Phylogenetic dating with confidence intervals using mean path lengths

Britton, Tom; Oxelman, Bengt; Vinnersten, Annika; Bremer, Kåre

doi:10.1016/s1055-7903(02)00268-3

Cited by 86 publications

(69 citation statements)

References 11 publications

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“…This appears not to be the case in this analysis (Fig. 2), and it is shown also by MPL analysis (Britton 2002;Britton et al 2002). The slow substitution rates in Rapateaceae and Bromeliaceae and to some extent in Sparganiaceae ϩ Typhaceae compared to the rest of the Poales is remarkable.…”

Section: Agementioning

confidence: 43%

“…The tree with branch lengths was input to mean-path-length (MPL) analysis (Britton 2002;Britton et al 2002) and nonparametric rate smoothing (NPRS; Sanderson 1997Sanderson , 1999. The MPL method is clock based, however, and also incorporates a clock test and a procedure for identifying precisely at which nodes of the tree significant deviations from the molecular clock occur (contrary to standard-likelihood ratio tests which consider the entire tree).…”

Section: Phylogenetic Datingmentioning

confidence: 99%

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Gondwanan Evolution of the Grass Alliance of Families (Poales)

2002

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Abstract. Phylogenetic interrelationships among all 18 families of Poales were assessed by cladistic analysis of chloroplast DNA rbcL and atpB sequences from 65 species. There are two well-supported main clades; the graminoid clade with Poaceae (grasses), Anarthriaceae, Centrolepidaceae, Ecdeiocoleaceae, Flagellariaceae, Joinvilleaceae, and Restionaceae; and the cyperoid clade with Cyperaceae, Juncaceae, and Thurniaceae. A sister group relationship between Poaceae and Ecdeiocoleaceae is identified with strong support. The sister group of this pair is Joinvilleaceae. These relationships help in elucidating the evolution of grasses and the grass spikelet. Dating of the tree was done by nonparametric rate smoothing of rbcL molecular evolution. Most Poales families date back to the Cretaceous Ͼ65 million years ago (mya). Dispersal-vicariance analysis indicates that the Poales originated in South America, the cyperoid clade in West Gondwana (South America or Africa), and the graminoid clade in East Gondwana (Australia). The Trans-Antarctic connection between South America and Australia, and its breakup about 35 mya, probably influenced the evolution of the Poales and the graminoid clade in particular, leading to vicariance between the continents, but the separation of Africa from the other Gondwanan areas, completed about 105 mya, is too old for such a relation.

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Section: Agementioning

confidence: 43%

Section: Phylogenetic Datingmentioning

confidence: 99%

Gondwanan Evolution of the Grass Alliance of Families (Poales)

2002

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“…We therefore carried out parallel analyses based on both models. To calculate confidence intervals for estimates of time since divergence, we used the mean path length method of Britton et al (2002). This method incorporates rate variation between branches into the estimate of uncertainty.…”

Section: Methodsmentioning

confidence: 99%

Phylogeography of the Pantropical Sea Urchin Tripneustes: Contrasting Patterns of Population Structure Between Oceans

2003

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Abstract. To understand how allopatric speciation proceeds, we need information on barriers to gene flow, their antiquity, and their efficacy. For marine organisms with planktonic larvae, much of this information can only be obtained through the determination of divergence between populations. We evaluated the importance of ocean barriers by studying the mitochondrial DNA phylogeography of Tripneustes, a pantropical genus of shallow water sea urchin. A region of cytochrome oxidase I (COI) was sequenced in 187 individuals from locations around the globe. The COI phylogeny agreed with a previously published phylogeny of bindin that barriers important to the evolution of Tripneustes are: (1) the cold water upwelling close to the tip of South Africa, (2) the Isthmus of Panama, (3) the long stretch of deep water separating the eastern from the western Atlantic, and (4) the freshwater plume of the Orinoco and the Amazon rivers between the Caribbean and the coast of Brazil. These barriers have previously been shown to be important in at least a subset of the shallow water marine organisms in which phylogeography has been studied. In contrast, the Eastern Pacific Barrier, 5000 km of deep water between the central and the eastern Pacific that has caused the deepest splits in other genera of sea urchins, is remarkably unimportant as a cause of genetic subdivision in Tripneustes. There is also no discernible subdivision between the Pacific and Indian Ocean populations of this genus. The most common COI haplotype is found in the eastern, central, and western Pacific as well as the Indian Ocean. Morphology, COI, and bindin data agree that T. depressus from the eastern Pacific and T. gratilla from the western Pacific are, in fact, the same species. The distribution of haplotype differences in the Indo-Pacific exhibits characteristics expected from a sea urchin genus with ephemeral local populations, but with high fecundity, dispersal, and growth: there is little phylogenetic structure, and mismatch distributions conform to models of recent population expansion on a nearly global scale. Yet, comparisons between local populations produce large and significant F ST values, indicating nonrandom haplotype distribution. This apparent local differentiation is only weakly reflected in regional divergence, and there is no evidence of isolation by distance in correlations between F ST values and either geographical or current distance. Thus, Tripneustes in the Indo-Pacific (but not in the Atlantic) seems to be one large metapopulation spanning two oceans and containing chaotic, nonequilibrium local variation, produced by the haphazard arrival of larvae or by unpredictable local extinction. To understand how allopatric speciation proceeds, we must deduce the nature, efficacy, and timing of barriers to gene flow between populations. For marine organisms with planktonic larvae, identification of such barriers is difficult, because these propagules disperse to an unknown extent in unpredictable directions. In broad outline, obstacles to di...

