evolution during this key episode in the history of life; biotic factors probably also played a role. The evidence for the role of biotic factors is considered in light of information from some problematic Cambrian taxa. These may show affinities with modern problematic pseudocoelomate phyla, although Cambrian and modern exponents differ dramatically in body size.     

Quantitative traits and diversification

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth-death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.     

Trees of unusual size: biased inference of early bursts from large molecular phylogenies

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the [Formula: see text]-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.     

FiSSE: A simple nonparametric test for the effects of a binary character on lineage diversification rates

It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model‐based tests of state‐dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple nonparametric statistical test (“FiSSE”) to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait‐dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait‐dependent extinction but can infer state‐dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood‐based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that nonparametric statistical approaches, such as FiSSE, provide an important complement to formal process‐based models for trait‐dependent diversification.     

The shape and temporal dynamics of phylogenetic trees arising from geographic speciation

Phylogenetic trees often depart from the expectations of stochastic models, exhibiting imbalance in diversification among lineages and slowdowns in the rate of lineage accumulation through time. Such departures have led to a widespread perception that ecological differences among species or adaptation and subsequent niche filling are required to explain patterns of diversification. However, a key element missing from models of diversification is the geographical context of speciation and extinction. In this study, we develop a spatially explicit model of geographic range evolution and cladogenesis, where speciation arises via vicariance or peripatry, and explore the effects of these processes on patterns of diversification. We compare the results with those observed in 41 reconstructed avian trees. Our model shows that nonconstant rates of speciation and extinction are emergent properties of the apportioning of geographic ranges that accompanies speciation. The dynamics of diversification exhibit wide variation, depending on the mode of speciation, tendency for range expansion, and rate of range evolution. By varying these parameters, the model is able to capture many, but not all, of the features exhibited by birth-death trees and extant bird clades. Under scenarios with relatively stable geographic ranges, strong slowdowns in diversification rates are produced, with faster rates of range dynamics leading to constant or accelerating rates of apparent diversification. A peripatric model of speciation with stable ranges also generates highly unbalanced trees typical of bird phylogenies but fails to produce realistic range size distributions among the extant species. Results most similar to those of a birth-death process are reached under a peripatric speciation scenario with highly volatile range dynamics. Taken together, our results demonstrate that considering the geographical context of speciation and extinction provides a more conservative null model of diversification and offers a very different perspective on the phylogenetic patterns expected in the absence of ecology.     

Cambrian agnostid communities in Tasmania

Jago, J. B.: Cambrian agnostid communities in Tasmania.
Two or possibly three different agnostid trilobite assemblages can be distinguished in the late Middle and early Upper Cambrian sequences of northern and western Tasmania. This is significant because in recent years agnostid trilobites have been widely used in local and international correlations of Middle and Upper Cambrian rocks. The three assemblages recognized are (1) an agnostid assemblage in which polymerid trilobites are abscnt, rare or present as thanatocoenotic fossils, (2) a ptychagnostid-non-nepeid assemblage, and (3) a nepeid-clavagnostid-peronopsid assemblage in which non-agnostid trilobites are abundant but ptychag-nostids are absent. It is proposed that assemblage (1) represents an open sea fauna, with assemblages (2) and (3) occurring in progressively shallower water.     

EXPLOSIVE EVOLUTIONARY RADIATIONS: DECREASING SPECIATION OR INCREASING EXTINCTION THROUGH TIME?

A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such "explosive-early" diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, "explosive early" patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.     

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Colless's coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability-generating models for bifurcating tree shapes. The Equal-Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.     

