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423 results for “Haplotypes”
Data from: Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes
Strong spatial sorting of genetic variation in contiguous populations is often explained by local adaptation or secondary contact following allopatric divergence. A third explanation, spatial sorting by stochastic effects of range expansion, has been considered less often though theoretical models suggest it should be widespread, if ephemeral. In a study designed to delimit species within a clade of venomous coralsnakes, we identified an unusual pattern within the Texas coral snake (Micrurus tener): strong spatial sorting of divergent mitochondrial (mtDNA) lineages over a portion of its range, but weak sorting of these lineages elsewhere. We tested three alternative hypotheses to explain this pattern—local adaptation, secondary contact following allopatric divergence, and range expansion. Collectively, near panmixia of nuclear DNA, the signal of range expansion associated sampling drift, expansion origins in the Gulf Coast of Mexico, and species distribution modeling suggest that the spatial sorting of divergent mtDNA lineages within M. tener has resulted from genetic surfing of standing mtDNA variation—not local adaptation or allopatric divergence. Our findings highlight the potential for the stochastic effects of recent range expansion to mislead estimations of population divergence made from mtDNA, which may be exacerbated in systems with low vagility, ancestral mtDNA polymorphism, and male-biased dispersal.
Data from: Intraspecific haplotype diversity in Cherleria sedoides L. (Caryophyllaceae) is best explained by chloroplast capture from an extinct species
Cherleria sedoides, a plant species widespread in alpine areas of the major European mountain ranges and in Scotland, contains two highly divergent chloroplast haplotype groups, one widespread (WH) and one present only in some populations in the Alps (AH). We investigated whether this haplotype diversity is the result of (1) intraspecific differentiation, (2) retention of an ancestral polymorphism or (3) hybridisation. For this purpose, 106 matK sequences from throughout the Caryophyllaceae and 80 trnQ-rps16 and psbD-trnT sequences of C. sedoides (51) and other species of Cherleria (29) were used for the construction of phylogenies and haplotype networks. As the two haplotype groups were never each other's closest relatives, haplotype diversity as a result of intraspecific differentiation is unlikely. Patterns of genetic differentiation within the WH and AH groups are very different. Whereas WH shows a radial pattern typical of rapid expansion, AH is divided into two divergent subgroups each containing more variation than the WH group. This suggests that the two haplotype groups have dissimilar histories and are therefore unlikely to represent an ancestral polymorphism. Instead, we conclude that the polymorphism is best interpreted as the result of hybridisation. As the WH and AH haplotype groups fall into Cherleria, but do not group with any extant species, we conclude that the rare AH group represents the original C. sedoides, and that the WH group was captured from another, now extinct, species of Cherleria.
Data from: Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region
Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
A positive correlation between species and genetic diversity (SGDC) has been proposed, consistent with neutral predictions in macroecology. We assessed the SGDC in tenebrionid beetle communities of the Aegean archipelago on fifteen islands of different sizes, distances to mainland, and ages of isolation. Alpha- and beta-diversity of species and haplotypes were assessed using sequences of >1000 individuals (mitochondrial Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We show that: (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland are factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated based on species, nuclear and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared to less dispersive lineages that are not sand-obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.
Data from: Haplotype structure, adaptive history and associations with exploratory behaviour of the DRD4 gene region in four great tit (Parus major) populations
The assessment of genetic architecture and selection history in genes for behavioural traits is fundamental to our understanding of how these traits evolve. The dopamine receptor D4 (DRD4) gene is a prime candidate for explaining genetic variation in novelty seeking behaviour, a commonly assayed personality trait in animals. Previously we showed that a single nucleotide polymorphism in exon 3 of this gene is associated with exploratory behaviour in at least one of four Western European great tit (Parus major) populations. These heterogeneous association results were explained by potential variable linkage disequilibrium (LD) patterns between this marker and the causal variant or by other genetic or environmental differences among the populations. Different adaptive histories are further hypothesized to have contributed to these population differences. Here, we genotyped 98 polymorphisms of the complete DRD4 gene including the flanking regions for 595 individuals of the four populations. We show that the LD structure, specifically around the original exon 3 SNP is conserved across the four populations and does not explain the heterogeneous association results. Study-wide significant associations with exploratory behaviour were detected in more than one haplotype block around exon 2, 3 and 4 in two of the four tested populations with different allele effect models. This indicates genetic heterogeneity in the association between multiple DRD4 polymorphisms and exploratory behaviour across populations. The association signals were in or close to regions with signatures of positive selection. We therefore hypothesize that variation in exploratory and other dopamine-related behaviour evolves locally by occasional adaptive shifts in the frequency of underlying genetic variants.
