scholarly journals The Genomic Selfing Syndrome Accompanies the Evolutionary Breakdown of Heterostyly

2020 ◽  
Vol 38 (1) ◽  
pp. 168-180
Author(s):  
Xin-Jia Wang ◽  
Spencer C H Barrett ◽  
Li Zhong ◽  
Zhi-Kun Wu ◽  
De-Zhu Li ◽  
...  
Keyword(s):  
Mating Systems ◽  
Sequence Divergence ◽  
Purifying Selection ◽  
Data Sets ◽  
Evolutionary Transition ◽  
Effective Population ◽  
Genomic Signatures ◽  
Self Fertilization ◽  
Selfing Syndrome ◽  
Selfing Species

Abstract The evolutionary transition from outcrossing to selfing can have important genomic consequences. Decreased effective population size and the reduced efficacy of selection are predicted to play an important role in the molecular evolution of the genomes of selfing species. We investigated evidence for molecular signatures of the genomic selfing syndrome using 66 species of Primula including distylous (outcrossing) and derived homostylous (selfing) taxa. We complemented our comparative analysis with a microevolutionary study of P. chungensis, which is polymorphic for mating system and consists of both distylous and homostylous populations. We generated chloroplast and nuclear genomic data sets for distylous, homostylous, and distylous–homostylous species and identified patterns of nonsynonymous to synonymous divergence (dN/dS) and polymorphism (πN/πS) in species or lineages with contrasting mating systems. Our analysis of coding sequence divergence and polymorphism detected strongly reduced genetic diversity and heterozygosity, decreased efficacy of purifying selection, purging of large-effect deleterious mutations, and lower rates of adaptive evolution in samples from homostylous compared with distylous populations, consistent with theoretical expectations of the genomic selfing syndrome. Our results demonstrate that self-fertilization is a major driver of molecular evolutionary processes with genomic signatures of selfing evident in both old and relatively young homostylous populations.

scholarly journals Estimating the Effective Number of Breeders From Heterozygote Excess in Progeny

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 1211-1216 ◽  
Author(s):  
Gordon Luikart ◽  
Jean-Marie Cornuet
Keyword(s):  
Mating Systems ◽  
Simulated Data ◽  
Data Sets ◽  
Effective Number ◽  
Effective Population ◽  
Heterozygote Excess ◽  
Accuracy And Precision ◽  
Effective Number Of Breeders ◽  
Hardy Weinberg Equilibrium ◽  
Simulated Data Sets

Abstract The heterozygote-excess method is a recently published method for estimating the effective population size (Ne). It is based on the following principle: When the effective number of breeders (Neb) in a population is small, the allele frequencies will (by chance) be different in males and females, which causes an excess of heterozygotes in the progeny with respect to Hardy-Weinberg equilibrium expectations. We evaluate the accuracy and precision of the heterozygote-excess method using empirical and simulated data sets from polygamous, polygynous, and monogamous mating systems and by using realistic sample sizes of individuals (15-120) and loci (5-30) with varying levels of polymorphism. The method gave nearly unbiased estimates of Neb under all three mating systems. However, the confidence intervals on the point estimates of Neb were sufficiently small (and hence the heterozygote-excess method useful) only in polygamous and polygynous populations that were produced by <10 effective breeders, unless samples included > ∼60 individuals and 20 multiallelic loci.

scholarly journals Population Genomics of the “Arcanum” Species Group in Wild Tomatoes: Evidence for Separate Origins of Two Self-Compatible Lineages

2021 ◽  
Vol 12 ◽  
Author(s):  
Ana M. Florez-Rueda ◽  
Mathias Scharmann ◽  
Morgane Roth ◽  
Thomas Städler
Keyword(s):  
Mating Systems ◽  
Population Genomics ◽  
Species Group ◽  
Nominal Species ◽  
Reproductive Barriers ◽  
Self Incompatibility ◽  
Effective Population ◽  
Demographic Models ◽  
Population Genomic ◽  
Selfing Syndrome

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the “Arcanum” group, comprising the nominal species Solanum arcanum, Solanum chmielewskii, and Solanum neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at different rates, given their distinct manifestations of the morphological “selfing syndrome.” Based on experimental crossings and transcriptome sequencing of a total of 39 different genotypes from as many accessions representing each species’ geographic range, we provide compelling evidence for deep genealogical divisions within S. arcanum; only the self-incompatible lineage known as “var. marañón” has close genealogical ties to the two self-compatible species. Moreover, there is evidence under multiple inference schemes for different geographic subsets of S. arcanum var. marañón being closest to S. chmielewskii and S. neorickii, respectively. To broadly characterize the population-genomic consequences of these recent mating-system transitions and their associated speciation events, we fit demographic models indicating strong reductions in effective population size, congruent with reduced nucleotide and S-locus diversity in the two independently derived self-compatible species.

