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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 161-176Article in journal (Refereed)
  • 2.
    Andersson, Jan O
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology. Mikrobiologi.
    A review of "Microbial Phylogeny and Evolution: Concepts and Controversies"2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 2, p. 359-361Article, book review (Other (popular science, discussion, etc.))
  • 3.
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    The New Foundations of Evolution: On the Tree of Life2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 1, p. 114-115Article, book review (Other (popular science, discussion, etc.))
  • 4. Bergsten, Johannes
    et al.
    Bilton, David T.
    Fujisawa, Tomochika
    Elliott, Miranda
    Monaghan, Michael T.
    Balke, Michael
    Hendrich, Lars
    Geijer, Joja
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Herrmann, Jan
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Foster, Garth N.
    Ribera, Ignacio
    Nilsson, Anders N.
    Barraclough, Timothy G.
    Vogler, Alfried P.
    The Effect of Geographical Scale of Sampling on DNA Barcoding2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 5, p. 851-869Article in journal (Refereed)
    Abstract [en]

    Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1%, sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from >7% for samples within 1 km, to <3.5% for samples up to >6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query, identifications considered uncertain (more than one species <1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95%, of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives smaller geographical scales deliver higher accuracy.

  • 5. Bergsten, Johannes
    et al.
    Bilton, David T.
    Fujisawa, Tomochika
    Elliott, Miranda
    Monaghan, Michael T.
    Balke, Michael
    Hendrich, Lars
    Geijer, Joja
    Herrmann, Jan
    Foster, Garth N.
    Ribera, Ignacio
    Nilsson, Anders N.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Barraclough, Timothy G.
    Vogler, Alfried P.
    The Effect of Geographical Scale of Sampling on DNA Barcoding2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 5, p. 851-869Article in journal (Refereed)
    Abstract [en]

    Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1%, sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from >7% for samples within 1 km, to <3.5% for samples up to >6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query, identifications considered uncertain (more than one species <1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95%, of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives smaller geographical scales deliver higher accuracy.

  • 6.
    Bergsten, Johannes
    et al.
    Naturhistoriska riksmuseet.
    Nilsson, Anders N.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ronquist, Fredrik
    Naturhistoriska riksmuseet.
    Bayesian Tests of Topology Hypotheses with an Example from Diving Beetles2013In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, no 5, p. 660-673Article in journal (Refereed)
    Abstract [en]

    We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.

  • 7.
    Bertrand, Yann
    et al.
    Södertörn University, School of Life Sciences. Muséum National d'Histoire Naturelle, Paris, France.
    Härlin, Mikael
    Södertörn University, School of Life Sciences.
    Stability and universality in the application of taxon names in phylogenetic nomenclature2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 5, p. 848-858Article in journal (Refereed)
  • 8.
    Bertrand, Yann
    et al.
    Södertörn university college;Museum National d'Histoire Naturelle, France.
    Härlin, Mikael
    Södertörn University College.
    Stability and universality in the application of taxon names in phylogenetic nomenclature2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 5, p. 848-858Article in journal (Refereed)
  • 9.
    Björklund, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Merilä, Juha
    Fluctuating asymmetry and measurement error1995In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 44, p. 97-101Article in journal (Refereed)
  • 10.
    Bogusz, Marcin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Whelan, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 218-231Article in journal (Refereed)
    Abstract [en]

    Phylogenetic tree inference is a critical component of many systematic and evolutionary studies. The majority of these studies are based on the two-step process of multiple sequence alignment followed by tree inference, despite persistent evidence that the alignment step can lead to biased results. Here we present a two-part study that first presents PaHMM-Tree, a novel neighbor joining-based method that estimates pairwise distances without assuming a single alignment. We then use simulations to benchmark its performance against a wide-range of other phylogenetic tree inference methods, including the first comparison of alignment-free distance-based methods against more conventional tree estimation methods. Our new method for calculating pairwise distances based on statistical alignment provides distance estimates that are as accurate as those obtained using standard methods based on the true alignment. Pairwise distance estimates based on the two-step process tend to be substantially less accurate. This improved performance carries through to tree inference, where PaHMM-Tree provides more accurate tree estimates than all of the pairwise distance methods assessed. For close to moderately divergent sequence data we find that the two-step methods using statistical inference, where information from all sequences is included in the estimation procedure, tend to perform better than PaHMM-Tree, particularly full statistical alignment, which simultaneously estimates both the tree and the alignment. For deep divergences we find the alignment step becomes so prone to error that our distance-based PaHMM-Tree outperforms all other methods of tree inference. Finally, we find that the accuracy of alignment-free methods tends to decline faster than standard two-step methods in the presence of alignment uncertainty, and identify no conditions where alignment-free methods are equal to or more accurate than standard phylogenetic methods even in the presence of substantial alignment error.

