The crucial role of genome-wide genetic variation in conservation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

Download Full-text

The crucial role of genome-wide genetic variation in conservation

10.1101/2021.07.05.451163 ◽

2021 ◽

Author(s):

Martin Kardos ◽

Ellie Armstrong ◽

Sarah W Fitzpatrick ◽

Samantha Hauser ◽

Philip Hedrick ◽

...

Keyword(s):

Genetic Variation ◽

Environmental Changes ◽

Population Viability ◽

Adaptive Potential ◽

Biodiversity Crisis ◽

Genome Wide ◽

Simulation Based ◽

Functional Genetic Variation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on the conservation of genome-wide genetic variation, and that this approach should be replaced with another that focuses instead on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that the conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations towards extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide variation on long-term population viability will only worsen the biodiversity crisis.

Download Full-text

Role of genome-wide mRNA-seq profiling in understanding the long-term sperm maintenance in the storage tubules of laying hens

Tropical Animal Health and Production ◽

10.1007/s11250-019-01821-5 ◽

2019 ◽

Vol 51 (6) ◽

pp. 1441-1447 ◽

Cited By ~ 1

Author(s):

Jilong Han ◽

Hafiz Ishfaq Ahmad ◽

Xunping Jiang ◽

Guiqiong Liu

Keyword(s):

Laying Hens ◽

Genome Wide

Download Full-text

AN EXPLORATORY STUDY OF STRATEGIC PLANNING BEHAVIOUR IN SMEs IN SINGAPORE/MALAYSIA CONTEXT

Journal of Enterprising Culture ◽

10.1142/s0218495893000142 ◽

1993 ◽

Vol 01 (02) ◽

pp. 255-278 ◽

Cited By ~ 1

Author(s):

B C GHOSH ◽

AIK-MENG LOW ◽

TECK-MENG TAN ◽

CHEE-ONN CHAN

Keyword(s):

Strategic Planning ◽

Risk Taking ◽

Exploratory Study ◽

Environmental Changes ◽

Information Gathering ◽

Extensive Literature ◽

Chief Executives ◽

Spouse Support

Strategic planning literature is extensive but how small and medium sized firms (SMEs) behave in response to environmental changes and how they incorporate such changes in their medium to long term plan has been insufficiently studied, in the writers’ view, especially in Singapore/Malaysia context. This research is dedicated towards finding a framework for such analysis and testing such framework in 15 local/regional companies. After an extensive literature review from sources which are both international and local, a fairly lengthy questionnaire was developed. As stated, 15 companies’ chief executives (or in their absence, someone equivalent) were interviewed and at the end of each interview a set of structured questions were asked to be filled in. The whole interview process itself took more than a month. The results have been analysed and highlighted. One main finding is that SMEs continue to be family-centred in a local/regional context especially. Among other findings were the process of information gathering which was chiefly informal, the dominance of CEO-centred management, opportunity-seeking and risk-taking in identifying strategies and finally, the role of the spouse-support. This research is multi-faced and deserves to be further explored. Herein lies its limitation as well as its promise. A research of this nature cannot claim to be fully conclusive and hence its natural incompleteness indicates further research continuation.

Download Full-text

The Role of Chloroplast Membrane Lipid Metabolism in Plant Environmental Responses

Cells ◽

10.3390/cells10030706 ◽

2021 ◽

Vol 10 (3) ◽

pp. 706

Author(s):

Ron Cook ◽

Josselin Lupette ◽

Christoph Benning

Keyword(s):

Environmental Conditions ◽

Environmental Changes ◽

Photosynthetic Apparatus ◽

Life Forms ◽

Membrane Lipid ◽

Chloroplast Membrane ◽

Class Composition ◽

Environmental Responses

Plants are nonmotile life forms that are constantly exposed to changing environmental conditions during the course of their life cycle. Fluctuations in environmental conditions can be drastic during both day–night and seasonal cycles, as well as in the long term as the climate changes. Plants are naturally adapted to face these environmental challenges, and it has become increasingly apparent that membranes and their lipid composition are an important component of this adaptive response. Plants can remodel their membranes to change the abundance of different lipid classes, and they can release fatty acids that give rise to signaling compounds in response to environmental cues. Chloroplasts harbor the photosynthetic apparatus of plants embedded into one of the most extensive membrane systems found in nature. In part one of this review, we focus on changes in chloroplast membrane lipid class composition in response to environmental changes, and in part two, we will detail chloroplast lipid-derived signals.

