Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

AbstractOngoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is critical for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group, a large taxonomic group that diverged ∼3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

Download Full-text

Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers

Plants ◽

10.3390/plants9091190 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1190 ◽

Cited By ~ 1

Author(s):

Eunju Seo ◽

Kipoong Kim ◽

Tae-Hwan Jun ◽

Jinsil Choi ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Principal Component ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Useful Knowledge ◽

Population Structure Analysis ◽

Group 3 ◽

Genetic Diversity Study

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

Download Full-text

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

PLoS Computational Biology ◽

10.1371/journal.pcbi.1004812 ◽

2016 ◽

Vol 12 (3) ◽

pp. e1004812 ◽

Cited By ~ 25

Author(s):

Andrej Kuritzin ◽

Tabea Kischka ◽

Jürgen Schmitz ◽

Gennady Churakov

Keyword(s):

Large Scale ◽

Incomplete Lineage Sorting ◽

Lineage Sorting

Download Full-text

Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

Mobile DNA ◽

10.1186/s13100-019-0187-y ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Jerilyn A. Walker ◽

◽

Vallmer E. Jordan ◽

Jessica M. Storer ◽

Cody J. Steely ◽

...

Keyword(s):

Large Scale ◽

Incomplete Lineage Sorting ◽

Genetic Relationships ◽

Whole Genome Sequence ◽

Lineage Sorting ◽

High Coverage ◽

Theropithecus Gelada ◽

Alu Insertion ◽

Genomic Markers ◽

Additional Support

Abstract Background Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput “poly-Detect” method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.

Download Full-text

De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Insects ◽

10.3390/insects11020101 ◽

2020 ◽

Vol 11 (2) ◽

pp. 101

Author(s):

Miao Wang ◽

Hanyu Li ◽

Huoqing Zheng ◽

Liuwei Zhao ◽

Xiaofeng Xue ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

De Novo ◽

Transcriptome Profiling ◽

Molecular Study ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Illumina Hiseq ◽

Vespa Velutina ◽

Genes Encoding

The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.

Download Full-text

Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

Frontiers in Plant Science ◽

10.3389/fpls.2020.619799 ◽

2021 ◽

Vol 11 ◽

Author(s):

Jinyuan Chen ◽

Guili Wu ◽

Nawal Shrestha ◽

Shuang Wu ◽

Wei Guo ◽

...

Keyword(s):

Phylogenetic Relationship ◽

Species Delimitation ◽

Large Scale ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Population Based ◽

Integrative Approach ◽

Morphological Evidence ◽

Sampling Errors ◽

Lineage Sorting

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.

Download Full-text

A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data

10.1101/587725 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jiafan Zhu ◽

Xinhao Liu ◽

Huw A. Ogilvie ◽

Luay K. Nakhleh

Keyword(s):

Large Scale ◽

Network Inference ◽

Incomplete Lineage Sorting ◽

Phylogenetic Network ◽

Biological Data ◽

Phylogenetic Networks ◽

Divide And Conquer ◽

Lineage Sorting ◽

Step Method ◽

Sequence Alignments

AbstractReticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting (ILS). However, these methods can only handle a small number of loci from a handful of genomes.In this paper, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological data sets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with existing methods. The results are a significant and promising step towards accurate, large-scale phylogenetic network inference.We implemented the algorithms in the publicly available software package PhyloNet (https://bioinfocs.rice.edu/PhyloNet)[email protected]

Download Full-text

Development and Characterization of PCR Markers in Cucumber

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.127.4.545 ◽

2002 ◽

Vol 127 (4) ◽

pp. 545-557 ◽

Cited By ~ 51

Author(s):

Gennaro Fazio ◽

Jack E. Staub ◽

Sang Min Chung

Keyword(s):

Large Scale ◽

Cost Effective ◽

Snp Markers ◽

Yield Component ◽

Nucleotide Polymorphisms ◽

Pcr Markers ◽

Dinucleotide Repeats ◽

Sequence Characterized Amplified Region ◽

Tetranucleotide Repeats ◽

Multiple Lateral Branching

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

Download Full-text

Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Genes ◽

10.3390/genes10090676 ◽

2019 ◽

Vol 10 (9) ◽

pp. 676 ◽

Cited By ~ 3

Author(s):

Farahani ◽

Maleki ◽

Mehrabi ◽

Kanouni ◽

Scheben ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Linkage Disequilibrium ◽

Large Scale ◽

Principal Component ◽

Snp Markers ◽

Genome Diversity ◽

High Genetic Diversity ◽

Breeding Programs ◽

Population Structure Analysis

Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.

Download Full-text

Design of SNP Markers for Aldabra Giant Tortoises using ddRAD-seq

10.21203/rs.3.rs-498085/v1 ◽

2021 ◽

Author(s):

F. Gözde Çilingir ◽

Dennis Hansen ◽

Arpat Ozgul ◽

Christine Grossen

Keyword(s):

Large Scale ◽

Wild Population ◽

Western Indian Ocean ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Sea Levels ◽

Breeding Populations ◽

Captive Populations ◽

Genome Wide ◽

Rising Sea Levels

Abstract The Aldabra giant tortoise ( Aldabrachelys gigantea ) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea . A total of 149 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.32 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea .

Download Full-text

Population Structure and Mitochondrial Polyphyly in North American Gadwalls (Anas Strepera)

The Auk ◽

10.1093/auk/124.2.444 ◽

2007 ◽

Vol 124 (2) ◽

pp. 444-462 ◽

Cited By ~ 2

Author(s):

Jeffrey L. Peters ◽

Kevin E. Omland

Keyword(s):

Population Structure ◽

Genetic Structure ◽

North America ◽

North American ◽

Incomplete Lineage Sorting ◽

Population Expansion ◽

Lineage Sorting ◽

Clade B ◽

Base Pair Fragment ◽

Anas Strepera

Abstract We examined population genetic structure in Gadwalls (Anas strepera) to test the prediction that female philopatry and fidelity to migratory flyways have contributed to the partitioning of mitochondrial variation across North America. Sequencing a 658–659 base-pair fragment of the mitochondrial DNA (mtDNA) control region from 348 Gadwalls, we found two distinct clades that were broadly intermixed across both breeding and nonbreeding populations. Clade A was abundant in North America as well as among published sequences from Eurasia. Clade B was sequenced from 5.5% of North American Gadwalls and was more similar to Asian Falcated Duck (A. falcata) haplotypes than to clade A haplotypes. Maximum likelihood indicated that Gadwall clade B haplotypes were a monophyletic group nested within Falcated Duck haplotypes, which suggests mtDNA introgression of clade B into Gadwalls. However, that topology was weakly supported, and we could not reject topologies that were consistent with incomplete lineage-sorting as the cause of mitochondrial polyphyly. Migratory flyways did not contribute significantly to population structure and, in general, we found a lack of genetic structure among most populations. However, Gadwalls sampled in Alaska and Washington were well differentiated from other populations. Coalescent analyses supported a historical population expansion for clade A, and this expansion could have contributed to the high genetic similarity among some populations but the strong differentiation of others. Female-mediated gene flow, along with both historical and contemporary population and range expansions, has likely contributed to the overall weak mtDNA structure in North American Gadwalls. Estructura Poblacional y Polifilia Mitocondrial en Anas strepera

Download Full-text