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36
Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Systematic Biology 54: 936–947
, 2005
"... Abstract.—Deserts are not usually considered biodiversity hotspots, but desert microbiotic crust communities exhibit a rich diversity of both eukaryotic and prokaryotic life forms. Like many communities dominated by microscopic organisms, they defy characterization by traditional species-counting ap ..."
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Abstract.—Deserts are not usually considered biodiversity hotspots, but desert microbiotic crust communities exhibit a rich diversity of both eukaryotic and prokaryotic life forms. Like many communities dominated by microscopic organisms, they defy characterization by traditional species-counting approaches to assessing biodiversity. Here we use exclusive molecular phylodiversity (E) to quantify the amount of evolutionary divergence unique to desert-dwelling green algae (Chlorophyta) in microbiotic crust communities. Given a phylogenetic tree with branch lengths expressed in units of expected substitutions per site, E is the total length of all tree segments representing exclusively desert lineages. Using MCMC to integrate over tree topologies and branch lengths provides 95 % Bayesian credible intervals for phylodiversity measures. We found substantial exclusive molecular phylodiversity based on 18S rDNA data, showing that desert lineages are distantly related to their nearest aquatic relatives. Our results challenge conventional wisdom, which holds that there was a single origin of terrestrial green plants and that green algae are merely incidental visitors rather than indigenous components of desert communities. We identify examples of lineage diversification within deserts and at least 12 separate transitions from aquatic to terrestrial life apart from the most celebrated transition leading to the embryophyte land plants. [Bayesian phylogenetics; biodiversity; exclusive molecular phylodiversity; microbiotic crusts.] Microbiotic crust communities occur worldwide in arid habitats and include diverse photosynthetic and
Mitochondrial and nuclear DNA sequences support a Cretaceous origin of Columbiformes and a dispersal-driven radiation in the Paleogene
- Syst. Biol
, 2007
"... Abstract. — Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 ..."
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Abstract. — Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous,
Trends in morphological evolution in homobasidiomycetes inferred using maximum likelihood: a comparison of binary and multistate approaches. Systematic Biology
"... Abstract. — The homobasidiomycetes is a diverse group of macrofungi that includes mushrooms, puffballs, coral fungi, and other forms. This study used maximum likelihood methods to determine if there are general trends (evolutionary tendencies) in the evolution of fruiting body forms in homobasidiomy ..."
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Abstract. — The homobasidiomycetes is a diverse group of macrofungi that includes mushrooms, puffballs, coral fungi, and other forms. This study used maximum likelihood methods to determine if there are general trends (evolutionary tendencies) in the evolution of fruiting body forms in homobasidiomycetes, and to estimate the ancestral forms of the homobasidiomycetes and euagarics clade. Character evolution was modeled using a published 481-species phylogeny under two character-coding regimes: additive binary coding, using DISCRETE, and multistate (five-state) coding, using MULTISTATE. Inferences regarding trends in character evolution made under binary coding were often in conflict with those made under multistate coding, suggesting that the additive binary coding approach cannot serve as a surrogate for multistate methods. MULTISTATE was used to develop a “minimal ” model of fruiting body evolution, in which the 20 parameters that specify rates of transformations among character states were grouped into the fewest possible rate categories. The minimal model required only four rate categories, one of which is approaching zero, and suggests the following conclusions regarding trends in evolution of homobasidiomycete fruiting bodies: (1) there is an active trend favoring the evolution of pileate-stipitate forms (those with a cap and stalk); (2) the hypothesis that the evolution of gasteroid forms (those with internal spore production, such as puffballs) is irreversible cannot be rejected; and (3) crustlike resupinate forms are not a particularly labile morphology. The latter finding contradicts the conclusions of a previous study that used binary character coding. Ancestral state reconstructions under binary coding suggest that the ancestor of the homobasidiomycetes was
Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Systematic Biology 63:293–308
, 2014
"... Abstract.—A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade’s history and subsequently slowdown in rate as niches become saturated—a so-called “Early Burst.” Although a common pattern in the fossil record, evidence for ..."
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Abstract.—A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade’s history and subsequently slowdown in rate as niches become saturated—a so-called “Early Burst.” Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst—the rate at which phenotypic evolution declines—is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows
Origins of cheating and loss of symbiosis in wild bradyrhizobium.
- J. Evol. Biol.,
, 2010
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Posterior mapping and posterior predictive distributions
- In Statistical methods in molecular
"... ”If we view statistics as a discipline in the service of science, and science as being an attempt to understand (i.e., model) the world around us, then the ability to reveal sensitivity of conclusions from fixed data to various model specifications, all of which are scientifically acceptable, is equ ..."
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”If we view statistics as a discipline in the service of science, and science as being an attempt to understand (i.e., model) the world around us, then the ability to reveal sensitivity of conclusions from fixed data to various model specifications, all of which are scientifically acceptable, is equivalent to the ability to reveal boundaries of scientific uncertainty. When sharp conclusions are not possible without obtaining more information, whether it be more data, new theory, or deeper understanding of existing data and theory, then it must be scientifically valuable and appropriate to expose this sensitivity and thereby direct efforts to seek the particular information needed to sharpen conclusions. ” Rubin [38] 1
Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera). New Phytologist
, 2011
"... Summary • Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, ecological conditions, and geographical context. Here, ..."
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Summary • Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, ecological conditions, and geographical context. Here, we examined two such predictions: that self-compatibility should be associated with the annual life history or extreme climatic conditions. • We analyzed data from a clade of plants remarkable for variation in breeding system, life history and climatic conditions (Oenothera, sections Anogra and Kleinia, Onagraceae). We used a phylogenetic comparative approach and Bayesian or hybrid Bayesian tests to account for phylogenetic uncertainty. Geographic information system (GIS)-based climate data and ecological niche modeling allowed us to quantify climatic conditions. • Breeding system and reproductive life span are not correlated in Anogra and Kleinia. Instead, self-compatibility is associated with the extremes of temperature in the coldest part of the year and precipitation in the driest part of the year. • In the 60 yr since this pattern was anticipated, this is the first demonstration of a relationship between the evolution of self-compatibility and climatic extremes. We discuss possible explanations for this pattern and possible implications with respect to anthropogenic climate change.
Evolutionary breakdown of pollination specialization in a Caribbean plant radiation
- New Phytologist
, 2010
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Habitat use affects morphological diversification in dragon lizards
"... One of the great questions in evolutionary biology concerns the causes of differences in diversity among clades. Ecological factors are often implicated to explain this pattern because the ecological circumstances avail- ..."
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One of the great questions in evolutionary biology concerns the causes of differences in diversity among clades. Ecological factors are often implicated to explain this pattern because the ecological circumstances avail-
The Effects of Flower Color Transitions on Diversification Rates in Morning Glories (Ipomoea
"... In On the Origin of Species, as well as in his other works, Darwin wrote extensively about evolution-ary changes within lineages and their causes. As is well-known, the mechanisms he described were fo- ..."
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In On the Origin of Species, as well as in his other works, Darwin wrote extensively about evolution-ary changes within lineages and their causes. As is well-known, the mechanisms he described were fo-