Download Full-text

Interaction between M. tuberculosis Lineage and Human Genetic Variants Reveals Novel Pathway Associations with Severity of TB

Pathogens ◽

10.3390/pathogens10111487 ◽

2021 ◽

Vol 10 (11) ◽

pp. 1487

Author(s):

Michael L. McHenry ◽

Eddie M. Wampande ◽

Moses L. Joloba ◽

LaShaunda L. Malone ◽

Harriet Mayanja-Kizza ◽

...

Keyword(s):

Genetic Variation ◽

Clinical Presentation ◽

Sub Saharan Africa ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Human Genomes ◽

Genome Wide ◽

Sub Saharan ◽

Cellular Replication

Tuberculosis (TB) remains a major public health threat globally, especially in sub-Saharan Africa. Both human and Mycobacterium tuberculosis (MTBC) genetic variation affect TB outcomes, but few studies have examined if and how the two genomes interact to affect disease. We hypothesize that long-term coexistence between human genomes and MTBC lineages modulates disease to affect its severity. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which we identified three MTBC lineages, of which one, L4.6-Uganda, is clearly derived and hence recent. We quantified TB severity using the Bandim TBscore and examined the interaction between MTBC lineage and human single-nucleotide polymorphisms (SNPs) genome-wide, in two independent cohorts of TB cases (n = 149 and n = 127). We found a significant interaction between an SNP in PPIAP2 and the Uganda lineage (combined p = 4 × 10−8). PPIAP2 is a pseudogene that is highly expressed in immune cells. Pathway and eQTL analyses indicated potential roles between coevolving SNPs and cellular replication and metabolism as well as platelet aggregation and coagulation. This finding provides further evidence that host–pathogen interactions affect clinical presentation differently than host and pathogen genetic variation independently, and that human–MTBC coevolution is likely to explain patterns of disease severity.

Download Full-text

Morphobiochemical features of plant adaptation in the Northern forest-steppe of Western Siberia

Bulletin of the State Nikitsky Botanical Gardens ◽

10.36305/0513-1634-2020-136-108-115 ◽

2021 ◽

pp. 108-115

Author(s):

O. O. Vronskaya ◽

O. L. Zandekova

Keyword(s):

Western Siberia ◽

Seasonal Development ◽

Forest Steppe ◽

Adaptive Potential ◽

Northern Forest ◽

The Family ◽

Phases Of Development ◽

Phenological Phases

The article presents the results of long-term research on the adaptive potential of plants of the genus Iris of the family Iridaceae in the Northern forest-steppe of Western Siberia. An assessment of the morphobiological features of irises was carried out, the timing of flowering and the amount of positive temperatures necessary for the onset of such phenological phases of development as regrowth, budding, flowering and fruiting were determined. The indicator role of phenolic compounds and peroxidase in iris leaves during seasonal development was revealed. The studied indicators can be used as an informative parameter for evaluating the state of plants for phyto-indication and introduction.

