scholarly journals Molecular evolution of ‘eye genes’ in blind beetles from the calcrete archipelago of Western Australia: evidence for neutral evolution of phototransduction genes

2018 ◽  
Vol 1 ◽  
Author(s):  
Barbara Langille ◽  
Terry Bertozzi ◽  
Simon Tierney ◽  
Andrew Austin ◽  
William Humphreys ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Western Australia ◽  
Sequence Data ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Evolution Theory ◽  
Beetle Species ◽  
Transcriptome Data ◽  
Surface Species ◽  
Relaxed Selection

Neutral evolution theory predicts that genes specific to the development/function of eyes in subterranean animals will evolve under relaxed selection, ultimately becoming pseudogenes. Independently evolved (3-8 million years ago) subterranean beetle (Dytiscidae) species of Western Australia have converged on eye loss, providing a powerful system to explore changes to the genome with respect to troglomorphic characters. Using next generation sequence data, we investigated the molecular evolution of ‘eye genes’ of subterranean beetle species to test if they are evolving neutrally. We used transcriptome data from five beetle species (three subterranean and two surface) to design baits for hybrid enrichment of 60 pigmentation and phototransduction genes from 31 subterranean and surface species. The current talk focuses on the results from the study of 8 photoreceptor genes that showed evidence for a lack of transcription or possible pseudogenisation in stygobitic species when compared to surface species. The mutations found in these genes included multiple insertions or deletions, resulting in frameshifts which led to the introduction of stop codons. Our study provides evidence for the parallel loss of key phototransduction genes, lending support to the neutral theory of regressive evolution.

scholarly journals The Rate of Molecular Evolution When Mutation May Not Be Weak

2018 ◽  
Author(s):  
A.P. Jason de Koning ◽  
Bianca D. De Sanctis
Keyword(s):  
Natural Selection ◽  
Molecular Evolution ◽  
Population Size ◽  
Mutation Rate ◽  
Molecular Clock ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Systematic Bias ◽  
Effective Population ◽  
Sequence Comparisons

AbstractOne of the most fundamental rules of molecular evolution is that the rate of neutral evolution equals the mutation rate and is independent of effective population size. This result lies at the heart of the Neutral Theory, and is the basis for numerous analytic approaches that are widely applied to infer the action of natural selection across the genome and through time, and for dating divergence events using the molecular clock. However, this result was derived under the assumption that evolution is strongly mutation-limited, and it has not been known whether it generalizes across the range of mutation pressures or the spectrum of mutation types observed in natural populations. Validated by both simulations and exact computational analyses, we present a direct and transparent theoretical analysis of the Wright-Fisher model of population genetics, which shows that some of the most important rules of molecular evolution are fundamentally changed by considering recurrent mutation’s full effect. Surprisingly, the rate of the neutral molecular clock is found to have population-size dependence and to not equal the mutation rate in general. This is because, for increasing values of the population mutation rate parameter (θ), the time spent waiting for mutations quickly becomes smaller than the cumulative time mutants spend segregating before a substitution, resulting in a net deceleration compared to classical theory that depends on the population mutation rate. Furthermore, selection exacerbates this effect such that more adaptive alleles experience a greater deceleration than less adaptive alleles, introducing systematic bias in a wide variety of methods for inferring the strength and direction of natural selection from across-species sequence comparisons. Critically, the classical weak mutation approximation performs well only when θ< 0.1, a threshold that many biological populations seem to exceed.

scholarly journals THE SELECTIVE VALUE OF ALLELES UNDERLYING POLYGENIC TRAITS

Genetics ◽  
1984 ◽  
Vol 108 (4) ◽  
pp. 1021-1033
Author(s):  
Michael Lynch
Keyword(s):  
Molecular Evolution ◽  
Genetic Drift ◽  
Genetic Variance ◽  
Neutral Theory ◽  
Mechanistic Explanation ◽  
Neutral Evolution ◽  
Stabilizing Selection ◽  
Average Effect ◽  
Absolute Value ◽  
The Mean

