Ion Transporter Gene Families as Physiological Targets of Natural Selection During Salinity Transitions in a Copepod

Physiology ◽  
2021 ◽  
Vol 36 (6) ◽  
pp. 335-349 ◽  
Author(s):  
Carol Eunmi Lee
Keyword(s):  
Natural Selection ◽  
Balancing Selection ◽  
Gene Families ◽  
Physiological Adaptation ◽  
Transporter Gene ◽  
Evolutionary Mechanisms ◽  
Ion Transporter ◽  
Species Invasions ◽  
Key Factor ◽  
Freshwater Invasions

Salinity is a key factor that structures biodiversity on the planet. With anthropogenic change, such as climate change and species invasions, many populations are facing rapid and dramatic changes in salinity throughout the globe. Studies on the copepod Eurytemora affinis species complex have implicated ion transporter gene families as major loci contributing to salinity adaptation during freshwater invasions. Laboratory experiments and population genomic surveys of wild populations have revealed evolutionary shifts in genome-wide gene expression and parallel genomic signatures of natural selection during independent salinity transitions. Our results suggest that balancing selection in the native range and epistatic interactions among specific ion transporter paralogs could contribute to parallel freshwater adaptation. Overall, these studies provide unprecedented insights into evolutionary mechanisms underlying physiological adaptation during rapid salinity change.

Genome-wide identification of polar auxin transporter gene families reveals a possible new polar auxin flow in inverted cuttings of Populus yunnanensis

Gene ◽  
2020 ◽  
pp. 145349
Author(s):  
An-Pei Zhou ◽  
Yuan-Yuan Zhong ◽  
Si-Qi Li ◽  
Xuan Fei ◽  
Pei-Hua Gan ◽  
...  
Keyword(s):  
Gene Families ◽  
Transporter Gene ◽  
Genome Wide ◽  
Auxin Transporter

scholarly journals Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

2020 ◽  
Vol 21 (5) ◽  
pp. 1752 ◽  
Author(s):  
Jin Yang ◽  
Jie Zhou ◽  
Hong-Jun Zhou ◽  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Gene Families ◽  
Small Scale ◽  
Transporter Gene ◽  
Promoter Regions ◽  
Network Analyses ◽  
Group I

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.

scholarly journals Identification and Analysis ofMedicago truncatulaAuxin Transporter Gene Families Uncover their Roles in Responses toSinorhizobium melilotiInfection

2015 ◽  
Vol 56 (10) ◽  
pp. 1930-1943 ◽  
Author(s):  
Chenjia Shen ◽  
Runqing Yue ◽  
Youhuang Bai ◽  
Rong Feng ◽  
Tao Sun ◽  
...  
Keyword(s):  
Gene Families ◽  
Transporter Gene

scholarly journals In Silico Genome-Wide Analysis of the ATP-Binding Cassette Transporter Gene Family in Soybean (Glycine max L.) and Their Expression Profiling

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Awdhesh Kumar Mishra ◽  
Jinhee Choi ◽  
Muhammad Fazle Rabbee ◽  
Kwang-Hyun Baek
Keyword(s):  
Gene Family ◽  
Abc Transporter ◽  
Abc Transporters ◽  
In Silico ◽  
Gene Families ◽  
Protein Domain ◽  
Atp Binding ◽  
Transporter Gene ◽  
Genome Wide ◽  
Atp Binding Cassette

ATP-binding cassette (ABC) transporters constitute one of the largest gene families in all living organisms, most of which mediate transport across biological membranes by hydrolyzing ATP. However, detailed studies of ABC transporter genes in the important oil crop, soybean, are still lacking. In the present study, we carried out genome-wide identification and phylogenetic and transcriptional analyses of the ABC gene family in G. max. A total of 261 G. max ABC (GmABCs) genes were identified and unevenly localized onto 20 chromosomes. Referring to protein-domain orientation and phylogeny, the GmABC family could be classified into eight (ABCA-ABCG and ABCI) subfamilies and ABCG were the most abundantly present. Further, investigation of whole genome duplication (WGD) signifies the role of segmental duplication in the expansion of the ABC transporter gene family in soybean. The Ka/Ks ratio indicates that several duplicated genes are governed by intense purifying selection during evolution. In addition, in silico expression analysis based on RNA-sequence using publicly available database revealed that ABC transporters are differentially expressed in tissues and developmental stages and in dehydration. Overall, we provide an extensive overview of the GmABC transporter gene family and it promises the primary basis for the study in development and response to dehydration tolerance.