Evolutionary Trends in the Ornamentation of Cambrian Solenopleuropsine Trilobites

A phylogeny of the Cambrian solenopleuropsine trilobites is constructed to evaluate the importance of differential speciation, extinction and developmental constraints in the evolutionary history of the clade. The transformation of the Pardailhania–Solenopleuropsis ( Manublesia )– Solenopleuropsis ( Solenopleuropsis ) lineages occurred during the mid Caesaraugustian–early Languedocian interval, with all measured morphological variables exhibiting continuous and gradual changes. Several evolutionary trends show tendencies towards an increase in tuberculation and its complexity on the anterior part of the cephalon. A mid Caesaraugustian anagenetic tendency is related to the influence of constant environmental conditions, whereas a late Caesaraugustian–early Languedocian cladogenetic tendency seems to have been an adaptative response to unstable environments. The Solenopleuropsinae clade has a well-preserved continuous fossil record over its full biogeographical range in the Mediterranean region. The sympatric evolution in centrally located populations (Mediterranean area) follows the model of phyletic gradualism, whilst a peripheral population in Avalonia gave rise (by allopatric speciation) to a distinct species, characterized by a variation in the relative size of the palpebral lobes, which may be evidence of a parallel evolution in the trends of ornamentation.     

Robustness of the approximate likelihood of the protracted speciation model

The protracted speciation model presents a realistic and parsimonious explanation for the observed slowdown in lineage accumulation through time, by accounting for the fact that speciation takes time. A method to compute the likelihood for this model given a phylogeny is available and allows estimation of its parameters (rate of initiation of speciation, rate of completion of speciation and extinction rate) and statistical comparison of this model to other proposed models of diversification. However, this likelihood computation method makes an approximation of the protracted speciation model to be mathematically tractable: it sometimes counts fewer species than one would do from a biological perspective. This approximation may have large consequences for likelihood‐based inferences: it may render any conclusions based on this method completely irrelevant. Here, we study to what extent this approximation affects parameter estimations. We simulated phylogenies from which we reconstructed the tree of extant species according to the original, biologically meaningful protracted speciation model and according to the approximation. We then compared the resulting parameter estimates. We found that the differences were larger for high values of extinction rates and small values of speciation‐completion rates. Indeed, a long speciation‐completion time and a high extinction rate promote the appearance of cases to which the approximation applies. However, surprisingly, the deviation introduced is largely negligible over the parameter space explored, suggesting that this approximate likelihood can be applied reliably in practice to estimate biologically relevant parameters under the original protracted speciation model.     

Simulating trees with a fixed number of extant species

In this paper, I develop efficient tools to simulate trees with a fixed number of extant species. The tools are provided in my open source R-package TreeSim available on CRAN. The new model presented here is a constant rate birth-death process with mass extinction and/or rate shift events at arbitrarily fixed times 1) before the present or 2) after the origin. The simulation approach for case (2) can also be used to simulate under more general models with fixed events after the origin. I use the developed simulation tools for showing that a mass extinction event cannot be distinguished from a model with constant speciation and extinction rates interrupted by a phase of stasis based on trees consisting of only extant species. However, once we distinguish between mass extinction and period of stasis based on paleontological data, fast simulations of trees with a fixed number of species allow inference of speciation and extinction rates using approximate Bayesian computation and allow for robustness analysis once maximum likelihood parameter estimations are available.     

Testing for a decline in diversity prior to extinction: Languedocian (latest mid‐Cambrian) distribution of cinctans (Echinodermata) in the Iberian Chains,NE Spain

Abstract: The middle Cambrian strata of the Iberian Chains (north‐eastern Spain) and the Montagne Noire (southern France) record an adaptative radiation of cinctans and trilobites, which spanned the Leonian–early Languedocian interval. A diachronous diversity peak was reached by both benthic groups when favourable palaeoenvironmental conditions (clayey vs. silty substrates) were established. The acme in diversity was followed by a gradual decline and a barren interval associated with the onset of the mid‐Languedocian regression, well constrained throughout the western Mediterranean region. For trilobites, the aftermath of the regression is characterized by a late‐Languedocian major faunal turnover of families, followed by a renewed Furongian–early Tremadocian radiation related to the stepwise immigration of trilobite invaders from northern and eastern Gondwana, under persistent transgressive conditions. In contrast, the cinctans reappeared only patchily in late‐Languedocian monospecific coquinas and finally disappeared before the Furongian. Thus, the late Languedocian is a crucial interval in which to analyse the decline in diversity and final extinction of cinctans in the aftermath of the mid‐Languedocian regression.     

HOW DOES ECOLOGICAL OPPORTUNITY INFLUENCE RATES OF SPECIATION,EXTINCTION, AND MORPHOLOGICAL DIVERSIFICATION IN NEW WORLD RATSNAKES (TRIBE LAMPROPELTINI)?