Download Full-text

Amitosis confers benefits of sex in the absence of sex to Tetrahymena

10.1101/794735 ◽

2019 ◽

Cited By ~ 1

Author(s):

Hao Zhang ◽

Joe A. West ◽

Rebecca A. Zufall ◽

Ricardo B. R. Azevedo

Keyword(s):

Genetic Variation ◽

Copy Number ◽

Environmental Changes ◽

Nuclear Division ◽

Biotic Interactions ◽

Deleterious Mutations ◽

Mutation Load ◽

Low Expectations ◽

Genetic Mechanisms

Sex appears to be the most successful reproductive strategy in eukaryotes despite its many costs1–3. While a complete explanation for sex’s success remains elusive, several evolutionary benefits of sex have been identified4, 5, such as, the purging of deleterious mutations6, 7, the accumulation of beneficial mutations8, 9, and an advantage in biotic interactions3, 10, 11. It is predicted that, by forgoing these benefits, asexual lineages are evolutionary dead-ends2, 12 due to genetic deterioration and/or an inability to adapt to environmental changes. Consistent with this prediction, many asexual lineages show signs of accelerated accumulation of deleterious mutations compared to their sexual relatives13–18. Despite these low expectations, some asexual eukaryotic lineages appear to be successful, including the ciliate Tetrahymena19. Here, we show that the mechanism of somatic nuclear division in Tetrahymena, termed amitosis, provides benefits similar to sex, allowing for the long-term success of asexual lineages. We found that, when compared to mitosis, amitosis with chromosome copy number control reduces mutation load deterministically, slows the accumulation of deleterious mutations under genetic drift, and accelerates adaptation. These benefits arise because, like sex, amitosis can generate substantial genetic variation in fitness among (asexual) progeny. Our results indicate that the ability of Tetrahymena to persist in the absence of sex may depend on non-sexual genetic mechanisms conferring benefits typically provided by sex, as has been found in other asexual lineages20–23.

Download Full-text

Genetic Susceptibility Loci for Childhood Acute Lymphoblastic Leukemia Among Japanese

Blood ◽

10.1182/blood.v126.23.3731.3731 ◽

2015 ◽

Vol 126 (23) ◽

pp. 3731-3731

Author(s):

Kevin Y Urayama ◽

Masatoshi Takagi ◽

Takahisa Kawaguchi ◽

Keitaro Matsuo ◽

Yoichi Tanaka ◽

...

Keyword(s):

Genetic Variation ◽

Acute Lymphoblastic Leukemia ◽

Lymphoblastic Leukemia ◽

Study Group ◽

Susceptibility Loci ◽

East Asians ◽

Childhood All ◽

Genome Wide

Abstract Scrutiny of the human genome through evaluation of common genetic variants has revealed hundreds of disease susceptibility loci. In childhood acute lymphoblastic leukemia (ALL), six regions that have replicated in several populations are now considered known susceptibility loci (ARID5B, IKZF1, CEBPE, CDKN2A, PIP4K2A, and GATA3), but their effects have yet to be fully confirmed in populations of non-European ancestry. Targeted validation attempts based on the same SNPs originally identified in European ancestral populations have been performed in East Asians, but findings have been inconsistent. This may be due to differences in linkage disequilibrium patterns, allele frequency, and/or magnitude of effect between Europeans and East Asians; thus a comprehensive characterization of genetic variation across the targeted genetic loci is required for an appropriate validation attempt in different populations. Using a large network of hospitals within the Tokyo Children's Cancer Study Group, saliva samples from previously diagnosed childhood ALL patients (aged 0-19 years) were collected between December 2012 and May 2015. Genome-wide single nucleotide polymorphism (SNP) genotyping was performed and resulted in the inclusion of a total of 570 ALL patients, with genetic data available for up to about 500,000 SNPs after quality control exclusions. Control genome-wide data were available for 2,712 previously genotyped samples from the Nagahama Study Group and Aichi Cancer Center Study, Japan. SNP imputation was performed on the combined case-control dataset using ShapeIT and Minimac3, and the 1000 Genomes Project Phase I Version 3 as the reference population. Tests of association between childhood ALL and all available SNP genotypes across the six genes (mentioned above) implicated in previous genome-wide association studies was performed using logistic regression and assuming a log-additive model of inheritance. Of the six genomic regions examined, SNPs within the IKZF1, ARID5B, and PIP4K2A genes showed a statistically significant association with childhood ALL risk after Bonferroni correction. SNPs with the strongest evidence of association for these three genes included rs7090445 (ARID5B, OR=1.75, P =3.7x10-17), rs12533431 (IKZF1, OR=1.43, P =4.3x10-5), and rs11013045 (PIP4K2A, OR=0.76, P =9.5x10-5). Further examination of these regions indicated a second independently associated locus within ARID5B. Furthermore, we observed that the same previously reported primary ALL susceptibility SNPs for IKZF1 (e.g. rs4132601, rs11978267) and PIP4K2A (e.g. rs10828317, rs7088318) were not associated in Japanese. This highlights the importance of considering regional genetic variation comprehensively when testing the role of previously implicated candidate regions in a different racial/ethnic population. Characterization of the role of CEBPE, CDKN2A, and GATA3 genetic variation in Japanese may benefit from greater statistical power and potentially additional coverage of SNPs within these regions. Disclosures No relevant conflicts of interest to declare.

