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38 results for “haplotype diversity”
Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction
Fig. 4. Mismatch distribution for mitochondrial haplotypes for 92 individuals of Brycon nattereri from the Laranjinha River.
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1601 individuals from 18 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognised as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study the sequence of eIF4E was analysed in 1090 barley landraces and non-current cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eIF4E haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 out of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest eIF4E may play a role in barley adaptation to local habitats.
Data from: Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity
High rates of gene duplication and the highest levels of functional allelic diversity in vertebrate genomes are the main hallmarks of the major histocompatibility complex (MHC), a multigene family with a primordial role in pathogen recognition. The usual tight linkage among MHC gene duplicates may provide an opportunity for the evolution of haplotypes that associate functionally divergent alleles and thus grant the transmission of optimal levels of diversity to coming generations. Even though such associations may be a crucial component of disease resistance, this hypothesis has been given little attention in wild populations. Here, we leveraged pedigree data from a barn owl (Tyto alba) population to characterize MHC haplotype structure across two MHC class I (MHC-I) and two MHC class IIB (MHC-IIB) duplicates, in order to test the hypothesis that haplotypes' genetic diversity is higher than expected from randomly associated alleles. After showing that MHC loci are tightly linked within classes, we found limited evidence for shifts towards MHC haplotypes combining high diversity. Neither amino acid nor functional within-haplotype diversity were significantly higher than in random sets of haplotypes, regardless of MHC class. Our results therefore provide no evidence for selection towards high-diversity MHC haplotypes in barn owls. Rather, high rates of convergent evolution may constrain the evolution of high-diversity haplotypes at MHC-I, while, in contrast, for MHC-IIB, fixed differences among loci may provide barn owls with already optimized functional diversity. This suggests that at the MHC-I and MHC-IIB, respectively, different evolutionary dynamics may govern the evolution of within-haplotype diversity.
Fig. 1 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 1: Distribution of P. acuta group in Canada, North America, Mexico and Cuba (A), Europe (B) and Serbia (C). Distribution of P. acuta in North and Central America (white circles) was compiled from the data of Wethington et al. (2009), Wethington & Guralnick (2004) and Kraus et al. (2014). The European (white circles) range is based on Wethington & Lydeard (2007), data and distribution in Serbia is based on Novaković (2014, black circles), and on our field sampling data (white circles).
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 in Molecular confirmation of the occurrence of Anguilla interioris (Actinopterygii: Anguilliformes) in North Maluku of Indonesia and mitochondrial DNA haplotype diversity among existing specimens
Figures 2–3. Mitochondrial cytochrome c oxidase subunit 1 (CO1) 551 bp sequence analyses. (2) Phylogenetic analysis based on maximum likelihood algorithm with the sample codes, GenBank or BOLD accession numbers and sample sites shown. Bootstrap percentages are shown at the tree nodes. (3) Haplotype network with the haplotypes labelled as H1 to H9. The circle size is proportional to the number of samples, and different sample sites are represented by different colours. Small white circle represents median vector which is the hypothesized or missing haplotype. Each dash on the line symbolizes one mutational step.
Data from: RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
Reduced representation genome-sequencing approaches based on restriction digestion are enabling large-scale marker generation and facilitating genomic studies in a wide range of model and nonmodel systems. However, sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework to mimic the biased recovery of chromosomes in restriction-based short-read sequencing experiments (RADseq). We analysed simulated DNA sequence datasets and compared known values from simulations with those that would be estimated using a RADseq approach from the same samples. We compare these 'true' and 'estimated' values of commonly used summary statistics, π, θw, Tajima's D and FST. We show that loci with missing haplotypes have estimated summary statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These biases are sensitive to nonequilibrium demography, such as bottlenecks and population expansion. In silico digests with 102 completely sequenced Drosophila melanogaster genomes yielded results similar to our findings from coalescent simulations. Though the potential of RADseq for marker discovery and trait mapping in nonmodel systems remains undisputed, our results urge caution when applying this technique to make population genetic inferences.
Supplementary material 1 from: Gariepy TD, Musolin DL, Konjević A, Karpun NN, Zakharchenko VY, Zhuravleva EN, Tavella L, Bruin A, Haye T (2021) Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia. NeoBiota 68: 53-77. https://doi.org/10.3897/neobiota.68.68915
Table S1. Collection information and GPS coordinates
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
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Data from: Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity
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Data from: An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations.
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Data from: RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
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An approach for estimating haplotype diversity from sequences with unequal lengths
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Rear-edge, low-diversity, and haplotypic uniformity in cold-adapted Bupleurum euphorbioides interglacial refugia populations
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Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures
GEO Series GSE250451. Homo sapiens. 12 samples. Type: Genome variation profiling by array.
List of specimens, species codes, localities (NI, Northern Iberia; CI, Central Iberia; SI, Southern Iberia; AU, Austria; BL, Bulgaria; CR, Croatia; CZ, Czech Republic; DK, Denmark; FR, France; GE, Germany; GR, Greece; HN, Hungary; SD, Sweden; SW, Switzerland; TK, Turkey), haplotypes codes for species and GenBank accession numbers of the samples used for an overall molecular screening of bat cryptic diversity in Iberia using a mtDNA cytb fragment in The Iberian contribution to cryptic diversity in European bats
List of specimens, species codes, localities (NI, Northern Iberia; CI, Central Iberia; SI, Southern Iberia; AU, Austria; BL, Bulgaria; CR, Croatia; CZ, Czech Republic; DK, Denmark; FR, France; GE, Germany; GR, Greece; HN, Hungary; SD, Sweden; SW, Switzerland; TK, Turkey), haplotypes codes for species and GenBank accession numbers of the samples used for an overall molecular screening of bat cryptic diversity in Iberia using a mtDNA cytb fragment
FIGURE 2 in High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962)
FIGURE 2: Three-dimensional plot of pairwise uncorrected p-distances for the cytochrome b (x-axis) and 16S rRNA (yaxis) markers. The number of observation (z-axis) indicates the number of times that a defined combination of cytochrome b – 16S distances has been observed.
FIGURE 4 in High haplotype diversity in a microendemic Malagasy gecko species, Lygodactylus mirabilis (Pasteur, 1962)
FIGURE 4: Mismatch distribution graph of the 27 mtDNA sequences (1251 bp, cytochrome b and 16S rRNA genes) in L. mirabilis. The solid line with diamonds represents the observed distribution curve and the diamonds are the relative frequencies of nucleotide differences between pair of individuals. The tick solid line represents the distribution expected from an expanding population. Dashed lines indicate the 95% confidence interval. Additional information can be found in the Materials and Methods.
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