scholarly journals Characterizing the genetic basis of trait evolution in the Mexican cavefish

2021 ◽  
Author(s):  
Camila Oliva ◽  
Nicole K Hinz ◽  
Wayne Robinson ◽  
Alexys M Barrett Thompson ◽  
Julianna Booth ◽  
...  
Keyword(s):  
Complex Traits ◽  
Morphological Traits ◽  
Prey Capture ◽  
Molecular Genetic ◽  
Startle Reflex ◽  
Fish Population ◽  
Multiple Traits ◽  
Genetic Changes ◽  
Behavioral Traits ◽  
Critical Gap

Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabits the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism and enhanced mechanosensory function. The infertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of behavioral and morphological traits. Taken together, this approach provides a novel system to identify genes that underlie naturally occurring genetic variation in morphological and behavioral traits.

scholarly journals Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

2019 ◽  
Author(s):  
Kerry A Geiler-Samerotte ◽  
Shuang Li ◽  
Charalampos Lazaris ◽  
Austin Taylor ◽  
Naomi Ziv ◽  
...  
Keyword(s):  
Single Cell ◽  
Complex Traits ◽  
Biological Systems ◽  
Evolutionary Medicine ◽  
Yeast Cells ◽  
Single Mutation ◽  
Multiple Traits ◽  
Genetic Changes ◽  
Ample Evidence ◽  
Controversial Topic

AbstractPleiotropy – when a single mutation affects multiple traits – is a controversial topic with far-reaching implications. Pleiotropy plays a central role in debates about how complex traits evolve and whether biological systems are modular or are organized such that every gene has the potential to affect many traits. Pleiotropy is also critical to initiatives in evolutionary medicine that seek to trap infectious microbes or tumors by selecting for mutations that encourage growth in some conditions at the expense of others. Research in these fields, and others, would benefit from understanding the extent to which pleiotropy reflects inherent relationships among phenotypes that correlate no matter the perturbation (vertical pleiotropy). Alternatively, pleiotropy may result from genetic changes that impose correlations between otherwise independent traits (horizontal pleiotropy). We distinguish these possibilities by using clonal populations of yeast cells to quantify the inherent relationships between single-cell morphological features. Then, we demonstrate how often these relationships underlie vertical pleiotropy and how often these relationships are modified by genetic variants (QTL) acting via horizontal pleiotropy. Our comprehensive screen measures thousands of pairwise trait correlations across hundreds of thousands of yeast cells and reveals ample evidence of both vertical and horizontal pleiotropy. Additionally, we observe that the correlations between traits can change with the environment, genetic background and cell-cycle position. These changing dependencies suggest a nuanced view of pleiotropy: biological systems demonstrate limited pleiotropy in any given context, but across contexts (e.g., across diverse environments and genetic backgrounds) each genetic change has the potential to influence a larger number of traits. Our method suggests that exploiting pleiotropy for applications in evolutionary medicine would benefit from focusing on traits with correlations that are less dependent on context.

scholarly journals Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo

2021 ◽  
Vol 12 ◽  
Author(s):  
Baoshun Shao ◽  
Hui Sun ◽  
Muhammad Jamil Ahmad ◽  
Nasser Ghanem ◽  
Hamdy Abdel-Shafy ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Complex Traits ◽  
Association Studies ◽  
Molecular Genetic ◽  
Reproductive Traits ◽  
Calving Interval ◽  
Genome Wide Association Studies ◽  
Multiple Traits ◽  
Age At First Calving ◽  
Genetic Features

Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.

