A model of macro-evolution as a branching process based on innovations

We introduce a model for the evolution of species triggered by generation of novel features and exhaustive combination with other available traits. Under the assumption that innovations are rare, we obtain a bursty branching process of speciations. Analysis of the trees representing the branching history reveals structures qualitatively different from those of random processes. For a tree with n leaves, the average distance of leaves from root scales as (log n)^2 to be compared to log n for random branching. The mean values and standard deviations for the tree shape indices depth (Sackin index) and imbalance (Colless index) of the model are compatible with those of real phylogenetic trees from databases. Earlier models, such as the Aldous' branching (AB) model, show a larger deviation from data with respect to the shape indices.Comment: 16 pages, 8 figures, 1 table, v2: minor corrections and addition

Stochastic Tree Models for Macroevolution: Development, Validation and Application

Phylogenetic trees capture the relationships between species and can be investigated by morphological and/or molecular data. When focusing on macroevolution, one considers the large-scale history of life with evolutionary changes affecting a single species of the entire clade leading to the enormous diversity of species obtained today. One major problem of biology is the explanation of this biodiversity. Therefore, one may ask which kind of macroevolutionary processes have given rise to observable tree shapes or patterns of species distribution which refers to the appearance of branching orders and time periods. Thus, with an increasing number of known species in the context of phylogenetic studies, testing hypotheses about evolution by analyzing the tree shape of the resulting phylogenetic trees became matter of particular interest. The attention of using those reconstructed phylogenies for studying evolutionary processes increased during the last decades. Many paleontologists (Raup et al., 1973; Gould et al., 1977; Gilinsky and Good, 1989; Nee, 2004) tried to describe such patterns of macroevolution by using models for growing trees. Those models describe stochastic processes to generate phylogenetic trees. Yule (1925) was the first who introduced such a model, the Equal Rate Markov (ERM) model, in the context of biological branching based on a continuous-time, uneven branching process. In the last decades, further dynamical models were proposed (Yule, 1925; Aldous, 1996; Nee, 2006; Rosen, 1978; Ford, 2005; Hernández-García et al., 2010) to address the investigation of tree shapes and hence, capture the rules of macroevolutionary forces. A common model, is the Aldous\\\'' Branching (AB) model, which is known for generating trees with a similar structure of \\\"real\\\" trees. To infer those macroevolutionary forces structures, estimated trees are analyzed and compared to simulated trees generated by models. There are a few drawbacks on recent models such as a missing biological motivation or the generated tree shape does not fit well to one observed in empirical trees. The central aim of this thesis is the development and study of new biologically motivated approaches which might help to better understand or even discover biological forces which lead to the huge diversity of organisms. The first approach, called age model, can be defined as a stochastic procedure which describes the growth of binary trees by an iterative stochastic attachment of leaves, similar to the ERM model. At difference with the latter, the branching rate at each clade is no longer constant, but decreasing in time, i.e., with the age. Thus, species involved in recent speciation events have a tendency to speciate again. The second introduced model, is a branching process which mimics the evolution of species driven by innovations. The process involves a separation of time scales. Rare innovation events trigger rapid cascades of diversification where a feature combines with previously existing features. The model is called innovation model. Three data sets of estimated phylogenetic trees are used to analyze and compare the produced tree shape of the new growth models. A tree shape statistic considering a variety of imbalance measurements is performed. Results show that simulated trees of both growth models fit well to the tree shape observed in real trees. In a further study, a likelihood analysis is performed in order to rank models with respect to their ability to explain observed tree shapes. Results show that the likelihoods of the age model and the AB model are clearly correlated under the trees in the databases when considering small and medium-sized trees with up to 19 leaves. For a data set, representing of phylogenetic trees of protein families, the age model outperforms the AB model. But for another data set, representing phylogenetic trees of species, the AB model performs slightly better. To support this observation a further analysis using larger trees is necessary. But an exact computation of likelihoods for large trees implies a huge computational effort. Therefore, an efficient method for likelihood estimation is proposed and compared to the estimation using a naive sampling strategy. Nevertheless, both models describe the tree generation process in a way which is easy to interpret biologically. Another interesting field of research in biology is the coevolution between species. This is the interaction of species across groups such that the evolution of a species from one group can be triggered by a species from another group. Most prominent examples are systems of host species and their associated parasites. One problem is the reconciliation of the common history of both groups of species and to predict the associations between ancestral hosts and their parasites. To solve this problem some algorithmic methods have been developed in recent years. But only a few host parasite systems have been analyzed in sufficient detail which makes an evaluation of these methods complex. Within the scope of coevolution, the proposed age model is applied to the generation of cophylogenies to evaluate such host parasite reconciliation methods. The presented age model as well as the innovation model produce tree shapes which are similar to obtained tree structures of estimated trees. Both models describe an evolutionary dynamics and might provide a further opportunity to infer macroevolutionary processes which lead to the biodiversity which can be obtained today. Furthermore with the application of the age model in the context of coevolution by generating a useful benchmark set of cophylogenies is a first step towards systematic studies on evaluating reconciliation methods

