Gene exchange across a postglacial contact zone in Fraxinus excelsior L.

Abstract Hybridization between divergent lineages of common ash Fraxinus excelsior L. was studied in Slovakia and adjacent regions of Hungary, the Czech Republic and Poland in the contact zone between two postglacial colonization routes originating from different glacial refugia. Thirty-eight common ash populations were studied using a combination of 6 maternally inherited chloroplast microsatellite markers and 7 biparentally inherited nuclear microsatellites (nSSR). Two predominant chloroplast lineages were identified, between which the boundary was very sharp. Populations containing a mixture of different haplotypes were found only in the immediate proximity of the boundary. Bayesian analysis of population structure based on nSSR loci revealed the existence of two clusters, which largely coincided with chloroplast lineages. Both haplotype frequencies and proportions of clusters identified by the Bayesian analysis exhibited a clinal transition over the hybrid zone, with cline widths of 36 km for chloroplast haplotype frequencies (reflecting gene flow by seeds) and 275 km for Bayesian clusters based on nSSR (reflecting gene flow by pollen and seeds). Chloroplast haplotype diversity increased along the boundary between lineages not only because of admixture, but also due to the presence of rare haplotypes. In contrast, diversity at nuclear loci did not exhibit any geographical trend.

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Spatial Scale Patterns of Genetic Diversity and Gene Flow in Populations of Sweet Detar (Detarium microcarpum Guill. & Perr.; Fabaceae)

10.21203/rs.3.rs-879012/v1 ◽

2021 ◽

Author(s):

Relique Ignace AGBO ◽

Antoine Missihoun ◽

David Montcho ◽

Rollande Dagba ◽

Paulin Sédah ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Molecular Analysis ◽

Haplotype Diversity ◽

Fixation Index ◽

Chloroplast Microsatellite ◽

Evolutionary Forces ◽

Detarium Microcarpum ◽

Polymorphism Rate ◽

Amova Analysis

Abstract The main objective of this study is to investigate the patterns of genetic diversity and phylogenetic relationships within populations of Detarium microcarpum (Fabaceae) relative to different spatial conditions. Seventy-eight (78) accessions of D. microcarpum belonging to six populations (Phytogeographic districts) were sampled. In order to have very good quality DNA for molecular analysis, an optimization of the DNA isolation protocol was made. The molecular analysis of the accessions was carried out using 7 chloroplast microsatellite markers. The polymorphism rate (P) is 85.71% and the Polymorphism Information Content (PIC) was in the range of 0.43 (Ntcp_9) to 0.73 (Ccmp_2) with an average of 0.59. Allelic richness (A) ranged from 1.41 to 2.85 with an average of 2.04. The observed heterozygosity (Ho) ranged from 0.23 to 0.60 with an average of 0.39. The expected heterozygosity (He) ranged from 0.43 to 0.60 with a mean of 0.50. Wright's fixation index (FIS) ranged from − 0.17 to 0.47. The effective allele (Ae) is between 1.77 and 2.53 with an average of 2.02. Wright differentiation index (FST) was 0.024. Phylogenetic analysis revealed that the NST value was significantly higher than the GST value (NST = 0.452; GST = 0.190; P < 0.05). A relatively low hd haplotype diversity is obtained (Hd = 0.320). AMOVA analysis showed that 17.35% of the variation existed within populations but 45.80% among populations within the species. Neighbor-Joining phylogenetic tree of D. microcarpum revealed three non-distinct clusters haplotypes showing the existence of gene flow between populations of the species. Our findings of genetic structure and gene flow of D. microcarpum populations based on different spatial conditions is caused by evolutionary forces such as scattering and pollination.

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Chloroplast DNA polymorphism reveals geographic structure and introgression in the Quercus crassifolia × Quercus crassipes hybrid complex in Mexico

Botany ◽

10.1139/b07-128 ◽

2008 ◽

Vol 86 (3) ◽

pp. 228-239 ◽

Cited By ~ 17

Author(s):

E. Tovar-Sánchez ◽

P. Mussali-Galante ◽

R. Esteban-Jiménez ◽

D. Piñero ◽

D. M. Arias ◽

...

