Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking

Howell, Neil; Howell, Corinna; Elson, Joanna L.

doi:10.1038/hdy.2008.52

Cited by 28 publications

(22 citation statements)

References 11 publications

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“…IM; mismatch distributions – see below) provide strong support for the HPD rate estimate, and for the similar molecular rates calculated from other species over Holocene timeframes and from pedigree data [16]–[18],[23],[24]. Although controversial [25],[26], as they are an order of magnitude or more faster than ‘traditional’ substitution rate estimates derived from interspecific phylogenetic datasets or the fossil record [24], these high intraspecific estimates have been quite consistent and are now well supported [16]–[18],[23],[24],[26].…”

Section: Resultssupporting

confidence: 63%

Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

et al. 2009

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Environmental change drives demographic and evolutionary processes that determine diversity within and among species. Tracking these processes during periods of change reveals mechanisms for the establishment of populations and provides predictive data on response to potential future impacts, including those caused by anthropogenic climate change. Here we show how a highly mobile marine species responded to the gain and loss of new breeding habitat. Southern elephant seal, Mirounga leonina, remains were found along the Victoria Land Coast (VLC) in the Ross Sea, Antarctica, 2,500 km from the nearest extant breeding site on Macquarie Island (MQ). This habitat was released after retreat of the grounded ice sheet in the Ross Sea Embayment 7,500–8,000 cal YBP, and is within the range of modern foraging excursions from the MQ colony. Using ancient mtDNA and coalescent models, we tracked the population dynamics of the now extinct VLC colony and the connectivity between this and extant breeding sites. We found a clear expansion signal in the VLC population ∼8,000 YBP, followed by directional migration away from VLC and the loss of diversity at ∼1,000 YBP, when sea ice is thought to have expanded. Our data suggest that VLC seals came initially from MQ and that some returned there once the VLC habitat was lost, ∼7,000 years later. We track the founder-extinction dynamics of a population from inception to extinction in the context of Holocene climate change and present evidence that an unexpectedly diverse, differentiated breeding population was founded from a distant source population soon after habitat became available.

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Section: Resultssupporting

confidence: 63%

Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

et al. 2009

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“…The use of molecular clocks has been extensively debated; for details see Bromham and Penny (2003), Hedges and Kumar (2003), Graur and Martin (2004), Bandelt (2008), Ho and Larson (2006) and Howell and Howell (2008). We acknowledge the uncertainties surrounding calibration points and estimated times of divergence should be interpreted with much caution.…”

Section: Phylogenetic Analysis and Datingmentioning

confidence: 96%

Did dung beetles arise in Africa? A phylogenetic hypothesis based on five gene regions

Sole

Scholtz

2010

Molecular Phylogenetics and Evolution

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“…Furthermore, non-synonymous substitutions were shown to be more frequent in terminal branches of the human mtDNA tree [22], [23], [24] and in younger clades compared to older clades [25]. There appears to be a continuous change in the mtDNA substitution rate with the slowest rate in between humans and apes, intermediate rate among human populations and the highest rate in pedigrees [13], [26].…”

Section: Introductionmentioning

confidence: 94%

“…Until recently, a linear molecular clock for the human mtDNA has been assumed and applied for dating the nodes of the tree [9]. On the other hand, time-dependence of the rate of accumulation of new mutations has been proposed based on several lines of evidence [10], [11], [12], [13], [14], [15], [16]. Notably, the phrase “accumulation of new mutations” can refer to different levels of genetic variation: it can be related to DNA replication errors left unrepaired in meiosis (observed in pedigree studies), however, in population studies it refers to the level of polymorphism and in interspecies comparisons to the number of fixed differences.…”

Section: Introductionmentioning

confidence: 99%

Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria

et al. 2009

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The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age.

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Molecular clock debate: Time dependency of molecular rate estimates for mtDNA: this is not the time for wishful thinking

Cited by 28 publications

References 11 publications

Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

Rapid Response of a Marine Mammal Species to Holocene Climate and Habitat Change

Did dung beetles arise in Africa? A phylogenetic hypothesis based on five gene regions

Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria

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