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Plant population genetics
Abstract
Over the last decade, there has been an exponential growth in interest and investigation of the problem of how best to conserve populations of endangered species. As a result, there is now a very extensive and widely scattered literature on this subject. Among recent papers which cite a large number of references are those of Boyce (1992), Ellstrand and Elam (1993) and Nunney and Campbell (1993). Soulé’s (1987) book gives a valuable survey of the subject, in which the chapter by Lande and Barrowclough (1987) deals with the population genetics of the problem. Much of this literature is concerned with the conservation of species where ex situ conservation is not a realistic alternative. The demographic and population genetics theory on which discussion of this broader issue is based, however, is also relevant to the special case of those species where the conservation of material in gene banks is possible. The purpose of this chapter is to give a brief outline of the population genetics theory on which discussion of in situ conservation is based and to introduce some of the terms and concepts used in the literature. We also indicate the kinds of experimental investigation of populations which are necessary to produce better recommendations about minimum viable population size than are possible at present.
... Genetic polymorphism of populations can be influenced by many factors, including the history of population, diversity of ecological factors etc. (see, e.g., Hartl, 1988). In Latvia, populations of L. loeselii provided age differences which are depending from the peculiarities of the habitat formation. ...
... There are different observations in some case studies (Hensen andOberprieler 2005, Stöcklin et al., 2009). Although generally after fragmentation of populations the genetic drift led to variability decrease (Hartl, 1988) later on some other abovementioned factors like the age of populations and ecological diversity can accelerate the genetic diversity. Therefore, the population size should be taken into consideration in context with other factors influencing genetic polymorphism. ...
According to the Global Strategy for Plant Conservation, 75% of endangered species should be preserved in ex situ collections till 2020. The genus Liparis has a lot of recognised taxons, but only one species, Liparis loeselii (L.) Rich., grows in Europe. L. loeselii is a rare and endangered orchid species occurring in Europe. In Latvia L. loeselii is classified as the third category of endangered and protected species. To develop the best conservation strategy, the knowledge concerning the genetic differences of protected plants in a particular area is crucial. For this purpose, the genetic diversity of L. loeselii populations from different Latvian habitats was tested. The inter-retrotransposon amplified polymorphism method (iPBS) was used for population genetic diversity evolution. In total, 54 accessions from nine habitats were collected and analysed. L. loeselii leaves have a high content of phenols that reduce the quality of extracted DNA. It was found that the percentage of polymorph loci varied among the populations of L. loeselii growing in different habitats; some of the populations were genetically homogeneous. The genetic diversity levels of L. loeselii populations are related with the population age and the growing conditions.
... For example, the last individuals of the dusky seaside sparrow (Ammodramus maritimus nigrescens) that were meant to be used in a breeding program turned out to be all male [5]. Deviations from equal sex ratios also reduce the genetically effective population size (N e ) relative to the census size (N c ) (Box 8.1), because N e = 4N m N f /(N m + N f ), with N m and N f being the number of mature males and females, respectively [6]. Sex ratio biases, therefore, reduce the genetic diversity and, hence, the evolutionary potential of a population, and may contribute to an extinction vortex, especially in small or declining populations [7]. ...
... • N c : census population size • N e : genetically effective population size, i.e. the size of an idealized model population that loses genetic diversity at the same rate as the study population [6]. ...
Sex differentiation is generally more labile in gonochoristic fish than it is, for example, in birds and mammals. Environmentally induced sex reversal is, therefore, often possible, and creates genotype‐phenotype mismatches that can be useful in population management. Interestingly, sex chromosomes of fish are typically not significantly decayed (i.e., all types of offspring of sex‐reversed individuals may be viable, including YY and WW individuals that can then often be sex reversed again). Releasing sex‐reversed fish, or releasing untreated YY and WW offspring of sex‐reversed fish, into natural populations can, therefore, affect the sex ratio of the population in the following generations and, hence, affect population growth.
Some types of releases are likely to boost population growth if the number of females are limiting (e.g., WW individuals to create female‐biased population sex ratios), while others can be used to reduce growth of undesired population (e.g., YY individuals to create male‐biased sex ratios). However, these ideas remain still largely untested. Key variables in respective population models are the effects of sex reversal and of unusual karyotypes on viability and reproduction under natural conditions. These key variables need to be determined to allow for data‐based models that can serve as basis for field trials.
... Haplotype phase and linkage disequilibrium (LD) between SNPs were estimated using IMPUTE2 version 2.3.2 [18] and Haploview version 4.2 [19] programs, respectively. We estimated D′ values among SNPs using R package "genetics" [20]. The LDs between pairs of the EGLN1 SNPs in four ethnic groups (East Asian, South Asian, European, and African populations) from the 1000 Genomes Project (http://www.internationalgenome.org/, [21]) were surveyed, employing LDlink web-based tools (https:// analysistools.nci.nih.gov/LDlink/, ...
... In the 46 subjects, the proportion of haplotype "GT" was the highest (32%), followed by "CT" (30%), "GC" (22%), and "CC" (16%). The proportions of diplotypes "CT/CT" (HL diplotype) and "GC/GC" (non-HL diplotype) were 20 and 11%, respectively. We compared time series variations of SpO 2 levels among individuals with different haplotypes (Fig. 4a) and diplotypes (Fig. 4b). ...
Background:
Recent studies have explored various genetic and physiological factors related to high-altitude adaptation in highlander populations. However, the effects of single nucleotide polymorphisms (SNPs), influencing such adaptation, on physiological responses to hypobaric hypoxia have not been examined in lowlanders with lowlander ancestry. Thus, we aimed to investigate the association between SNPs around the EGLN1 genomic region, possibly involved in high-altitude adaptation, and physiological changes to hypobaric hypoxia exposure in a cohort of Japanese lowlanders.
Methods:
Physiological data were obtained from 46 healthy Japanese male students under different atmospheric pressure conditions (equivalent to sea level and altitudes of 2500 and 4000 m). Genotypes of seven SNPs around EGLN1 were determined in all subjects by PCR-direct sequencing or TaqMan SNP genotyping assay.
Results:
Results of the association study suggest that percutaneous arterial oxygen saturation (SpO2) responses of individuals with rs12097901 and rs2790859 alleles, whose frequencies are high in highlander populations (HL alleles), may be susceptible to acute hypobaric hypoxia. SpO2levels of individuals with HL alleles were lower than those of individuals with non-HL alleles. At the same time, the subjects with HL alleles did not appear to have any remarkable hematological or pulmonary features that may counteract the low levels of SpO2. One may hypothesize that the low SpO2levels in HL allele carriers could be a risk factor for acute mountain sickness in Japanese population.
Conclusions:
Our findings suggest that rs12097901 and rs2790859 genotypes affect SpO2responses and may be associated with the susceptibility to acute hypobaric hypoxia in Japanese population.
... Statistical analyses were conducted in R version 3.3.1 [28] unless stated otherwise. Genotype Hardy-Weinberg equilibrium (HWE) was tested by chi-squared test or Fisher's exact test (package::function, genetics [29]::HWE.chisq and HWE.exact). Pairwise D' and r 2 were calculated to estimate linkage disequilibrium (LD) between loci within a gene (genetics [29]::LD). ...
... and HWE.exact). Pairwise D' and r 2 were calculated to estimate linkage disequilibrium (LD) between loci within a gene (genetics [29]::LD). ABCB1 haplotypes were inferred using PHASE 2.1 [30,31] as previously described [32]; individuals were excluded from further haplotype analysis if their haplotype pairs had low confidence predictions (predicted probability <0.8) due to missing genotype data or rare genotype combinations. Common haplotypes were defined based on a frequency of greater than 0.05. ...
