scholarly journals Genetic Divergence between Two Sympatric Ecotypes of Phalaenopsis pulcherrima on Hainan Island

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 446
Author(s):  
Xiangyu Hu ◽  
Siren Lan ◽  
Xiqiang Song ◽  
Fusun Yang ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Reproductive Isolation ◽  
Hainan Island ◽  
Nutrient Content ◽  
Soil Conditions ◽  
Island Population ◽  
Ecological Differentiation ◽  
Ecotypic Differentiation ◽  
High Level

Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear geographical isolation in Phalaenopsis pulcherrima, a Southeast Asia endemic and endangered orchid. The soil of the red leaf ecotype has a higher water content and nutrient content than the green ecotype. What is the genetic structure of the two ecotypes? Is there complete or partial reproductive isolation between the two ecotypes? In this work, leaf reflection of the two ecotypes in P. pulcherrima were compared, to illustrate their difference in leaf color. The genetic differentiation between two ecotypes was examined, using ISSR and SRAP markers to determine the genetic structure of the populations. Our results showed that the green ecotype had reflectance spectrum peaks at 530 nm and 620 nm, while in the red ecotype, the peak at 530 nm was absent. A total of 165 ISSR and SRAP loci showed a high level of genetic diversity within the green ecotype, and analyses of the population structure revealed two genetic clusters that corresponded to the red and green ecotypes. The percentage of variation between the two ecotypes (24.55%) was greater than the percentage of variation among the populations (16.54%)—indicating partial reproductive isolation, high genetic differentiation, and that ecological differentiation has been more important than geographical barriers among populations within ecotypes. Most pairwise FST values between the populations within either ecotype on Hainan Island were less than 0.15; however, the FST between both the Thai and Malaysian populations and the Hainan Island population was greater than 0.25, due to South China sea isolation. Ecotypic differentiation is an important part of speciation; therefore, we must take into account the axes along which lineages sort, when formulating protection strategies.

scholarly journals Genomic differentiation in an endemic Philippine genus (Aves: Sarcophanops) due to geographic isolation on recently disassociated islands

2019 ◽  
Author(s):  
Luke C Campillo ◽  
Joseph D. Manthey ◽  
Robert C. Thomson ◽  
Peter A. Hosner ◽  
Robert G. Moyle
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Deep Structure ◽  
Island Population ◽  
Geographic Isolation ◽  
Recent Period ◽  
Genetic Sampling ◽  
Genome Wide ◽  
Species Analysis

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

scholarly journals Microsatellite Polymorphism and Genetic Structure of Florida Mottled Duck Populations

The Condor ◽  
2002 ◽  
Vol 104 (2) ◽  
pp. 424-431 ◽  
Author(s):  
Christen L. Williams ◽  
Richard C. Brust ◽  
Olin E. Rhodes Jr
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Habitat Loss ◽  
Microsatellite Loci ◽  
Nuclear Dna ◽  
Gene Frequencies ◽  
Limited Distribution ◽  
Mottled Duck ◽  
Anas Fulvigula ◽  
High Level

Abstract Little is understood concerning the effects regional isolation and habitat loss have had upon the genetic structure of Mottled Ducks (Anas fulvigula), a nonmigratory waterfowl species with a limited distribution. Our objective was to identify nuclear DNA-based markers for Mottled Ducks and determine levels of subdivision among populations in Florida. We screened 13 microsatellite primer pairs and identified six microsatellite loci that were variable in Mottled Ducks. These markers revealed a low level of genetic differentiation and a high level of genetic exchange among four Mottled Duck subpopulations within Florida. Over all populations, single-locus expected heterozygosities over the six loci surveyed ranged from 0.13–0.85. There were no significant differences in gene frequencies among the populations examined, and the Fst over 5 biparental loci was not different from zero. Our analysis of the Florida Mottled Duck population indicated high levels of heterozygosity and no evidence of genetic subdivision among breeding units. Polimorfismo en Microsatélites y Estructura Genética en Poblaciones de Anas fulvigula Resumen. Se tiene escaso conocimiento acerca de los efectos del aislamiento regional y de la pérdida de hábitat sobre la estructura genética de poblaciones de Anas fulvigula, un ave acuática no migratoria de distribución restringida. Nuestro objetivo fue identificar marcadores genéticos de ADN para A. fulvigula y determinar los niveles de subdivisión entre poblaciones en Florida. Examinamos 13 pares de iniciadores (i.e., primers) para microsatélites e identificamos seis loci que fueron variables en A. fulvigula. Estos marcadores revelaron un bajo nivel de diferenciación genética y un alto grado de intercambio genético entre cuatro subpoblaciones de A. fulvigula en Florida. Para todas las poblaciones, la heterocigocidad esperada en un locus varió entre 0.13–0.85 para los seis loci examinados. No hubo diferencias significativas en las frecuencias génicas entre las subpoblaciones examinadas, y el valor de Fst para los 5 loci biparentales no fue diferente de cero. Nuestros análisis de las poblaciones de A. fulvigula de Florida indicaron altos niveles de heterocigocidad y no mostraron evidencia de subdivisión genética entre las unidades reproductivas.