Data from: Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes
Females choose specific mates in order to produce fitter offspring. However, several factors interfere with females' control over fertilization of their eggs, including sneaker males and phenotypically unpredictable allele segregation during meiosis. Mate choice at the individual level thus provides only a poor approximation for obtaining the best genetic match. Consequently, post-copulatory sperm selection by female oocytes has been proposed as a mechanism to achieve complementary combinations of parental haplotypes. Here, using controlled in vitro fertilization of three-spined stickleback eggs, we find haplotype-specific fertilization bias towards gametes with complementary major histocompatibility complex (MHC) immunogenes. The resulting zygote (and thus offspring) genotypes exhibit an intermediate level of individual MHC diversity that was previously shown to confer highest pathogen resistance. Our finding of haplotype-specific gamete selection thus represents an intriguing mechanism for fine-tuned optimization of the offspring's immune gene composition and an evolutionary advantage in the Red Queen dynamics of host-parasite coevolution.
Data from: Strong nuclear differentiation contrasts with widespread sharing of plastid DNA haplotypes across taxa in European purple saxifrages (Saxifraga sect. Porphyrion subsect. Oppositifoliae)
The purple saxifrages, Saxifraga sect. Porphyrion subsect. Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. A multitude of taxa has been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting we show that some taxa indeed form strongly supported genetic entities best recognized on the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana, S. speciosa), while others (S. murithiana, S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s. s. is phylogenetically incoherent. Plastid DNA sequence data show very limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s. s., S. retusa) share the same set of haplotypes. In the widespread species S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered, which exhibit a geographic rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are likely responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, seems, however, insufficient to break down species barriers.
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Phased (reconstructed) haplotypes
<p>Phased (reconstructed) haplotypes of Merinoland lambs and F1 crosses</p>
FIGURE 7. Haplotype parsimony networks for ITS1 in A comparative study of populations of Ectopleura crocea and Ectopleura ralphi (Hydrozoa, Tubulariidae) from the Southwestern Atlantic Ocean
FIGURE 7. Haplotype parsimony networks for ITS1+5.8S (A) and COI (B) for the different populations of Ectopleura crocea and Ectopleura ralphi of the Southwestern Atlantic Ocean. Black circles for the Argentine haplotypes, white ones for Brazilian localities; the sizes of the circles are proportional to the number of localities sharing the haplotype; small black circles represent hypothetical or unsampled haplotypes. Lines connecting circles represent one substitution step. Note that A BO/MP samples differ from JU/PA/BO only by an indel of three base pairs (AAT/– – –). Locality codes are represented inside the circles as MA: Macaé, JU: Juréia, PA: Paraná, BO: Bombas, MP: Mar del Plata.
FIGURE 3. Haplotype network for P in Phylogeny and genetic variation within the widely distributed Bluntnose Minnow, Pimephales notatus (Cyprinidae), in North America
FIGURE 3. Haplotype network for P. notatus. Median-joining haplotype network for the mitochondrial (cytb) gene examined for P. notatus. Each circle represents a different haplotype; circle sizes are proportional to the number of individuals possessing a particular haplotype. Major drainages are represented by different colors. Small red dots represent missing (unsampled or extinct) haplotypes. Lines between circles represent one mutational step, and numbers presented are the number of mutations between haplotypes. Dotted-square-lines depict two major lineages resolved in mtDNA phylogenetic analyses. Dotted-circle depicts a subclade represented in detail (inset). One specimen from P. tenellus was included for comparisons.