Tacrolimus (TAC) is a first‐line immunosuppressant used to prevent organ rejection after kidney transplantation. There is large inter‐individual variability in its pharmacokinetics. Single nucleotide polymorphisms (SNPs) in genes encoding TAC metabolising enzymes cytochromes P450 3A4/5 (CYP3A4/5), P‐glycoprotein efflux transporter (ABCB1), their expression regulator pregnane X receptor (NR1I2), and CYP3A co‐factor cytochrome P450 reductase (POR), have been studied for their effects on tacrolimus disposition. However, except for CYP3A5*3, controversies remain about their roles in predicting dose‐adjusted trough blood TAC concentrations (C0/D). This study aimed to investigate the effects of ABCB1 (61A>G, 1199G>A, 1236C>T, 2677G>T and 3435C>T), CYP3A4*22, CYP3A5*3, NR1I2 (8055C>T, 63396C>T and ‐25385C>T) and POR*28 SNPs on TAC C0/D. In total, 165 kidney transplant recipients were included in this study. SNPs were genotyped by probe‐based real‐time polymerase chain reaction. Associations between log‐transformed whole blood TAC C0/D (measured at 1 and 3 months post‐transplant) and genotypes/haplotypes were assessed by linear mixed effects analysis, controlling for age, sex and haematocrit. It was observed that CYP3A5 expressors (*1/*1 + *1/*3) (P = 5.5×10‐16) and ABCB1 61G allele carriers (P = 0.001) had lower log‐transformed TAC C0/D (56% and 26% lower geometric mean TAC C0/D, respectively) and accounted for approximately 30% and 4%, respectively, of log‐transformed TAC C0/D variability in the first 3 months post‐transplant. In conclusion, CYP3A5*3 is a major, and ABCB1 61A>G is a novel, although minor, genetic factor affecting TAC C0/D in kidney transplant recipients.
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... Because of this, the commonly used Hardy-Weinberg proportion test for X-chromosomal markers considers only females in the test [74], as implemented in the popular software for genetic studies, PLINK [69,70]. Some other computer programs for the Hardy-Weinberg proportion test, such as the functions in the R package "genetics" for genetic studies [75], do not distinguish between the autosomal and X-chromosomal markers in the test. That is, it is left to the user to decide how to deal with the hemizygous males when testing Hard-Weinberg proportions for X-chromosomal markers [74]. ...
... Several functions or packages have been developed for the purpose of testing Hardy-Weinberg proportions. We first focus on the functions available in the population genetic package "genetics" [75], and then introduce several other packages developed specifically for the Hardy-Weinberg proportion exact test. The "genetics" package has two functions, HWE.chisq and HWE.exact, for testing the departure from Hardy-Weinberg proportions based on the chi-squared and exact tests, respectively. ...
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson’s chi-squared goodness-of-fit test and the exact test. Pearson’s chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case–control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
... ecogeographic/genetic/trait) is distributed within and among populations throughout the target territory. For each CWR, if no studies on ecogeographic/genetic/trait diversity have been carried out, Lawrence and Marshall (1997) have recommended the conservation of five populations from the most ecogeographically diverse sites in order to maximize genetic diversity conservation. The determination of the actual number of sites is, nevertheless, likely to be dictated by the financial and human resources available for implementation. ...
The Interactive Toolkit for Crop Wild Relative Conservation Planning is designed to provide guidance to plan and implement active in situ and ex situ conservation of crop wild relatives at any geographic scale. The conservation recommendations that result from this national CWR conservation planning process are used to develop National Strategic Action Plans (NSAP) (or National Strategies) for the conservation and sustainable use of CWR. The interactive online version of the toolkit is available at: http://www.cropwildrelatives.org/conservation-toolkit/.
... = (k-1) (s-1), en donde k es el número de alelos diferentes, N el número de organismos y s el número de muestras (Workman y Niswander, 1970). Se estimó el número de migrantes por generación de acuerdo a N e m = (Fst -1 -1)/2 (Hartl, 1988). Debido a que las truchas recolectadas en el Arroyo El Mocho Bill fueron translocadas de la localidad de Arroyo El Largo, estas dos localidades se reconocen como una sola área de muestreo y se compara con las recolectadas en los otros arroyos. ...
La trucha Yaqui pertenece a un grupo de truchas nativas no descritas del género Oncorhynchus del Noroeste de México. Estudios morfológicos y moleculares postulan a la trucha Yaqui como una nueva especie exclusiva para las cuencas de los ríos Yaqui, Mayo y Casas Grandes y, evolutivamente muy cercana a la trucha arcoíris, Oncorhynchus mykiss. El conocimiento de su historia natural es escaso. Se estudió la variabilidad genética poblacional y su estatus de conservación en su distribución en Sonora en la región de Mesa Tres Ríos. Se muestrearon seis arroyos de aguas frías (localidades) en la región de Mesa Tres Ríos en dos vertientes geográficas en la búsqueda de estructura genética poblacional. Se analizaron 61 secuencias completas de la región control del ADN mitocondrial. Se obtuvieron nueve haplotipos, tres de ellos se encontraron en ambas vertientes de las localidades del área estudiada. Los resultados mostraron una baja diferenciación genética poblacional (Fst = 0.08035) y un moderado número de migrantes por generación (Nem = 5.72), que resulta en una falta de estructura poblacional y sustenta la hipótesis de una sola población de trucha Yaqui en las vertientes muestreadas de la región de Mesa Tres Ríos, Sonora.
... LD) between the disease locus and the marker locus n generations ago, where ( ) ( ) n P MA is the haplotype frequency of ( ) MA n generations ago. From standard genetic theory (Equation (1.10) of Hartl[22]), the LD at the present time is θ is the recombination fraction between the disease locus and the marker locus. Thus, ...
Population stratification is always a concern in association analysis. There is a debate on the extent of the problem in less extreme situations (Thomas and Witte [1], Wacholder et al. [2]). Wacholder et al.[3] and Ardlie et al. [4] showed that hidden population structure is not a serious threat to case-control designs. We propose a method of assessing the seriousness of the population stratification before designing association studies. If population stratification is not a serious problem, one may consider using case-control study instead of family-based design to get more power. In a case-control design, we compare chi-square statistics from a structured population (a union of two subpopulations) and a homogeneous population with the same prevalence and allele frequencies. We provide an explicit formula to calculate the chi-square statistics from 17 parameters, such as proportions of subpopulation, allele frequencies in subpopulations, etc. We choose these factors because they have potential to cause false associations. Each parameter takes a random value in a chosen range. We then calculate the likelihood of getting opposite conclusions in the structured and the homogeneous populations. This is the likelihood of having false positives caused by population stratification. The advantage of this method is to provide a cost effective way to choose between using case-control data and using family data before actually collecting those data. We conclude that sample sizes have a significant effect on the likelihood of false positive caused by population stratification. The larger the sample size is, the more likely to have false positive if the population structure is ignored. If the sample size will be smaller than 200 by budget constraints, then case-control study may be a better choice because of its power.
... The "Beringian Standstill" model places the ancestral Native American population in the Beringian refugium during much or all of the LGM (2, 5-7), where it was geographically isolated from the Siberian population by uninhabitable areas in northeastern Asia and unable to expand into the Americas because of the coalesced Laurentide and Cordilleran ice sheets (Fig. 1B). The genetic isolation is a key point, as evolution occurs more readily in the absence of gene flow (59). The FADS polymorphisms and EDAR V370A likely existed in the pre-LGM ancestral populations [although the allele is not present in Denisovans (60)]. ...