Genetic differentiation in populations of the cestode Bothriocephalus acheilognathi (Cestoda, Pseudophyllidea) as revealed by eight microsatellite markers

Parasitology ◽  
2003 ◽  
Vol 126 (5) ◽  
pp. 493-501 ◽  
Author(s):  
H. Y. LUO ◽  
P. NIE ◽  
Y. A. ZHANG ◽  
W. J. YAO ◽  
G. T. WANG
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Random Mating ◽  
Genetic Structure Of Populations ◽  
Bothriocephalus Acheilognathi ◽  
The Mean ◽  
High Level ◽  
Cross Fertilization

The genetic structure of populations of the fish cestode, Bothriocephalus acheilognathi collected from Bailianhe Reservoir (BLH), Changshou (CSH) and Liangzi (LZH) Lakes was investigated by using 8 microsatellite loci. A total of 108 adult worms were genotyped at each of the 8 loci. For the 3 populations, the mean number of alleles per locus ranged from 2·38 to 5·5, and the mean expected heterozygosity ranged from 0·432 to 0·559. The average polymorphic information content (PIC) was from 0·384 to 0·492. The significant Fis values indicated non-random mating within LZH and BLH populations. On the other hand, when samples were further classified into subpopulations at the level of host fish species, no or little heterozygote deficiency was detected at most loci, showing that cross-fertilization, predominantly, but not exclusively, must have occurred within the subpopulations. Microsatellite markers also revealed an unexpected high level of genetic differentiation, as measured by Rst and Nm values or by δu2 genetic distance among subpopulations from different hosts. Factors influencing the population genetic structure and the parasite host specificity are discussed.

scholarly journals Genomic differentiation in an endemic Philippine genus (Aves: Sarcophanops) due to geographic isolation on recently disassociated islands

2019 ◽  
Author(s):  
Luke Campillo ◽  
Joseph D. Manthey ◽  
Robert C. Thomson ◽  
Peter A. Hosner ◽  
Robert G. Moyle
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Deep Structure ◽  
Island Population ◽  
Geographic Isolation ◽  
Recent Period ◽  
Genetic Sampling ◽  
Genome Wide ◽  
Species Analysis

Phylogeographic studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation, but remains relatively undocumented perhaps because the current episode of island isolation started relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide RAD markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

scholarly journals Genomic differentiation in an endemic Philippine genus (Aves: Sarcophanops) owing to geographical isolation on recently disassociated islands

2020 ◽  
Vol 131 (4) ◽  
pp. 814-821
Author(s):  
Luke C Campillo ◽  
Joseph D Manthey ◽  
Robert C Thomson ◽  
Peter A Hosner ◽  
Robert G Moyle
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Deep Structure ◽  
Island Population ◽  
Geographical Isolation ◽  
Isolated Populations ◽  
Genetic Sampling ◽  
Genome Wide ◽  
Species Analysis

Abstract Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but remains relatively undocumented, perhaps because the current episode of island isolation started in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (RAD) markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and a sister species, Sarcophanops steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

2017 ◽  
Vol 54 ◽  
pp. 134-140
Author(s):  
H. S. Rudoman ◽  
V. M. Balatsky ◽  
V. Y. Nor ◽  
V. O. Vovk
Keyword(s):  
Genetic Structure ◽  
Information Content ◽  
Analysis Of Variance ◽  
Farm Animals ◽  
Daily Weight Gain ◽  
Fixation Index ◽  
Its Sequencing ◽  
Large White ◽  
Stage Of Development ◽  
High Level

