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Karlin EF. A Comparison of Entropic Diversity and Variance in the Study of Population Structure. ENTROPY (BASEL, SWITZERLAND) 2023; 25:492. [PMID: 36981380 PMCID: PMC10048111 DOI: 10.3390/e25030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/10/2023] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).
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Affiliation(s)
- Eric F Karlin
- School of Theoretical & Applied Science, Ramapo College, Mahwah, NJ 07430, USA
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2
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Capo-chichi LJA, Elakhdar A, Kubo T, Nyachiro J, Juskiw P, Capettini F, Slaski JJ, Ramirez GH, Beattie AD. Genetic diversity and population structure assessment of Western Canadian barley cooperative trials. FRONTIERS IN PLANT SCIENCE 2023; 13:1006719. [PMID: 36699829 PMCID: PMC9868428 DOI: 10.3389/fpls.2022.1006719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.
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Affiliation(s)
- Ludovic J. A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Joseph Nyachiro
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Patricia Juskiw
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Jan J. Slaski
- Ecosystems and Plant Sciences, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
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Climate-Driven Adaptive Differentiation in Melia azedarach: Evidence from a Common Garden Experiment. Genes (Basel) 2022; 13:genes13111924. [DOI: 10.3390/genes13111924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/04/2022] Open
Abstract
Studies of local adaptation in populations of chinaberry (Melia azedarach L.) are important for clarifying patterns in the population differentiation of this species across its natural range. M. azedarach is an economically important timber species, and its phenotype is highly variable across its range in China. Here, we collected M. azedarach seeds from 31 populations across its range and conducted a common garden experiment. We studied patterns of genetic differentiation among populations using molecular markers (simple sequence repeats) and data on phenotypic variation in six traits collected over five years. Our sampled populations could be subdivided into two groups based on genetic analyses, as well as patterns of isolation by distance and isolation by environment. Significant differentiation in growth traits was observed among provenances and families within provenances. Geographic distance was significantly correlated with the quantitative genetic differentiation (QST) in height (HEIT) and crown breadth. Climate factors were significantly correlated with the QST for each trait. A total of 23 climatic factors were examined. There was a significant effect of temperature on all traits, and minimum relative humidity had a significant effect on the survival rate over four years. By comparing the neutral genetic differentiation (FST) with the QST, the mode of selection acting on survival rate varied, whereas HEIT and the straightness of the main trunk were subject to the same mode of selection. The variation in survival rate was consistent with the variation in genetic differentiation among populations, which was indicative of local adaptation. Overall, our findings provide new insights into the responses of the phenological traits of M. azedarach to changes in the climate conditions of China.
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Kánainé Sipos D, Csenki-Bakos K, Ősz Á, Bokor Z, Kotrik L, Żarski D, Ittzés I, Urbányi B, Kovács B. Twelve new microsatellite loci of Eurasian perch Perca fluviatilis Linnaeus, 1758. Biol Futur 2021; 72:385-393. [PMID: 34554558 DOI: 10.1007/s42977-021-00087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
The Eurasian perch (Perca fluviatilis Linnaeus, 1758) is native to almost entire Eurasia. For over the last two decades, this species became an important candidate for intensive freshwater aquaculture due to its high consumer's acceptance and overall market value. Hence, the intensive production of Eurasian perch has increased considerably allowing effective domestication; there is still a need for the development of effective selective breeding programmes allowing its further expansion. This process, in turn, can be significantly facilitated by molecular genetics. The genetic information of Eurasian perch and its populations is limited. Up to date information of regarding genetic diversity of many populations is still missing, including microsatellites for Eurasian perch, which could be useful during the selective breeding programmes allowing parental assignment and/or to follow heritability of desired traits. In this study, we have developed and characterized new polymorphic microsatellites. Subsequently, those 12 markers have been used further to compare two Hungarian and one Polish Eurasian perch populations. The Hungarian stocks had high genetic similarity (with low diversity), as we assumed, while the Polish population differed significantly. All populations deviated significantly from the Hardy-Weinberg equilibrium, and heterozygote deficiency was detected in all, showing the presence of an anthropogenic effect.
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Affiliation(s)
- Dóra Kánainé Sipos
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Katalin Csenki-Bakos
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Ágnes Ősz
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Zoltán Bokor
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - László Kotrik
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Daniel Żarski
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland
| | - István Ittzés
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary.,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute for Conservation of Natural Resources, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. Str. 1, 2100, Gödöllő, Hungary. .,Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter K. Str. 1, 2100, Gödöllő, Hungary.