Several genome-wide association studies reveal that a variant of the Ectodysplasin A Receptor (EDAR) has an additive effect on human incisorshoveling, such that the presence of one or two alleles of V370A corresponds to a moderate or strong degree of shoveling. We analyzed shoveling for 5,333 individuals from 54 archaeological populations across Eurasia and the Western Hemisphere. We use an evolutionary quantitative approach to test the hypothesis that genetic drift alone can account for the shift in phenotypic mean between Asian and Western Hemisphere populations, as the latter demonstrate much higher frequencies and degrees of shoveling. We employ a range of theoretical extremes for heritability estimates (0.05 to 1), a range of possible phenotypic variances (0.86 to 1.23), and a generation time of 25 years across 100 to 400 generations. We find that all combinations of parameter values within published ranges reject the neutral hypothesis with 95% confidence, suggesting that the increase in incisor shoveling observed in Native American populations is the result of selection. This finding accords with the genomic evidence that reveals strong selection for the EDAR V370A allele. This concurrence of dental and genomic data places the selection event on V370A within the Beringian refugium during the Last Glacial Maximum, a region that is environmentally extreme due its very low levels of ultraviolet radiation exposure. We hypothesize that the phenotypic target of selection was likely the pleiotropically related ductal branching of the mammary gland rather than incisor shoveling.
... To understand the behavior in Eq. (6), let us assume that the mutation rate µ is so low that the population may have only two alleles at most, i.e., one is resident and denoted by A, and the other is mutant and denoted by a. These alleles are related to the expected progeny sex ratio but independent of the probability for the carrier to be a parent of the next generation [16]. Let x and X be the expected progeny sex ratios of a and A, respectively. ...
A question in evolutionary biology is why the number of males is approximately equal to that of females in many species, and Fisher's theory of equal investment answers that it is the evolutionarily stable state. The Fisherian mechanism can be given a concrete form by a genetic model based on the following assumptions: (1) Males and females mate at random. (2) An allele acts on the father to determine the expected progeny sex ratio. (3) The offspring inherits the allele from either side of the parents with equal probability. The model is known to achieve the 1:1 sex ratio due to the invasion of mutant alleles with different progeny sex ratios. In this study, however, we argue that mutation plays a more subtle role in that fluctuations caused by mutation renormalize the sex ratio and thereby keep it away from 1:1 in general. This finding shows how the sex ratio is affected by mutation in a systematic way, whereby the effective mutation rate can be estimated from an observed sex ratio.
... This is also consistent with the work on genetic variation in Prunus Africana showing that genetic distinctness and differentiation of populations may arise from geographic and ecological isolation (Dawson et al., 1999). Hartl (1988) suggested that an Fst range of 0-0.05, 0.05-0.15, 0.15-0.25 and above 0.25 indicates little, moderate, large and very large differentiation, respectively. ...
... Genski diverzitet po jednom lokusu je definiran kao: Prekid izolacije ("isolate breaking") se odnosi na pojavu da kada subpopulacije (bivše izoliranê populacije) ostvaruju sekundarni kontakt ili se stapaju, usljed čega se reduciraju frekvencije homozigotnih genotipova. Ovaj fenomen je suprotan Wahlundovom principu (Hartl 1988). ...
... Whereas for outbred stocks it is not about individual uniformity. The population should remain constant with common phenotypic characteristics but with genetic polymorphism and large variety in allelic forms of the individuals (Hardy 2012;Hartl 2000;Hartl & Clark 2007). ...
Refinement strategies in breeding and keeping of laboratory mice play a pivotal role in assuring the best possible solution as long as animal based research is indispensable. Furthermore, Refinement is one of the three Rs proclaimed by Russel and Burch in 1959 that found their way into the current European legislative on the protection of animals used for scientific purposes. In Germany a majority of 72,83 percent of all vertebrates used in experiments are mice, totaling over two million individuals. Almost all used laboratory mice are descendants of the house mouse (Mus musculus). The domestication of mice started at the beginning of the 17th century, when mice were kept and bred for different intentions and led to its proceeding domestication. In Great Britain mice were already in the focus as objects of study, but they were as well popular within amateur breeders that created the so-called “fancy mice”. Subsequent and more and more professional breeding led to the emerging of the first inbred mouse strains in 1909. This launched a cascade that enables researchers today to draw on a reservoir of over 450 inbred strains of mice. The necessity of mouse models becomes visible when keeping in mind that almost 90% of the 106 Nobel Prizes awarded for Physiology or Medicine included research relying on them. To understand the basic needs of laboratory mice it is essential to have a closer look at their ancestors. They are still living among us as wild mice with either a feral, non-commensal way of life or they live as commensals associated with humans. The domestication did not change much in the behavior of mice as they still are nocturnal animals with a strong basic need for living in a group. But some of the basic changes coming along with domestication are applicable for laboratory mice as well, as they are usually less aggressive and more easily to tame than their wild relatives. The experimental aspect of the thesis consists of two parts that both contribute to gain knowledge about minimizing the lifelong experience of pain, suffering, distress or long-lasting harm for laboratory mice. The first part aims to refine the breeding methods and the second part is a new approach to create a mouse-human relationship as well as to add a new form of enrichment - cognitive enrichment. The evaluation of different breeding conditions is consistent with data found in literature that in not profitable conditions postnatal litter loss reaches numbers up to 50 percent. In detail, the present study evaluated the impact of an impoverished, a super-enriched and a standard-enriched condition from the prenatal period until weaning of the offspring. A solid and constant breeding success was discovered in the standard enriched cage. The superenriched condition did provide more unpalatable results concerning litter loss and pup growth. The most prominent finding was the detrimental high litter losses and the delayed pup development in the impoverished condition. The result that the highest prevalence of pup mortality occurred during the first four days after birth, leads to the conclusion, that if the usually counting of pups at weaning is going on, a huge amount of infant death is not recorded. To get a hint of how much influence the prenatal condition has on the maternal quality and thus on the offspring’s development, we tested a group with a change of the condition from impoverished and super-enriched to standard enrichment on P1. The swapping did not result in a prevention of perinatal litter loss. But one can estimate, that there was a certain effect of the variation in enrichment as the neonatal weight gap between the groups was closed until weaning. But not just a tribute to Refinement is approached but due to a better knowledge of the prevention of litter loss, a reduction of the animal number can be realized. We successfully overcame the challenge to create a positively connoted mouse-human relationship and to introduce a PRT into the keeping of laboratory mice. Previous research provided the information that gentle handling protocols contribute to more relaxed mice. Enrichment is one major factor enabling mice to interact with their surroundings, and by manipulating things, they gain control over their environment. Control and the possibility to predict what is likely to happen next have a deep impact on the stress level. This study concentrated on clicker-training with one intention of an escalated handling protocol and with another intention of providing a new form of enrichment- cognitive enrichment. In clickertraining positive reinforcement consists of a chain of two reinforcers. The primary reinforcer is the food reward and a second reinforcer- a click is added to build up a time bridge between the strengthened behavior and an upcoming reward. Our little fellow creatures differ in their personality, even though they have an equal genetic background and born and raised under the same conditions. The food reward must address the motivation of each mouse, because motivation is the underlying reason why mice are participating in training. Further the cognitive abilities of mice turned out to be more than enough to perform the assigned tasks. The clicker-training of mice turned out to be quite simple. The evaluation of different behavioral experiments stress that trained mice are more confident in the interaction with humans and show less stress related and less depression like behaviors. In addition, stress reduction leads to a lower variability among experimental mice which results in a reduction of the amount of needed subjects and leads to data with a higher quality. This study proposes that clicker-training improves Refinement as well as reduction and thereby contributes in the implementation of the 3R-principle of Russel and Burch.
... The default sett ing was left and the "-x15" was added to provide 15 repetitions of algorithm and choice of the best one. To test the Hardy-Weinberg equilibrium and linkage disequilibrium, the package "genetics" in R software was used [29]. Basic characteristics were described by absolute and relative frequencies for categorical variables and median (5-95 percentile) for continuous va- riable. ...