The Age of Nonsynonymous and Synonymous Mutations in Animal mtDNA and Implications for the Mildly Deleterious Theory

Genetics ◽  
1999 ◽  
Vol 153 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Rasmus Nielsen ◽  
Daniel M Weinreich
Keyword(s):  
Dna Sequences ◽  
Purifying Selection ◽  
Data Sets ◽  
Deleterious Mutations ◽  
Synonymous Mutations ◽  
Weak Evidence ◽  
Mitochondrial Data ◽  
The Mean ◽  
Excess Number ◽  
Neutral Mutations

Abstract McDonald/Kreitman tests performed on animal mtDNA consistently reveal significant deviations from strict neutrality in the direction of an excess number of polymorphic nonsynonymous sites, which is consistent with purifying selection acting on nonsynonymous sites. We show that under models of recurrent neutral and deleterious mutations, the mean age of segregating neutral mutations is greater than the mean age of segregating selected mutations, even in the absence of recombination. We develop a test of the hypothesis that the mean age of segregating synonymous mutations equals the mean age of segregating nonsynonymous mutations in a sample of DNA sequences. The power of this age-of-mutation test and the power of the McDonald/Kreitman test are explored by computer simulations. We apply the new test to 25 previously published mitochondrial data sets and find weak evidence for selection against nonsynonymous mutations.

Low reproductive success of hay-scented fern (Dennstaedtia punctilobula) regardless of inbreeding level or time since disturbance

Botany ◽  
2014 ◽  
Vol 92 (12) ◽  
pp. 911-915 ◽  
Author(s):  
Kathryn M. Flinn ◽  
Matthew M. Loiacono ◽  
Hannah E. Groff
Keyword(s):  
Reproductive Success ◽  
Mating Systems ◽  
Tree Regeneration ◽  
Single Individual ◽  
Dennstaedtia Punctilobula ◽  
Self Fertilization ◽  
Sporophyte Production ◽  
Inbreeding Level ◽  
Native Invasive ◽  
Selfing Ability

Self-fertilization can facilitate the colonization of new habitats because it allows a single individual to found a population. Here we investigated the relationship between mating systems and colonization in hay-scented fern (Dennstaedtia punctilobula (Michx.) T.Moore). Throughout eastern North America, this species has been called a “native invasive” for its tendency to dominate forest understories disturbed by logging, inhibiting tree regeneration. Thus, it is important to understand the mechanisms of its spread. We hypothesized that if populations were founded through selfing, then populations disturbed more recently would retain higher selfing ability; this pattern would demonstrate an important link between mating systems and colonization. For four populations logged at different times in the past, we compared the sporophyte production of gametophytes at different levels of inbreeding (intragametophytic selfing, intergametophytic selfing, and outcrossing) using laboratory crosses. Across all treatments, only 9.8% of gametophytes formed sporophytes (N = 400 gametophytes). Neither inbreeding level nor time since disturbance affected sporophyte production. Selfing ability did not differ across populations logged at different times; there was no interaction between inbreeding level and time since disturbance. The low reproductive success of D. punctilobula, regardless of inbreeding level or time since disturbance, suggests that population establishment and expansion via sexual reproduction may be relatively rare in this clonal species.

Establishment of local adaptation in partly self-fertilizing populations

Genetics ◽  
2021 ◽  
Author(s):  
Bogi Trickovic ◽  
Sylvain Glémin
Keyword(s):  
Local Adaptation ◽  
Pollen Dispersal ◽  
Theoretical Background ◽  
Weak Selection ◽  
Dominance Level ◽  
Self Fertilization ◽  
Protected Polymorphism ◽  
And Migration ◽  
Closed Form Approximation ◽  
Selfing Species

Abstract Populations often inhabit multiple ecological patches and thus experience divergent selection, which can lead to local adaptation if migration is not strong enough to swamp locally adapted alleles. Conditions for the establishment of a locally advantageous allele have been studied in randomly mating populations. However, many species reproduce, at least partially, through self-fertilization, and how selfing affects local adaptation remains unclear and debated. Using a two-patch branching process formalism, we obtained a closed-form approximation under weak selection for the probability of establishment of a locally advantageous allele (P) for arbitrary selfing rate and dominance level, where selection is allowed to act on viability or fecundity, and migration can occur via seed or pollen dispersal. This solution is compared to diffusion approximation and used to investigate the consequences of a shift in a mating system on P, and the establishment of protected polymorphism. We find that selfing can either increase or decrease P, depending on the patterns of dominance in the two patches, and has conflicting effects on local adaptation. Globally, selfing favors local adaptation when locally advantageous alleles are (partially) recessive, when selection between patches is asymmetrical and when migration occurs through pollen rather than seed dispersal. These results establish a rigorous theoretical background to study heterogeneous selection and local adaptation in partially selfing species.