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An Information-theoretic approach to dimensionality reduction in data science. INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2021. [DOI: 10.1007/s41060-021-00272-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Tadesse M, Kebede M, Girma D. Genetic Diversity of Tef [ Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers. Int J Genomics 2021; 2021:6672397. [PMID: 33977102 PMCID: PMC8087483 DOI: 10.1155/2021/6672397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/29/2022] Open
Abstract
Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp-320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon's information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.
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Affiliation(s)
- Mahilet Tadesse
- Adama Science and Technology University, Department of Applied Biology, P. O. Box 1888, Adama, Ethiopia
- Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P. O. Box 32, Debre Zeit, Ethiopia
| | - Mulugeta Kebede
- Adama Science and Technology University, Department of Applied Biology, P. O. Box 1888, Adama, Ethiopia
| | - Dejene Girma
- Ethiopian Institute of Agricultural Research, National Agricultural Biotechnology Research Center, P.O. Box 249, Holetta, Ethiopia
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Latacz M, Rozmus D, Fiedorowicz E, Snarska J, Jarmołowska B, Kordulewska N, Savelkoul H, Cieślińska A. Vitamin D Receptor ( VDR) Gene Polymorphism in Patients Diagnosed with Colorectal Cancer. Nutrients 2021; 13:200. [PMID: 33440610 PMCID: PMC7826796 DOI: 10.3390/nu13010200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly occurring neoplasias in humans. The prevalence of CRC rates is still rising. Although the exact background of the disease still remains unknown, it is believed that CRC may not only be a result of environmental factors, but also genetic ones. One of the mechanisms underlying CRC might be the vitamin D pathway, as CRC is the most closely linked neoplasia to vitamin D deficiency. This study shows a possible association of the vitamin D receptor (VDR) polymorphisms FokI, BsmI, ApaI, and TaqI with CRC susceptibility. A total of 103 patients diagnosed with CRC (61 men and 42 women, aged 57-82 years) and 109 healthy people (50 men and 59 women, aged 47-68 years) were genotyped using PCR-RFLP for FokI, BsmI, ApaI, and TaqI. None of the single nucleotide polymorphisms (SNPs) individually increased or decreased the risk of CRC. The evaluation of haplotypes revealed two that might enhance the likelihood of CRC development: taB (OR = 30.22; 95% CI 2.81-325.31; p = 0.01) and tAb (OR = 3.84; 95% CI 1.29-11.38; p = 0.01). In conclusion, genotyping is an easy and robust procedure that needs to be performed only once in a lifetime. A creation of a relevant SNP's panel might contribute to the identification of the groups that are at the greatest risk of CRC.
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Affiliation(s)
- Maria Latacz
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
- Faculty of Medicine, Collegium Medicum, University of Warmia and Mazury, 10-082 Olsztyn, Poland
| | - Dominika Rozmus
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
| | - Ewa Fiedorowicz
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
| | - Jadwiga Snarska
- Department of General Surgery, Faculty of Medical Sciences, Collegium Medicum, University of Warmia and Mazury, 10-082 Olsztyn, Poland;
| | - Beata Jarmołowska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
| | - Natalia Kordulewska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
| | - Huub Savelkoul
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University and Research, 6700 AH Wageningen, The Netherlands;
| | - Anna Cieślińska
- Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (M.L.); (D.R.); (E.F.); (B.J.); (N.K.)