Background:
Adaptive response to hypoxia is regulated by several mechanisms and transcription factors, including hypoxia-inducible factors (HIFs). Activation of HIF-1α is associated with increased expression of P-glycoprotein and multidrug resistance in cancer cells. In this retrospective study, we analyzed candidate single-nucleotide polymorphisms (SNPs) in HIF-1α and HIF-1β associated with risk of monoclonal gammopathy of undetermined significance (MGUS) or multiple myeloma (MM).
Patients and methods:
Genotypes of SNPs associated with hypoxia were determined in an independent cohort of monoclonal gammopathies (MG) (275 MM and 228 MGUS patients) and in 219 cancer-free controls by real time polymerase chain reaction allelic discrimination.
Results:
When MM patients were compared to controls, protective role of CG genotype compared to CC in HIF-1β (rs2228099) for MM development was observed (OR = 0.65; CI 0.45-0.95; p = 0.026). Even after adjustment for patients' age and body mass index (BMI), there were significantly lower odds (OR = 0.55; p = 0.045) of developing MM patients of CG genotype in comparison to CC genotype. Log-rank test confirmed association of GT haplotype (rs11549467, rs2057482) in HIF-1α with better overall survival (median 41.8 months; (CI 35.1-48.5)) for "none GT" and median 93.8 months (CI 31.3-156.4) for "at least one GT" haplotype (p = 0.0500). Further, significant associations between SNPs in MDR1 and outcome of MM were found in 110 MM patients that underwent bortezomib-based treatment.
Conclusion:
Our study showed a genetic predisposition for risk of MG development and/or outcome of MM patients; nevertheless, further studies are needed to confirm our initial analysis. Key words: multiple myeloma - hypoxia - genotype - polymorphism - qPCR.
... Mesoamerican dry forests and coastal dunes contain the ecosystems and evolutionary processes that originated, mold, and maintain wild cotton diversity and its interactions. These evolutionary services (Faith et al., 2010;Bailey, 2011;Rudman et al., 2017) are essential for species conservation, because preserving this genetic diversity allows the capacity to adapt to environmental changes (Ellstrand, 1992;Hartl, 2000). However, the factors that mold each part of the wild-to-domesticated complex are different; for example, the conservation of native traditional varieties depends to a great extent on the communities that cultivate them, their management techniques, and interests (Zhang et al., 2007). ...
The domestication syndrome of many plants includes changes in their mating systems. The evolution of the latter is shaped by ecological and genetic factors that are particular to an area. Thus, the reproductive biology of wild relatives must be studied in their natural distribution to understand the mating system of a crop species as a whole. Gossypium hirsutum (upland cotton) includes both domesticated varieties and wild populations of the same species. Most studies on mating systems describe cultivated cotton as self-pollinated, while studies on pollen dispersal report outcrossing; however, the mating system of upland cotton has not been described as mixed and little is known about its wild relatives. In this study we selected two wild metapopulations for comparison with domesticated plants and one metapopulation with evidence of recent gene flow between wild relatives and the crop to evaluate the mating system of cotton’s wild-to-domesticated complex. Using classic reproductive biology methods, our data demonstrate that upland cotton presents a mixed mating system throughout the complex. Given cotton’s capacity for outcrossing, differences caused by the domestication process in cultivated individuals can have consequences for its wild relatives. This characterization of the diversity of the wild relatives in their natural distribution, as well as their interactions with the crop, will be useful to design and implement adequate strategies for conservation and biosecurity.
... The "Beringian Standstill" model places the ancestral Native American population in the Beringian refugium during much or all of the LGM (2, 5-7), where it was geographically isolated from the Siberian population by uninhabitable areas in northeastern Asia and unable to expand into the Americas because of the coalesced Laurentide and Cordilleran ice sheets (Fig. 1B). The genetic isolation is a key point, as evolution occurs more readily in the absence of gene flow (59). The FADS polymorphisms and EDAR V370A likely existed in the pre-LGM ancestral populations [although the allele is not present in Denisovans (60)]. ...
Significance
The frequency of the human-specific EDAR V370A isoform is highly elevated in North and East Asian populations. The gene is known to have several pleiotropic effects, among which are sweat gland density and ductal branching in the mammary gland. The former has led some geneticists to argue that the near-fixation of this allele was caused by selection for modulation of thermoregulatory sweating. We provide an alternative hypothesis, that selection instead acted on the allele’s effect of increasing ductal branching in the mammary gland, thereby amplifying the transfer of critical nutrients to infants via mother’s milk. This is likely to have occurred during the Last Glacial Maximum when a human population was genetically isolated in the high-latitude environment of the Beringia.
... LD between each of these 101 SNPs and all other (12,893) SNPs in the data set was calculated for each population using Genepop V4 (Rousset 2008). SNPs in significant LD (Benjamini and Yekutieli adjusted P value < 0.05) were taken for LD network analysis within their respective population (highland n ¼ 576, lowland n ¼ 618) using the genetics (Warnes et al. 2013) and LDna (Kemppainen et al. 2015) packages in R. Parameters for cluster emergence were jEj (the minimum edges or number of connections between loci) set at 20 and phi (factor used to determine the minimum observed change in R 2 allowed when adding new loci to a cluster) set at 2. Resulting clusters were plotted using the igraph package in R (Csardi and Nepusz 2006). ...
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences.
... Each pairwise distance estimated from TreeMix involves the distance from a terminal tip to an internal node plus the distance from that internal node to a second terminal tip and thus is an estimate of 2F ST , assuming equal sample size (Weir and Hill 2002). We estimated divergence time using the esti-matorsN e ¼ĥ 4l and 1 ÀF ST ¼ 1 À 1 2Ñe t , in which t is generations,l is mutations per generation per site,F ST ¼ is half of the pairwise distance from TreeMix, andÑ e is the harmonic mean of the estimated effective population sizesN e (Weir and Hill 2002), assuming thatF ST ¼ 0 at t ¼ 0 (Hartl 2000). We estimatedN e using the mlrho autosomal heterozygositiesĤ reported in the Simons Genome Diversity Project (Mallick et al. 2016) and the relationshipĥ ¼Ĥ 1ÀĤ . ...
The Hadza and Sandawe populations in present-day Tanzania speak languages containing click sounds and therefore thought to be distantly related to southern African Khoisan languages. We analyzed genome-wide genotype data for individuals sampled from the Hadza and Sandawe populations in the context of a global data set of 3,528 individuals from 163 ethno-linguistic groups. We found that Hadza and Sandawe individuals share ancestry distinct from and most closely related to Omotic ancestry; share Khoisan ancestry with populations such as ≠Khomani, Karretjie, and Ju/’hoansi in southern Africa; share Niger-Congo ancestry with populations such as Yoruba from Nigeria and Luhya from Kenya, consistent with migration associated with the Bantu Expansion; and share Cushitic ancestry with Somali, multiple Ethiopian populations, the Maasai population in Kenya, and the Nama population in Namibia. We detected evidence for low levels of Arabian, Nilo-Saharan, and Pygmy ancestries in a minority of individuals. Our results indicate that west Eurasian ancestry in eastern Africa is more precisely the Arabian parent of Cushitic ancestry. Relative to the Out-of-Africa migrations, Hadza ancestry emerged early whereas Sandawe ancestry emerged late.
... Linkage disequilibrium (LD), expressed as a correlation coefficient between markers (r 2 ), was calculated using the filtered SNP data set containing all 1,391 lines from the experiment and the LD function of the "genetics" R package (Warnes, Gorjanc, Leisch, & Man, 2013). ...
