scholarly journals MEASURING GENE FLOW AMONG POPULATIONS HAVING HIGH LEVELS OF GENETIC FRAGMENTATION

Genetics ◽  
1984 ◽  
Vol 106 (2) ◽  
pp. 293-308
Author(s):  
Allan Larson ◽  
David B Wake ◽  
Kay P Yanev
Keyword(s):  
Gene Flow ◽  
Flow Parameter ◽  
Alternative Methods ◽  
Stabilizing Selection ◽  
Gene Exchange ◽  
Epigenetic Factors ◽  
Effective Population ◽  
Population Number ◽  
Genetic Structures ◽  
Future Work

ABSTRACT We present an analysis of the genetic structures of 22 species of salamanders, with regard to levels of gene flow among populations. We estimate the gene flow parameter, Nm (the product of the effective population number and rate of migration among populations) using two alternative methods described by Wright and Slatkin. For most species, these two methods give approximately congruent estimates of Nm; when estimates differ, the method of Wright produces values slightly larger than those derived by the method of Slatkin. We analyze these results in light of independently derived historical inferences of the fragmentation of populations. This analysis suggests that the Nm values calculated from protein polymorphisms may contain information more relevant to historical patterns of gene exchange than to the current population dynamics; moderately large values of Nm may be calculated for species containing populations known to be no longer exchanging genes. Application of a method for estimating the maximum possible rate of gene exchange among populations indicates that, for most species studied here, gene flow among populations probably is no greater than the mutation rate. We suggest that most plethodontid species cannot be viewed as units whose cohesion is maintained by continuing gene exchange. Furthermore, we suggest that phenotypic uniformity among populations is not easily explained by hypotheses of continual stabilizing selection and propose that future work concentrate upon clarification of the genetic and epigenetic factors conferring self-maintenance or autopoietic properties on living systems.

Paternity analysis with microsatellites in a Danish Abies nordmanniana clonal seed orchard reveals dysfunctions

2006 ◽  
Vol 36 (4) ◽  
pp. 1054-1058 ◽  
Author(s):  
O K Hansen ◽  
E D Kjær
Keyword(s):  
Asymptotic Variance ◽  
Seed Orchard ◽  
Paternity Analysis ◽  
Effective Population ◽  
Population Number ◽  
Clonal Seed Orchard ◽  
Relative Contribution ◽  
Male Gametes ◽  
Abies Nordmanniana ◽  
The Status

A paternity analysis using five microsatellite markers was conducted in a Danish clonal seed orchard with 13 Abies nordmanniana (Stev.) Spach clones. The purpose was to investigate potential seed-orchard dysfunctions, with special emphasis on nonequal pollen contributions and selfing. Male paternity was found for 232 seedlings germinated from seeds collected on three ramets, each of eight clones, and the relative contribution of each clone to the gene pool of male gametes was calculated. Furthermore, 49 ramets were genotyped to check for erroneous grafting. The effect of an unbalanced male contribution was quantified by means of two measures: (1) the status number (NS), which reflects buildup of coancestry in the seed-orchard crop as a result of a low number of clones and an unequal male contribution, and (2) the asymptotic variance effective population number (Ne(v)). The contributions by pollen donors from the 13 clones were highly skewed. Three clones were fathers to more than 75% of the progenies, while making up only 24% of the ramets in the seed orchard. Four clones sired no progenies at all. The unequal contribution on the male side corresponded to NS = 4.2 and Ne(v) = 5.8. Some selfing was observed, which may give rise to concern if clonal seed orchards with few clones are established. The estimated maximum pollen contamination from outside the seed orchard was 4.3%. No grafting–labelling errors were identified.

scholarly journals Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

2021 ◽  
Author(s):  
Gregory Thom ◽  
Camila C. Ribas ◽  
Eduardo Shultz ◽  
Alexandre Aleixo ◽  
Cristina Y. Miyaki
Keyword(s):  
Genetic Diversity ◽  
Spatial Patterns ◽  
Amazon Basin ◽  
Population Connectivity ◽  
Alternative Methods ◽  
Forest Species ◽  
Effective Population ◽  
Habitat Specificity ◽  
Heterogeneous Distribution ◽  
Solimões River

