Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice

Yamane, Kyoko; Yano, Kentarô; Kawahara, Takuji

doi:10.1093/dnares/dsl012

Cited by 120 publications

(104 citation statements)

References 31 publications

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“…We used the substitution models reported above and the relaxed molecular clock model (uncorrelated lognormal) for both chloroplast and ITS. For chloroplast regions, we used the substitution rate previously estimated for chloroplast noncoding regions, 1Á52 Â 10 À9 per nucleotide year À1 (Yamane et al, 2006). For ITS, Kay et al (2006) estimated the mutation rates for different Angiospermae families.…”

Section: Phylogeographical Reconstructionmentioning

confidence: 99%

Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary

Lima

Telles

Chaves

et al. 2017

Ann Bot

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Background and Aims Cyclic glaciations were frequent throughout the Quaternary and this affected species distribution and population differentiation worldwide. The present study reconstructed the demographic history and dispersal routes of Eugenia dysenterica lineages and investigated the effects of Quaternary climate change on its spatial pattern of genetic diversity.Methods A total of 333 individuals were sampled from 23 populations and analysed by sequencing four regions of the chloroplast DNA and the internal transcribed spacer of the nuclear DNA. The analyses were performed using a multi-model inference approach based on ecological niche modelling and statistical phylogeography.Key Results Coalescent simulation showed that population stability through time is the most likely scenario. The palaeodistribution dynamics predicted by the ecological niche models revealed that the species was potentially distributed across a large area, extending over Central-Western Brazil through the last glaciation. The lineages of E. dysenterica dispersed from Central Brazil towards populations at the northern, western and south-eastern regions. A historical refugium through time may have favoured lineage dispersal and the maintenance of genetic diversity.Conclusions The results suggest that the central region of the Cerrado biome is probably the centre of distribution of E. dysenterica and that the spatial pattern of its genetic diversity may be the outcome of population stability throughout the Quaternary. The lower genetic diversity in populations in the south-eastern Cerrado biome is probably due to local climatic instability during the Quaternary.

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Section: Phylogeographical Reconstructionmentioning

confidence: 99%

Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary

Lima

Telles

Chaves

et al. 2017

Ann Bot

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“…The effective population size was estimated from the mutation parameter . Time to most recent common ancestor (TMRCA) was estimated based on Bayesian phylogenetic analysis implemented in BEAST 1.7.4 (Drummond & Rambaut 2007), and mutation rates previously estimated for chloroplast non-coding regions were used to get time in years (Yamane et al 2006). We also constrained the basal node to be no older than 55.5 Myr, in the Early Eocene, which corresponds to the earliest known occurrence of the genus Caryocar on the pollen fossil record from Venezuela (Rull 2000).…”

Section: (Caryocaraceae)mentioning

confidence: 99%

Recovering the demographical history of a Brazilian Cerrado tree species Caryocar brasiliense: coupling ecological niche modeling and coalescent analyses

Collevatti¹,

Lima-Ribeira²,

Souza-Neto³

et al. 2012

NatCon

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Here we studied the demographical history of Caryocar brasiliense (Caryocaraceae), by coupling ecological niche modeling (ENM) and statistical phylogeography. Analyses were based on the polymorphism of 147 individuals sampled in 12 populations for the chloroplast genome. C. brasiliense presented low genetic diversity but high population genetic differentiation, which is not correlated with geographical distances among localities. The most ancient lineage divergence from southern and western Cerrado boundaries occurred around ~3.3 ± 2.3 Myr BP. The simulation of demographic scenarios showed that the diversity pattern found so far for C. brasiliense is most likely due to a range retraction during the last glacial maximum (LGM, 21 kyr BP), leading to multiple refugia. The paleodistribution models and coalescent analyses strongly suggest that the current distribution of C. brasiliense is wider than during the dry periods of the Quaternary.

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“…The statistical test [Likelihood ratio = 2 9 (lnL1 -lnL0)], with L0 representing the probability of the null hypothesis and number of degree of freedom n-2 (with n being the number of taxa), was calculated with LRT calculator Mode (optionl) implemented in ModelTest v3.7 (Ratio = 30.497070, this is not significant at the alpha level of 0.0100). Based on the hypothesis of a molecular clock, the divergence time (T) between two lineages was estimated using the sequence divergence and the average rate of nucleotide substitutions by calculating T = DXY/2r where r = 0.8 ± 0.04 9 10-9 mutations per site per year in chloroplast intergenic regions (Yamane et al 2006).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogeography and conservation perspectives of an endangered macaronesian endemic: Picconia azorica (Tutin) Knobl. (Oleaceae)

Ferreira

Piredda

Bagnoli³

et al. 2010

Eur J Forest Res

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AB The Azores provide an excellent field test for research activities aimed\ud at developing conservation strategies for endangered tree species. In\ud this work, the urgency to promote Picconia azorica conservation programs\ud addressed (a) insights into the biotaxonomy of the species (including an\ud evaluation of its origin and relationships with the only congeneric\ud species of P. azorica: P. excelsa from the Canary and Madeira islands)\ud and (b) the evaluation of P. azorica genetic diversity. Plastid DNA\ud sequence analysis and molecular markers (RFLP and SSR) were used for\ud this purpose. Phylogenetic data suggest the monophyly of Picconia and\ud support a late Miocene divergence of the two species. Three polymorphic\ud cpSSR loci allowed the identification of five different haplotypes in P.\ud azorica. Uniqueness and relictuality of lineages are presented and\ud discussed. Picconia azorica intra-specific diversity patterns revealed\ud low genetic diversity and a weak genetic structure, which could result\ud from long-lasting ecological stability and efficient inter-island seed\ud movement that have been severely affected in recent times. The species\ud survival is at risk, and we suggest management practices focusing on ex\ud situ and in situ conservation units based on eco-genetic data.\ud Additional measures contributing to mild erosion of the genepool and to\ud remove barriers to seed dispersal are indicated

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Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice

Cited by 120 publications

References 31 publications

Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary

Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary

Recovering the demographical history of a Brazilian Cerrado tree species Caryocar brasiliense: coupling ecological niche modeling and coalescent analyses

Phylogeography and conservation perspectives of an endangered macaronesian endemic: Picconia azorica (Tutin) Knobl. (Oleaceae)

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