A bigger brain for a more complex environment

2020 ◽  
Vol 31 (8) ◽  
pp. 803-816
Author(s):  
Umberto di Porzio
Keyword(s):  
Human Brain ◽  
Cognitive Abilities ◽  
Molecular Genetic ◽  
Adult Size ◽  
Genetic Changes ◽  
Cultural Challenges ◽  
Birth Canal ◽  
Newborn Brain ◽  
Neuronal Interactions ◽  
The Brain

AbstractThe environment increased complexity required more neural functions to develop in the hominin brains, and the hominins adapted to the complexity by developing a bigger brain with a greater interconnection between its parts. Thus, complex environments drove the growth of the brain. In about two million years during hominin evolution, the brain increased three folds in size, one of the largest and most complex amongst mammals, relative to body size. The size increase has led to anatomical reorganization and complex neuronal interactions in a relatively small skull. At birth, the human brain is only about 20% of its adult size. That facilitates the passage through the birth canal. Therefore, the human brain, especially cortex, develops postnatally in a rich stimulating environment with continuous brain wiring and rewiring and insertion of billions of new neurons. One of the consequence is that in the newborn brain, neuroplasticity is always turned “on” and it remains active throughout life, which gave humans the ability to adapt to complex and often hostile environments, integrate external experiences, solve problems, elaborate abstract ideas and innovative technologies, store a lot of information. Besides, hominins acquired unique abilities as music, language, and intense social cooperation. Overwhelming ecological, social, and cultural challenges have made the human brain so unique. From these events, as well as the molecular genetic changes that took place in those million years, under the pressure of natural selection, derive the distinctive cognitive abilities that have led us to complex social organizations and made our species successful.

scholarly journals Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders

2021 ◽  
Vol 11 (4) ◽  
pp. 435
Author(s):  
Andreas-Christian Hade ◽  
Mari-Anne Philips ◽  
Ene Reimann ◽  
Toomas Jagomäe ◽  
Kattri-Liis Eskla ◽  
...  
Keyword(s):  
Alcohol Use ◽  
Molecular Genetic ◽  
Brain Structures ◽  
Thalamic Nuclei ◽  
Genetic Changes ◽  
Molecular Changes ◽  
Gabaergic Neurotransmission ◽  
And Control ◽  
Upregulated Genes

The Mediodorsal (MD) thalamus that represents a fundamental subcortical relay has been underrepresented in the studies focusing on the molecular changes in the brains of subjects with alcohol use disorder (AUD). In the current study, MD thalamic regions from AUD subjects and controls were analyzed with Affymetrix Clariom S human microarray. Long-term alcohol use induced a significant (FDR ≤ 0.05) upregulation of 2802 transcripts and downregulation of 1893 genes in the MD thalamus of AUD subjects. A significant upregulation of GRIN1 (glutamate receptor NMDA type 1) and FTO (alpha-ketoglutarate dependent dioxygenase) was confirmed in western blot analysis. Immunohistochemical staining revealed similar heterogenous distribution of GRIN1 in the thalamic nuclei of both AUD and control subjects. The most prevalent functional categories of upregulated genes were related to glutamatergic and GABAergic neurotransmission, cellular metabolism, and neurodevelopment. The prevalent gene cluster among down-regulated genes was immune system mediators. Forty-two differentially expressed genes, including FTO, ADH1B, DRD2, CADM2, TCF4, GCKR, DPP6, MAPT and CHRH1, have been shown to have strong associations (FDR p < 10−8) with AUD or/and alcohol use phenotypes in recent GWA studies. Despite a small number of subjects, we were able to detect robust molecular changes in the mediodorsal thalamus caused by alcohol emphasizing the importance of deeper brain structures such as diencephalon, in the development of AUD-related dysregulation of neurocircuitry.

Molecular Genetic Changes in Alveolar Soft Part Sarcoma

1998 ◽  
Vol 18 (6) ◽  
pp. 529-543
Author(s):  
Agnes S. Chan ◽  
Jeremy A. Squire ◽  
Paul Thorner ◽  
Maria Zielenska
Keyword(s):  
Soft Part ◽  
Molecular Genetic ◽  
Alveolar Soft Part Sarcoma ◽  
Genetic Changes

scholarly journals Molecular genetic changes in gastric carcinoma

2021 ◽  
Vol 6 ◽  
pp. 30-46
Author(s):  
Juhi Singh ◽  
Puneet Kumar ◽  
Khushi Verma ◽  
Satyender Kumar Tiwary ◽  
Gopeshwar Narayan ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Gastric Carcinoma ◽  
Wide Spectrum ◽  
Molecular Genetic ◽  
Survival Rates ◽  
High Throughput Analysis ◽  
Genetic Changes ◽  
Genetic Level ◽  
New Biomarkers