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimoes River, Western Amazon, South America Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

scholarly journals RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

2021 ◽  
Author(s):  
Jelmer Wijtze Poelstra ◽  
B. Karina Montero ◽  
Jan Lüdemann ◽  
Ziheng Yang ◽  
S. Jacques Rakotondranary ◽  
...  
Keyword(s):  
Gene Flow ◽  
Contact Zone ◽  
Mouse Lemur ◽  
Biological Processes ◽  
Microsatellite Data ◽  
Ancestral Gene ◽  
Mouse Lemurs ◽  
Low Levels ◽  
Future Work ◽  
Lemur Species

Despite being one of the most fundamental biological processes, the process of speciation remains poorly understood in many groups of organisms. Mouse lemurs are a species-rich genus of small primates endemic to Madagascar, whose diversity has only recently been uncovered using genetic data and is primarily found among morphologically cryptic, allopatric populations. To assess to what extent described species represent reproductively isolated entities, studies are needed in areas where mouse lemur taxa come into contact. Hybridization has previously been reported in a contact zone between two closely related mouse lemur species (Microcebus murinus and M. griseorufus) based on microsatellite data. Here, we revisit this system using RADseq data for populations in, near, and far from the contact zone, including many of the individuals that had previously been identified as hybrids. Surprisingly, we find no evidence for admixed nuclear ancestry in any of the individuals. Re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Using coalescent-bases analyses, we also show an overall lack of recent gene flow between the two species, and low levels of ancestral gene flow. Combined with evidence for local syntopic occurrence, these data indicate that M. murinus and M. griseorufus are reproductively isolated. Finally, we estimate that they diverged less than a million years ago, suggesting that completion of speciation is relatively rapid in mouse lemurs. Future work should focus on the underpinnings of reproductive isolation in this cryptic primate radiation, which are mostly unknown. Our study also provides a cautionary tale for the inference of hybridization with microsatellite data.

scholarly journals Molecular markers applying in forest trees gene pool conservation

2009 ◽  
pp. 101-113
Author(s):  
Jelena Milovanovic ◽  
Mirjana Sijacic-Nikolic
Keyword(s):  
Population Genetics ◽  
Molecular Markers ◽  
Gene Flow ◽  
Gene Pool ◽  
Statistical Power ◽  
Forest Trees ◽  
Effective Population ◽  
Migration Patterns ◽  
Geographic Diversity ◽  
Marker Loci

Many studies performed during the last years demonstrated the usefulness of neutral molecular markers in the field of conservation and population genetics of forest trees, in particular to understand the importance of migration patterns in shaping current genetic and geographic diversity and to measure important parameters such as effective population size, gene flow and past bottleneck. During the next years, a large amount of data at marker loci or at sequence level is expected to be collected, and to become excellent statistical power for the assessment of biological and evolutionary value.

scholarly journals Resistance of melon cultivars to Bemisia tabaci biotype B

2012 ◽  
Vol 30 (4) ◽  
pp. 600-606 ◽  
Author(s):  
Edson LL Baldin ◽  
José Paulo GF da Silva ◽  
Luiz Eduardo R Pannuti
Keyword(s):  
Bemisia Tabaci ◽  
Plant Resistance ◽  
Chemical Control ◽  
Alternative Methods ◽  
Silverleaf Whitefly ◽  
Trichome Density ◽  
Breeding Programs ◽  
Biotype B ◽  
Future Work ◽  
Bemisia Tabaci Biotype B

The silverleaf whitefly, Bemisia tabaci biotype B, is currently one of the most important pests of melon, causing direct and indirect damage to plants, and significantly reducing production in the field. Due to the need for alternative methods of chemical control in melon crops, the melon cultivars AF-646, AF-682, Don Luis, Frevo, Jangada, Nilo, Vereda, Amarelo Ouro and Hales Best were assessed at field, greenhouse, and laboratory trials for resistance to whitefly B. tabaci biotype B. In general, 'Hales Best' and 'Amarelo Ouro' were the most resistant, showing oviposition non-preference against whitefly. The trichome density is associated with the variation in oviposition on the cultivars and should be further investigated in future work. These results may be helpful in melon breeding programs, focusing on plant resistance to B. tabaci biotype B.

