Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

2014 ◽  
Vol 23 (11) ◽  
pp. 2699-2711 ◽  
Author(s):  
Nicholas J. Marra ◽  
Andrea Romero ◽  
J. Andrew DeWoody
Keyword(s):  
Natural Selection ◽  
Genetic Basis ◽  
Rna Seq ◽  
Heteromyid Rodents

scholarly journals The genomics of adaptation

2012 ◽  
Vol 279 (1749) ◽  
pp. 5024-5028 ◽  
Author(s):  
Jacek Radwan ◽  
Wiesław Babik
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Royal Society ◽  
Genetic Basis ◽  
Genomic Data ◽  
Evolutionary Change ◽  
Introductory Article ◽  
Technological Advances ◽  
A Genome ◽  
Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

scholarly journals Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Duan Chu ◽  
Lai Wei
Keyword(s):  
Amino Acids ◽  
Natural Selection ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Translation Efficiency ◽  
Maize Genome ◽  
Rna Seq ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
The Relationship

Abstract Background Synonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated codon could base pair with the same anticodon as the original, the mutation is termed an isoaccepting mutation. An interesting but less-studied type of codon bias is codon co-occurrence bias. There is a trend to cluster the isoaccepting codons in the genome. The proposed advantage of codon co-occurrence bias is that the tRNA released from the ribosome E site could be quickly recharged and subsequently decode the following isoaccepting codons. This advantage would enhance translation efficiency. In plant species, whether there are signals of positive selection on isoaccepting mutations in the codon co-occurred regions has not been studied. Results We termed polymorphic mutations in coding regions using publicly available RNA-seq data in maize (Zea mays). Next, we classified all synonymous mutations into three categories according to the context, i.e., the relationship between the focal codon and the previous codon, as follows: isoaccepting, nonisoaccepting and nonsynonymous. We observed higher fractions of isoaccepting mutations in the isoaccepting context. If we looked at the minor allele frequency (MAF) spectrum, the isoaccepting mutations have a higher MAF in the isoaccepting context than that in other regions, and accordingly, the nonisoaccepting mutations have a higher MAF in the nonisoaccepting context. Conclusion Our results indicate that in regions with codon co-occurrence bias, natural selection maintains this pattern by suppressing the nonisoaccepting mutations. However, if the consecutive codons are nonisoaccepting, mutations tend to switch these codons to become isoaccepting. Our study demonstrates that the codon co-occurrence bias in the maize genome is selectively maintained by natural selection and that the advantage of this trend could potentially be the rapid recharging and reuse of tRNAs to increase translation efficiency.

scholarly journals Positive selection and fast turnover rate in tumor suppressor genes reveal how cetaceans resist cancer

2020 ◽  
Author(s):  
Daniela Tejada-Martinez ◽  
João Pedro de Magalhães ◽  
Juan C. Opazo
Keyword(s):  
Natural Selection ◽  
Tumor Suppressor ◽  
Positive Selection ◽  
Tumor Suppressor Genes ◽  
Turnover Rate ◽  
Genetic Basis ◽  
Large Body ◽  
Nijmegen Breakage Syndrome ◽  
Chromosome Break ◽  
Suppressor Genes

AbstractCetaceans are the longest-lived species of mammals and the largest in the history of the planet. They have developed mechanisms against diseases like cancer, however their underlying molecular and genetic basis remain unknown. The goal of this study was to investigate the role of natural selection in the evolution of tumor suppressor genes in cetaceans. We found signal of positive selection 29 tumor suppressor genes and duplications in 197 genes. The turnover rate of tumor suppressor genes was almost 6 times faster in cetaceans when compared to other mammals. Those genes with duplications and with positive selection are involved in important cancer regulation mechanisms (e.g. chromosome break, DNA repair and biosynthesis of fatty acids). They are also related with multiple ageing and neurological disorders in humans (e.g. Alzheimer, Nijmegen breakage syndrome, and schizophrenia). These results provide evolutionary evidence that natural selection in tumor suppressor genes could act on species with large body sizes and extended life span, providing insights into the genetic basis of disease resistance. We propose that the cetaceans are an important model in cancer, ageing and neuronal, motor and behavior disorders.

scholarly journals Genes Associated with SLE Are Targets of Recent Positive Selection

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Paula S. Ramos ◽  
Stephanie R. Shaftman ◽  
Ralph C. Ward ◽  
Carl D. Langefeld
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Lupus Erythematosus ◽  
Genetic Basis ◽  
Ethnic Disparities ◽  
Future Research ◽  
Risk Alleles ◽  
Recent Positive Selection ◽  
Risk Variants ◽  
Genomic Regions

