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At least 19 recordsLinked to original sources

Phylogeny, ancestors and anagenesis in the hominin fossil record

Probabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary pattern by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a dataset of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Au. afarensis; Au. garhi is ancestral to Homo; H. antecessor is ancestral to H. heidelbergensis, which in turn is ancestral to both H. sapiens and H. neanderthalensis. These results show a benefit of accommodating direct ancestry in phylogenetics. By so doing, quantitative results align more closely with previous qualitative expectations.

evolutionary biology

What do ossification sequences tell us about the origin of extant amphibians?

ABSTRACTThe controversial origin of extant amphibians has been studied using several sources of data and methods, including phylogenetic analyses of morphological data, molecular dating, stratigraphic data, and integration of ossification sequence data, but a consensus has failed to emerge. We have compiled five datasets to assess the relative support for six competing hypotheses about the origin of extant amphibians: a monophyletic origin among temnospondyls, a monophyletic origin among lepospondyls, a diphyletic origin among both temnospondyls and lepospondyls, a diphyletic origin among temnospondyls alone, and two variants of a triphyletic origin, in which anurans and urodeles come from different temnospondyl taxa while caecilians come from lepospondyls and are either closer to anurans and urodeles or to amniotes. Our datasets comprise ossification sequences of up to 107 terminal taxa and up to eight cranial bones, and up to 65 terminal taxa and up to seven appendicular bones, respectively. Among extinct taxa, only two or three temnospondyl can be analyzed simultaneously for cranial data, but this is not an insuperable problem because each of the six tested hypotheses implies a different position of temnospondyls and caecilians relative to other sampled taxa. For appendicular data, more extinct taxa can be analyzed, including some lepospondyls and the finned tetrapodomorph Eusthenopteron, in addition to temnospondyls. The data are analyzed through maximum likelihood, and the AICc (corrected Akaike Information Criterion) weights of the six hypotheses allow us to assess their relative support. By an unexpectedly large margin, our analyses of the cranial data support a monophyletic origin among lepospondyls; a monophyletic origin among temnospondyls, the current near-consensus, is a distant second. All other hypotheses are exceedingly unlikely according to our data. Surprisingly, analysis of the appendicular data supports triphyly of extant amphibians within a clade that unites lepospondyls and temnospondyls, contrary to all molecular and recent paleontological phylogenies, but this conclusion is not very robust.View Full Text

paleontology

A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data

Our understanding of macroevolutionary patterns of adaptive evolution has greatly increased with the advent of large-scale phylogenetic comparative methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an adaptive process of divergence and selection. However, inference of the dynamics of adaptive landscapes from comparative data is complicated by interpretational difficulties, lack of identifiability among parameter values and the common requirement that adaptive hypotheses must be assigned a priori. Here we develop a reversible-jump Bayesian method of fitting multi-optima OU models to phylogenetic comparative data that estimates the placement and magnitude of adaptive shifts directly from the data. We show how biologically informed hypotheses can be tested against this inferred posterior of shift locations using Bayes Factors to establish whether our a priori models adequately describe the dynamics of adaptive peak shifts. Furthermore, we show how the inclusion of informative priors can be used to restrict models to biologically realistic parameter space and test particular biological interpretations of evolutionary models. We argue that Bayesian model-fitting of OU models to comparative data provides a framework for integrating of multiple sources of biological data--such as microevolutionary estimates of selection parameters and paleontological timeseries--allowing inference of adaptive landscape dynamics with explicit, process-based biological interpretations.

Evolutionary Biology

Burrow architectural types of the Atlantic ghost crab, Ocypode quadrata (Fabricius, 1787) (Brachyura: Ocypodidae), in Brazil

A broad range of aspects from paleontology to physiology of the ghost crabs Ocypode quadrata have been studied worldwide. These crabs have been used as ecological indicators of the levels of anthropogenic impacts on sandy beaches. Our aim is to report the variety of burrow architecture types constructed by ghost crabs Ocypode quadrata on beaches of Maceio, Brazil. We found 20 types of burrows that differ in shape (number of axes, number of openings, orientation of blind end, number of branches). The slash-shaped burrows (type C) were the most frequent shape, followed by types K (spiral) and E (Y-shaped). Type C also showed the largest opening diameter and length ranges. Burrow types F, J, P, S and T were the least frequent. The G-test for goodness of fit to a time-independent uniform frequency distribution (G = 417.61; d.f. = 18; p < 0.005) reject the hypothesis that burrow types are constructed randomly (uniform distribution). The dominance of type C burrows and other simple-type burrows over more elaborate types indicates preference for simplicity.

Ecology

A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach--the CPP on Mass Extinction Times (CoMET) model--provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.

