Rates and patterns of chloroplast DNA evolution.

Clegg, Michael T.; Gaut, Brandon S.; Learn, Gerald H.; Morton, Brian R.

doi:10.1073/pnas.91.15.6795

Cited by 392 publications

(303 citation statements)

References 44 publications

(43 reference statements)

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“…Furthermore, the only significant recent migration detected is from southwestern Europe into Central Europe, and not the other way around. Unless we posit that the Iberia-specific genetic variation evolved rapidly since an introduction (and this is unlikely due to the low mutation rate of cpDNA (Clegg et al, 1994)), the genetic diversity observed in Iberian populations is not compatible with introduction from Central Europe.…”

Section: Discussionmentioning

confidence: 99%

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Fuentes-Utrilla¹,

Venturas²,

Hollingsworth³

et al. 2013

Heredity

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Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France.

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Section: Discussionmentioning

confidence: 99%

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Fuentes-Utrilla¹,

Venturas²,

Hollingsworth³

et al. 2013

Heredity

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“…We included all insertion or deletion events (indels) in our data set and coded them as either present or absent. We are aware that non-coding regions of the cpDNA are prone to repeated independent evolution of the same indels (Clegg et al 1994). Independently derived indels probably had little e¡ect on our topology because ¢ve out of the seven indels were autapomorphic and the topology of the cpDNA phylogeny when all indels were deleted was almost identical to the topology when all indels were included but it was less well resolved.…”

Section: Methodsmentioning

confidence: 99%

“…Exclusion of these characters did not change the general topological structure of the trees. The nature of the evolution of chloroplast sequences in non-coding regions is complex (Clegg et al 1994), and we sometimes found two to four adjacent bases that appeared to have mutated in tandem. Therefore, we limited the e¡ect of these regions on our phylogenetic estimation by coding them as single changes.…”

Section: Methodsmentioning

confidence: 99%

“…Within species, some cpDNA introns and intragenic spacer regions evolve at a su¤ciently high rate to allow detection of variation (McCauley 1994;Clegg et al 1994). Although mtDNA sequences are largely conserved within plant species, intraspeci¢c mtDNA structural variation often results from intragenomic recombination that generates gene rearrangements (Palmer 1992;Fragoso et al 1989).…”

Section: Introductionmentioning

confidence: 99%

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Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes inSilene vulgaris

Olson

McCauley

2000

Proc. R. Soc. Lond. B

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Both the chloroplast and mitochondrial genomes are used extensively in studies of plant population genetics and systematics. In the majority of angiosperms, the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) are each primarily transmitted maternally, but rare biparental transmission is possible. The extent to which the cpDNA and mtDNA are in linkage disequilibrium is argued to be dependent on the ¢delity of co-transmission and the population structure. This study reports complete linkage disequilibrium between cpDNA and mtDNA haplotypes in 86 individuals from 17 populations of Silene vulgaris, a gynodioecious plant species. Phylogenetic analysis of cpDNA and mtDNA haplotypes within 14 individuals supports a hypothesis that the evolutionary histories of the chloroplasts and mitochondria are congruent within S. vulgaris, as might be expected if this association persists for long periods. This provides the ¢rst documentation of the evolutionary consequences of long-term associations between chloroplast and mitochondrial genomes within a species. Factors that contribute to the phylogenetic and linkage associations, as well as the potential for intergenomic hitchhiking resulting from selection on genes in one organellar genome are discussed.

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“…Likewise, inaccurate calibration will bias the resulting estimates for other divergences. Equally seriously, however, heterogeneous rates of evolution among lineages are well known (3)(4)(5)(6)(7), and a failure to recognize such heterogeneity can compromise resulting estimates of divergence times. Inadequate sampling of taxa, coupled with rate heterogeneity, can compound the problem.…”

mentioning

confidence: 99%

Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

Soltis

Savolainen

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

232

152

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Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are attributed to the inadequacy of the fossil record, but many potential sources of error can affect molecular-based estimates. In this study, we minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes. Age estimates varied because of gene effects, codon position, lineage effects, method of inferring branch lengths, and whether or not rate constancy was assumed. However, even methods designed to ameliorate the effects of rate heterogeneity among lineages could not accommodate the substantially slower rates observed in Marattia ؉ Angiopteris and in the tree ferns. Both of these clades of ferns have undergone dramatic decelerations in their rates of molecular evolution and are ''molecular living fossils,'' consistent with their relative morphological stasis for the past 165-200 million years. Similar discrepancies between the fossil record and molecular-based age estimates noted in other studies may also be explained in part by violations of rate constancy among lineages.

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Rates and patterns of chloroplast DNA evolution.

Abstract: The chloroplast genome (cpDNA) of plants has been a focus of research In plant molecular evolution and systematics. Several features of this genome have facilitated molecular evolutionary analyses. First

Cited by 392 publications

References 44 publications

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes inSilene vulgaris

Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils

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