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Sahu PK, Mondal S, Sao R, Vishwakarma G, Kumar V, Das BK, Sharma D. Genome-wide association mapping revealed numerous novel genomic loci for grain nutritional and yield-related traits in rice ( Oryza sativa L.) landraces. 3 Biotech 2020; 10:487. [PMID: 33123454 DOI: 10.1007/s13205-020-02467-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
A core set of 190 rice landraces were used to decipher the genetic structure and to discover the chromosomal regions containing QTLs, affecting the grain micro-nutrients, fatty acids, and yield-related traits by using 148 molecular markers in this study. Landraces were categorized into three sub-groups based on population stratification study and followed by neighbor-joining tree and principal component analysis. Analysis of variance revealed abundant variations among the landraces for studied traits with less influence of environmental factors. Genome Wide Association Studies (GWAS) revealed 22 significant and consistent QTLs through marker trait association (MTAs) for 12 traits based on 2 years and pooled analysis. Out of 22 QTLs, three have been reported earlier while 19 QTLs are novel. Interestingly, 13 QTLs out of 22 were explained more than 10% phenotypic variance. Association of RM1148 and RM205 with Days to 50% flowering was comparable with flowering control genes Ghd8/qDTH8 and qDTH9, respectively. Similarly, Zn content was associated with RM44, which is situated within the QTL qZn8-1. Moreover, significant association of RM25 with oleic acid content was closely positioned with QTL qOle8. Association of RM7434 with grain yield/plant; RM184 with spikelet fertility %; R3M10, R9M42 with hundred seed weight; RM536, RM17467, RM484, RM26063 with Fe content; RM44, RM6839 with Zn content are the major outcomes of this study. In addition, association of R11M23 with days to 50% flowering, panicle length and total spikelets per panicle are explained the possible occurrence of pleiotropism among these traits. Prominent rice landraces viz., Anjani (early maturity); Sihar (extra dwarf); Gangabaru (highest grain yield/plant); Karhani (highest iron content); Byalo-2 (highest zinc content) and Kadamphool (highest oleic acid) were identified through this study. The present study will open many avenues towards utilization of these QTLs and superior landraces in rice breeding for developing nutrition-rich high yielding varieties.
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Affiliation(s)
- Parmeshwar K Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Vikash Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - B K Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094 India
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh 492012 India
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Gopaulchan D, Motilal LA, Kalloo RK, Mahabir A, Moses M, Joseph F, Umaharan P. Genetic diversity and ancestry of cacao ( Theobroma cacao L.) in Dominica revealed by single nucleotide polymorphism markers. Genome 2020; 63:583-595. [PMID: 32853534 DOI: 10.1139/gen-2019-0214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cacao (Theobroma cacao L.), an introduced tree crop in Dominica, is important for foreign exchange earnings from fine or flavour cocoa. The genetic structure of farmed cacao in Dominica was examined to identify varieties for conservation, breeding, and propagation to improve their cocoa industry. Cacao trees (156) from 73 sites over seven geographical regions were genotyped at 192 single nucleotide polymorphism (SNP) markers. Identity, regional differentiation, phylogenetic, multi-variate, ancestry, and core collection analyses were performed. Farmed cacao germplasm had moderate gene diversity (He = 0.320 ± 0.005) from generally unique trees, but cocoa growing regions were genetically similar. Synonymous matching (16.3%) showed that some clonal material was supplied to farmers. Cacao trees were mainly mixed from Amelonado, Criollo, Iquitos, Contamana, and Marañon ancestries, with predominantly Amelonado-Criollo hybrids. Criollo ancestry, linked to fine or flavour cocoa, was found at more than 30% in 28 unique trees. Forty-five trees, containing the SNP diversity of cacao in Dominica, are recommended as a core germplasm collection. This study identifies promising trees for improving cocoa quality; provides genetic evidence that community, regional, or country-wide pooling would not compromise the exclusive fine or flavour cocoa industry; and discusses other implications towards improving the Dominican cocoa industry.
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Affiliation(s)
- David Gopaulchan
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Lambert A Motilal
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Rena K Kalloo
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Amrita Mahabir
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Marissa Moses
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
| | - Franklyn Joseph
- The Ministry of Agriculture, Land and Fisheries, the Government of the Commonwealth of Dominica
| | - Pathmanathan Umaharan
- Cocoa Research Centre, Sir Frank Stockdale Bldg., The University of the West Indies, St. Augustine, 330912, Trinidad, Trinidad and Tobago
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10
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Giunchi D, Mucci N, Bigi D, Mengoni C, Baldaccini NE. Feral pigeon populations: their gene pool and links with local domestic breeds. ZOOLOGY 2020; 142:125817. [PMID: 32763653 DOI: 10.1016/j.zool.2020.125817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 10/24/2022]
Abstract
Columba livia is a wild bird whose domestication has led to a large number of pigeon breeds. The occasional loss or straying of domestic birds determined the origin of feral pigeons, which are now widespread all around the world. In this study, we assumed that the main contribution to feral populations is provided by domestic breeds reared in the same areas. We tested this hypothesis by analysing the variability of 12 microsatellite loci in nine Italian feral populations sampled in areas with different intensities of breeding and selecting domestic breeds. We included in the analysis samples belonging to ten domestic lineages commonly bred in Italy. The pattern of geographic differentiation of feral populations turned out to be rather complex and only partially explained by the geographic distance between populations. This pattern can be understood only when the domestic breeds were included in the analysis. In particular, feral populations located in regions with a long-lasting tradition of pigeon breeding showed a high level of admixture with domestic breeds, in particular with Racing Homer and Piacentino. Ferals from Bolzano, Venice and Sassari were characterized by unique genetic components, mostly not shared by other feral populations and by the considered domestic breeds. Our results further emphasize the complex genetic structure of feral populations whose origin can be properly investigated by taking into account the pool of domestic pigeons bred in the considered area.