One of the top priorities at the present stage of development of pig breeding remains the development of a set of measures aimed at increasing the resistance animals to various diseases, especially – to colibacteriosis .One of the recent and effective approaches to prevent colibacillosis is using markers of selection; it involves pig genotyping by genome locuses. Chosen locuses are associated with animal sensitivity to the disease and selection of the results of genotyping of animals with increased resistance. Due to researches, one of such locuses is alpha-fukozyltrasferаza 1 gene (FUT1). Gene FUT1 is located in chromosome 6. As a result of its sequencing in the swine breeds of Large White and Swedish Landrace, single-nucleotide polymorphism (g.307 G > A SNP) has been detected. AA genotype determines the resistance of animals to colibacteriosis, while AG and GG genotypes are susceptible to this disease. According to the results of previous studies, the positive effect of allele A was determined not only on the resistance of pigs to colibacteriosis, but also on indicators of fattening and meat productivity and on reproductive performance. In Ukraine, the studies of polymorphism FUT1 g.307 G > A SNP were held fragmentedly and only on certain populations of Ukrainian Meat and Large White breed but without establishing its association with the indicators of productivity of pigs. The aim of our work was to study the genetic structure of Ukrainian Large White breeds, type 1 and the establishment of association. g. 307 G > A SNP FUT1 gene with pigs indicators of productivity. For research the 96 samples of hair were used. DNA isolation from samples with biomaterial were carried out using ion exchange resin Chelex-100. Genotyping was performed by PCR-RFLP by method of Jorgensen et al. (2006). Using DNA analysis of this breeds locus FUT1 was determined by genetic structure. Allele frequency of allele G (0,573) and allele A (0,427) was established The distribution of genotype frequencies was not statistically significantly different from the theoretically expected, calculated by the Hardy-Weinberg criterion. Thus, according to the locus of FUT1 g.307 G > A, the breeds investigated are in a state close to the genetic equilibrium. The negative value of the fixation index by the locus FUT1 g.307 G > A indicates an excess of heterozygotes in the population, and hence the lack of targeted selection for this marker. The valuation was performed by calculating the PIC (polymorphic information content) – information content of polymorphism marker. In the analyzed pig herd for this marker, the PIC has an average value (0,367), which indicates the high level of polymorphism of the given locus and is favorable for the possibility of conducting a search for links between individual genotypes and indicators of productivity. To establish the association g.307 G > A SNP FUT1 gene with indicators of animal productivity, a one-way analysis of variance of the experimental data was used. Based on the results of a one-way analysis of variance, a significant effect of the genotypes of the FUT1gene (g.1849 G > C) on the indicator of the average daily weight gain (р ≤ 0,001), the thickness of the bacon at the level of the VI-VII vertebrae (p ≤ 0.01), reaching live weight of 100 kg (р ≤ 0,001) and breeding index of fattening qualities (р ≤ 0,01) was found. The parameter of the influence of the genetic factor on the test feature was 28,54%, 10,4%, 33,4% and 8,8% respectively. According to the investigated indicators of productivity, animals with genotype AA, which determines resistance to colibacteriosis, dominated the animals with genotypes GG and AG. Based on the results of our research and pre-published data, the multiple effect of the g.307 G > A SNP FUT1 gene is observed, which is associated with the indicators of productivity, which again confirms the polygenicity of the quantitative trait loci of farm animals. Taking into account a high level of polymorphism of the investigated gene and reliable associations of genotypes with indicators of productivity found, it can be recommended to carry out breeding of pigs using genetic information of the g.307 G > A SNP gene FUT1.

Geographic Variation in Dominance of Spinosad Resistance in Colorado Potato Beetles (Coleoptera: Chrysomelidae)

2020 ◽  
Author(s):  
Coby Klein ◽  
Mitchell Baker ◽  
Andrei Alyokhin ◽  
David Mota-Sanchez
Keyword(s):  
New York ◽  
Long Island ◽  
New York State ◽  
The United States ◽  
Island Population ◽  
Potato Beetle ◽  
Rate Of Increase ◽  
Short Period ◽  
Leptinotarsa Decemlineata Say ◽  
High Level

Abstract Eastern New York State is frequently the site of Colorado potato beetle (Leptinotarsa decemlineata, Say) populations with the highest observed levels of insecticide resistance to a range of active ingredients. The dominance of a resistant phenotype will affect its rate of increase and the potential for management. On organic farms on Long Island, L. decemlineata evolved high levels of resistance to spinosad in a short period of time and that resistance has spread across the eastern part of the Island. Resistance has also emerged in other parts of the country as well. To clarify the level of dominance or recessiveness of spinosad resistance in different parts of the United States and how resistance differs in separate beetle populations, we sampled in 2010 beetle populations from Maine, Michigan, and Long Island. In addition, a highly resistant Long Island population was assessed in 2012. All populations were hybridized with a laboratory-susceptible strain to determine dominance. None of the populations sampled in 2010 were significantly different from additive resistance, but the Long Island population sampled in 2012 was not significantly different from fully recessive. Recessive inheritance of high-level resistance may help manage its increase.

