Evidence for Time Dependency of Molecular Rate Estimates

Ho, Simon Y. W.; Shapiro, Beth; Phillips, Matthew J.; Cooper, Alan; Drummond, Alexei J.

doi:10.1080/10635150701435401

Cited by 256 publications

(266 citation statements)

References 69 publications

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“…Smaller fluctuations in the more recent past, especially the lake level drop of *260 m during the last glacial maximum (*20 KYA), also had a profound impact on the current genetic structure of rock-dwelling cichlid species Scholz et al, 2007;McGlue et al, 2008). We have previously noted difficulties in aligning molecular datings of population divergence and growth with the geological datings of lake level fluctuations (Koblmüller et al, 2011;Sefc et al, 2016); in particular, the age of recent demographic events may be overestimated due to the potential time dependency of the molecular clock (Ho et al, 2007) in combination with comparatively ancient calibration points ) and large confidence intervals around substitution rates inferred from recent events (Genner et al, 2010b). In this light, although the reconstructed dates do not match exactly, divergence between A. compressiceps and A. calvus and the first wave of population expansion in A. compressiceps may be connected with lake level fluctuations during the megadroughts, and the more recent population size expansions in A. compressiceps and A. calvus may be associated with fluctuations during the last glacial maximum.…”

Section: Recently Diverged Species With Similar Demographic Historiesmentioning

confidence: 99%

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

et al. 2016

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Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, 'isolation-with-migration' models indicated that divergence between the two Altolamprologus species was recent (67-142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.

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Section: Recently Diverged Species With Similar Demographic Historiesmentioning

confidence: 99%

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

et al. 2016

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“…However, it has been argued that the clock rate slows down with time owing to purifying selection [13], which would result in an underestimate of the time to the most recent common ancestor (tMRCA). This concept has received little attention for bacteria, although it may apply to Helicobacter pylori.…”

Section: Introductionmentioning

confidence: 99%

How old are bacterial pathogens?

Achtman¹

2016

Proc. R. Soc. B.

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Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori , which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis , the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis . Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.

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“…Using this approach, a decay in nucleotide substitution rates with time has been identified across the population-species transition [3,4]. However, both the magnitude and the timing of any decay are hotly contested [5 -7], with particular focus on errors that may arise from the use of ancient DNA sequences to infer molecular rates [8 -10].…”

Section: Introductionmentioning

confidence: 99%

Post-glacial partitioning of mitochondrial genetic variation in the field vole

Herman

Searle

2011

Proc. R. Soc. B.

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Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12 000 years BP) rather than the Last Glacial Maximum (LGM, ca 24 000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 Â 10 27 substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.

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Evidence for Time Dependency of Molecular Rate Estimates

Cited by 256 publications

References 69 publications

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

How old are bacterial pathogens?

Post-glacial partitioning of mitochondrial genetic variation in the field vole

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