The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
... Humans are morphologically very different from chimpanzees, yet the amount of protein divergence between the two species is very small. This has led to the hypothesis that morphological evolution is related more to changes in regulatory genes, as opposed to structural genes (Hartl, 1981). Theories have emerged attempting to calculate times of divergence from presumed common ancestors. ...
... Zhao et al. (2006) inferred the potential factors involved in marker segregation distortion of an F 2 population of rice by calculating the allele frequency (p and q) and the distribution of F 2 genotype frequency (p 2 :2pq:q 2 ). According to the Hardy-Weinberg principle for a gene with two alleles, homogeneity of allele frequency (p = q) and F 2 genotype frequency distribution is expected in the absence of disturbing forces such as mate choice, mutation, selection, genetic drift, gene flow, and meiotic drive (Hartl, 1987). Deviation of allele frequency from the expected ratio as determined by Chi-squared test indicates the occurrence of gametophytic selection, whereas deviation from the expected genotype frequency indicates zygotic selection (Zhao et al., 2006). ...
p>Distorted marker segregation is a common phenomenon in interspecific cross of various crops. Previous mapping study of early
blight fungus (Alternaria solani) resistance loci showed 52% marker distortion in the genetic linkage map of 176 F2 progenies
derived from Solanum lycopersicum cv. Solentos × S. arcanum LA2157. The objectives of this study were to analyze in detail the
marker segregation in the map and to determine the cause of segregation distortion by calculating the allele and genotype
frequencies of each marker. Out of 371 mapped markers, 192 markers deviated from the expected Mendelian ratio of 1 : 2 : 1.
Distorted markers occurred in all chromosomes, ranging from 1% to 92%. Surplus of S. arcanum homozygotes contributed most
to the skewness (40%), followed by heterozygotes (18%), and S. lycopersicum homozygotes (5%). The allele frequencies of 152
markers deviated from the expected allele homogeneity frequency, indicating that their segregation might be affected by
gamethophytic selection. Sixty-one markers deviated from the expected F2 genotype frequency distribution, indicating that their
segregation might be influenced by zygotic selection. Thirty-seven of the distorted markers showed deviation from expected
frequencies of allele homogeneity and F2 genotype frequency distribution. Distorted markers can be retained in linkage analysis
since chromosomal regions containing distorted markers showed linkage with early blight fungus resistance loci. Further
identification of the mechanism contributing segregation distortion requires detailed and extensive mapping studies.</p
... The results presented here are counted as an additional case study on this issue and thus comparable in scope to the seminal works by Carroll and Boyd (1992, and related works) on the soapberry bug J. haematoloma, and Singer et al. (1993, and related works) on the checkerspot butterfly Euphydryas editha (Boisduval) (Lepidoptera: Nymphalidae). It should be noted, however, that the evolutionary change in the host-use ability of a particular population of insects, as an outcome of the changes in allele frequency, could result from migration as well as adaptation by natural selection (Hartl 2000). ...
Investigations of the ongoing evolutionary change of host specificity, especially of that in the initial phase, contribute largely to our understanding of the mechanisms responsible for the diversification of phytophagous insects. However, empirical studies of this aspect in natural systems are very scanty. In the present study, we document the evolutionary change of the degree of adaptation to an introduced legume centro by adults and larvae of the herbivorous ladybird beetle Henosepilachna vigintioctopunctata (Fabricius), which depends normally on various solanaceous plants. Results obtained through experiments conducted in seven successive years revealed a fluctuating degree of adaptation, but with a gradual increase, to centro by H. vigintioctopunctata, showing a tendency towards host plant generalization. Of particular importance, our results suggest that both host plant specialization and generalization are possible evolutionary outcomes of a dynamic initial phase of ongoing host range expansion. In addition, results of quantitative genetic analyses on larval development and other circumstantial evidence suggested that the evolutionary trajectories to specialization/generalization are largely determined by ecological conditions rather than by the insects' intrinsic genetic architecture. We also discuss some special aspects of acquisition of, and adaptation to, novel hosts by H. vigintioctopunctata and other herbivorous beetles, of which adults also feed on plant leaves.
... There are four evolutionary forces that may shape the genetic structure of popualtions. They are migration, mutation, selection, and genetic drift (Hartl, 2001). The breeding populations are closed populations that migration as responsible force shaping the genetic structure can be omitted. ...
p>Selective breeding aiming at improving the performance of economically important traits acts by exploiting population’s phenotypic variance. Due to the relationship between phenotype and genotype, selection on phenotype may also affect the profile of genotype. This study was aimed to monitor the impact of three generations of mass selection for fast growth in African catfish, Clarias gariepinus , on genetic variability, assessed by microsatellite. A total of 350 fish representing four populations, namely a composite base population (G-0), selected lines of the first generation (G-1) to the third generation (G-3), were sampled. The samples were screened for their genetic diversity using five microsatellite loci1 namely cga01, cga02, cga03, cga05, and cga09. Several genetic parameters including number of allele (A), allelic richness (AR), observed (Ho) and expected (He) heterozygosity, and fixation index (Fis) were evaluated. The results showed that there was a slight increase in the value of diversity indices in the G-1 relative to the G-0 and to the other two generations. Among these parameters, the number of allele seemed to be the most sensitive parameter in detecting genetic changes. All populations experienced heterozygote deficit and positive fixation index indicating the phenomena of inbreeding. Overall, selection for growth for three generations in African catfish breeding program resulted in significant genetic differentiation between populations. Further, the level of genetic differentiation seemed to accumulate along with the number of generaton in breeding program. However, selection did not result in a decline in genetic diversity within population. A relatively short period of the program, along with the use a high number of broodstock (mating pairs) to produce each generation seems to be able to maintain the stability of genetic diversity of the population.</p
... In order to determine the appropriate window size to identify genes near our top SNPs, we examined linkage disequilibrium (LD) decay profiles. LD between markers was calculated as the correlation coefficient (r 2 ) between pairs of genotypes using the 'genetics' package in R (Warnes et al. 2013), which uses maximum-likelihood estimation for uncertain haplotypes. For each scaffold containing a SNP in the top 0.1% of the BSLMM iterations (see genomewide association analysis and beaksize prediction), LD was estimated between every possible pair of bi-allelic sites. ...
Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using Restriction site Associated DNA (RAD-seq), we characterized 32,569 single-nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genome-wide association study (GWAS). Principal Components Analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: Delta-Like 1 Homolog (DLK1) and High Mobility Group AT-Hook 2 (HMGA2). Our results suggest that 1) key adaptive traits are associated with a small fraction of the genome (11 out of 32,569 SNPs), 2) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and 3) micro- and macro-evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions. This article is protected by copyright. All rights reserved.
... When using the Hardy-Weinberg Equilibrium (HWE), it is always assumed that the population is composed of a large number of diploid, randomly mating individuals that are free from mutation and migration (Hartl, 1988). It is also a common assumption that the markers being analyzed are inherited in a Mendelian fashion, and are selectively neutral. ...
DNA analysis is a ubiquitous tool to identify variation within populations. By using microsatellites, highly variable genetic loci distributed throughout the entire nuclear genome, genetic characteristics can be identified in the population. Genetic variation in the black bear, Ursus americanus, was characterized through samples gathered from the Maine population. In total, five loci were characterized for analysis. In order to aid in wildlife forensic cases, I examined genetic variations in black bears. The range of observed heterozygosity for the population sample was 0.729-0.871; the number of alleles per locus ranged from 7 to 15. Sampling the population and determining the frequencies of the alleles can introduce information about the genetic characteristics of the population. The allele frequencies that have been recorded here can be used in cases to determine if two unknown samples are from a single individual, or to determine that samples came from different animals. Analysis of the information can also aid in the knowledge of population structure and genetic diversity within the population. With the characterization of individuals within a family, multiple paternity, a phenomenon seen in several different taxa, can be observed. In this population study, however, multiple paternity was not observed.