ABSTRACT To define the genetic and ecological circumstances that are conductive to evolution via genetic drift at the allelic level, the selection coefficient for a constituent allele of arbitrary effect is derived for a polygenic character exposed to stabilizing selection. Under virtually all possible conditions, alleles within the class for which the absolute value of the average effect is &lt;10-2 phenotypic standard deviations are neutral with respect to each other. In addition, when the mean phenotype is at the optimum and the genetic variance is in selection-drift-mutation equilibrium, a considerable amount of neutral evolution is expected in the class of alleles with intermediate effects on the phenotype. These results help clarify how molecular evolution via genetic drift may occur at a locus despite intense selection and provide a potential mechanistic explanation for the neutral theory of molecular evolution.

scholarly journals Tripartite genome of all species

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 195
Author(s):  
MengPing Long ◽  
TaoBo Hu
Keyword(s):  
Molecular Evolution ◽  
Neutral Theory ◽  
Variable Region ◽  
The Other ◽  
Genome Architecture ◽  
Evolution Theory ◽  
Functional Variation ◽  
As Species ◽  
Genomic Regions ◽  
Maximum Genetic Diversity

Neutral theory has dominated the molecular evolution field for more than half a century, but it has been severely challenged by the recently emerged Maximum Genetic Diversity (MGD) theory. However, based on our recent work of tripartite human genome architecture, we found that MGD theory may have overlooked the regulatory but variable genomic regions that increase with species complexity. Here we propose a new molecular evolution theory named Increasing Functional Variation (IFV) hypothesis. According to the IFV hypothesis, the genome of all species is divided into three regions that are ‘functional and invariable’, ‘functional and variable’ and ‘non-functional and variable’. While the ‘non-functional and variable’ region decreases as species become more complex, the other two regions increase.

scholarly journals Molecular Evolution of the Avian CHD1 Genes on the Z and W Sex Chromosomes

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1903-1912 ◽  
Author(s):  
Anna-Karin Fridolfsson ◽  
Hans Ellegren
Keyword(s):  
Molecular Evolution ◽  
Sex Chromosomes ◽  
Sequence Data ◽  
Neutral Evolution ◽  
Z Chromosome ◽  
W Chromosome ◽  
Effective Population ◽  
Synonymous Substitutions ◽  
Nonsynonymous Substitutions ◽  
Female Specific

Abstract Genes shared between the nonrecombining parts of the two types of sex chromosomes offer a potential means to study the molecular evolution of the same gene exposed to different genomic environments. We have analyzed the molecular evolution of the coding sequence of the first pair of genes found to be shared by the avian Z (present in both sexes) and W (female-specific) sex chromosomes, CHD1Z and CHD1W. We show here that these two genes evolve independently but are highly conserved at nucleotide as well as amino acid levels, thus not indicating a female-specific role of the CHD1W gene. From comparisons of sequence data from three avian lineages, the frequency of nonsynonymous substitutions (Ka) was found to be higher for CHD1W (1.55 per 100 sites) than for CHD1Z (0.81), while the opposite was found for synonymous substitutions (Ks, 13.5 vs. 22.7). We argue that the lower effective population size and the absence of recombination on the W chromosome will generally imply that nonsynonymous substitutions accumulate faster on this chromosome than on the Z chromosome. The same should be true for the Y chromosome relative to the X chromosome in XY systems. Our data are compatible with a male-biased mutation rate, manifested by the faster rate of neutral evolution (synonymous substitutions) on the Z chromosome than on the female-specific W chromosome.

