Polyploidy can Confer Superiority to West African Acacia senegal (L.) Willd. Trees

Diallo, Adja Madjiguene; Nielsen, Lene Rostgaard; Kjær, Erik Dahl; Petersen, Karen Koefoed; Ræbild, Anders

doi:10.3389/fpls.2016.00821

Cited by 35 publications

(31 citation statements)

References 55 publications

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“…Under both scenarios, the relative fraction of polyploid DOs surviving at the end of the experiment increased with increasing levels of food removal, overcoming the population of nonpolyploid DOs when the environmental challenge introduced in terms of food reduction was strong enough. Taken as whole, these results suggest that WGDs are usually maladaptive under stable environments, but may actually confer an adaptive advantage under certain environmental constraints, which seems in agreement with recent 'real-life' observations (6,(27)(28)(29).…”

Section: Discussionsupporting

confidence: 90%

Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution

Yao

Carretero‐Paulet

Peer

2019

Preprint

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The potential role of whole genome duplication (WGD) in evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary 'dead end', there is growing evidence that the long-term establishment of polyploidy might be linked to environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete non-polyploids at times of environmental upheaval remain indefinable. Here, we improved our recently developed bio-inspired framework, combining an artificial genome with an agent-based system, to form a population of so-called Digital Organisms (DOs), to examine the impact of WGD on evolution under different environmental scenarios mimicking extinction events of varying strength and frequency. We found that, under stable environments, DOs with non-duplicated genomes formed the majority, if not all, of the population, whereas the numbers of DOs with duplicated genomes increased under dramatically challenging environments. After tracking the evolutionary trajectories of individual artificial genomes in terms of sequence and encoded gene regulatory networks (GRNs), we propose that increased complexity, modularity, and redundancy of duplicated GRNs might provide DOs with increased adaptive potential under extinction events, while ensuring mutational robustness of the whole GRN. Our results confirm the usefulness of our computational simulation in studying the role of WGD in evolution and adaptation, helping to overcome the traditional limitations of evolution experiments with model organisms, and provide some additional insights into how genome duplication might help organisms to compete for novel niches and survive ecological turmoil.

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Section: Discussionsupporting

confidence: 90%

Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution

Yao

Carretero‐Paulet

Peer

2019

Preprint

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“…Several studies have suggested that polyploids often have a greater chance to survive an extreme environment compared to diploids because they can undergo rapid morphological innovation [5,22,41,42,43,44]. As a pantropical genus, Ceratopteris displays greater heat tolerance and intolerance to cooler temperatures than the temperate taxon [45].…”

Section: Discussionmentioning

confidence: 99%

Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates

Zhang

Wang

Zhang

et al. 2019

IJMS

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Whole-genome duplications (WGDs) are widespread in plants and frequently coincide with global climatic change events, such as the Cretaceous–Tertiary (KT) extinction event approximately 65 million years ago (mya). Ferns have larger genomes and higher chromosome numbers than seed plants, which likely resulted from multiple rounds of polyploidy. Here, we use diploid and triploid material from a model fern species, Ceratopteris thalictroides, for the detection of WGDs. High-quality RNA-seq data was used to infer the number of synonymous substitutions per synonymous site (Ks) between paralogs; Ks age distribution and absolute dating approach were used to determine the age of WGD events. Evidence of an ancient WGD event with a Ks peak value of approximately 1.2 was obtained for both samples; however, the Ks frequency distributions varied significantly. Importantly, we dated the WGD event at 51–53 mya, which coincides with the Paleocene-Eocene Thermal Maximum (PETM), when the Earth became warmer and wetter than any other period during the Cenozoic. Duplicate genes were preferentially retained for specific functions, such as environment response, further support that the duplicates may have promoted quick adaption to environmental changes and potentially resulted in evolutionary success, especially for pantropical species, such as C. thalictroides, which exhibits higher temperature tolerance.

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“…Polyploidization, the duplication of entire genomes either via hybridization between different species (allopolyploidy) or within single species (autopolyploidy), is recognized as an important mode of speciation especially in plants (Estep et al ., 2014; Vamosi et al ., 2018). Polyploids are suggested to have higher genome plasticity (Leitch & Leitch, 2008) allowing adaptation to different environments in both plants (Leitch & Leitch, 2008; te Beest et al ., 2012; Diallo et al ., 2016; Han et al ., 2020) and animals (Schoenfelder & Fox, 2015). Thus, polyploidization can be a first step in ecological speciation and adaptive radiation (Rundle & Nosil, 2005).…”

Section: Major Speciation Models Of Tropical African Biodiversitymentioning

confidence: 99%

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

et al. 2020

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Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid‐Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo‐climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo‐climatic factors impacting the diversification of the sub‐Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

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Polyploidy can Confer Superiority to West African Acacia senegal (L.) Willd. Trees

Cited by 35 publications

References 55 publications

Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution

Using digital organisms to investigate the effect of whole genome duplication in (artificial) evolution

Dating Whole Genome Duplication in Ceratopteris thalictroides and Potential Adaptive Values of Retained Gene Duplicates

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

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