Download Full-text

Genetics of psoriasis: a basis for precision medicine

Precision Clinical Medicine ◽

10.1093/pcmedi/pbz011 ◽

2019 ◽

Vol 2 (2) ◽

pp. 120-130 ◽

Cited By ~ 3

Author(s):

Delin Ran ◽

Minglong Cai ◽

Xuejun Zhang

Keyword(s):

Genetic Variation ◽

Precision Medicine ◽

Genetic Factors ◽

Genome Wide Association Study ◽

Direct Sequencing ◽

Disease Prediction ◽

Inflammatory Skin Disease ◽

Polygenic Inheritance ◽

Genome Wide

AbstractPsoriasis is an inflammatory skin disease with a background of polygenic inheritance. Both environmental and genetic factors are involved in the etiology of the disease. In the last two decades, numerous studies have been conducted through linkage analysis, genome-wide association study (GWAS), and direct sequencing to explore the role of genetic variation in disease pathogenesis and progression. To date, >80 psoriasis susceptibility genes have been identified, including HLA-Cw6, IL12B, IL23R, and LCE3B/3C. Some genetic markers have been applied in disease prediction, clinical diagnosis, treatment, and new drug development, which could further explain the pathogenesis of psoriasis and promote the development of precision medicine. This review summarizes related research on genetic variation in psoriasis and explores implications of the findings in clinical application and the promotion of a personalized medicine project.

Download Full-text

Open Issues in Evolutionary Robotics

Evolutionary Computation ◽

10.1162/evco_a_00172 ◽

2016 ◽

Vol 24 (2) ◽

pp. 205-236 ◽

Cited By ~ 48

Author(s):

Fernando Silva ◽

Miguel Duarte ◽

Luís Correia ◽

Sancho Moura Oliveira ◽

Anders Lyhne Christensen

Keyword(s):

Evolutionary Computation ◽

Autonomous Robots ◽

Behavioral Control ◽

Evolutionary Robotics ◽

Simulation Based ◽

Canonical Approach ◽

Task Specification ◽

Open Issues

One of the long-term goals in evolutionary robotics is to be able to automatically synthesize controllers for real autonomous robots based only on a task specification. While a number of studies have shown the applicability of evolutionary robotics techniques for the synthesis of behavioral control, researchers have consistently been faced with a number of issues preventing the widespread adoption of evolutionary robotics for engineering purposes. In this article, we review and discuss the open issues in evolutionary robotics. First, we analyze the benefits and challenges of simulation-based evolution and subsequent deployment of controllers versus evolution on real robotic hardware. Second, we discuss specific evolutionary computation issues that have plagued evolutionary robotics: (1) the bootstrap problem, (2) deception, and (3) the role of genomic encoding and genotype-phenotype mapping in the evolution of controllers for complex tasks. Finally, we address the absence of standard research practices in the field. We also discuss promising avenues of research. Our underlying motivation is the reduction of the current gap between evolutionary robotics and mainstream robotics, and the establishment of evolutionary robotics as a canonical approach for the engineering of autonomous robots.

Download Full-text