The Simulated Evolution of Biochemical Guilds: Reconciling Gaia Theory and Natural Selection

1999 ◽  
Vol 5 (4) ◽  
pp. 291-318 ◽  
Author(s):  
Keith Downing ◽  
Peter Zvirinsky
Keyword(s):  
Natural Selection ◽  
Artificial Life ◽  
Large Scale ◽  
Resource Competition ◽  
Nutrient Recycling ◽  
Nutrient Ratios ◽  
Evolutionary Mechanisms ◽  
Life Model ◽  
Gaia Theory ◽  
Implicit Coordination

Gaia theory, which states that organisms both affect and regulate their environment, poses an interesting problem to Neo-Darwinian evolutionary biologists and provides an exciting set of phenomena for artificial-life investigation. The key challenge is to explain the emergence of biotic communities that are capable, via their implicit coordination, of regulating large-scale biogeochemical factors such as the temperature and chemical composition of the biosphere, but to assume no evolutionary mechanisms beyond contemporary natural selection. Along with providing an introduction to Gaia theory, this article presents simulations of Gaian emergence based on an artificial-life model involving genetic algorithms and guilds of simple metabolizing agents. In these simulations, resource competition leads to guild diversity; the ensemble of guilds then manifests life-sustaining nutrient recycling and exerts distributed control over environmental nutrient ratios. These results illustrate that standard individual-based natural selection is sufficient to explain Gaian self-organization, and they help clarify the relationships between two key metrics of Gaian activity: recycling and regulation.

Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1216-1229 ◽  
Author(s):  
Qingyang Huang ◽  
Alex Beharav ◽  
Youchun Li ◽  
Valery Kirzhner ◽  
Eviatar Nevo
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Wild Barley ◽  
Permutation Test ◽  
Balancing Selection ◽  
Real Data ◽  
Hordeum Spontaneum ◽  
Data Sets ◽  
Total Genetic Diversity ◽  
Ssr Loci

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun–rock (11 genotypes), (ii) sun–soil (18 genotypes), (iii) shade–soil (11 genotypes), and (iv) shade–rock (14 genotypes). Fifty-four genotypes were tested for ecological–genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun–rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, GST was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun–rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).Key words: natural selection, genetic diversity, microsatellites, adaptation, Hordeum spontaneum, wild barley, microsite divergence.

scholarly journals Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

2007 ◽  
Vol 274 (1611) ◽  
pp. 861-869 ◽  
Author(s):  
Elvira de Eyto ◽  
Philip McGinnity ◽  
Sofia Consuegra ◽  
Jamie Coughlan ◽  
Jarle Tufto ◽  
...  
Keyword(s):  
Natural Selection ◽  
Atlantic Salmon ◽  
Balancing Selection ◽  
Natural Populations ◽  
Class Ii ◽  
Major Histocompatibility ◽  
Genotype Frequencies ◽  
Fitness Consequences ◽  
In The Wild ◽  
Class Ii Alpha

Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon ( Salmo salar ) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.

scholarly journals Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress

FEBS Journal ◽  
2010 ◽  
Vol 277 (14) ◽  
pp. 2954-2969 ◽  
Author(s):  
ChenJia Shen ◽  
YouHuang Bai ◽  
SuiKang Wang ◽  
SaiNa Zhang ◽  
YunRong Wu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Sorghum Bicolor ◽  
Expression Profile ◽  
Gene Families ◽  
Transporter Gene ◽  
Auxin Transporter

scholarly journals Pragmatics and Language Evolution

2017 ◽  
Author(s):  
Marieke Woensdregt ◽  
Kenny Smith
Keyword(s):  
Natural Selection ◽  
Social Learning ◽  
Cultural Evolution ◽  
Computational Models ◽  
Language Use ◽  
Language Evolution ◽  
Biological Evolution ◽  
Cognitive Capacity ◽  
Food Sources ◽  
Evolutionary Mechanisms