The reasons for the ethnic disparities in the prevalence of systemic lupus erythematosus (SLE) and the relative high frequency of SLE risk alleles in the population are not fully understood. Population genetic factors such as natural selection alter allele frequencies over generations and may help explain the persistence of such common risk variants in the population and the differential risk of SLE. In order to better understand the genetic basis of SLE that might be due to natural selection, a total of 74 genomic regions with compelling evidence for association with SLE were tested for evidence of recent positive selection in the HapMap and HGDP populations, using population differentiation, allele frequency, and haplotype-based tests. Consistent signs of positive selection across different studies and statistical methods were observed at several SLE-associated loci, includingPTPN22,TNFSF4,TET3-DGUOK,TNIP1,UHRF1BP1,BLK, andITGAMgenes. This study is the first to evaluate and report that several SLE-associated regions show signs of positive natural selection. These results provide corroborating evidence in support of recent positive selection as one mechanism underlying the elevated population frequency of SLE risk loci and supports future research that integrates signals of natural selection to help identify functional SLE risk alleles.

Thermal potentiation and mineralogical evolution in the Bivalvia (Mollusca)

1998 ◽  
Vol 72 (6) ◽  
pp. 991-1010 ◽  
Author(s):  
Joseph G. Carter ◽  
Enriqueta Barrera ◽  
Michael J. S. Tevesz
Keyword(s):  
Natural Selection ◽  
Genetic Basis ◽  
Outer Part ◽  
Outer Shell ◽  
Shell Layer ◽  
Soft Bottom ◽  
Prismatic Shell ◽  
Calcite Deposition ◽  
Fracture Localization ◽  
Bivalve Shells

The most important factor controlling the timing of Phanerozoic mineralogical evolution in the Bivalvia appears to be thermal potentiation of calcite deposition in colder marine and estuarine environments. Cold temperature has promoted mineralogical evolution in the Bivalvia by kinetically facilitating (potentiating) initially weak biological controls for calcite, thereby exposing their genetic basis to natural selection. Calcite has evolved in bivalve shells for a variety of selective advantages, including resistance to dissolution; resistance to chemical boring by algae and gastropods; reduced shell density in swimming and soft-bottom reclining species; enhanced flexibility in simple prismatic shell layers; and fracture localization and economy of secretion in association with certain foliated structures.Endogenous calcite in bivalve shells varies from biologically induced to weakly and strongly biologically controlled. Biologically controlled calcite generally first appears in bivalve shells as an impersistent component of the outer shell layer, only later, in some groups, expanding to include the entire outer and then part or all of the middle and inner shell layers. The initial stages of mineralogical evolution are shown by certain modern Mytilidae, Veneridae and Petricolidae. In the latter two families, the calcite occurs as conellae in the outer part of the outer shell layer. Calcitic conellae in the inner shell layer of Pliocene Mercenaria are not barnacle plates, as previously indicated, but endogenous calcite comparable in origin to other venerid conellae. Their occurrence in Mercenaria may reflect thermal potentiation of weak biological controls for calcite, as well as local detachment of the secretory mantle epithelium near the pallial and adductor musculature.

scholarly journals Development and Application of a PCR-Based Molecular Marker for the Identification of High Temperature Tolerant Cabbage (Brassica oleracea var. capitata) Genotypes

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 116
Author(s):  
Hayoung Song ◽  
Myungjin Lee ◽  
Byung-Ho Hwang ◽  
Ching-Tack Han ◽  
Jong-In Park ◽  
...  
Keyword(s):  
High Temperature ◽  
Molecular Marker ◽  
Brassica Oleracea ◽  
Inbred Line ◽  
Genetic Basis ◽  
Soft Rot ◽  
Inbred Lines ◽  
Rna Seq ◽  
F2 Population ◽  
Pcr Based Molecular Marker