... La evolución puede ser definida como "los cambios acumulados en la composición genética de una población" (Hartl 2000). Dicha evolución acumulativa ocurre primariamente por el cambio en las frecuencias alélicas y genotípicas de las poblaciones a través del tiempo y el espacio, y estos cambios son modulados por las llamadas fuerzas evolutivas: la mutación, el flujo génico, la deriva genética y la selección. ...
La diversidad genética es un requisito para el cambio evolutivo. Por consiguiente, la conservación de la diversidad genética dentro de las especies es importante para asegurar el potencial de adaptación en un medio ambiente cambiante. La variación genética de los rasgos de importancia adaptativa se puede medir mediante la observación de la variación fenotípica en los ensayos de ambiente común.
De acuerdo a su área de distribución y productividad potencial, Nothofagus pumilio (Poepp. et Endl.) es la especie arbórea nativa más importantes de la Patagonia. Se halla en bosques puros en el límite superior arbóreo a ambos lados de la Cordillera de los Andes. El objetivo de este estudio fue evaluar la variación geográfica y genética de poblaciones naturales de la especie en rasgos cuantitativos potencialmente adaptativos. Se muestrearon poblaciones naturales de la Provincia de Chubut representando los tres gradientes ambientales más relevantes de su área de distribución: latitudinal, altitudinal y de precipitación. Se analizó variación natural en caracteres seminales y se instalaron ensayos de ambiente común en los que se evaluaron variables correspondientes a plántulas en invernadero y plantines en campo. Con los datos obtenidos se estudió variación en caracteres cuantitativos entre y dentro de poblaciones. Los resultados principales muestran evidencias de variación clinal y ecotípica en los gradientes latitudinal y altitudinal, respectivamente, con indicios de adaptación local en el caso del gradiente altitudinal. También se verificó variación genética entre morfotipos. En algunas de las variables consideradas se registró una importante diversidad genética, tanto entre como dentro de poblaciones, mientras que en otras la diversidad fue muy baja.
En la discusión se da cuenta del complejo patrón de variación geográfica y genética de la especie, presumiblemente determinado por factores históricos (probablemente relacionado con la última glaciación) y la presión de selección que opera actualmente. Las diferencias fueron evidentes en los gradientes evaluados y entre los diferentes tipos de caracteres, operando procesos de adaptación local y plasticidad fenotípica en un equilibrio variable.
Palabras claves: adaptación, conservación, plasticidad fenotípica, genética cuantitativa, Nothofagus pumilio.
... Furthermore, even if both migrants identified by Hast (2010) were completely heterozygous, and assuming both individuals successfully reproduced, their genes would likely have had a negligible impact on diversity considering the rapidly growing founding population of bears (Nei et al. 1975, Kekkonen et al. 2012). Though possible because of new allele admixtures from immigration (Hartl 2000, Frankham et al. 2003), the level of linkage disequilibrium we observed in the 2010–2012 dataset (>51% of pairings) would be accompanied by increased H E and H O , and the effective number of breeders would likely be higher than what we observed (Nunney 1993, Miller et al. 2009). A low number of breeders at BSF was supported by a parentage analysis (2014) discovered that a reintroduced black bear population in Arkansas exhibited relatively constant genetic diversity since reintroduction as well, and posited that this may have been the result of a high population growth rate. ...
Reintroduced populations are vulnerable to demographic and environmental stochasticity, deleterious genetic effects, and reduced population fitness, all of which can increase extinction probability. Population viability is principle to determining the status of reintroduced populations and for guiding management decisions. To attempt to reestablish black bear (Ursus americanus) populations in the central Appalachians, two reintroductions using small founder groups occurred during the 1990s in the Big South Fork area along the Kentucky-Tennessee border (BSF) and in the Jefferson National Forest along the Kentucky-Virginia border (KVP). My objectives were to estimate demographic and genetic parameters, and to evaluate long-term viability and reintroduction success for the KVP and BSF black bear populations. The KVP grew rapidly to 317–751 bears with a significantly female-biased sex ratio by 2013. Spatially explicit capture-recapture models suggested KVP recolonization may continue to the southwest and northeast along linear mountain ridges. Based on radio-monitoring during 2010–2014, high adult female survival and moderate mean litter sizes were estimated in both populations. All mortality was anthropogenic and males were 4.13 times more likely to die than females. Two-cub litters were most probable in the BSF, whereas the KVP had similar probabilities of two- and three-cub litters. The average annual mortality that occurred during the study period was sustainable and allowed for moderate growth (λKVP = 1.10; λBSF = 1.13). Continued mortality at the higher 2015 rate, however, resulted in probabilities of ≥25% population decline over 10 years of 0.52–0.53 and 0.97–0.98 in the KVP and BSF, respectively. Rapid population growth during the 13–17 years post-reintroduction and the overlapping generations inherent to bears retained genetic diversity. Cumulative findings indicated both reintroductions were successful at establishing viable, self-sustaining populations over the long-term. The anthropogenic mortality rate during 2015, if sustained, could cause precipitous declines in these populations. Reimplementation of annual vital rate monitoring and conservative harvests should be considered. Connectivity may be established between these two reintroduced black bear populations if growth and recolonization continue.
... The generation to which an SPF macaque (n = 929) belongs was defined as 1 plus the maximum of the sire and dam generation numbers. 11 Table 1 lists the number of samples tested per generation. Arlequin 10 also was used to compute Weir and Cockerham pairwise F ST 37 values among age cohorts and among generations of animals, to assess the degree of divergence due to genetic drift. ...
The SPF breeding program at the Caribbean Primate Research Center supplies Indian-origin rhesus macaques of known genetic and virologic background for biomedical research. In this study, population genetic analyses using 14 short tandemrepeat sequences showed that the SPF colony has remained genetically homogenous over time, with sufficient amounts of heterozygosity and minimal stratification from its founders. Intergenerational studies indicated that an average of 7 alleles have been retained, inbreeding levels have remained low, and the degree of Indian ancestry is one of the highest among several national primate research centers. The relative low genetic diversity in the free-ranging population as well as in the captive SPF and conventional colonies when compared with that of other primate centers indicates that the free-ranging population, from which the captive-colony animals were derived, has experienced significant founder effects and genetic drift during the years after its establishment. This study supports the historical origin of the free-ranging population and confirms the high value of this resource for biomedical research. Current genetic diversity levels within the SPF colony can be ensured with the practice of colony management approaches such as equalizing male:female ratios in each SPF breeding group and increasing breeding group sizes. Introducing new Indian-origin macaques from other captive colonies might help to maximize the genetic diversity of the breeding stock. Furthermore, genetic estimates must be used to rank breeders according to their genetic value or their genome uniqueness to increase founder-genome representation and curb future genetic bottlenecks and allele loss. ©2016 by the American Association for Laboratory Animal Science.
... Fst values were indicative of low population differentiation (0.001881–0.003901) across sub regions, thus indicate that more than 99% of total diversity can be attributable to within population's variation [9]. We suggest considering these regions as a single population for routine use in forensic analysis, these results were consistent with previous studies and they stressed that populations surveyed in this study belong to the so-called Central Andean region of Colombia [10]. ...
p>Population Structure of Trichogrammatoidea armigera,
Egg Parasitoid of Helicoverpa armigera Based on RAPDPCR
Analysis. Bahagiawati, Damayanti Buchari, Nurindah,
H. Rizjaani, Dwinita W. Utami, B. Sahari, and A.
Sari. Genetic structures of Trichogrammatoidea armigera
(Hymenoptera: Trichogrammatidae), the egg parasitoid of
Helicoverpa armigera (Lepidoptera: Noctuidae) were studied.