Inferring evolutionary processes from DNA sequence data

2019 ◽  
pp. 145-172
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet
Keyword(s):  
Molecular Evolution ◽  
Dna Sequence ◽  
Genetic Markers ◽  
Dna Sequences ◽  
Sequence Data ◽  
Neutral Theory ◽  
Evolutionary Genetics ◽  
Haplotype Structure ◽  
Dna Sequence Data ◽  
Neutrality Tests

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if different sequences were simply treated as different alleles. This chapter introduces some important methods and concepts applicable to the analysis of DNA-sequence data. The null models for analyzing sequence data are derived from the neutral theory of molecular evolution. Historically, however, the neutral theory has made a large impact on evolutionary genetics. Therefore, this chapter starts by reviewing its important contribution. Then, important parameters and statistics for analyzing sequence variation are introduced, including a plethora of neutrality tests. The chapter ends with a cautious focus on the powerful tool of genome scan analysis and its utility for identifying regions of the genomes potentially under selection. This includes a section on more recently derived statistics which incorporate information on haplotype structure.

Molecular evolution of homologous gene sequences in germline-limited and somatic chromosomes of Acricotopus

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 732-741 ◽  
Author(s):  
Wolfgang Staiber
Keyword(s):  
Molecular Evolution ◽  
Dna Sequences ◽  
Sequence Data ◽  
Structural Evolution ◽  
5S Rdna ◽  
Oligonucleotide Primer ◽  
Homologous Gene ◽  
Gene Sequences ◽  
Nucleotide Substitutions ◽  
Degenerate Oligonucleotide

The origin of germline-limited chromosomes (Ks) as descendants of somatic chromosomes (Ss) and their structural evolution was recently elucidated in the chironomid Acricotopus. The Ks consist of large S-homologous sections and of heterochromatic segments containing germline-specific, highly repetitive DNA sequences. Less is known about the molecular evolution and features of the sequences in the S-homologous K sections. More information about this was received by comparing homologous gene sequences of Ks and Ss. Genes for 5.8S, 18S, 28S, and 5S ribosomal RNA were choosen for the comparison and therefore isolated first by PCR from somatic DNA of Acricotopus and sequenced. Specific K DNA was collected by microdissection of monopolar moving K complements from differential gonial mitoses and was then amplified by degenerate oligonucleotide primer (DOP)-PCR. With the sequence data of the somatic rDNAs, the homologous 5.8S and 5S rDNA sequences were isolated by PCR from the DOP-PCR sequence pool of the Ks. In addition, a number of K DOP-PCR sequences were directly cloned and analysed. One K clone contained a section of a putative N-acetyltransferase gene. Compared with its homolog from the Ss, the sequence exhibited few nucleotide substitutions (99.2% sequence identity). The same was true for the 5.8S and 5S sequences from Ss and Ks (97.5%–100% identity). This supports the idea that the S-homologous K sequences may be conserved and do not evolve independently from their somatic homologs. Possible mechanisms effecting such conservation of S-derived sequences in the Ks are discussed.Key words: microdissection, DOP-PCR, germline-limited chromosomes, molecular evolution.

Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

2012 ◽  
Vol 60 (1) ◽  
pp. 32 ◽  
Author(s):  
Laurence J. Clarke ◽  
Duncan I. Jardine ◽  
Margaret Byrne ◽  
Kelly Shepherd ◽  
Andrew J. Lowe
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Structure ◽  
Western Australia ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Conservation Strategies ◽  
New Taxon ◽  
Near Surface ◽  
Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

scholarly journals Nucleotide sequences of highly repeated DNAs; compilation and comments

1982 ◽  
Vol 39 (1) ◽  
pp. 1-30 ◽  
Author(s):  
George L. Gabor Miklos ◽  
Amanda Clare Gill
Keyword(s):  
Satellite Dna ◽  
Germ Line ◽  
Sequence Data ◽  
Allelic Variation ◽  
Neutral Theory ◽  
Natural Populations ◽  
Evolutionary Significance ◽  
Nucleotide Sequence Data ◽  
A Genome ◽  
Repeated Dnas

SummaryThe nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequence per se is unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles of neutral and selective mechanisms in the evolution of highly repeated DNA.Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at the cellular level is unlikely to prove profitable.The presence or in some cases the amount of satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regions rec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.

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