Gastric cancer remains highly prevalent and accounts for a notable proportion of global cancer mortality and this is associated with poor survival rates. Understanding the molecular genetic changes of gastric carcinoma may offer an insight into its pathogenesis helps in identifying new biomarkers, aid prognostication, and novel treatment targets. Over a past few decades, advances in technology and high throughput analysis have improved understanding of the molecular genetic aspects of gastric cancer. In this article, hierarchy of the changes at genetic and molecular level including several aspects which are heterogenous and represents a wide spectrum such as tumor suppressor genes, oncogenes, cellcycle regulators, apoptosis, cell-adhesion molecules, loss of heterozygosity, microsatellite instability, and epigenetic changes. The classification of gastric carcinoma at molecular and genetic level as well as hereditary gastric carcinoma is elaborated. The molecular genetic aspects regarding pathogenesis, changes and aberrations of all genes and pathways which are involved in gastric cancer are addressed in this review.

scholarly journals Metabolic and molecular-genetic changes in the liver during carbon tetrachloride intoxication

2020 ◽  
Vol 99 (9) ◽  
pp. 996-1000
Author(s):  
Denis O. Karimov ◽  
Tatyana G. Kutlina ◽  
Guzel’ F. Mukhammadiyeva ◽  
Yana V. Valova ◽  
Samat S. Baygildin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Blood Serum ◽  
Pearson Correlation ◽  
Molecular Genetic ◽  
Experimental Studies ◽  
Pcr Amplification ◽  
Statistical Processing ◽  
Male Rats ◽  
Clinical Test ◽  
Genetic Changes

Introduction. Toxic hepatitis (TH) is a complex and multifaceted disease, the development of which is mediated by a complex of biochemical and molecular genetic interactions. The current understanding of the pathogenesis of TH and, as a consequence, its treatment is based on standardization of the phenotype of the disease, often without taking into account metabolic disorders within the cells. Material and methods. experimental studies were performed on white outbred male rats weighing 200-220 g. A 50% solution of TCM was used as a toxicant. Biochemical studies were performed on a laboratory medical photometer “Stat Fax 3300” using clinical test kits and control materials manufactured by Vector-Best LLC. Liver tissue for histological examination was subjected to the standard histological procedure and paraffin embedding. Sections 5-7 μm thick were stained with hematoxylin-eosin. Gene expression analysis was performed using real-time PCR amplification on a RotorGene instrument (QIAGEN). Statistical processing of experimental data was performed using the Pearson correlation coefficient and one-way analysis of variance (ANOVA). The results were considered reliable at p <0.05. Results. As a result of the analysis of the correlation of the expression of the studied genes and the level of biochemical parameters, it was found that the correlation of the expression of the Nfe2l2 and Gstm1 genes was r = 0.812 (p = 0.0001). The dynamics of gene expression of Chek, Gstm1, Gstp1, Nfe2l2, had a negative correlation with the level of AST activity in blood serum. And the expression of the genes Chek, Gclc, Gstm1, Nfe2l2, Ripk, Sod1 with an index of ALT activity in the blood serum. After 72 hours, the expression of almost all of the studied genes became multidirectional. And the correlation between indices is often not determined. An analysis of the relationship between the level of cytolysis enzymes and the correlation level of the studied genes showed that after 72 hours the correlation was observed in the Gstm1, Hmox, and Sod1 genes with the levels of AST and ALT.

Complex Traits in Natural Populations

2020 ◽  
pp. 263-290
Author(s):  
Daniel L. Hartl
Keyword(s):  
Complex Traits ◽  
Population Genomics ◽  
Association Studies ◽  
Natural Populations ◽  
Complex Diseases ◽  
Stabilizing Selection ◽  
Phenotypic Evolution ◽  
Genetic Changes ◽  
Number Of Genes ◽  
Almost All

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

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