Impact of Ice Ages on the genetic structure of trees and shrubs

Lascoux, Martin; Palmé, Anna; Cheddadi, Rachid; Latta, Robert G.

doi:10.1098/rstb.2003.1390

Cited by 116 publications

(109 citation statements)

References 45 publications

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“…3c and Supplementary Table 16). This probably reflects allopatric division during the last Ice Age, followed by subsequent admixture when the two populations rejoined after ice-sheet retreat, as has been suggested on the basis of chloroplast DNA evidence 25 . The small number of ancestral populations is probably due to the high degree of interbreeding within birch populations; as a wind-pollinated species, birch pollen can spread more than 1,000 km 26 .…”

Section: 6mentioning

confidence: 61%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

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Forest ecosystems maintain a large share of Northern Hemisphere biodiversity. Boreal forests comprise roughly 30% of global forest area 1 and contain the highest tree density among climate zones 2 . Moreover, boreal regions are undergoing extensive climate change. Annual temperature increases exceeding 1.5 °C are projected to result in a warming of 4-11 °C by the end of this century, with little concomitant increase in precipitation 1 . At this pace, climate zones will shift northward at a greater speed than trees can migrate 3 . To understand how future populations of forest trees may respond to climate change, it is essential to uncover past and present signatures of molecular adaptation in their genomes. Silver birch, B. pendula, is a pioneer species in boreal forests of Eurasia. Flowering of the species can be artificially accelerated 4 , giving it an advantage over other tree species with published genome sequences (such as poplar 5 , spruce 6 , and pine 7 ) for the optimization of fiber and biomass production.Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch.Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightlylinked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.A full list of affiliations appears at the end of the paper.

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Section: 6mentioning

confidence: 61%

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi¹,

Smolander²,

Nieminen³

et al. 2017

Nat Genet

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237

253

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“…While these arguments have previously been put forward (e.g. Lascoux et al 2004), data to support these claims remained scarce, at least in plants, and were largely absent in forest trees until recently.…”

Section: Introductionmentioning

confidence: 95%

Past demography in forest trees: what can we learn from nuclear DNA sequences that we do not already know?

Lascoux

Pyhäjärvi

Källman

et al. 2008

Plant Ecology & Diversity

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Acquiring nuclear DNA sequences in forest tree species is becoming easier as molecular tools are developing rapidly and we now have at our disposal an array of theoretical methods to carry out statistical inferences from multilocus sequence variation. In the present article we use results from two recent studies of nuclear DNA sequence polymorphism in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) to illustrate what additional insights to each species' history can be gained compared with classical phylogeographic studies based on chloroplast or mitochondrial DNA. The sampling schemes and statistical analyses used in these two studies were similar facilitating a comparison between them. In both cases we inferred the presence of a rather severe bottleneck predating the Last Glacial Maximum (∼18,000 years ago). This result is discussed in relation to recent reassessments of the fossil pollen record and to its implication for our understanding of adaptation. Finally we briefly outline some suggestions for future research.

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“…Using DNA information, Petit et al (2002) have been able to describe in detail the spread of oak into northern Europe. Synthesis involving both fossil pollen and modern genetic data offers considerable potential for the future (Lascoux et al 2004). Distribution change of species on subcontinental and continental scales involves, potentially, an enormous increase in the numbers of individuals constituting the species concerned.…”

Section: (C) Stasismentioning

confidence: 99%

Continuing the debate on the role of Quaternary environmental change for macroevolution

Bennett

2004

Phil. Trans. R. Soc. Lond. B

100

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The Quaternary has been a period of dramatic environmental change for the past 1.8 Myr, with major shifts in distributions and abundances of terrestrial and marine organisms. The evolutionary consequences of this have been debated since the nineteenth century. However, the lack of accurate relative and absolute time-scales for evolutions and environmental change inhibited progress. We do now have an understanding of time-scales. Palaeoecology has demonstrated the individualistic nature of species' response to environmental change, but lacks a means of determining ancestry. DNA characterization of modern populations in relation to their distributions nicely complements palaeoecological results by contributing ancestry. The chance to understand how species originate and the causal factors of speciation (environmental change or otherwise) may be within reach.

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Impact of Ice Ages on the genetic structure of trees and shrubs

Cited by 116 publications

References 45 publications

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Past demography in forest trees: what can we learn from nuclear DNA sequences that we do not already know?

Continuing the debate on the role of Quaternary environmental change for macroevolution

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