Global warming accelerates the development of high temperature (HT)- and high humidity (HH)-tolerant varieties. This is further facilitated by the identification of HTHH-tolerant genes and the development of molecular markers based on these genes. To identify genes involved in HTHH tolerance in cabbage (Brassica oleracea var. capitata), we performed RNA-seq analysis of two inbred lines, BN1 (HTHH-tolerant) and BN2 (HTHH-susceptible), and selected trehalose 6- phosphate phosphatase I-2 (BoTPPI-2) as one of the HTHH-tolerant-associated genes. We also developed a segregating F2 population from a cross between BN1 and BN2. RNA-seq results showed that BoTPPI-2 transcript levels were high in the HTHH-tolerant inbred line BN1, but not detectable in the HTHH-susceptible inbred line BN2. The expression pattern of BoTPPI-2 was not related to the expression of heat shock-related genes. Soft rot resistance, used as an indicator of HTHH tolerance, was higher in BN1 than in BN2. F2 individuals similar to BN1 with respect to phenotype appeared to be HTHH-tolerant, whereas BN2-types were susceptible to HTHH. Analysis of the genomic DNA revealed the presence of a long terminal repeat (LTR; ca. 4.6 kb) in the ninth intron of the BoTPPI-2_BN2 allele, thereby suppressing its transcription and exhibiting HTHH phenotype. Except for the LTR insertion, the sequence of BoTPPI-2_BN2 was almost identical to that of BoTPPI-2_BN1. On the basis of the LTR and BoTPPI-2 sequences, we developed a molecular marker to identify HTHH-tolerant genotypes and validated its efficiency using F2 individuals, inbred lines, and cultivars from diverse sources. The marker explained the genetic basis of HTHH tolerance in at least 80%, but not 100%, of the cabbage genotypes. Thus, additional markers associated with HTHH tolerance are needed for perfect selection.

scholarly journals Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species

2020 ◽  
Author(s):  
Joanna F D Hagen ◽  
Cláudia C Mendes ◽  
Shamma R Booth ◽  
Javier Figueras Jimenez ◽  
Kentaro M Tanaka ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Genetic Basis ◽  
Posterior Lobe ◽  
Rna Seq ◽  
New Genes ◽  
Genital Development ◽  
Rapid Diversification ◽  
Gene Regulatory ◽  
Phenotypic Diversification ◽  
Morphological Differences

Abstract In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These appendages are used for grasping the female during mating and so their divergence is most likely driven by sexual selection. Mapping studies indicate a highly polygenic and generally additive genetic basis for these morphological differences. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid phenotypic diversification. Here, we used new D. simulans/D. mauritiana introgression lines on chromosome arm 3L to generate higher resolution maps of posterior lobe and clasper differences between these species. We then carried out RNA-seq on the developing genitalia of both species to identify the expressed genes and those that are differentially expressed between the two species. This allowed us to test the function of expressed positional candidates during genital development in D. melanogaster. We identified several new genes involved in the development and possibly the evolution of these genital structures, including the transcription factors Hairy and Grunge. Furthermore, we discovered that during clasper development Hairy negatively regulates tartan (trn), a gene known to contribute to divergence in clasper morphology. Taken together, our results provide new insights into the regulation of genital development and how this has evolved between species.

scholarly journals Nothing in Evolution Makes Sense Except in the Light of DNA

2010 ◽  
Vol 9 (2) ◽  
pp. 87-97 ◽  
Author(s):  
Steven T. Kalinowski ◽  
Mary J. Leonard ◽  
Tessa M. Andrews
Keyword(s):  
Natural Selection ◽  
Dna Sequences ◽  
Genetic Basis ◽  
Cognitive Conflict ◽  
Preliminary Evidence ◽  
Biology Students ◽  
Lamarckian Evolution ◽  
Student Misconceptions

Natural selection is one of the most important concepts for biology students to understand, but students frequently have misconceptions regarding how natural selection operates. Many of these misconceptions, such as a belief in “Lamarckian” evolution, are based on a misunderstanding of inheritance. In this essay, we argue that evolution instructors should clarify the genetic basis of natural selection by discussing examples of DNA sequences that affect fitness. Such examples are useful for showing how natural selection works, for establishing connections between genetics and evolution, and for creating cognitive conflict within students having misconceptions. We describe several examples of genes that instructors might use during lectures, and present preliminary evidence from our classroom that an evolution curriculum rich in DNA sequences is effective at reducing student misconceptions of natural selection.

scholarly journals Deep evolutionary origin of limb and fin regeneration

2018 ◽  
Author(s):  
Sylvain Darnet ◽  
Aline C. Dragalzew ◽  
Danielson B. Amaral ◽  
Andrew W. Thompson ◽  
Amanda N. Cass ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Expression Profiles ◽  
Genetic Program ◽  
Common Origin ◽  
Evolutionary Origin ◽  
Rna Seq ◽  
Genetic Pathways ◽  
Fin Regeneration ◽  
Cichlid Species ◽  
Spotted Gar

Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of complete limb and paired fin regeneration, respectively. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in Polypterid fishes (Cladistia). Whether complete appendage regeneration in sarcopterygians and actinopterygians evolved independently or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-seq analysis to provide support for a common origin of a paired appendage regeneration in osteichthyes (bony vertebrates). We show that, in addition to Polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of all major actinopterygian clades: the American paddlefish, (Chondrostei), the spotted gar (Holostei), as well as in two cichlid species, the white convict and the oscar (Teleostei). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a pan-osteichthyes genetic program of appendage regeneration. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

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