scholarly journals Impact of mating systems on patterns of sequence polymorphism in flowering plants

2006 ◽  
Vol 273 (1604) ◽  
pp. 3011-3019 ◽  
Author(s):  
Sylvain Glémin ◽  
Eric Bazin ◽  
Deborah Charlesworth
Keyword(s):  
Life History ◽  
Genome Evolution ◽  
Mating Systems ◽  
Life History Traits ◽  
Gc Content ◽  
Sequence Polymorphism ◽  
Effective Population ◽  
Recombination Rates ◽  
Woody Perennial ◽  
Evolutionary Changes

A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping the patterns of genetic diversity within and among species. Among them, mating systems are thought to have important influences on molecular diversity and genome evolution. Selfing is expected to reduce effective population size, N e , and effective recombination rates, directly leading to reduced polymorphism and increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results directly from selfing or indirectly from evolutionary changes, such as small flowers and low pollen output, leading to greater differentiation of molecular markers than under outcrossing. The lower effective recombination rate increases the likelihood of hitch-hiking, further reducing within-deme diversity of selfers and thus increasing their genetic differentiation. There are also indirect effects on molecular evolutionary processes. Low N e reduces the efficacy of selection; in selfers, selection should thus be less efficient in removing deleterious mutations. The rarity of heterozygous sites in selfers leads to infrequent action of biased conversion towards GC, which tends to increase sequences' GC content in the most highly recombining genome regions of outcrossers. To test these predictions in plants, we used a newly developed sequence polymorphism database to investigate the effects of mating system differences on sequence polymorphism and genome evolution in a wide set of plant species. We also took into account other life-history traits, including life form (whether annual or perennial herbs, and woody perennial) and the modes of pollination and seed dispersal, which are known to affect enzyme and DNA marker polymorphism. We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism.

scholarly journals Mating system and recombination affect molecular evolution in four Triticeae species

2008 ◽  
Vol 90 (1) ◽  
pp. 97-109 ◽  
Author(s):  
A. HAUDRY ◽  
A. CENCI ◽  
C. GUILHAUMON ◽  
E. PAUX ◽  
S. POIRIER ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Mating System ◽  
Mating Systems ◽  
Genetic Load ◽  
Gc Content ◽  
Aegilops Speltoides ◽  
Effective Population ◽  
Recombination Rates ◽  
Biased Gene Conversion ◽  
Evolution Of Genomes

SummaryMating systems and recombination are thought to have a deep impact on the organization and evolution of genomes. Because of the decline in effective population size and the interference between linked loci, the efficacy of selection is expected to be reduced in regions with low recombination rates and in the whole genome of self-fertilizing species. At the molecular level, relaxed selection is expected to result in changes in the rate of protein evolution and the pattern of codon bias. It is increasingly recognized that recombination also affects non-selective processes such as the biased gene conversion towards GC alleles (bGC). Like selection, this kind of meiotic drive in favour of GC over AT alleles is expected to be reduced in weakly recombining regions and genomes. Here, we investigated the effect of mating system and recombination on molecular evolution in four Triticeae species: two outcrossers (Secale cereale and Aegilops speltoides) and two selfers (Triticum urartu and Triticum monococcum). We found that GC content, possibly driven by bGC, is affected by mating system and recombination as theoretically predicted. Selection efficacy, however, is only weakly affected by mating system and recombination. We investigated the possible reasons for this discrepancy. A surprising one is that, in outcrossing lineages, selection efficacy could be reduced because of high substitution rates in favour of GC alleles. Outcrossers, but not selfers, would thus suffer from a ‘GC-induced’ genetic load. This result sheds new light on the evolution of mating systems.

scholarly journals Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life‐history traits and climatic conditions

2019 ◽  
Vol 224 (4) ◽  
pp. 1642-1656 ◽  
Author(s):  
Pavel Trávníček ◽  
Martin Čertner ◽  
Jan Ponert ◽  
Zuzana Chumová ◽  
Jana Jersáková ◽  
...  
Keyword(s):  
Life History ◽  
Genome Size ◽  
Life History Traits ◽  
Gc Content ◽  
Climatic Conditions ◽  
Adaptive Potential ◽  
Plant Life

scholarly journals Switch in Codon Bias and Increased Rates of Amino Acid Substitution in the Drosophila saltans Species Group

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 339-350 ◽  
Author(s):  
Francisco Rodríguez-Trelles ◽  
Rosa Tarrío ◽  
Francisco J Ayala
Keyword(s):  
Rapid Evolution ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Species Group ◽  
Effective Population ◽  
Recombination Rates ◽  
Mutation Pressure ◽  
Saltans Group ◽  
Codon Use ◽  
Population Numbers

Abstract We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated.

scholarly journals Coalescent times, life history traits and conservation concerns: an example from four shark species from the Indo-Pacific

2021 ◽  
Author(s):  
Pierre Lesturgie ◽  
Serge Planes ◽  
Stefano Mona
Keyword(s):  
Population Structure ◽  
Life History ◽  
Life History Traits ◽  
New Caledonia ◽  
Demographic History ◽  
Conservation Strategies ◽  
Shark Species ◽  
Effective Population ◽  
Demographic Models ◽  
Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescent pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

scholarly journals Revealing life-history traits by contrasting genetic estimations with predictions of effective population size

2018 ◽  
Vol 32 (4) ◽  
pp. 817-827 ◽  
Author(s):  
Gili Greenbaum ◽  
Sharon Renan ◽  
Alan R. Templeton ◽  
Amos Bouskila ◽  
David Saltz ◽  
...  
Keyword(s):  
Life History ◽  
Population Size ◽  
Effective Population Size ◽  
Life History Traits ◽  
Effective Population

scholarly journals Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

2010 ◽  
Vol 20 (8) ◽  
pp. 1001-1009 ◽  
Author(s):  
J. Romiguier ◽  
V. Ranwez ◽  
E. J. P. Douzery ◽  
N. Galtier
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Gc Content ◽  
Mammalian Genomes

Fishing-induced evolution and changing reproductive ecology of fish: the evolution of steepness

2010 ◽  
Vol 67 (10) ◽  
pp. 1708-1719 ◽  
Author(s):  
Katja Enberg ◽  
Christian Jørgensen ◽  
Marc Mangel
Keyword(s):  
Life History ◽  
Fisheries Management ◽  
Life Histories ◽  
Life History Traits ◽  
Management Practice ◽  
Total Biomass ◽  
Evolutionary Changes ◽  
Stock Biomass ◽  
Spawning Stock ◽  
Stock Recruitment

Fishing can induce evolutionary changes in individual life history traits, leading to fish that mature smaller and younger and with larger gonads, so that they reproduce more intensely. The steepness of a stock–recruitment relationship is commonly defined as the fraction of recruitment of an unfished population obtained when the spawning stock biomass is 20% of its unfished level. We use a model of harvest-induced evolutionary change to understand how the steepness of the stock–recruitment relationship changes due to fishing. If the true spawning stock biomass is known, the stock–recruitment relationship changes little under fishing-induced evolution and there is little concern for fisheries management. When management is based on a total biomass – recruitment relationship, recruitment may be underestimated, which is also of little concern from a sustainability perspective. However, when the number of spawners – recruitment relationship is used to forecast recruitment, management practice that ignores the evolution of steepness may overestimate recruitment and therefore recommend catches that exceed safe biological limits. Using outdated maturity ogives underestimates spawning stock biomass, which results in steeper and higher stock–recruitment relationships as life histories evolve. Although of little concern for sustainability, this may pose challenges for practical fisheries management.

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