The Western Stemmed Point Tradition: Evolutionary Perspectives on Cultural Change in Projectile Points During the Pleistocene-Holocene Transition

In this thesis I analyze the cultural techniques of Paleoindians in North America by examining the diversification and fusion of stemmed projectile point traditions using an evolutionary analysis. The Western Stemmed Point tradition has an extensive regional and temporal distribution throughout the Intermountain West and High Plains during the Paleoindian period. In an effort to determine how stemmed projectile point technologies relate to each other, I applied a phylogenetic approach to construct heritable patterns of projectile point histories. By measuring the physical traits of those points and using a macro-evolutionary theoretical approach, changes in artifact form can be acquired and heritable processes understood. This process was further complicated by our understanding of how culture is learned and shared. Techniques can be learned as individual units or even as sets of units, resulting in the differential persistence of individual traits. This analysis indicated that projectile point traits for blade and haft characteristics evolved in a mosaic fashion creating distinct patterns of vertical and horizontal transmission across space and time. Furthermore, the haft characteristics created important results that support the eastward expansion of stemmed projectile point traditions from the west

Clownfishes evolution below and above the species level.

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels

Chance in the Modern Synthesis

The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” or “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. In the following, we first offer a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance. We do not take these to be an exhaustive taxonomy of all possible ways in which chance meaningfully figures in explanations in evolutionary biology. These are simply five common uses of the term by biologists at this period. They will serve to organize our summary of the collected references to chance and the analysis and discussion of the following questions: • What did synthesis authors understand by chance? • How did these authors see chance operating in evolution? • Did their appeals to chance increase or decrease over time during the synthesis? That is, was there a “hardening” of the synthesis, as Gould claimed (1983)

Macro- and Microevolution of Languages: Exploring Linguistic Divergence with Approaches from Evolutionary Biology