scholarly journals Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

2020 ◽  
Author(s):  
Solomon T C Chak ◽  
Juan Antonio Baeza ◽  
Phillip Barden
Keyword(s):  
Molecular Evolution ◽  
Genome Evolution ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Effective Population ◽  
Protein Coding ◽  
Marine Realm ◽  
Snapping Shrimps

Abstract Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.

scholarly journals Molecular bases for the selection of the chromophore of animal rhodopsins

2015 ◽  
Vol 112 (50) ◽  
pp. 15297-15302 ◽  
Author(s):  
Hoi Ling Luk ◽  
Federico Melaccio ◽  
Silvia Rinaldi ◽  
Samer Gozem ◽  
Massimo Olivucci
Keyword(s):  
Excited States ◽  
Sequence Divergence ◽  
Evolutionary Transition ◽  
Structure Changes ◽  
Bovine Rhodopsin ◽  
Key Factor ◽  
Pcc 7120 ◽  
Molecular Bases ◽  
Amino Acid Sequence Divergence ◽  
Selection Of

The functions of microbial and animal rhodopsins are triggered by the isomerization of their all-trans and 11-cis retinal chromophores, respectively. To lay the molecular basis driving the evolutionary transition from the all-trans to the 11-cis chromophore, multiconfigurational quantum chemistry is used to compare the isomerization mechanisms of the sensory rhodopsin from the cyanobacterium Anabaena PCC 7120 (ASR) and of the bovine rhodopsin (Rh). It is found that, despite their evolutionary distance, these eubacterial and vertebrate rhodopsins start to isomerize via distinct implementations of the same bicycle-pedal mechanism originally proposed by Warshel [Warshel A (1976) Nature 260:678–683]. However, by following the electronic structure changes of ASR (featuring the all-trans chromophore) during the isomerization, we find that ASR enters a region of degeneracy between the first and second excited states not found in Rh (featuring the 11-cis chromophore). We show that such degeneracy is modulated by the preorganized structure of the chromophore and by the position of the reactive double bond. It is argued that the optimization of the electronic properties of the chromophore, which affects the photoisomerization efficiency and the thermal isomerization barrier, provided a key factor for the emergence of the striking amino acid sequence divergence observed between the microbial and animal rhodopsins.

scholarly journals Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hong Zhang ◽  
Yirong Wang ◽  
Xinkai Wu ◽  
Xiaolu Tang ◽  
Changcheng Wu ◽  
...  
Keyword(s):  
Driving Forces ◽  
Mrna Translation ◽  
Purifying Selection ◽  
Wide Distribution ◽  
Open Reading Frames ◽  
Translation Regulation ◽  
Effective Population ◽  
Upstream Open Reading Frames ◽  
Functional Peptides ◽  
Regulatory Functions

AbstractUpstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.

Large testes and brain sizes in odontocetes (order Cetacea, suborder Odontoceti): the influence of mating system on encephalization

2014 ◽  
Vol 92 (8) ◽  
pp. 721-726 ◽  
Author(s):  
Trish C. Kelley ◽  
Jeff W. Higdon ◽  
Steven H. Ferguson
Keyword(s):  
Sexual Conflict ◽  
Mating Systems ◽  
Sexual Size Dimorphism ◽  
Negative Relationship ◽  
Data Sets ◽  
Mass Measurements ◽  
Data Set ◽  
Brain Mass ◽  
Terrestrial Mammals ◽  
Machiavellian Intelligence

Little is known about their mating systems, but odontocetes may utilize the same types of mating systems as terrestrial mammals. Species with relatively large testes are likely to be polygynandrous, while species with smaller testes and greater sexual size dimorphism (SSD) are predicted to be polygynous. The “Machiavellian intelligence or sexual conflict” hypothesis predicts that polygynadrous species also evolved larger brains both to coerce conspecifics to mate and to resist mating attempts by undesirable mates. The “costly tissue” hypothesis predicts that species investing heavily in testes invest less in brain tissue and vice versa to conserve energy. Residual testes and brain mass measurements were used to test the sexual conflict and costly tissue hypotheses in 40 species of odontocetes. Correlations were performed on both raw data and independent contrasts to control for phylogeny. There was a significant positive correlation between residual testes mass and SSD in both data sets, and between residual testes mass and residual brain mass in the non-phylogenetically controlled data set. Results indicate a negative relationship between increased testes masses and SSD in odontocetes. There was no support for the costly tissue hypothesis. Support for Machiavellian intelligence or sexual conflict hypothesis was found only when phylogenetic effects were not considered.

Sign in / Sign up

Export Citation Format

Share Document