Keyword(s):

Parental Species ◽

Diversity Index ◽

Hot Spot ◽

Haplotype Diversity ◽

Hybrid Zones ◽

Chloroplast Microsatellite ◽

Colonization Routes ◽

Allopatric Populations ◽

Genetic Structure Of Populations ◽

Hybrid Complex

Quercus crassifolia H. & B. and Quercus crassipes H. & B. are two common temperate forest species in Mexico that form hybrids when they occur in mixed (sympatric) areas. In this study, we used chloroplast microsatellite haplotypes to infer phylogeographic patterns onto the genetic structure of populations of both parental species, thus defining probable colonization routes throughout Mexico. Haplotype diversity in seven hybrid zones and four allopatric sites with nonmixed (allopatric) populations of both putative parental species was analyzed. To determine the expansion and colonization routes for the two species, we carried out a nested clade phylogeographic analysis that would allow us to infer the haplotype correspondence to a phylogeographical approach. In spite of sharing many common populations, we determined that there is a different genetic historical colonization for Q. crassipes and for Q. crassifolia. Hybrid populations had the highest levels of genetic variation (Gv), Shannon diversity index (H), and haplotype number (nh) in comparison with nonmixed/allopatric populations of their putative parentals. Furthermore, populations of hybrid zones showed the highest values of genetic differentiation FST, RST . Moreover, both species share four distinctive cpDNA haplotypes, which were most likely acquired by introgression through hybrids located in several populations throughout the Eje Neovolcánico area. This last region was confirmed to be a “hot spot” for oak diversity, a place in which different maternal lineages merged.

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

10.1101/2021.08.12.455854 ◽

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.

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HLA Haplotype Frequencies and Genetic Profiles of the Kuwaiti Population

Medical Principles and Practice ◽

10.1159/000499593 ◽

2019 ◽

Vol 29 (1) ◽

pp. 39-45 ◽

Cited By ~ 1

Author(s):

Reem Ameen ◽

Salem H. Al Shemmari ◽

Steven G.E. Marsh

Keyword(s):

Middle Eastern ◽

Venous Blood ◽

Haplotype Diversity ◽

Principal Component ◽

Hla Class I ◽

Class Ii ◽

Class I ◽

Haplotype Frequencies ◽

Kuwaiti Population ◽

Genetic Profiles

Objective: The aim of this study was to assess the HLA haplotype frequencies and genetic profiles of the Kuwaiti population. Materials and Methods: Whole venous blood was obtained from 595 healthy, unrelated Kuwaiti volunteers. The study population was genotyped for HLA class I (HLA-A, HLA-B, and HLA-C) and class II (HLA-DRB1 and HLA-DQB1) loci using sequence-specific oligonucleotide (SSO) probe-based hybridization and high-resolution HLA genotyping. Haplotype frequencies were estimated using an implementation of the expectation maximization algorithm that resolves both phase and allelic ambiguity. The Kuwaiti population was compared with other populations from the US National Marrow Donor Program (NMDP), by running a principal component analysis (PCA) on the relevant haplotype frequencies. Results: The most common HLA class I alleles in Kuwait were HLA-A*02:01g, HLA-C*06:02g, and HLA-B*50:01g with frequencies of 16, 14, and 12%, respectively. The most common HLA class II alleles in Kuwait were HLA-DQB1*02:01g and HLA-DRB1*07:01 with frequencies of 29.7 and 16.5%, respectively. The most common Kuwaiti haplotype observed was HLA-A*02:01g∼HLA-C*06:02g∼HLA-B*50:01g∼HLA-DRB1*07:01∼HLA-DQB1*02:01g at a frequency of 2.3%. The PCA demonstrated close genetic proximity of the Kuwaiti population with Middle Eastern, Southeast Asian, and North African populations in the NMDP. Conclusion: Identifying the haplotype diversity in the Kuwaiti population will contribute to the selection of an HLA-match for HSCT, disease associations, pharmacogenomics, and knowledge of population HLA diversity.

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Contribution to bionomy of Hylesinus fraxini (Coleoptera: Curculionidae: Scolytinae) and its monogamy in the Czech Republic

Forestry Journal ◽

10.1515/forj-2015-0032 ◽

2015 ◽

Vol 61 (4) ◽

pp. 240-245

Author(s):

Karolina Lukášová ◽

Soňa Zimová

Keyword(s):