Comparative host–parasite population genetic structures: obligate fly ectoparasites on Galapagos seabirds

Parasitology ◽  
2013 ◽  
Vol 140 (9) ◽  
pp. 1061-1069 ◽  
Author(s):  
IRIS I. LEVIN ◽  
PATRICIA G. PARKER
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Sequence Data ◽  
Population Genetic Study ◽  
Haemosporidian Parasite ◽  
Dna Sequence Data ◽  
Sula Granti ◽  
Breeding Attempt ◽  
Genetic Structures

SUMMARYParasites often have shorter generation times and, in some cases, faster mutation rates than their hosts, which can lead to greater population differentiation in the parasite relative to the host. Here we present a population genetic study of two ectoparasitic flies, Olfersia spinifera and Olfersia aenescens compared with their respective bird hosts, great frigatebirds (Fregata minor) and Nazca boobies (Sula granti). Olfersia spinifera is the vector of a haemosporidian parasite, Haemoproteus iwa, which infects frigatebirds throughout their range. Interestingly, there is no genetic differentiation in the haemosporidian parasite across this range despite strong genetic differentiation between Galapagos frigatebirds and their non-Galapagos conspecifics. It is possible that the broad distribution of this one H. iwa lineage could be facilitated by movement of infected O. spinifera. Therefore, we predicted more gene flow in both fly species compared with the bird hosts. Mitochondrial DNA sequence data from three genes per species indicated that despite marked differences in the genetic structure of the bird hosts, gene flow was very high in both fly species. A likely explanation involves non-breeding movements of hosts, including movement of juveniles, and movement by adult birds whose breeding attempt has failed, although we cannot rule out the possibility that closely related host species may be involved.

Judgments of Learning

2015 ◽  
Author(s):  
Matthew G. Rhodes
Keyword(s):  
Memory Performance ◽  
Methodological Approach ◽  
Judgments Of Learning ◽  
Alternative Methods ◽  
Theoretical Frameworks ◽  
Theoretical Approaches ◽  
History Of Research ◽  
History Of ◽  
Combine Information ◽  
Future Work

Several decades of research have examined predictions of future memory performance—typically referred to as judgments of learning (JOLs). In this chapter, I first discuss the early history of research on JOLs and their fit within a leading metacognitive framework. A common methodological approach has evolved that permits the researcher to investigate the correspondence between JOLs and memory performance, as well as the degree to which JOLs distinguish between information that is or is not remembered. Factors that influence each aspect of the accuracy of JOLs are noted and considered within theoretical approaches to JOLs. Thus far, research on JOLs had yielded a number of findings and promising theoretical frameworks that will continue to be refined. Future work will benefit by considering how learners combine information to arrive at a judgment, the implications of alternative methods of measuring JOLs, and the potential for JOLs to influence memory.

scholarly journals Detecting selection with a genetic cross

2020 ◽  
Vol 117 (36) ◽  
pp. 22323-22330
Author(s):  
Hunter B. Fraser
Keyword(s):  
Skin Color ◽  
Evolutionary Biology ◽  
Neutral Evolution ◽  
Sign Test ◽  
Stabilizing Selection ◽  
Mrna Levels ◽  
Effective Population ◽  
Phenotypic Data ◽  
Genetic Cross ◽  
Selected Traits

Distinguishing which traits have evolved under natural selection, as opposed to neutral evolution, is a major goal of evolutionary biology. Several tests have been proposed to accomplish this, but these either rely on false assumptions or suffer from low power. Here, I introduce an approach to detecting selection that makes minimal assumptions and only requires phenotypic data from ∼10 individuals. The test compares the phenotypic difference between two populations to what would be expected by chance under neutral evolution, which can be estimated from the phenotypic distribution of an F2cross between those populations. Simulations show that the test is robust to variation in the number of loci affecting the trait, the distribution of locus effect sizes, heritability, dominance, and epistasis. Comparing its performance to the QTL sign test—an existing test of selection that requires both genotype and phenotype data—the new test achieves comparable power with 50- to 100-fold fewer individuals (and no genotype data). Applying the test to empirical data spanning over a century shows strong directional selection in many crops, as well as on naturally selected traits such as head shape in HawaiianDrosophilaand skin color in humans. Applied to gene expression data, the test reveals that the strength of stabilizing selection acting on mRNA levels in a species is strongly associated with that species’ effective population size. In sum, this test is applicable to phenotypic data from almost any genetic cross, allowing selection to be detected more easily and powerfully than previously possible.

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