  • 11.
    Bokma, F
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Speciation and Patterns of Diversity2010In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 59, no 3, p. 365-367Article, book review (Refereed)
  • 12.
    Bokma, Folmer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Time, species, and separating their effects on trait variance in clades2010In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 59, no 5, p. 602-607Article in journal (Refereed)
  • 13.
    Bokma, Folmer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Baek, Seung Ki
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    50 years of inordinate fondness2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 2, p. 251-256Article in journal (Refereed)
  • 14.
    Bokma, Folmer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Godinot, Marc
    Maridet, Olivier
    Ladeveze, Sandrine
    Costeur, Loic
    Sole, Floreal
    Gheerbrant, Emmanuel
    Peigne, Stephane
    Jacques, Florian
    Laurin, Michel
    Testing for Deperet's Rule (Body Size Increase) in Mammals using Combined Extinct and Extant Data2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 98-108Article in journal (Refereed)
    Abstract [en]

    Whether or not evolutionary lineages in general show a tendency to increase in body size has often been discussed. This tendency has been dubbed "Cope's rule" but because Cope never hypothesized it, we suggest renaming it after Deperet, who formulated it clearly in 1907. Deperet's rule has traditionally been studied using fossil data, but more recently a number of studies have used present-day species. While several paleontological studies of Cenozoic placental mammals have found support for increasing body size, most studies of extant placentals have failed to detect such a trend. Here, we present a method to combine information from present-day species with fossil data in a Bayesian phylogenetic framework. We apply the method to body mass estimates of a large number of extant and extinct mammal species, and find strong support for Deperet's rule. The tendency for size increase appears to be driven not by evolution toward larger size in established species, but by processes related to the emergence of new species. Our analysis shows that complementary data from extant and extinct species can greatly improve inference of macroevolutionary processes.

  • 15. Britton, Tom
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Jaquet, David
    Lundqvist, Samuel
    Bremer, Kåre
    Estimating divergence times in large phylogenetic trees2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, p. 741-752Article in journal (Refereed)
    Abstract [en]

    A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.

  • 16. Brysting, Anne K.
    et al.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Huber, Katharina T.
    Moulton, Vincent
    Brochmann, Christian
    Untangling complex histories of genome mergings in high polyploids2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 3, p. 467-476Article in journal (Refereed)
    Abstract [en]

    Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.

  • 17.
    Edler, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Gothenburg, Sweden.
    Guedes, Thais
    Zizka, Alexander
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Antonelli, Alexandre
    Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 197-204Article in journal (Refereed)
    Abstract [en]

    Biogeographical regions (bioregions) reveal how different sets of species are spatially grouped and therefore are important units for conservation, historical biogeography, ecology, and evolution. Several methods have been developed to identify bioregions based on species distribution data rather than expert opinion. One approach successfully applies network theory to simplify and highlight the underlying structure in species distributions. However, this method lacks tools for simple and efficient analysis. Here, we present Infomap Bioregions, an interactive web application that inputs species distribution data and generates bioregion maps. Species distributions may be provided as georeferenced point occurrences or range maps, and can be of local, regional, or global scale. The application uses a novel adaptive resolution method to make best use of often incomplete species distribution data. The results can be downloaded as vector graphics, shapefiles, or in table format. We validate the tool by processing large data sets of publicly available species distribution data of the world's amphibians using species ranges, and mammals using point occurrences. We then calculate the fit between the inferred bioregions and WWF ecoregions. As examples of applications, researchers can reconstruct ancestral ranges in historical biogeography or identify indicator species for targeted conservation.