Evolutionary Biology

Estimating diversification rates from the fossil record

Diversification rates are estimated from phylogenies, typically without fossils, except in paleontological studies. By nature, rate estimations depend heavily on the time data provided in phylogenies, which are divergence times and (when used) fossil ages. Among these temporal data, fossil ages are by far the most precisely known (divergence times are inferences calibrated with fossils). We propose a method to compute the likelihood of a phylogenetic tree with fossils in which the only known time information is the fossil ages.\n\nTesting our approach on simulated data shows that the maximum likelihood rate estimates from the phylogenetic tree shape and the fossil dates are almost as accurate as the ones obtained by taking into account all the data, including the divergence times. Moreover they are substantially more accurate than the estimates obtained only from the exact divergence times (without taking into account the fossil record).

Evolutionary Biology

A new model for ancient DNA decay based on paleogenomic meta-analysis

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation.

genomics

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

Divergence time estimation -- the calibration of a phylogeny to geological time -- is a integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. While these (essentially model-violation) results are robust (and probably common in empirical data sets), we note a further alternative: that the configuration of the statistical inference problem alone (i.e., the parameters, their relationships, and associated priors) precluded the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the various calibration densities specified for fossil-calibrated nodes), that with no data present at all, an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions, indicating an absence of relevant information in the data. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they essentially anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared, especially for parameters of direct interest. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently. [marginal priors; information content; diptych; divergence time estimation; fossil record; BEAST; angiosperms.]

evolutionary biology

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100042).\n\nReconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.

evolutionary biology

Evolutionary history of New World monkeys revealed by molecular and fossil data

New World monkeys (parvorder Platyrrhini) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, the ancestral morphology, and the evolution of the distribution of the clade. Here we integrate paleontological and molecular evidence to investigate the evolutionary dynamics of extinct and extant platyrrhines. We develop an analytical framework to infer ancestral states, the evolution of body mass, and changes in latitudinal ranges through time. Our results show that extant platyrrhines originated some 5-10 million years earlier than previously assumed, likely dating back to the Middle Eocene ([~] 43 million years ago, Ma). The estimated ancestral platyrrhine was strikingly small - weighing [~] 0.4 kg, as compared to the largest modern species over 10 kg - matching the size of their presumed Eocene North African ancestors. Small-sized callitrichines (marmosets and tamarins) retained a small body mass throughout their evolutionary history, thus challenging the hypothesis of phyletic dwarfism as an explanation to their adaptive traits. In contrast, a rapid change in body mass range took place as the three families diverged between the Late Oligocene and the Early Miocene. That period also marks a peak in diversity of fossil platyrrhines and is associated with their widest latitudinal range, expanding as far to the South as Patagonia. This geographic expansion is temporally coincident with a significant increase in platyrrhine population size inferred from genomic data, and with warm and humid climatic conditions linked to the Miocene Climatic Optimum and the lower elevation of the Andes. These results unveil the early evolution of an iconic group of monkeys and showcase the advantages of integrating fossil and molecular data for estimating evolutionary rates and trends.

evolutionary biology

Complex multicellularity in fungi: evolutionary convergence, single origin, or both?

Complex multicellularity comprises the most advanced level of organization evolved on Earth. It has evolved only a few times in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not seen in other lineages. In this article we review ecological, paleontological, developmental and genomic aspects of complex multicellularity in fungi and discuss the general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8-12 distinct fungal lineages, which show a patchy phylogenetic distribution, yet share some of the genetic mechanisms underlying complex multicellular development. To mechanistically explain the patchy distribution of complex multicellularity across the fungal tree of life we identify four key observations that need to be considered: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these; the universal conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain its pervasive occurrence in across the fungal tree of life.

evolutionary biology

Bayesian and likelihood placement of fossils on phylogenies from quantitative morphometrics

AO_SCPLOWBSTRACTC_SCPLOWJointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.

evolutionary biology

Bracketing phenotypic limits of mammalian hybridization

An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian paleontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between gray and ringed seals. We analyzed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology, and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species-pairs known to hybridize. In contrast, morphological and developmental analyses show gray and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that gray-ringed seal hybridization is not limited to captivity. Taken together, gray and ringed seals appear to be in an adaptive radiation phase of evolution, showing large morphological differences relative to their comparatively modest genetic distance. Because morphological similarity does not always correlate with genetic distance in nature, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.

evolutionary biology

Counterbalancing the time-dependence effect on the human mitochondrial DNA molecular clock