Ecological adaptive radiation theory predicts an increase in both morphological and specific diversification when organisms colonize new environments. Accordingly, bursts of morphological diversification, characterized by low within‐subclade morphological disparity, may be associated with these increases in speciation rates. Conversely, increasing species density, reduction in available habitat, or increasing extinction rates are expected to cause rates of diversification to decline. We test these hypotheses by examining the tempo and mode of speciation in the lampropeltinine snakes, a morphologically variable group that colonized the New World ～24 million years ago and radiated throughout the Miocene. We show that specific diversification increased early in the history of the group, and that most morphological variation is partitioned among, rather than within subclades. These patterns provide further evidence for the hypothesis that morphological variation tends to be strongly partitioned among lineages when clades undergo early bursts of species diversification. A reduction in speciation rates may be indicative of density dependent effects due to a saturation of available ecological opportunity, rather than increases in extinction rates at the onset of the Pleistocene/Pliocene glacial cycles. This evidence runs counter to the general Pleistocene species pump model.     

EXTINCTION DURING EVOLUTIONARY RADIATIONS: RECONCILING THE FOSSIL RECORD WITH MOLECULAR PHYLOGENIES

Recent application of time‐varying birth–death models to molecular phylogenies suggests that a decreasing diversification rate can only be observed if there was a decreasing speciation rate coupled with extremely low or no extinction. However, from a paleontological perspective, zero extinction rates during evolutionary radiations seem unlikely. Here, with a more comprehensive set of computer simulations, we show that substantial extinction can occur without erasing the signal of decreasing diversification rate in a molecular phylogeny. We also find, in agreement with the previous work, that a decrease in diversification rate cannot be observed in a molecular phylogeny with an increasing extinction rate alone. Further, we find that the ability to observe decreasing diversification rates in molecular phylogenies is controlled (in part) by the ratio of the initial speciation rate (Lambda) to the extinction rate (Mu) at equilibrium (the LiMe ratio), and not by their absolute values. Here we show in principle, how estimates of initial speciation rates may be calculated using both the fossil record and the shape of lineage through time plots derived from molecular phylogenies. This is important because the fossil record provides more reliable estimates of equilibrium extinction rates than initial speciation rates.     

DO GEOLOGICAL OR CLIMATIC PROCESSES DRIVE SPECIATION IN DYNAMIC ARCHIPELAGOS? THE TEMPO AND MODE OF DIVERSIFICATION IN SOUTHEAST ASIAN SHREWS

Geological and climatic processes potentially alter speciation rates by generating and modifying barriers to dispersal. In Southeast Asia, two processes have substantially altered the distribution of land. Volcanic uplift produced many new islands during the Miocene–Pliocene and repeated sea level fluctuations during the Pleistocene resulted in intermittent land connections among islands. Each process represents a potential driver of diversification. We use a phylogenetic analysis of a group of Southeast Asian shrews ( Crocidura ) to examine geographic and temporal processes of diversification. In general, diversification has taken place in allopatry following the colonization of new areas. Sulawesi provides an exception, where we cannot reject within-island speciation for a clade of eight sympatric and syntopic species. We find only weak support for temporally declining diversification rates, implying that neither volcanic uplift nor sea level fluctuations had a strong effect on diversification rates. We suggest that dynamic archipelagos continually offer new opportunities for allopatric diversification, thereby sustaining high speciation rates over long periods of time, or Southeast Asian shrews represent an immature radiation on a density-dependent trajectory that has yet to fill geographic and ecological space.     