  • 18.
    Ekman, Stefan
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Andersen, Heidi Lie
    Universitetet i Bergen.
    Wedin, Mats
    Naturhistoriska riksmuseet.
    The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota)2008In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 57, no 1, p. 141-156Article, review/survey (Refereed)
    Abstract [en]

    Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasinglyfrequent. They rely on constancy of character state change rates over trees, a correlation between neutral geneticchange and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions.This investigation explored the outcomes of a variety of methods for reconstructing discrete ancestral state in the ascus apexof the Lecanorales, a group containing the majority of lichen-forming ascomycetes. Evolution of this character complex hasbeen highly controversial in lichen systematics for more than two decades. The phylogeny was estimated using BayesianMarkov chain Monte Carlo inference on DNA sequence alignments of three genes (small subunit of the mitochondrialrDNA, large subunit of the nuclear rDNA, and largest subunit of RNA polymerase II). We designed a novel method forassessing the suitable number of discrete gamma categories, which relies on the effect on phylogeny estimates rather thanon likelihoods. Ancestral state reconstructions were performed using maximum parsimony and maximum likelihood ona posterior tree sample as well as two fully Bayesian methods. Resulting reconstructions were often strikingly differentdepending on the method used; different methods often assign high confidence to different states at a given node. Thetwo fully Bayesian methods disagree about the most probable reconstruction in about half of the nodes, even when similarlikelihood models and similar priors are used. We suggest that similar studies should use several methods, awaiting animproved understanding of the statistical properties of the methods. A Lecanora-type ascus may have been ancestral in theLecanorales. State transformations counts, obtained using stochastic mapping, indicate that the number of state changes is12 to 24, which is considerably greater than the minimum three changes needed to explain the four observed ascus apextypes. Apparently, the ascus in the Lecanorales is far more apt to change than has been recognized. Phylogeny correspondswell with morphology, although it partly contradicts currently used delimitations of the Crocyniaceae, Haematommataceae,Lecanoraceae, Megalariaceae, Mycoblastaceae, Pilocarpaceae, Psoraceae, Ramalinaceae, Scoliciosporaceae, and Squamarinaceae.

  • 19.
    Ekman, Stefan
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Blaalid, Rakel
    The Devil in the Details: Interactions between the Branch-Length Prior and Likelihood Model Affect Node Support and Branch Lengths in the Phylogeny of the Psoraceae2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 4, p. 541-561Article in journal (Refereed)
    Abstract [en]

    In popular use of Bayesian phylogenetics, a default branch-length prior is almost universally applied without knowing how a different prior would have affected the outcome. We performed Bayesian and maximum likelihood (ML) inference of phylogeny based on empirical nucleotide sequence data from a family of lichenized ascomycetes, the Psoraceae, the morphological delimitation of which has been controversial. We specifically assessed the influence of the combination of Bayesian branch-length prior and likelihood model on the properties of the Markov chain Monte Carlo tree sample, including node support, branch lengths, and taxon stability. Data included two regions of the mitochondrial ribosomal RNA gene, the internal transcribed spacer region of the nuclear ribosomal RNA gene, and the protein-coding largest subunit of RNA polymerase II. Data partitioning was performed using Bayes' factors, whereas the best-fitting model of each partition was selected using the Bayesian information criterion (BIC). Given the data and model, short Bayesian branch-length priors generate higher numbers of strongly supported nodes as well as short and topologically similar trees sampled from parts of tree space that are largely unexplored by the ML bootstrap. Long branch-length priors generate fewer strongly supported nodes and longer and more dissimilar trees that are sampled mostly from inside the range of tree space sampled by the ML bootstrap. Priors near the ML distribution of branch lengths generate the best marginal likelihood and the highest frequency of "rogue" (unstable) taxa. The branch-length prior was shown to interact with the likelihood model. Trees inferred under complex partitioned models are more affected by the stretching effect of the branch-length prior. Fewer nodes are strongly supported under a complex model given the same branch-length prior. Irrespective of model, internal branches make up a larger proportion of total tree length under the shortest branch-length priors compared with longer priors. Relative effects on branch lengths caused by the branch-length prior can be problematic to downstream phylogenetic comparative methods making use of the branch lengths. Furthermore, given the same branch-length prior, trees are on average more dissimilar under a simple unpartitioned model compared with a more complex partitioned models. The distribution of ML branch lengths was shown to better fit a gamma or Pareto distribution than an exponential one. Model adequacy tests indicate that the best-fitting model selected by the BIC is insufficient for describing data patterns in 5 of 8 partitions. More general substitution models are required to explain the data in three of these partitions, one of which also requires nonstationarity. The two mitochondrial ribosomal RNA gene partitions need heterotachous models. We found no significant correlations between, on the one hand, the amount of ambiguous data or the smallest branch-length distance to another taxon and, on the other hand, the topological stability of individual taxa. Integrating over several exponentially distributed means under the best-fitting model, node support for the family Psoraceae, including Psora, Protoblastenia, and the Micarea sylvicola group, is approximately 0.96. Support for the genus Psora is distinctly lower, but we found no evidence to contradict the current classification.

