Estimating Speciation and Extinction Rates for Phylogenies of Higher Taxa

Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time xcut, and fully unresolved thereafter, so that for all subclades, stem age > xcut > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations. [Birth-death process; higher taxa; macroevolution; phylogenetics.

Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation

Abstract Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.

Artificial neural networks can learn to estimate extinction rates from molecular phylogenies

Molecular phylogenies typically consist of only extant species, yet they allow inference of past rates of extinction, because. recently originated species are less likely to be extinct than ancient species. Despite the simple structure of the assumed underlying speciation-extinction process, parametric functions to estimate extinction rates from phylogenies turned out to be complex and often difficult to derive. Moreover, these parametric functions are specific to a particular process (e.g. complete species level phylogeny with constant birth and death rates) and a particular type of data (e.g. times between bifurcations). Here, it is shown that artificial neural networks can substitute for parametric estimation functions once they have been sufficiently trained on simulated data. This technique can in principle be used for different processes and data types, and because it circumvents the time-consuming and difficult task of deriving parametric estimation functions, it may greatly extend the possibilities to make macro-evolutionary inferences from molecular phylogenies. This novel approach is explained, applied to estimate speciation and extinction rates from a molecular phylogeny of the reef fish genus Naso (Acanturidae), and its performance is compared to that of maximum likelihood estimation. (c) 2006 Elsevier Ltd. All rights reserved

Why most birds are small – a macro-ecological approach to the evolution of avian body size

Abstract There are more small-bodied species of birds than those having large bodies. Generally, and relative to occurrance in any one place, small-bodied species also contain more individuals than large-bodied species. The same patterns have been documented for several groups of higher organisms for example, snakes, flowering plants and mammals, which suggests that there exists a general reason "why", which applies to other groups of species as well as to birds. This thesis attempts to identify this reason. In the first place, it is possible that most species happened to become small-bodied by chance. Simulations of neutral body-size evolution indicate however that the observed bias towards small size is stronger than that accounted for by neutral evolution. Then, the most plausible explanation for why most species are small is that small-bodied species speciate faster. However, statistical analyses accounting for historical relatedness of present-day species indicate no relation between body size and the rate of speciation. Finally, instead of little by little, the dominance of small species may have arisen suddenly, when approximately 65 million years ago (presumably) a large meteorite hit the earth, causing mass extinctions. However, analysis of body sizes and genetic differences of extant species reveals that while avian species numbers were approximately halved, the catastrophe affected small and large species equally. Thus, the reason why most species are small does not seem to be due to differential rates of speciation or extinction. Instead, the cause appears to be in the tempo and mode of evolution. It was found by analysis of extant species' body size that probably most differences in body size between species arise at the moment of speciation. Differences between small-bodied species are smaller than between large-bodied species and probably this difference also has its origin at the moment of speciation. Consequently, groups of small species stay small whereas groups of large species are more variable in body size, so that in the end most species are small.Tiivistelmä Maailman noin 10 000 lintulajin joukossa pienikokoisia lajeja on enemmän kuin suurikokoisia. Yleensä pienkokoiset lajit ovat myös yksilömääriltään suurempia kuin samalla paikalla esiintyvät suurikokoiset lajit. Koska sama ilmiö on havaittu monissa muissa suurissa eliöryhmissä (esim. nisäkkäät, käärmeet ja kukkakasvit), on ilmeistä, että on olemassa yhteinen syy, joka pätee niin linnuissa kuin muissakin eliöryhmissä. Tämän väitöskirjan tavoite on selvittää, mikä tämä yhteinen syy voisi olla. Ensinnäkin on mahdollista, että suurin osa lajeista on kehittynyt pienikokoisiksi aivan sattumalta. Ruumiin koon evoluution simulaatiot kuitenkin osoittavat, että on hyvin epätodennäköistä, että neutraali evoluutio olisi johtanut pienikokoisten lajien suuriin määrään havaitussa määrin. Toinen mahdollinen selitys ilmiölle on, että pienikokoiset lajit lajiutuvat nopeammin. Tilastolliset analyysit, jotka ottavat huomioon nykyisin elävien lajien sukulaisuussuhteet, osoittavat ettei ruumin koon ja lajiutumisen vauhdin välillä ole yhteyttä. Kolmas mahdollinen selitys pienikokoisten lajien suurelle määrällä on historiallinen. On mahdollista, että pienikokoisten lajien suhteellisen suuri määrä syntyi nopeasti noin 65 miljoonaa vuotta sitten tapahtuneen massasukupuuton seurauksena, joka fossiiliaineiston perusteella kohdistui erityisesti suurikokoisiin maaeläimiin (esimerkiksi dinosauruksiin). Vertaileva analyysi nykyään elävien lintulajien ruumiin koosta ja geneettisistä eroista osoittaa, että vaikka suuri osa lintulajeista hävisi massasukupuutossa, tämä katastrofi karsi lajeja riippumatta niiden ruumiin koosta. Näyttää siis siltä, etteivät erot lajiutumisen tai sukupuuttojen esiintymisessä selitä sitä, että suurin osa lajeista on pienikokoisia. Tämän tutkimuksen tulosten perusteella syy näyttäisi sen sijaan olevan ruumiin koon kehityksen vauhdissa ja siinä tavassa, jolla kehitys yleensä etenee. Analyysi nykyisten lajien ruumiin koosta paljasti, että suurin osa eroista lajien välillä syntyy (evolutiiviessa aikataulussa) suhteellisen nopeasti lajiutumistapahtuman yhteydessä (punktualismi) eikä vähitellen pitkien aikojen kuluessa (gradualismi), kuten yleensä oletetaan. Kehityslinjojen sisällä pienikokoisten lajien väliset erot ruumiin koossa olivat pienempiä kuin isokokoisten lajien väliset erot - ja todennäköisesti myöskin tämä ero syntyy lajiutumisen yhteydessä. Tämä johtaa evoluution kuluessa tilanteeseen, että alunperin pienikokoisista lajeista kehittyneet lajit ovat myös pienikokoisia, kun taas isokokoisten lajien kehityslinjoissa on nähtävissä huomattavasti paljon enemmän vaihtelua ruumiin koossa. Näiden seurauksena eliöstöissä suurin osa lajeista lopulta on pienikokoisia

Estimating speciation and extinction rates for phylogenies of higher taxa

ISSN:1063-5157ISSN:1076-836

Data from: Estimating speciation and extinction rates for phylogenies of higher taxa

Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and families) are each represented as a single lineage. We show that previous methods implicitly assumed that such subclades are defined by randomly (or in an extreme deterministic way) choosing the edges that define the subclades from the complete species phylogeny. We show that these methods produce biased results if higher taxa are defined in a different manner. We introduce strict higher level phylogenies where subclades are defined so that the phylogeny is fully resolved from its origin to time xcut, and fully unresolved thereafter, so that for all subclades, stem age > xcut > crown age. We present estimates of speciation and extinction rates from a phylogeny of birds in which this subclade definition was applied. However, for most higher level phylogenies in the literature, it is unclear how higher taxa were defined, but often such phylogenies can be easily transformed into strict higher level phylogenies, as we illustrate by estimating speciation and extinction rates from a near-complete but only partly resolved species-level phylogeny of mammals. The accuracy of our methods is verified using simulations