Supplementary Data - Haplotype-based inference of recent effective population size in modern and ancient DNA samples
<p>This repository contains the simulated data analyzed in our manuscript titled "Haplotype-based Inference of Recent Effective Population Size in Modern and Ancient DNA Samples".The data is split into 7 datasets. </p><p><strong>- demographies.tar.gz</strong>: the simulated demographic models.<br><strong>- modern_data.tar.gz:</strong> simulated SNP-araray data. The genotypes were simulated under 4 demographic histories (see demographies.tar.gz) for 256 samples and under 10 different random seeds (Replicate 1-10). Additionally, Replicates 11 and 12 include simulations at larger sample sizes. Note that the results at lower sample sizes can be obtained by keeping the first N samples of the simulated files.<br><strong>- true_ibd.tar.gz :</strong> This dataset contains the IBD segments from the simulated modern_data (ground truth from ARGON simulator).<br><strong>- ancient_data.tar.gz</strong> dataset contains simulated aDNA data. The dataset contains data simulated at different coverages (MISSING_$M, where $M = exp(-coverage)), sample sizes, demographic models, and random seeds. Split into three parts. See below for instructions on how to reconstruct the dataset. <br><strong>- structure.tar.gz</strong> and<strong> admixture.tar.gz :</strong> contain the data simulated under more complex demographic histories involving 2 isolated populations (structure) or a single population undergoing a recent admixture event (admixtuer.tar.gz). The manuscript provides more details about the demographic histories.<br>- <strong>imputed.tar.gz</strong> dataset contains simulated imputed aDNA data. Each region was simulated independently. Each folder corresponds to a chromosome arm and contains:<br> - data.anc_array.npy: list of the SNPs included in the analysis (simulating a 1240k array)<br> - data.glimpse.vcf.gz: phased ancient population data as phased by GLIMPSE v1<br> - data.glimpse.vcf.gz.csi: index for the above VCF file<br> - data.imputed.vcf.gz: imputed ancient population data (unphased, including dosages and genotype posteriors)<br> - data.imputed.vcf.gz.csi: index file for the above VCF<br> - data.map.gz: genetic map for GLIMPSE (tab-separated format: pos chr cM)<br> - data.ref.tsv.gz: file used for calculating genotype likelihoods with BCFtools mpileup command to use as input for GLIMPSE (format: chromosome position ref_allele,alt_allele)<br> - data.ref.tsv.gz.tbi: index for the above file<br> - data.ref.vcf.gz: simulated sequencing data from the reference panel<br> - data.ref.vcf.gz.csi: index file for the above VCF<br> - data.target_ground_truth.vcf.gz: simulated sequencing data for the ancient population (ground truth)<br> - datalist.txt: list of genotype likelihood files for each target individual (to be used for merging into a single file)<br> - data.temp.map.gz: genetic map for data creation with msprime simulator (format: chr position rate(cM/Mb) cM)<br> - data.tree -> msprime simulator output containing all samples, both reference panel samples and ancient population samples<br> - data.vcf.gz: VCF containing ground truth sequencing data, phased genotypes for reference panel samples and for ancient population samples<br> - dataref.fa.fai: index for reference fasta file used during reads creation</p><p> </p><p>Note that some of the datasets have been split into multiple parts, for example admixed.tar.gz has been split into three different parts admixed.tar.gz-part-aa, admixed.tar.gz-part-ab, and admixed.tar.gz-part-ac<br>You can get the data by typing:</p><p>cat admixed.tar.gz.part-* > admixed.tar.gz</p><p><br> </p>
Fig. 3. Haplotype network for 419 in Across mountains and ocean: species delimitation and historical connectivity in Holarctic and Arctic-Alpine wolf spiders (Lycosidae, Pardosa)
Fig. 3. Haplotype network for 419 specimens of P. saltuaria species group based on mitochondrial COI data. Haplotypes are colored based on morphological identification. Each line is 1 mutation step.