Czech Republic ◽

Bark Beetle ◽

Bark Beetles ◽

Second Generation ◽

Female Offspring ◽

Fraxinus Excelsior ◽

The Czech Republic ◽

Gallery System

Abstract This study focused on bionomics of the ash bark beetle Hylesinus fraxini (Panzer 1779). The study area was at Jílové u Prahy in the Central Bohemian Region of the Czech Republic. In February 2014, three common ash (Fraxinus excelsior) trees were felled and Hylesinus fraxini infestation was subsequently observed from March. Beetles were collected from 20 debarked logs and dissected under stereomicroscope, and their sex was determined. Five logs with bark beetles were placed into photoeclectors. Beetles that emerged were collected and put into the second photoeclector with fresh ash wood to determine whether they would establish the second generation. The analysis showed that each gallery system with a pair of bark beetles contained one male with only one female. If one adult of H. fraxini was found in the gallery system, it was usually female. Therefore, possible polygamy of Hylesinus fraxini was not confirmed in Central Bohemia. Maternal gallery length significantly correlated with the number of eggs laid per female. Offspring beetles did not establish the second generation, as only maturation feeding occurred in fresh wood.

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Gene flow of common ash (Fraxinus excelsior L.) in a fragmented landscape

PLoS ONE ◽

10.1371/journal.pone.0186757 ◽

2017 ◽

Vol 12 (10) ◽

pp. e0186757 ◽

Cited By ~ 7

Author(s):

Devrim Semizer-Cuming ◽

Erik Dahl Kjær ◽

Reiner Finkeldey

Keyword(s):

Gene Flow ◽

Fraxinus Excelsior ◽

Fragmented Landscape

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Characterization and primer development for amplification of chloroplast microsatellite regions of Fraxinus excelsior

Journal of Plant Research ◽

10.1007/s10265-005-0223-5 ◽

2005 ◽

Vol 118 (5) ◽

pp. 339-341 ◽

Cited By ~ 13

Author(s):

M. E. Harbourne ◽

G. C. Douglas ◽

S. Waldren ◽

T. R. Hodkinson

Keyword(s):

Fraxinus Excelsior ◽

Chloroplast Microsatellite

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The microsatellite polymorphism and gene flow in the contact zone of four common shrew (Sorex araneus L., Mammalia) chromosome races

Biology Bulletin ◽

10.1134/s1062359011050062 ◽

2011 ◽

Vol 38 (5) ◽

pp. 425-433 ◽

Cited By ~ 1

Author(s):

O. O. Grigoryeva ◽

A. G. Shestak ◽

S. G. Potapov ◽

Yu. M. Borisov ◽

S. Yu. Irkhin ◽

...

Keyword(s):

Gene Flow ◽

Contact Zone ◽

Common Shrew ◽

Sorex Araneus ◽

Microsatellite Polymorphism ◽

Chromosome Races ◽

Common Shrew Sorex Araneus

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Genetic population structure of mangrove jack, Lutjanus argentimaculatus (Forsskål)

Marine and Freshwater Research ◽

10.1071/mf02142 ◽

2003 ◽

Vol 54 (2) ◽

pp. 127 ◽

Cited By ~ 20

Author(s):

Jennifer R. Ovenden ◽

Raewyn Street

Keyword(s):

Population Structure ◽

Gene Flow ◽

Allelic Variation ◽

Gene Diversity ◽

Haplotype Diversity ◽

Genetic Population Structure ◽

Western Coast ◽

Base Pairs ◽

Genetic Population ◽

Lutjanus Argentimaculatus

Translocations of mangrove jack, Lutjanus argentimaculatus (Forsskål 1775), to increase angling opportunities in artificial impoundments are foreshadowed in Queensland. To evaluate genetic population structure before translocations occur, mangrove jack were collected from three sites on the Queensland coast and from one site on the north-western coast of Western Australia. Allelic variation at four dinucleotide microsatellite loci was high: gene diversity (heterozygosity) ranged from 0.602 to 0.930 and allelic counts from 10 to 24. Genetic differentiation among collection sites was weak: estimates of FST were 0.002 for all four sites, and less (FST = 0.001) across a major biogeographical boundary (the Torres Strait region). Nucleotide sequence from two mitochondrial regions (control, 375 base pairs, and ATPase, 415 base pairs) was obtained from a subset of the Australian and additional Indo-Pacific (Indonesian and Samoan) mangrove jack. Haplotype diversity was high (control region, 33 haplotypes for 34 fish; ATPase region, 13 haplotypes for 56 fish). Phylogenetic analysis of mitochondrial DNA sequence data could not discern a relationship between tree topology and geography. These results suggest that mangrove jack in Queensland, and possibly throughout Australia, experience high levels of gene flow. The artificial gene flow caused by permitted translocations is unlikely to exceed natural levels. Fine-scale ecological matching between donor and recipient populations may increase stocking success, and is important if translocation is needed as a species recovery tool in the future.

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