The
            <i>Amborella</i>
            Genome and the Evolution of Flowering Plants

Palmer, Jeffrey D.; Ammiraju, Jetty S.S.; Ralph, Paula E.; Rounsley, Steve; Talag, Jason D.; Wanke, Stefan; Wing, Rod A.; Chang, Tien-Hao; Lan, Tianying; Ayyampalayam, Saravanaraj; Burnette, James M.; Farrell, Nina; Walts, Brandon; Wessler, Susan R.; Zhang, Xiaoyu; Lyons, Eric; Sankoff, David; Tang, Haibao; Zheng, Chunfang; Carretero‐Paulet, Lorenzo; Estill, James C.; Jiao, Yuannian; Liu, Kun; Mei, Wenbin; Wafula, Eric; Altman, Naomi; Arikit, Siwaret; Axtell, Michael J.; Chanderbali, André S.; Chen, Feng; Chen, Jian-Qun; Chiang, Vincent L.; Paoli, Emanuele De; Determann, Ronald; Fogliani, Bruno; Guo, Caixia; Harholt, Jesper; Harkess, Alex; Job, Claudette; Job, Dominique; Kim, Sangtae; Kong, Hongzhi; Li, Guanglin; Li, Lin; Liu, Jie; Mā, Hong; Meyers, Blake C.; Park, Jongsun; Qi, Xuchen; Rajjou, Loïc; Burtet‐Sarramegna, Valérie; Sederoff, Ron; Shahid, Saima; Sun, Ying-Hsuan; Ulvskov, Peter; Villegente, Matthieu; Xue, Jia‐Yu; Yeh, Ting‐Feng; Yu, Xianxian; Zhai, Jixian; Acosta, Juan J.; Albert, Victor A.; Barbazuk, W. Bradley; Bruenn, Riva A.; Chamala, Srikar; Kochko, Alexandre de; dePamphilis, Claude W.; Der, Joshua P.; Herrera‐Estrella, Luis; Ibarra-Laclette, Enrique; Kirst, Matias; Leebens‐Mack, James H.; Pissis, Solon P.; Poncet, Valérie; Schuster, Stephan C.; Soltis, Douglas E.; Soltis, Pamela S.; Tomsho, Lynn P.

doi:10.1126/science.1241089

Cited by 752 publications

(413 citation statements)

References 86 publications

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“…In particular, because PSMC is applied to a single diploid genome, it has been used to infer population size histories in numerous species for which one or more genome sequences are available, in many cases finding support for large changes in population size (Groenen et al 2012;Albert et al 2013;Prado-Martinez et al 2013;Zhan et al 2013;Freedman et al 2014;Green et al 2014;Wallberg et al 2014;Auton et al 2015;Lamichhaney et al 2015). Our findings suggest that natural selection may alter the shape of, and inflate the degree of change in, these inferred histories.…”

Section: Discussionmentioning

confidence: 63%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.KEYWORDS population genetics; positive selection; demographic inference T HE widespread availability of population genomic data has spurred a new generation of studies aimed at understanding the histories of natural populations from a host of model and nonmodel organisms alike. In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al. 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al. 2007;Goebel et al. 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al. 2007;Garrick et al. 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 198...

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Section: Discussionmentioning

confidence: 63%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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“…4-7). Although it has been repeatedly noted that polyploidy events correlate with some major plant radiations (2,8,9), the specific roles that tandem duplicates play in species-or lineage-specific plant adaptation remain more poorly explored.…”

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confidence: 99%

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

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

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Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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“…However, because this exemplar analysis does not include genome sequences from basal angiosperms, it cannot distinguish gene families originating before or soon after the earliest diversification of angiosperms. Amborella is thought to be the single living sister species to other extant flowering plants, and the Amborella trichopoda genome, which is finished but not yet available for large-scale analysis, will provide a valuable reference for reconstructing ancestral angiosperm gene content (http://www.amborella.org/) [54].…”

Section: Ancestral Genome Modification At Key Evolutionary Nodesmentioning

confidence: 99%

Polyploidy-associated genome modifications during land plant evolution

Jiao

Paterson

2014

Phil. Trans. R. Soc. B

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The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.

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The Amborella Genome and the Evolution of Flowering Plants

Cited by 752 publications

References 86 publications

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Polyploidy-associated genome modifications during land plant evolution

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