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“…An advantage of Bayesian approaches is that 95% confidence intervals around age estimates are directly reported by available software. Another approach that provides confidence intervals around estimates is the mean path length method, which assumes a strict clock but allows multiple calibrations [94].…”

Section: Gnetummentioning

confidence: 99%

Relaxed molecular clocks for dating historical plant dispersal events

Renner

2005

Trends in Plant Science

217

184

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Age estimation from molecular sequences has emerged as a powerful tool for inferring when a plant lineage arrived in a particular area. Knowing the tenure of lineages within a region is key to understanding the evolution of traits, the evolution of biotic interactions, and the evolution of floras. New analytical methods model change in substitution rates along individual branches of a phylogenetic tree by combining molecular data with time constraints, usually from fossils. These 'relaxed clock' approaches can be applied to several gene regions that need not all have the same substitution rates, and they can also incorporate multiple simultaneous fossil calibrations. Since 1995, at least 100 plant biogeographic studies have used molecular-clock dating, and about a fifth has used relaxed clocks. Many of these report evidence of long-distance dispersal. Meta-analyses of studies from the same geographic region can identify directional biases because of prevailing wind or water currents and the relative position and size of landmasses.Inferring past plant dispersal: from which data and why? The geographic ranges of the lineages seen today are often interrupted by large expanses of inhospitable habitat, for example, an ocean. This raises questions about how and when they acquired their disjunct habitats. When lineages arrive in new habitats they will usually diverge and sometimes speciate, therefore, dating dispersal and lineage splits has broad implications for understanding rates of diversification [1], the evolution of biota [2,3] and associated faunas [4][5][6], and the time taken for species to adapt to novel environments [7][8][9][10]. Recent biogeographic studies that have included time estimates have revealed strikingly fast diversification rates in some floras, such as the Cape Region of South Africa, the recency of species accumulation even in ancient lineages, such as ferns [1], and the persistence of precarious mutualisms over many millions of years, such as the interactions between figs and fig wasps and between yucca and yucca moths [4,6].The ideal materials from which to estimate the ages of lineages and their presence in particular places are abundant fossils. However, isolated fossils often provide only screenshots from which we extrapolate in time and space. Extinction followed by recolonization is particularly difficult to infer from the fossil record. It is often more parsimonious to interpret the history of taxa with extended fossil records in a framework of continuity [11,12]. Yet, there is ample direct evidence of rapid species expansions following dispersal from the study of invasive species, phylogeographic molecular data, and natural experiments such as Krakatau, an island sterilized by a massive eruption in 1883 [13][14][15][16].The idea of dating the divergence of lineages from the time-dependent change of their genomes, the molecular clock hypothesis, is 40 years old [17], and plant geographers have applied sequence-or protein-based dating since the 1990s [18][19][20][21][22][23][24][25][...

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Phylogenetic dating with confidence intervals using mean path lengths

Cited by 86 publications

References 11 publications

Gondwanan Evolution of the Grass Alliance of Families (Poales)

Gondwanan Evolution of the Grass Alliance of Families (Poales)

Phylogeography of the Pantropical Sea Urchin Tripneustes: Contrasting Patterns of Population Structure Between Oceans

Relaxed molecular clocks for dating historical plant dispersal events

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