The ecological dynamics of clade diversification and community assembly

Clades diversify in an ecological context, but most macroevolutionary models do not directly encapsulate ecological mechanisms that influence speciation and extinction. A data set of 245 chordate, arthropod, mollusk, and magnoliophyte phylogenies had a majority of clades that showed rapid lineage accumulation early with a slowing more recently, whereas a small but significant minority showed accelerated lineage accumulation in their recent histories. Previous analyses have demonstrated that macroevolutionary birth-death models can replicate the pattern of slowing lineage accumulation only by a strong decrease in speciation rate with increasing species richness and extinction rate held extremely low or absent. In contrast, the metacommunity model presented here could generate the full range of patterns seen in the real phylogenies by simply manipulating the degree of ecological differentiation of new species at the time of speciation. Specifically, the metacommunity model predicts that clades showing decelerating lineage accumulation rates are those that have diversified by ecological modes of speciation, whereas clades showing accelerating lineage accumulation rates are those that have diversified primarily by modes of speciation that generate little or no ecological diversification. A number of testable predictions that integrate data from molecular systematics, community ecology, and biogeography are also discussed.     

Differences between subfamilies in diversification process of the Early and Middle Permian fusulinid fauna in South China

Based on the fusulinid occurrence records from a computerized database of stratigraphic distribution, statistic comparisons have been conducted to disclose the differences among six subfamilies (constituting the major part of the fusulinid fauna) in generic and specific diversities, rates of speciation and extinction, and changes in the rates and others during the diversification process of the fusulinid fauna in Early and Middle Permian in South China. Our results reveal that: (1) significant differences exist in the diversification pattern of different taxa and (2) the rates of speciation and extinction in Schwagerininae are statistically higher than those in the others. Furthermore, the high rate of speciation in Schwagerininae contributed to the higher rate of diversification of the fusulinid fauna in Early Permian, whereas the lower rate of diversification in the Middle Permian has resulted from the ubiquitous low rates of speciation in all major taxa in the fauna, such as Schwagerininae, Neoschwagerininae, Verbeekininae, Sumatrininae, and Misellininae.     

The Nature of Evolutionary Radiations: A Case Study Involving Devonian Trilobites

Evolutionary radiations, times of profound diversification of species against a broader background of more muted evolutionary change, have long been considered one of the fundamental patterns in the fossil record. Further, given the important role geological, environmental, and climatic processes play in causing speciation, analyzing the biogeographic context of radiations can yield important insight into their evolutionary mechanisms. In this study we examine biogeographic patterns and quantify rates of speciation in a diverse group of Devonian trilobites, the calmoniids, that has been hailed as a classic paleontological example of an evolutionary radiation. In particular, a phylogenetic biogeographic analysis—modified Brooks Parsimony Analysis—was used to examine the processes and geographic setting of speciation within the group. Results indicate that the Malvinokaffric Realm was a geographically complex area, and this geographic complexity created various opportunities for speciation via geodispersal and vicariance that created the fuel that fed the speciation in these taxa. Part of the geographic complexity was created not only by the inherent geologic backdrop of the region, but the overlying changes of sea level rise and fall. Rates of speciation were highest when sea level was lowest. Low sea level encouraged isolation of faunas in different tectonic basins. By contrast, sea level rise facilitated range expansion and geodispersal to other distinct tectonic basins, and speciation rates concomitantly fell; however, the taxa with the expanded ranges were later fodder for diversification when sea level fell again. Here we present a view of evolutionary radiations driven fundamentally by external abiotic factors—geology and climate—that cause range expansion and opportunities for geographic isolation with resultant rapid speciation.     

Abnormalities in early Paleozoic trilobites from central and eastern China

Malformations are common in trilobites, but the majority of described specimens are from Europe and North America. Only a few abnormal trilobites have been reported from China. Ten abnormal trilobites from Cambrian, Ordovician and Silurian strata in central and eastern China are documented. The abnormal Ordovician trilobites are found for the first time in China. All malformations occur in the thoraxes and pygidia, and were caused by a sub-lethal predatory attack, genetic or embryological malfunction, or injury sustained during molting. It is difficult to identify the predators of the six injured trilobites, but potential predators include Cambrian non-trilobite arthropods, Ordovician cephalopods, and Silurian eurypterids, chondrichthyes or cephalopods, even cannibalistic trilobites. Abnormal specimens caused by sub-lethal predatory attacks mainly occur in Cambrian strata in China and other areas in the world, and are rare in post-Cambrian strata. This pattern may reflect the rise of predators and increased predation in the post-Cambrian, which led to an increased trilobite fatality rate, thus reducing the probability that injured specimens would become fossilized.