Pragmatics is the branch of linguistics that deals with language use in context. It looks at the meaning linguistic utterances can have beyond their literal meaning (implicature), and also at presupposition and turn taking in conversation. Thus, pragmatics lies on the interface between language and social cognition. From the point of view of both speaker and listener, doing pragmatics requires reasoning about the minds of others. For instance, a speaker has to think about what knowledge they share with the listener to choose what information to explicitly encode in their utterance and what to leave implicit. A listener has to make inferences about what the speaker meant based on the context, their knowledge about the speaker, and their knowledge of general conventions in language use. This ability to reason about the minds of others (usually referred to as “mindreading” or “theory of mind”) is a cognitive capacity that is uniquely developed in humans compared to other animals. What we know about how pragmatics (and the underlying ability to make inferences about the minds of others) has evolved. Biological evolution and cultural evolution are the two main processes that can lead to the development of a complex behavior over generations, and we can explore to what extent they account for what we know about pragmatics. In biological evolution, changes happen as a result of natural selection on genetically transmitted traits. In cultural evolution on the other hand, selection happens on skills that are transmitted through social learning. Many hypotheses have been put forward about the role that natural selection may have played in the evolution of social and communicative skills in humans (for example, as a result of changes in food sources, foraging strategy, or group size). The role of social learning and cumulative culture, however, has been often overlooked. This omission is particularly striking in the case of pragmatics, as language itself is a prime example of a culturally transmitted skill, and there is solid evidence that the pragmatic capacities that are so central to language use may themselves be partially shaped by social learning. In light of empirical findings from comparative, developmental, and experimental research, we can consider the potential contributions of both biological and cultural evolutionary mechanisms to the evolution of pragmatics. The dynamics of types of evolutionary processes can also be explored using experiments and computational models.

scholarly journals An evolutionary compass for detecting signals of polygenic selection and mutational bias

2017 ◽  
Author(s):  
Lawrence H. Uricchio ◽  
Hugo C. Kitano ◽  
Alexander Gusev ◽  
Noah A. Zaitlen
Keyword(s):  
Crohn’S Disease ◽  
Natural Selection ◽  
Educational Attainment ◽  
Population Stratification ◽  
Mutational Bias ◽  
Summary Statistics ◽  
Mutation Bias ◽  
Trait Variation ◽  
Evolutionary Mechanisms ◽  
Polygenic Selection

Selection and mutation shape genetic variation underlying human traits, but the specific evolutionary mechanisms driving complex trait variation are largely unknown. We developed a statistical method that uses polarized GWAS summary statistics from a single population to detect signals of mutational bias and selection. We found evidence for non-neutral signals on variation underlying several traits (BMI, schizophrenia, Crohn’s disease, educational attainment, and height). We then used simulations that incorporate simultaneous negative and positive selection to show that these signals are consistent with mutational bias and shifts in the fitness-phenotype relationship, but not stabilizing selection or mutational bias alone. We additionally replicate two of our top three signals (BMI and educational attainment) in an external cohort, and show that population stratification may have confounded GWAS summary statistics for height in the GIANT cohort. Our results provide a flexible and powerful framework for evolutionary analysis of complex phenotypes in humans and other species, and offer insights into the evolutionary mechanisms driving variation in human polygenic traits.Impact summaryMany traits are variable within human populations and are likely to have a substantial and complex genetic component. This implies that mutations that have a functional impact on complex human traits have arisen throughout our species’ evolutionary history. However, it remains unclear how processes such as natural selection may have acted to shape trait variation at the genetic and phenotypic level. Better understanding of the mechanisms driving trait variation could provide insights into our evolutionary past and help clarify why it has been so difficult to map the preponderance of causal variation for common heritable diseases.In this study, we developed and applied methods for detecting signatures of mutation bias (i.e., the propensity of a new variant to be either trait-increasing or trait-decreasing) and natural selection acting on trait variation. We applied our approach to several heritable traits, and found evidence for both natural selection and mutation bias, including selection for decreased BMI and decreased risk for Crohn’s disease and schizophrenia.While our results are consistent with plausible evolutionary scenarios shaping a range of traits, it should be noted that the field of polygenic selection detection is still new, and current methods (including ours) rely on data from genome-wide association studies (GWAS). The data produced by these studies may be vulnerable to certain cryptic biases, especially population stratification, which could induce false selection signals. We therefore repeated our analyses for the top three hits in a cohort that should be less susceptible to this problem – we found that two of our top three signals replicated (BMI and educational attainment), while height did not. Our results highlight both the promise and pitfalls of polygenic selection detection approaches, and suggest a need for further work disentangling stratification from selection.

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