Figure 2. Phylogenetic relationships among Viverra tangalunga inferred from mtDNA haplotypes from the concatenated 797 in The distribution of the Malay civet Viverra tangalunga (Carnivora: Viverridae) across Southeast Asia: natural or human-mediated dispersal?
Figure 2. Phylogenetic relationships among Viverra tangalunga inferred from mtDNA haplotypes from the concatenated 797-bp mitochondrial control region and cytochrome b sequences. Trees for each of the three analyses (neighbour joining, maximum likelihood, and Bayesian inference) had similar topologies. Numbers above the branches represent bootstrap support, with only values> 60% shown. Numbers in parentheses represent the number of individuals sharing the same haplotype; haplotype codes are listed in Appendix S3.
Data from: Alignment of COI haplotypes from museum samples of Diptera of forensic importance
<p>Necrophagous Diptera are the most important group of insects used for the purposes of forensic entomology. While the most utilized fly family in this context is the family Calliphoridae, there is a number of other families, which can be of a great importance during real case investigations. This article analyses the necrophagous flies of all families recorded from 160 real cases in Switzerland in between 1993-2007. A total of 56 species belonging to 16 families was identified with Calliphoridae being the most dominant family (90,63 % of all cases), followed by Muscidae (26,25 %), Sarcophagidae (19,38 %), Phoridae (14,38 %) and Fanniidae (12,50 %). For specimens that were difficult to identify morphologically, a new PCR primer has been specifically designed for the amplification of a short, informative COI barcode in degraded museum samples of forensically important Diptera taxa. The richest family in terms of species was the family Muscidae with 16 species. <em>Fannia fuscula</em> and <em>Fannia monilis</em> were recorded from human cadavers for the first time. The study highlights the importance of different fly families in forensic investigation, enhancing our comprehension of their prevalence and dispersion in real cases in Central Europe. The results pave the way for additional exploration, especially regarding the involvement of less frequently observed species in forensic entomology.</p>
Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure
<p>Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, which<br>reduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (<em>Sylvia atricapilla</em>), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve due<br>to reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.</p>
Salt Water Exposure Exacerbates the Negative Response of Phragmites australis Haplotypes to Sea-Level Rise
<p>Dataset associated with the 2024 publication in the <em>Plants</em> journal dealing with <em>Phragmites australis </em>response to abiotic factors associated with rising sea levels. </p>
Supplementary tables for chapter 3: "Haplotype-resolved transcriptomics defines the inheritance and genetic architecture of response to Citrus Greening Disease"
<p>Dissertation chapter 3: "<span>Haplotype-resolved transcriptomics defines the inheritance and genetic architecture of response to Citrus Greening Disease"</span></p>
FIGURE 4. COI haplotype networks. A in Three New Species of Deep-Sea Wood-Associated Sea Stars (Asteroidea: Caymanostellidae) from the Eastern Pacific
FIGURE 4. COI haplotype networks. A—Caymanostella scrippscognaticausa sp. nov. locality network; B—Caymanostella davidalani sp. nov. locality network; C—Caymanostella davidalani sp. nov. depth network.
EXO5 common haplotypes MD simulation data
<p>Molecular Dynamics simulation data for WT, G172V, L151P and G172V+D115N EXO5, bound to a single-strand DNA, as found in PDB 7LW9. .gro, .pdb, .top and .tpr files are provided for the starting structure, along with compressed .xtc trajectories for all simulation replicas, and an .mdp file with the simulation parameters. The trajectories do not include the first 960 ns of simulation, considered as the equilibration cutoff. The .xtc files contain one frame per 100 ps, with all molecules and atoms except water.</p>
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