Egg masses of H. armigera were collected from fields of
several locations in West Java and East Java with different
distances among them and two distinct cultural practices,
i.e., monoculture and polyculture. Genetic relationships
among T. armigera populations that emerged from the collected
H. armigera eggs were analysed by the RAPD-PCR
technique using four oligonucleotide primers. The four
primers revealed 55 presumptive polymorphic loci that were
used to estimate the population structures. The estimated
values of Fixation Index (Fst) was 0.16, indicating that there
was a division of the populations into subpopulations. This
Fst value implied the present of reproductive isolation
among the populations that might be due to their low
migration rate (1.3 insect per generation). This low migration
rate indicated the present of low level of gene flow among
the populations. A dendrogram resulted from the NTSYS
analysis indicated that the West Java and East Java populations
of the egg parasitoid had quite wide genetic distances,
while within each of the populations there was a subdivision
of minor populations. This finding has an important implication
on the program to release Trichogramma spp. as a biological
control agent. The release of the parasitoid cannot be
done randomly, because if we pick up a minor population,
the starter or the released population will mate with the
local population and multiply, thus the inundation will fail to
control the target pest.</p
An apple (Malus × domestica Borkh.) core collection was established using 19 SSR markers in 1,344 apple germplasm samples using the PowerCore program. For this, 166 accessions were selected using a heuristic strategy, accounting for about 12.4% of the entire collection. The core collection had an allelic loci retention ratio of 100%, and no significant differences were observed in the number of alleles, Shannon’s information index, observed heterozygosity, expected heterozygosity, major allele frequency, or polymorphic information content between the core and the entire collection, as indicated by t-tests and Levene’s test. Analysis of molecular variance also revealed no significant genetic variation between the core and the entire collection. For all apple accessions, the genetic relationship, assessed using neighbor-joining analysis, was divided into five clusters, and the population structure had the highest value at k = 2. The first two axes in the principal coordinate analysis accounted for 14.00% and 9.85% of the total variance, and the core collection was distributed in a scattered pattern across the plot of the entire collection. The 166-apple core set constructed here is recommended for use as the core collection for the Korean apple germplasm.
The milkfish, Chanos chanos, is a commercially important cultured species which is distributed throughout south and southeast Asian countries. Captive breeding and seed production techniques have been standardized recently in India and there is a need for analyzing its population structure along the Indian coast. A total of 80 samples from four different locations across the Indian coast were analyzed by using ATPase 6/8 genes. Analysis revealed the existence of 25 haplotypes across populations with the haplotype diversity in the range of 0.5684–0.8053 and the nucleotide diversity varied from 0.001838 to 0.002519. The variation within and among populations accounted for 97.43% and 2.75%, respectively. The observed FST values were found to be non-significant (p > 0.05). Results from this study indicated that there is lack of genetic divergence between the populations of milkfish along the Indian coast.
Microsatellites play an important role when investigating population and ecological genetics, although high effort in development and genotyping constitute a technical constraint and remains a major bottleneck. Here we use a microsatellite genotyping approach utilizing sequences of amplicons for allele calling (SSR-GBS) based on Illumina that requires less effort and time. The approach consist of development of highly polymorphic loci, sequencing of multiplexed PCR amplified microsatellites on an Illumina Miseq PE 300 platform and bioinformatic treatment of the sequenced data using custom scripts. The procedure allows automation in allele calling, which can be more reliably replicated and thereby removes biases that might prevent concatenation of datasets from different analyses. Additionally, the methodology enhances information content in the sequenced data beyond the traditional amplicon length (AL) approaches. Using 26 newly developed microsatellite markers and SSR-GBS we investigate the population genetic assessment of anthropogenically altered populations of East African Nile tilapia to show the potential of this genotyping approach. More precisely, we compare genotypic data generated considering AL and whole amplicon information (WAI). We found that genotypes based on WAI are not only able to recover a higher number of alleles but also a more detailed genetic structure pattern. We discuss the capability and importance of WAI allele calling and show perspectives for implementation in the future conservation genetic studies. More specifically, we demonstrate how the current markers and techniques might contribute useful information for studies concerning resources sustainable exploitation and conservation using the East African Nile tilapia.
The known distribution of Pleurotopsis longinqua is restricted to southeastern Australia, New Zealand, Patagonia, and the northern Pacific coast of North America. Previous studies demonstrated that isolates from all of these areas were sexually compatible (i.e., were the same biological species). Intercompatibility studies, however, did not provide information about genetic (evolutionary) relationships among the disjunct populations. Restriction fragment patterns of the nuclear ribosomal ITS1-5.8S-ITS2 were compared for isolates from each geographical region to estimate genetic divergence. Only one enzyme, Taq I, discriminated between different collections. To further examine genetic divergence, the ITS1-5.8S-ITS2 region was sequenced for one collection from each geographical area. Only four base-pair differences were observed among isolates from New Zealand, Argentina and Washington State. The remarkable similarity of these collections suggests that the current disjunct distribution is not very old.
The typical framework for studies and models of bloom dynamics of toxigenic algae is based on environmental determinants (e.g., light, nutrients) of cell growth rate and toxin production rate. There is mounting evidence, however, of grazer control of toxin production, which then may impact cell growth. This thesis examines the costs and benefits of grazer-induced toxin production in the toxigenic dinoflagellate Alexandrium catanella. Paralytic Shellfish Toxin (PST) production was significantly increased regardless of growth phase when cells were contemporaneously exposed directly or indirectly to grazers, relative to cells not exposed to grazers. The same effect was observed for cells that had been previously exposed to grazers regardless of nutrient regime. In contrast, the pattern for cell growth rate was the opposite – cells directly or indirectly exposed to grazers showed lower growth rates than unexposed cells, with little effect of growth phase or nutrient regime. The results suggest a trade-off between toxin production and growth rate. A subsequent experiment confirmed a trade-off using toxin production rate and the relative expression of a cell growth gene, which is correlated with cell division rate. A fitness tax equivalent to a reduction in cell division rate of 56% was evident when grazers induced cells to increase toxin production. This grazer-mediated fitness tax should be incorporated in population dynamic models of toxigenic prey. Costs and benefits of toxin production were simultaneously tested in laboratory studies that measured net cell growth rates of three Alexandrium catanella strains that differed in PST production (low, moderate and high PST production, respectively) versus a gradient of grazing pressure. Both the moderate toxigenic and the high toxigenic strain showed a fitness benefit relative to the low toxigenic strain; however, the highest benefit was derived in the moderate toxigenic strain, which also reduced cell size and increased cell division rate in response to grazing. This suggests that in addition to toxin production other mechanisms of defense are simultaneously expressed, adding complexity to the study of defense mechanisms.
The scale‐eating cichlid fish Perissodus microlepis is a textbook example of bilateral asymmetry due to its left or right‐bending heads and of negative frequency‐dependent selection, which is proposed to maintain this stable polymorphism. The mechanisms that underlie this asymmetry remain elusive. Several studies had initially postulated a simple genetic basis for this trait, but this explanation has been questioned, particularly by reports observing a unimodal distribution of mouth shapes. We hypothesize that this unimodal distribution might be due to a combination of genetic and phenotypically plastic components. Here, we expanded on previous work by investigating a formerly identified candidate SNP associated to mouth laterality, documenting inter‐individual variation in feeding preference using stable isotope analyses, and testing their association with mouth asymmetry. Our results suggest that this polymorphism is influenced by both a polygenic basis and inter‐individual non‐genetic variation, possibly due to feeding experience, individual specialization, and intraspecific competition. We introduce a hypothesis potentially explaining the simultaneous maintenance of left, right, asymmetric and symmetric mouth phenotypes due to the interaction between diverse eco‐evolutionary dynamics including niche construction and balancing selection. Future studies will have to further tease apart the relative contribution of genetic and environmental factors and their interactions in an integrated fashion.