There are more than 7000 languages in the world, and many of these have emerged through linguistic divergence. While questions related to the drivers of linguistic diversity have been studied before, including studies with quantitative methods, there is no consensus as to which factors drive linguistic divergence, and how. In the thesis, I have studied linguistic divergence with a multidisciplinary approach, applying the framework and quantitative methods of evolutionary biology to language data. With quantitative methods, large datasets may be analyzed objectively, while approaches from evolutionary biology make it possible to revisit old questions (related to, for example, the shape of the phylogeny) with new methods, and adopt novel perspectives to pose novel questions. My chief focus was on the effects exerted on the speakers of a language by environmental and cultural factors. My approach was thus an ecological one, in the sense that I was interested in how the local environment affects humans and whether this human-environment connection plays a possible role in the divergence process. I studied this question in relation to the Uralic language family and to the dialects of Finnish, thus covering two different levels of divergence. However, as the Uralic languages have not previously been studied using quantitative phylogenetic methods, nor have population genetic methods been previously applied to any dialect data, I first evaluated the applicability of these biological methods to language data. I found the biological methodology to be applicable to language data, as my results were rather similar to traditional views as to both the shape of the Uralic phylogeny and the division of Finnish dialects. I also found environmental conditions, or changes in them, to be plausible inducers of linguistic divergence: whether in the first steps in the divergence process, i.e. dialect divergence, or on a large scale with the entire language family. My findings concerning Finnish dialects led me to conclude that the functional connection between linguistic divergence and environmental conditions may arise through human cultural adaptation to varying environmental conditions. This is also one possible explanation on the scale of the Uralic language family as a whole. The results of the thesis bring insights on several different issues in both a local and a global context. First, they shed light on the emergence of the Finnish dialects. If the approach used in the thesis is applied to the dialects of other languages, broader generalizations may be drawn as to the inducers of linguistic divergence. This again brings us closer to understanding the global patterns of linguistic diversity. Secondly, the quantitative phylogeny of the Uralic languages, with estimated times of language divergences, yields another hypothesis as to the shape and age of the language family tree. In addition, the Uralic languages can now be added to the growing list of language families studied with quantitative methods. This will allow broader inferences as to global patterns of language evolution, and more language families can be included in constructing the tree of the world’s languages. Studying history through language, however, is only one way to illuminate the human past. Therefore, thirdly, the findings of the thesis, when combined with studies of other language families, and those for example in genetics and archaeology, bring us again closer to an understanding of human history.Monet maailman yli 7000 kielestä ovat syntyneet erkaantumisprosessin kautta. Tällöin yhdestä kielestä muotoutuu eri tekijöiden vaikutuksesta aikojen saatossa useampia kieliä. Kielten erkaantumiseen vaikuttavia tekijöitä on tutkittu aiemminkin ja myös laskennallisia menetelmiä käyttäen. Vielä on kuitenkin epäselvää mitkä kaikki tekijät voivat vaikuttaa kielten erkaantumiseen ja miten. Tutkin väitöskirjassani kielten erkaantumiseen vaikuttavia tekijöitä. Lähestymistapani on monitieteinen, sillä sovellan laskennallisia evoluutiobiologian menetelmiä ja teorioita kieliaineistoon. Laskennalliset menetelmät mahdollistavat suurien aineistojen objektiivisen analysoinnin, kun taas evoluutiobiologisen lähestymistavan avulla voin muodostaa uudenlaisia tutkimuskysymyksiä ja käyttää uusia menetelmiä vastatakseni aiemmin esitettyihin kysymyksiin (esimerkiksi sukupuun muotoon liittyen). Tutkimuksessani keskityin selvittämään kielten erkaantumista ihmisen ekologian kannalta. Toisin sanoen olin kiinnostunut ympäristö- ja/tai kulttuuritekijöiden vaikutuksesta kielenpuhujiin ja siitä, voiko tämä kytkös olla osallisena kielten erkaantumisprosessissa. Tutkin kysymystä tämän prosessin kahdessa eri vaiheessa: sen alussa ennen kuin eriytyminen on kokonaan tapahtunut, ja sen jo tapahduttua. Murteiden eriytyminen vastaa prossessin alkuvaihetta, ja tutkin sitä suomen kielen murreaineistoa käyttäen. Tapahtuneita erkaantumisia tutkin sukupuista, joita tein uralilaisten kielten sanastoaineistosta. Koska uralilaisia kieliä ei ole aiemmin tutkittu vastaavanlaisin laskennallisin menetelmin eikä käyttämiäni populaatiogenetiikan menetelmiä ole käytetty aiemmin mihinkään murreaineistoon, testasin aluksi näiden menetelmien soveltuvuutta aineistojeni analysointiin. Totesin biologisten menetelmien soveltuvan kieliaineiston analysointiin, sillä tulokseni vastasivat perinteisiä näkemyksiä sekä uralilaisen sukupuun muodosta että suomen murrejaosta. Lisäksi havaitsin, että erot ympäristöoloissa mahdollisesti vaikuttavat kielten erkaantumiseen. Tämä oli havaittavissa niin eriytymisprosessin varhaisissa vaiheissa murteiden välillä kuin myös koko kieliryhmän eriytymisiä tutkittaessa. Koska ihmisten tiedetään usein sopeutuvan vallitseviin ympäristöolosuhteisiin kulttuurisopeumien avulla, päättelin murretutkimusteni tuloksista, että juuri kieltenpuhujien kulttuurinen sopeutuminen paikallisiin ympäristöolosuhteisiin saattaisi toimia puhujapopulaatioita erottavana tekijänä ja täten kytköksenä ympäristöerojen ja kielellisen erkaantumisen välillä. Tämä voisi mahdollisesti selittää myös uralilaisten kielten erkaantumisia. Väitöstutkimukseni tulokset tuovat uusia näkemyksiä kielten erkaantumiseen niin paikallisella kuin maailmanlaajuisellakin tasolla. Havaintoni ympäristöerojen mahdollisesta vaikutuksesta suomen murteiden muotoutumisessa herättää kysymyksen löytöni yleistettävyydestä myös muihin kieliin ja niiden murteisiin. Koska murteiden erkaantuminen on ensimmäinen vaihe kielen eriytymisprosessissa, on murteiden muotoutumista tutkimalla mahdollista myös selvittää, mitkä tekijät ovat aikaansaaneet maailmanlaajuisen kielten kirjon. Tästä syystä tarvitaan vastaavanlaisia tutkimuksia myös muiden kielten murteista. Esitän väitöskirjassani myös uralilaisten kielten laskennallisesti tehdyn sukupuun, jota voidaan verrata vastaavilla menetelmillä tehtyihin muiden kieliryhmien puihin. Tämän vertailun kautta on mahdollista selvittää onko kielisukupuiden muodossa jotain maailmanlaajuisia säännönmukaisuuksia, josta voi edelleen tehdä päätelmiä kieliin vaikuttavista lainalaisuuksista. Ihmiskunnan historian ja esihistorian selvittäminen on haasteellinen palapeli, jossa eri tieteenalojen palasia yhteen sovittelemalla voidaan päästä lähemmäksi yleistä ymmärrystä menneisyydestä. Väitöstutkimukseni on pieni osa tätä kokonaisuutta, mutta yhdistelemällä havaintojani niin muista kieliryhmistä tehtyihin havaintoihin kuin myös esimerkiksi arkeologian ja genetiikan tuloksiin, olemme taas askeleen lähempänä tätä tavoitetta.Siirretty Doriast