scholarly journals Genetic Differentiation of Archachatina marginata Populations from Three Vegetation Zones Using Radom Amplified Polymorphic DNA Polymerase Chain Reaction

2015 ◽  
Vol 7 (3) ◽  
pp. 372-381
Author(s):  
Comfort O. AFOLAYAN ◽  
Michael Olugemi AWODIRAN
Keyword(s):  
Genetic Differentiation ◽  
Principal Component ◽  
Ammonium Bromide ◽  
Vegetation Zones ◽  
Suitable Parameter ◽  
Variable Feature ◽  
Canonical Variates ◽  
Cetyl Trimethyl Ammonium ◽  
High Level ◽  
Dna Profiles

The genetic differentiation of Archachatina marginata populations from three different zones of Nigeria was studied with a view to delimiting them into sub-species. One hundred and nineteen (119) snail specimens were collected, comprising of forty (40) specimens from Yenagoa (Mangrove forest) and from Kabba (Guinea Savanna) and thirty nine (39) specimens were from Ile-Ife (Rainforest). Eight parameters of the shell specimens of A. marginata which included height of shell, width of shell, aperture height, aperture width, spire length, spire width, penultimate whorl length and first whorl length were subjected to Principal Component Analysis (PCA) and Canonical Variates Analysis (CVA) to delimit the populations into sub-species. DNA of the various populations was extracted from the foot muscle using CTAB (Cetyl Trimethyl Ammonium Bromide) method, which was subjected to RAPD analysis. The RAPD studies employed five (5) oligonucleotide primers (OPB – 17, OPH – 12, OPH – 17, OPI – 06 and OPU – 14) to amplify DNA from 27 samples of A. marginata selected. All five primers produced different band patterns, and the number of fragments amplified per primer varied. Among them, OPB- 17 gave DNA profiles with more numerous bands than the others primers. Both PCA and CVA produced overlapped clusters of A. marginata specimens from the three vegetation zones. The height of shell was observed to be the most variable feature and preferably the most suitable parameter for population grouping. Analysis of the proportions of polymorphic loci and band sharing based on similarity indices for A. marginata samples indicated a relatively high level of genetic variation in the populations from the three areas.

Contrasting patterns of genetic structure and disequilibrium in populations of a stone-cased caddisfly (Tasimiidae) from northern and southern Australia

2008 ◽  
Vol 59 (3) ◽  
pp. 235 ◽  
Author(s):  
Alicia Slater Schultheis ◽  
Richard Marchant ◽  
Jane Margaret Hughes
Keyword(s):  
Genetic Structure ◽  
Genetic Differentiation ◽  
Adult Emergence ◽  
Conclusive Evidence ◽  
Emergence Patterns ◽  
Freshwater Invertebrate ◽  
Gene Coi ◽  
Hardy Weinberg Equilibrium ◽  
New Recruits ◽  
Genetic Patchiness

In marine and freshwater invertebrate populations, microscale genetic differentiation or ‘genetic patchiness’ is thought to result from variation in the abundance and genetic composition of new recruits at a particular location. In the present study, the role of the adult emergence patterns in genetic patchiness was examined using mtDNA and two microsatellite loci to compare patterns of genetic differentiation in asynchronously (subtropical) and synchronously emerging (temperate) populations of the stone-cased caddisfly Tasimia palpata. A 550 base pair region of the mitochondrial cytochrome c oxidase subunit I gene (COI) was sequenced in at least 14 individuals from each population. Genetic structure was detected only at the reach scale in the subtropical populations and no genetic differentiation was detected in temperate populations. There were more deviations from Hardy–Weinberg equilibrium (HWE) in subtropical populations than in temperate populations where 44% and 12.5%, respectively, of tests for deviations from HWE were significant. Although distinct patterns of genetic structure and deviations from HWE were observed in the subtropical and temperate populations of T. palpata, no conclusive evidence was found to suggest that the differences are caused by differences in emergence patterns. We hypothesise that genetic patchiness must be caused by post-recruitment processes, most likely the preservation of oviposition ‘hotspots’ in subtropical streams.

scholarly journals Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

2021 ◽  
Author(s):  
Guai-qiang Chai ◽  
Yizhong Duan ◽  
Peipei Jiao ◽  
Zhongyu Du ◽  
Furen Kang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Association Studies ◽  
Natural Populations ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Future Design ◽  
Ammopiptanthus Nanus ◽  
Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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