We propose a new method for estimating the coalescent age of phylogenetically related sequences that takes into account the observed time dependency of molecular rate estimates. Applying this method to human mitochondrial DNA data we have obtained significantly older ages for the main events of human evolution than in previous estimates. These ages are in close agreement with the most recent archaeological and paleontological records.

evolutionary biology

Time calibrated morpho-molecular classification of Nassellaria (Radiolaria)

Nassellaria are marine radiolarian protists belonging to the Rhizaria lineage. Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.

molecular biology

Osmunda pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and fossil evidence in the phylogeny of Osmundaceae

The systematic classification of Osmundaceae has long remained controversial. Recent molecular data indicate that Osmunda is paraphyletic, and needs to be separated into Osmundastrum and Osmunda s. str. Here we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Osmunda pulchella and five additional, newly identified Jurassic Osmunda species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as ancestral members of modern genera and subgenera. Altogether, the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can be elegantly reconciled under the assumption that Osmunda is indeed monophyletic; the recently proposed root-placement in Osmundaceae--based solely on molecular data--likely results from un- or misinformative out-group signals.

Paleontology

Community stability and selective extinction during Earth’s greatest mass extinction

We modelled the resilience and transient dynamics of terrestrial paleocommunities from the Karoo Basin, South Africa, around the Permian-Triassic mass extinction. Using recently refined biostratigraphic data that suggest two pulses of extinction leading up to the Permian-Triassic boundary, we show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became stable during the mass extinction. Modelled food webs before and after the mass extinction have lower resilience and less stable transient dynamics compared to random food webs lacking in functional structure but of equal species richness. They are, however, more stable than random food webs of equal richness but with randomized functional structure. In contrast, models become increasingly more resilient and have more stable transient dynamics, relative to the random models, as the mass extinction progressed. The increased stability of the community that resulted from the first pulse of extinction was driven by significant selective extinction against small-bodied amniotes, and significantly greater probabilities of survival of large-bodied amniotes. These results point to a positive relationship between evolved patterns of functional diversity and emergent community dynamics, with observed patterns being more stable than alternative possibilities.\n\nSignificanceAnthropogenic impacts on modern ecosystems have no precedents in human history. The fossil record does contain episodes of severe biodiversity crises, but incomplete preservation and low temporal resolution make it difficult to equate fossil data to modern ecological processes. We examined terrestrial paleocommunities from Earths most severe mass extinction, the Permian-Triassic mass extinction (PTME), and modelled their dynamic stabilities. We show that during times of low extinction, paleocommunities were no more stable than randomly assembled communities, but they became more stable during the mass extinction. Increased stability resulted mostly from selective extinction and survival based on vertebrate body size. Whether modern communities will behave similarly depends on the similarity between human drivers and those of the PTME.

Paleontology

Fables and foibles: a critical analysis of the Palaeoflora database and the Coexistence approach for palaeoclimate reconstruction

The \"Coexistence Approach\" is a mutual climate range (MCR) technique combined with the nearest-living relative (NLR) concept. It has been widely used for palaeoclimate reconstructions based on Eurasian plant fossil assemblages, most of them palynofloras (studied using light microscopy). The results have been surprisingly uniform, typically converging to subtropical, per-humid or monsoonal conditions. Studies based on the coexistence approach have had a marked impact in literature, generating over 10,000 citations thus far. However, recent studies have pointed out inherent theoretical and practical problems entangled in the application of this widely used method. But so far little is known how results generated by the coexistence approach are affected by subjective errors, data errors, and violations of the basic assumptions. The majority of Coexistence Approach studies make use of the Palaeoflora database (the combination of which will be abbreviated to CA+PF). Testing results produced by CA+PF studies has been hindered by the general unavailability of the contents in the underlying Palaeoflora database; two exceptions are the mean-annual temperature tolerances and lists of assigned associations between fossils and nearest-living relatives. Using a recently published study on the Eocene of China, which provides the first usable insight into the data structure of the Palaeoflora database, we compare the theory and practice of Coexistence Approach using the Palaeoflora database (CA+PF). We show that CA+PF is riddled by association and climate data error. We reveal the flaws in the application of CA, which is often in stark contrast to the theory of the method. We show that CA+PF is highly vulnerable against numerous sources of errors, mainly because it lacks safeguards that could identify unreliable data. We demonstrate that the CA+PF produces coherent, pseudo-precise results even for artificially generated, random plant assemblages. Alternative MCR-NLR methods can surpass the most imminent deficits of CA, and may be used as a stop-gap until more accurate bioclimatic and distribution data on potential Eurasian NLRs, and theoretically- and statistically-robust methods will become available. Finally, general guidelines are provided for the future application of methods using the mutual climatic range with nearest living relatives approach when reconstructing climate from plant fossil assemblages.

Paleontology