  • 20.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Svennblad, Bodil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Britton, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics2003In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 52, no 5, p. 665-673Article in journal (Refereed)
    Abstract [en]

    Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so.

  • 21.
    Frajman, Bozo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating2009In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 58, no 3, p. 328-345Article in journal (Refereed)
    Abstract [en]

    We used four potentially unlinked nuclear DNA regions from the gene   family encoding the second largest subunit of the RNA polymerases, as   well as the psbE-petG spacer and the rps16 intron from the chloroplast   genome, to evaluate the origin of and relationships within Heliosperma   (Sileneae, Caryophyllaceae). Relative dates of divergence times are   used to discriminate between hybridization and gene duplication/loss as   alternative explanations for topological conflicts between gene trees.   The observed incongruent relationships among the three major lineages   of Heliosperma are better explained by homoploid hybridization than by   gene duplication/losses because species branching events exceed gene   coalescence times under biologically reasonable population sizes and   generation times, making lineage sorting an unlikely explanation. The  origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have   been involved in the origin of Heliosperma, one most closely related to   the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

  • 22.
    Grimm, Guido
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Kapli, Paschalia
    3Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece.
    Bomfleur, Benjamin
    Swedish Museum of Natural History, Department of Paleobiology.
    McLoughlin, Stephen
    Swedish Museum of Natural History, Department of Paleobiology.
    Renner, Susanne
    Using more than the oldest fossils: Dating Osmundaceae with three Bayesian clock approaches2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 396-405Article in journal (Refereed)
    Abstract [en]

    A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved—“node dating” (ND) inBEAST, “total evidence” (TE) dating in MrBayes, and the “fossilized birth–death” (FBD) in FDPPDiv—to infer divergence times in the royal ferns. Osmundaceae have 16–17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils,we included up to 36 rhizomes and frond compression/impression fossils, which for TE datingwere scored for 33morphological characters.We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution.

  • 23.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Krause, Johannes
    Sawyer, Susanna
    Valente, Luis M.
    Bailey, Sebastian
    Finstermeier, Knut
    Sabin, Richard
    Gilissen, Emmanuel
    Sonet, Gontran
    Nagy, Zoltan T.
    Lenglet, Georges
    Mayer, Frieder
    Savolainen, Vincent
    Next-Generation Museomics Disentangles One of the Largest Primate Radiations2013In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 62, no 4, p. 539-554Article in journal (Refereed)
    Abstract [en]

    Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA data set from museum specimens, we document how NGS technologies can “unlock” museum collections, thereby helping to unravel the tree-of-life. [Museum collection; next-generation DNA sequencing; primate radiation; speciation; target capture.]

  • 24.
    Hansen, T. F.
    et al.
    Oslo University.
    Bartoszek, Krzysztof
    Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg.
    Interpreting the evolutionary regression: The interplay between observational and biological errors in phylogenetic comparative studies2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, p. 413-425Article in journal (Refereed)
    Abstract [en]

    Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations fromthe estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicatingthat they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation inregression studies. In particular, we discuss the interplay of biological deviations with deviations due to observationalor measurement errors, which are also important in comparative studies based on estimated species means. We showhow bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and eitherobservational or biological error in the predictor variables. We show how all these biases can be estimated and correctedfor in the presence of phylogenetic correlations.We present general formulas for incorporating measurement error in linearmodels with correlated data. We also show how alternative regression models, such as major axis and reduced major axisregression, which are often recommended when there is error in predictor variables, are strongly biased when there isbiological variation in any part of the model.We argue that such methods should never be used to estimate evolutionary orallometric regression slopes.