Thousands of tropical tree species provide timber, fuel, food, fodder and other ecosystem services for local and global communities. Yet, knowledge about the status and trends of tropical tree genetic diversity, which provides the basis for conservation and sustainability, remains limited. Nevertheless, the number of molecular studies is rapidly increasing thanks to technological advances and reduced costs. DNA markers provide ways to identify species or describe the genetic diversity of populations that can be used for gene conservation and restoration programs. Increasingly, molecular methods are also being used to identify the origin of timber to help combat illegal logging. Technical developments are also facilitating studies of adaptive traits, with expressed gene analysis offering real potential for detecting adaptive genetic diversity. Combining information from molecular studies with ecological and socioeconomic information related to, for instance, current and predicted species distribution, protected area networks or competing land use demands, enables the identification of the most suitable gene conservation, management or restoration strategies for each species. In this chapter we review advances in the development and application of molecular markers in conservation planning, landscape restoration and DNA forensics of tropical tree species, and discuss future directions.
Human-induced biological invasions are common worldwide and often have negative impacts on wildlife and human societies. Several studies have shown evidence for selection on invaders after introduction to the new range. However, selective processes already acting prior to introduction have been largely neglected. Here we tested whether such early selection acts on known behaviour-related gene variants in the yellow-crowned bishop (Euplectes afer), a pet-traded African songbird. We tested for non-random allele frequency changes after trapping, acclimation and survival in captivity. We also compared the native source population with two independent invasive populations. Allele frequencies of two SNPs in the dopamine receptor D4 (DRD4) gene – known to be linked to behavioural activity in response to novelty in this species – significantly changed over all early invasion stages. They also differed between the African native population and the two invading European populations. The two-locus genotype associated with reduced activity declined consistently, but strongest at the trapping stage. Overall genetic diversity did not substantially decrease and there is little evidence for new alleles in the introduced populations, indicating that selection at the DRD4 gene predominantly worked on the standing genetic variation already present in the native population. Our study demonstrates selection on a behaviour-related gene during the first stages of a biological invasion. Thus, pre-establishment stages of a biological invasion do not only determine the number of propagules that are introduced (their quantity), but also their phenotypic and genetic characteristics (their quality). This article is protected by copyright. All rights reserved.
An individual-based simulation model was created to examine genetic variability, time until fixation and spatial genetic structure in a continuously distributed population. Previous mathematical models for continuously distributed populations have the difficulty that the assumption of independent reproduction and independent dispersal of offspring cause clumped spatial distribution and thus violate an assumption of random spatial distribution. In this study, this problem is avoided by considering the dispersal behavior of offspring. The simulation results showed that the inbreeding effective population size estimated by the rate of decrease of heterozygosity during the first 15 generations corresponds to the neighborhood size calculated by the standard deviation of the dispersal distance (σT ). This inbreeding effective population size does not greatly change with the area of simulation when the densities and σT are the same. However, the inbreeding effective population size estimated by heterozygosity using the first 500 generations is larger than the neighborhood size calculated by the dispersal distance and increases with the area of simulation with the same densities. The variance effective population size, estimated by time until fixation of alleles, increases with dispersal distance (σT ) and with the area of simulation given the same densities. The inbreeding effective population size and variance effective population size were smaller than the actual population size unless σT is sufficiently large (2 σT > approximate L/2, where L is a side of the simulation square).
Recent advances in genotyping with high-density markers allow researchers access to genomic variants including rare ones. Linkage disequilibrium (LD) is widely used to provide insight into evolutionary history. It is also the basis for association mapping in humans and other species. Better understanding of the genomic LD structure may lead to better-informed statistical tests that can improve the power of association studies. Although rare variant associations with common diseases (RVCD) have been extensively studied recently, there is very limited understanding, and even controversial view of LD structures among rare variants and between rare and common variants. In fact, many popular RVCD tests make the assumptions that rare variants are independent. In this report, we show that two commonly used LD measures are not capable of detecting LD when rare variants are involved. We present this argument from two perspectives, both the LD measures themselves and the computational issues associated with them. To address these issues, we propose an alternative LD measure, the polychoric correlation, that was originally designed for detecting associations among categorical variables. Using simulated as well as the 1000 Genomes data, we explore the performances of LD measures in detail and discuss their implications in association studies.
A range of dilutions (1:1 to 1:320) of ethanolic extracts of dried tissues of the macroalgae, Osmundaria serrata and Zonaria subarticulata were made. These dilutions were incorporated into fungal growth media and their influence on the germination of spores of Aspergillus niger and Alternaria sp., and the colony growth of Rhizoctonia solani after breaking of scerotial dormancy, observed. Pure ethanol inhibited spore germination and colony growth by up to 100 %, but the toxicity of ethanol decreased with increasing dilution and showed hormetic trends. The presence of macroalgal factors ameliorated the toxicity of pure ethanol to different percentages but showed both amelioratory and inhibitory influences on the action of the different dilutions of ethanol on spore germination or colony growth. The data are discussed in the light of other examples of hormesis and the need to isolate the active macroalgal factors.
In taxonomic study of closely related taxa, numerical data seem to be insufficiently used or discussed. In this study actual sizes of various parts in male genitalia and their ratios (to forewing length) are compared and discussed. Generally ratios are considered to be useful for eliminating the environmental effects, as seen in the case that male genitalia of Delias oraia are proved clearly larger than those of Delias belisama. Meanwhile it is clarified through the discussion that there are such a character that is hardly effected by the environment, and that is therefore very important to discuss the speciation and biological evolution in related taxa.
The importance of considering genetic variation in conservation of rare plants is well understood (Falk and Holsinger 1991; Hamrick and Godt 1996; Rieseberg and Swensen 1996). In addition, the importance of considering genetic diversity in plant reintroduction has been well argued (Fenster and Dudash 1994; Mistretta 1994; Havens 1998; Falk et al. 2001, 2006; Hufford and Mazer 2003). As a result, various guidelines for collecting propagules (primarily seed) for reintroduction based on genetic theory have been put forth (Knapp and Rice 1994; Center for Plant Conservation 1996; McKay et al. 2005). Here I review the tenets of restoration genetics before discussing the means of measuring genetic diversity in species slated for reintroduction. Current collection guidelines for reintroduction and examples of empirical studies that have measured genetic variation before, during, and after reintroduction are presented and evaluated. Lastly, further arguments for the inclusion of genetic data in reintroduction practice are presented, with a brief discussion of the issue of managed relocation and how genetic data may inform the future of plant reintroduction in a changing climate.
Life history traits play an important role in the level and distribution of genetic diversity, and comparing closely related species with similar life histories can provide insight into the determinants of genetic variation in plant populations. In this study, we used variations of one chloroplast DNA fragment, one nuclear gene, and six microsatellites to compare the levels and distributions of genetic diversity in four widespread Typha species from China. Surveys were conducted on 898 individuals from 120 sites. The individuals of all four species formed monophyletic clades and distinct genetic clusters, suggesting no hybridization between T. angustifolia and T. latifolia in China. The levels of cpDNA nucleotide diversity followed the order T. latifolia > T. laxmannii > T. angustifolia > T. orientalis, whereas the genetic diversity in nDNA and nSSR of T. laxmannii and T. angustifolia was higher than that of T. latifolia. In T. angustifolia, T. laxmannii, and T. orientalis, more than half of genetic variation occurred within populations, and in T. latifolia, most of genetic variation occurred among populations. The variation in the levels and distributions of genetic diversity among the four species can be attributed to differences in inflorescence characteristics which either limit or enhanced outcrossing rates.
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