Allopatry increases the balance of phylogenetic trees during radiation under neutral speciation

The shape of a phylogenetic tree is defined by the sequence of speciation events, represented by its branching points, and extinctions, represented by branch interruptions. In a neutral scenario of parapatry and isolation by distance, species tend to branch off the original population one after the other, leading to highly unbalanced trees. In this case the degree of imbalance, measured by the normalized Sackin index, grows linearly with species richness. Here we claim that moderate values of imbalance for trees with large number of species can occur if the geographic distribution involves more than one deme (allopatry) and speciation is parapatric within demes. The combined values of balance (normalized Sackin index) and species richness provide an estimate of how many demes were involved in the process if it happened in such neutral scenario. We also show that the spatial division in demes moderately slows down the diversification process, portraying a neutral mechanism for structuring the branch length distribution of phylogenetic trees

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

A number of approaches for studying macroevolution using phylogenetic trees have been developed in the last few years. Here, we present RPANDA, an R package that implements model‐free and model‐based phylogenetic comparative methods for macroevolutionary analyses. The model‐free approaches implemented in RPANDA are recently developed approaches stemming from graph theory that allow summarizing the information contained in phylogenetic trees, computing distances between trees, and clustering them accordingly. They also allow identifying distinct branching patterns within single trees. RPANDA also implements likelihood‐based models for fitting various diversification models to phylogenetic trees. It includes birth–death models with i) constant, ii) time‐dependent and iii) environmental‐dependent speciation and extinction rates. It also includes models with equilibrium diversity derived from the coalescent process, as well as a likelihood‐based inference framework to fit the individual‐based model of Speciation by Genetic Differentiation, which is an extension of Hubbell's neutral theory of biodiversity. RPANDA can be used to (i) characterize trees by plotting their spectral density profiles (ii) compare trees and cluster them according to their similarities, (iii) identify and plot distinct branching patterns within trees, (iv) compare the fit of alternative diversification models to phylogenetic trees, (v) estimate rates of speciation and extinction, (vi) estimate and plot how these rates have varied with time and environmental variables and (vii) deduce and plot estimates of species richness through geological time. RPANDA provides investigators with a set of tools for exploring patterns in phylogenetic trees and fitting various models to these trees, thereby contributing to the ongoing development of phylogenetics in the life sciences