  • 25.
    Hansen, Thomas F.
    et al.
    Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway.
    Bartoszek, Krzysztof
    Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden.
    Interpreting the evolutionary regression: The interplay between observational and biological errors in phylogenetic comparative studies2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 3, p. 413-425Article in journal (Refereed)
    Abstract [en]

    Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations fromthe estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicatingthat they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation inregression studies. In particular, we discuss the interplay of biological deviations with deviations due to observationalor measurement errors, which are also important in comparative studies based on estimated species means. We showhow bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and eitherobservational or biological error in the predictor variables. We show how all these biases can be estimated and correctedfor in the presence of phylogenetic correlations.We present general formulas for incorporating measurement error in linearmodels with correlated data. We also show how alternative regression models, such as major axis and reduced major axisregression, which are often recommended when there is error in predictor variables, are strongly biased when there isbiological variation in any part of the model.We argue that such methods should never be used to estimate evolutionary orallometric regression slopes.

  • 26.
    Höhna, Sebastian
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics.
    Drummond, Alexei J.
    Guided Tree Topology Proposals for Bayesian Phylogenetic Inference2012In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 61, no 1, p. 1-11Article in journal (Refereed)
    Abstract [en]

    Increasingly, large data sets pose a challenge for computationally intensive phylogenetic methods such as Bayesian Markov chain Monte Carlo (MCMC). Here, we investigate the performance of common MCMC proposal distributions in terms of median and variance of run time to convergence on 11 data sets. We introduce two new Metropolized Gibbs Samplers for moving through tree space. MCMC simulation using these new proposals shows faster average run time and dramatically improved predictability in performance, with a 20-fold reduction in the variance of the time to estimate the posterior distribution to a given accuracy. We also introduce conditional clade probabilities and demonstrate that they provide a superior means of approximating tree topology posterior probabilities from samples recorded during MCMC.

  • 27.
    Höhna, Sebastian
    et al.
    Stockholms universitet.
    Heath, Tracy A.
    Boussau, Bastien
    Landis, Michael J.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Huelsenbeck, John P.
    Probabilistic graphical model representation in phylogenetics2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 753-771Article in journal (Refereed)
    Abstract [en]

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis–Hastings or Gibbs sampling of the posterior distribution.

  • 28.
    Höhna, Sebastian
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics. University of California, USA.
    Heath, Tracy A.
    Boussau, Bastien
    Landis, Michael J.
    Ronquist, Fredrik
    Huelsenbeck, John P.
    Probabilistic Graphical Model Representation in Phylogenetics2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 753-771Article in journal (Refereed)
    Abstract [en]

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution.

  • 29.
    Höhna, Sebastian
    et al.
    Stockholm University, Faculty of Science, Department of Mathematics. University of California, USA.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 726-736Article in journal (Refereed)
    Abstract [en]

    Programs for Bayesian inference of phylogeny currently implement a unique and inot signxed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be speciinot signed interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-speciinot signcation language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous inot sign,exibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our inot signeld. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at ext-link-type=uri xlink:href=http://www.RevBayes.com>http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.].

  • 30. Höhna, Sebastian
    et al.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 726-736Article in journal (Refereed)
  • 31. Jondelius, Ulf
    et al.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hooge, Matthew
    Raikova, Olga I.
    How the Worm Got its Pharynx: Phylogeny, Classification and Bayesian Assessment of Character Evolution in Acoela2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 6, p. 845-871Article in journal (Refereed)
    Abstract [en]

    Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.

  • 32. Klopfstein, Seraina
    et al.
    Vilhelmsen, Lars
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1089-1103Article in journal (Refereed)
  • 33.
    Kocot, Kevin
    et al.
    University of Alabama.
    Struck, Torsten
    Natural History Museum, Department of Research and Collections, University of Oslo.
    Merkel, Julia
    Johannes Gutenberg University.
    Waits, Damien
    Auburn University.
    Todt, Christiane
    University Museum of Bergen.
    Brannock, Pamela
    Auburn University.
    Weese, David
    Auburn University.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Moroz, Leonid
    The Whitney Laboratory for Marine Bioscience.
    Lieb, Bernhard
    Johannes Gutenberg University.
    Halanych, Kenneth
    Auburn University.
    Phylogenomics of Lophotrochozoa with consideration of systematic error2017In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 66, no 2, p. 256-282Article in journal (Refereed)
    Abstract [en]

    Phylogenomic studies have improved understanding of deep metazoan phylogeny and show promise for resolving incongruences among analyses based on limited numbers of loci. One region of the animal tree that has been especially difficult to resolve, even with phylogenomic approaches, is relationships within Lophotrochozoa (the animal clade that includes molluscs, annelids, and flatworms among others). Lack of resolution in phylogenomic analyses could be due to insufficient phylogenetic signal, limitations in taxon and/or gene sampling, or systematic error. Here, we investigated why lophotrochozoan phylogeny has been such a difficult question to answer by identifying and reducing sources of systematic error. We supplemented existing data with 32 new transcriptomes spanning the diversity of Lophotrochozoa and constructed a new set of Lophotrochozoa-specific core orthologs. Of these, 638 orthologous groups (OGs) passed strict screening for paralogy using a tree-based approach. In order to reduce possible sources of systematic error, we calculated branch-length heterogeneity, evolutionary rate, percent missing data, compositional bias, and saturation for each OG and analyzed increasingly stricter subsets of only the most stringent (best) OGs for these five variables. Principal component analysis of the values for each factor examined for each OG revealed that compositional heterogeneity and average patristic distance contributed most to the variance observed along the first principal component while branch-length heterogeneity and, to a lesser extent, saturation contributed most to the variance observed along the second. Missing data did not strongly contribute to either. Additional sensitivity analyses examined effects of removing taxa with heterogeneous branch lengths, large amounts of missing data, and compositional heterogeneity. Although our analyses do not unambiguously resolve lophotrochozoan phylogeny, we advance the field by reducing the list of viable hypotheses. Moreover, our systematic approach for dissection of phylogenomic data can be applied to explore sources of incongruence and poor support in any phylogenomic dataset. 

  • 34. Linder, Martin
    et al.
    Britton, Tom
    Stockholm University, Faculty of Science, Department of Mathematics.
    Sennblad, Bengt
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Evaluation of Bayesian Models of Substitution Rate Evolution-Parental Guidance versus Mutual Independence2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 3, p. 329-342Article in journal (Refereed)
    Abstract [en]

    We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.

  • 35.
    Linder, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Britton, Tom
    Sennblad, Bengt
    Evaluation of Bayesian Models of Substitution Rate Evolution-Parental Guidance versus Mutual Independence2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 3, p. 329-342Article in journal (Refereed)
    Abstract [en]

    We have evaluated the performance of two classes of probabilistic models for substitution rate variation over phylogenetic trees. In the first class, branch rates are considered to be independent and identically distributed (i.i.d.) stochastic variables. Three versions with respect to the underlying distribution (Gamma, Inverse Gaussian, and LogNormal) are considered. The i.i.d. models are compared with the autocorrelated (AC) model, where rates of adjacent nodes in the tree are AC, so that a node rate is LogNormal distributed around the rate of the parent node. The performance of different models is evaluated using three empirical data sets. For all data sets, it was clear that all tested models extracted substantial knowledge from data when posterior divergence time distributions were compared with the prior distributions and, furthermore, that they clearly outperformed a molecular clock. Moreover, the descriptive power of the i.i.d. models, as evaluated by Bayes factors, was either equal to or clearly better than that of the AC model. The latter effect increased with extended taxon sampling. Likewise, under none of the models could we find compelling evidence, in any of the data sets, for rate correlation between adjacent branches/nodes. These findings challenge previous suggestions of universality of autocorrelation in sequence evolution. We also performed an additional comparison with a divergence time prior including calibration information from fossil evidence. Adding fossil information to the prior had negligible effect on Bayes factors and mainly affected the width of the posterior distribution of the divergence times, whereas the relative position of the mean divergence times were largely unaffected.

  • 36.
    Mindell, David P
    et al.
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Sorenson, Michael D
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Dimcheff, Derek E
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Hasegawa, M
    Ast, Jennifer C
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Yuri, Tamaki
    University of Michigan, Museum of Zoology and Department of Ecology and Evolutionary Biology.
    Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes1999In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 48, p. 138-152Article in journal (Refereed)
  • 37.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Aristotle’s Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. — By J. David Archibald2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 5, p. 892-895Article, book review (Other academic)
  • 38.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 39.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals. By Paul Sanghera2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 40.
    Morrison, David A.
    Section for Parasitology, Swedish University of Agricultural Sciences.
    Is the tree of life the best metaphor, model, or heuristic for phylogenetics?2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 4, p. 628-638Article in journal (Refereed)
  • 41.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Multiple Sequence Alignment Methods — Edited by David J. Russell2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 4, p. 690-692Article, book review (Other academic)
  • 42.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Taxonomy of Australian Mammals. By Stephen Jackson and Colin Groves2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 2, p. 346-348Article, book review (Other academic)
  • 43.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Biology and Identification of the Coccidia (Apicomplexa) of Marsupials of the World. Donald W. Duszynski.2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 722-724Article, book review (Other academic)
  • 44.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Book of Trees: Visualizing Branches of Knowledge — By Manuel Lima. Design for Information: an Introduction to the Histories, Theories, and Best Practices Behind Effective Information Visualizations. — By Isabel Meirelles.2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 363-365Article, book review (Other academic)
  • 45.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Invention of Nature: The Adventures of Alexander von Humboldt, the Lost Hero of Science (UK). The Invention of Nature: Alexander von Humboldt’s New World (USA). By Andrea Wulf2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 6, p. 1117-1119Article, book review (Other academic)
  • 46.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Monkey’s voyage: how improbable journeys shaped the history of life. €”by Alan de Queiroz.2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 847-849Article in journal (Other academic)
  • 47.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Tree of Life: Evolution and Classification of Living Organisms .—Edited by Pablo Vargas and Rafael Zardoya; translated by Anne Louise2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 546-548Article, book review (Other academic)
  • 48.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Understanding Evolution .— By Kostas Kampourakis2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1121-1122Article, book review (Other academic)
  • 49.
    Nater, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kawakami, Takeshi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1000-1017Article in journal (Refereed)
    Abstract [en]

    Using genetic data to resolve the evolutionary relationships of species is of major interest in evolutionary and systematic biology. However, reconstructing the sequence of speciation events, the so-called species tree, in closely related and potentially hybridizing species is very challenging. Processes such as incomplete lineage sorting and interspecific gene flow result in local gene genealogies that differ in their topology from the species tree, and analyses of few loci with a single sequence per species are likely to produce conflicting or even misleading results. To study these phenomena on a full phylogenomic scale, we use whole-genome sequence data from 200 individuals of four black-and-white flycatcher species with so far unresolved phylogenetic relationships to infer gene tree topologies and visualize genome-wide patterns of gene tree incongruence. Using phylogenetic analysis in nonoverlapping 10-kb windows, we show that gene tree topologies are extremely diverse and change on a very small physical scale. Moreover, we find strong evidence for gene flow among flycatcher species, with distinct patterns of reduced introgression on the Z chromosome. To resolve species relationships on the background of widespread gene tree incongruence, we used four complementary coalescent-based methods for species tree reconstruction, including complex modeling approaches that incorporate post-divergence gene flow among species. This allowed us to infer the most likely species tree with high confidence. Based on this finding, we show that regions of reduced effective population size, which have been suggested as particularly useful for species tree inference, can produce positively misleading species tree topologies. Our findings disclose the pitfalls of using loci potentially under selection as phylogenetic markers and highlight the potential of modeling approaches to disentangle species relationships in systems with large effective population sizes and post-divergence gene flow.

  • 50.
    Nylander, Johan A. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Olsson, Urban
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Zoology.
    Sanmartin, Isabel
    Accounting for phylogenetic uncertainty in biogeography: A Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves2008In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 57, no 2, p. 257-268Article in journal (Refereed)
    Abstract [en]

    The phylogeny of the thrushes (Aves: Turdus) has been difficult to reconstruct due to short internal branches and lack of node support for certain parts of the tree. Reconstructing the biogeographic history of this group is further complicated by the fact that current implementations of biogeographic methods, such as dispersal-vicariance analysis (DIVA; Ronquist, 1997), require a fully resolved tree. Here, we apply a Bayesian approach to dispersal-vicariance analysis that accounts for phylogenetic uncertainty and allows a more accurate analysis of the biogeographic history of lineages. Specifically, ancestral area reconstructions can be presented as marginal distributions, thus displaying the underlying topological uncertainty. Moreover, if there are multiple optimal solutions for a single node on a certain tree, integrating over the posterior distribution of trees often reveals a preference for a narrower set of solutions. We find that despite the uncertainty in tree topology, ancestral area reconstructions indicate that the Turdus clade originated in the eastern Palearctic during the Late Miocene. This was followed by an early dispersal to Africa from where a worldwide radiation took place. The uncertainty in tree topology and short branch lengths seems to indicate that this radiation took place within a limited time span during the Late Pliocene. The results support the role of Africa as a probable source area for intercontinental dispersals as suggested for other passerine groups, including basal diversification within the songbird tree.

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