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Affiliation(s)
- Dimitri Giunchi
- Dipartimento di Biologia, Università di Pisa, Via Volta 6, 56126, Pisa, Italy.
| | - Nadia Mucci
- Area per la Genetica della Conservazione (BIO-CGE), Dipartimento per il monitoraggio e la tutela dell'ambiente e per la conservazione della biodiversità, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Cà Fornacetta, 9, 40064, Ozzano dell'Emilia, Italy.
| | - Daniele Bigi
- Department of Agricultural and Food Science (DISTAL), University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Chiara Mengoni
- Area per la Genetica della Conservazione (BIO-CGE), Dipartimento per il monitoraggio e la tutela dell'ambiente e per la conservazione della biodiversità, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Via Cà Fornacetta, 9, 40064, Ozzano dell'Emilia, Italy
| | - N Emilio Baldaccini
- Dipartimento di Biologia, Università di Pisa, Via Volta 6, 56126, Pisa, Italy
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11
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Incipient sympatric speciation via host race formation in Phengaris arion (Lepidoptera: Lycaenidae). ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-019-00418-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe plausibility of sympatric speciation is still debated despite increasing evidence, such as host races in insects. This speciation process may be occurring in the case of the two phenological forms of the obligatorily myrmecophilous Phengaris arion. The main goal of our research was to study the nature and causes of difference between these forms focusing primarily on the incipient speciation via host races. Molecular analyses based on highly variable microsatellites together with Wolbachia screening, male genitalia morphometrics and host ant studies were carried out on four syntopic sample pairs. Our results show that the two phenological forms of P. arion may meet the criteria for host plant races. They coexist in sympatry in certain parts of the species range which is allowed by the adaptation to the distinct phenology of the host plants. Negative selection acts against the intermediate individuals which are on the wing in the inappropriate time frame. Thus, disruptive selection affects and produces bimodal distributions of phenotypes. However, the phenology of food plants is not entirely distinct and fluctuates year by year. Therefore, the two forms can exchange genes occasionally depending on the length of the time slot when they can meet with each other. Consequently, the reproductive isolation could not be completed and the existence of the two arion forms may represent only an incipient stage of sympatric speciation. It is also clear that Wolbachia is likely not a driver of sympatric speciation in this case.
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Xiong B, Zhang L, Dong S, Zhang Z. Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China. PeerJ 2020; 8:e8304. [PMID: 31915585 PMCID: PMC6944114 DOI: 10.7717/peerj.8304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 11/27/2019] [Indexed: 11/20/2022] Open
Abstract
Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.
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Affiliation(s)
- Biao Xiong
- College of Tea Science, Guizhou University, Guiyang, China
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Zhang X, Han LL, Hong X, Jiang P, Niu YF, Wang ZQ, Cui J. Genotyping and Phylogenetic Position of Trichinella spiralis Isolates from Different Geographical Locations in China. Front Genet 2019; 10:1093. [PMID: 31737057 PMCID: PMC6834790 DOI: 10.3389/fgene.2019.01093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022] Open
Abstract
In China, the nematode Trichinella spiralis is the main aetiological agent of human trichinellosis. We performed multi-locus microsatellite typing of T. spiralis isolates to improve the current knowledge of the evolution and population diversity. First, seven polymorphic microsatellite loci were used to infer the genetic diversity of T. spiralis collected in 10 endemic regions. Then, a Bayesian model-based STRUCTURE analysis, a clustering based on the neighbor-joining method, and a principal coordinate analysis (PCA) were performed to identify the genetic structure. Finally, the phylogenetic position of Chinese isolates was explored based on six mitochondrial and nuclear genetic markers (cox1, cytb, 5S ISR, ESV, ITS1, and 18S rDNA) using the maximum likelihood and Bayesian methods. In addition, the divergence time was estimated with multiple genes using an uncorrelated log-normal relaxed molecular-clock model. A total of 16 alleles were detected in 2,310 individuals (1,650 muscle larvae and 660 adult worms) using seven loci. The STRUCTURE analysis indicated that the T. spiralis isolates could be organized and derived from the admixture of two ancestral clusters, which was also substantiated through the clustering analysis based on the allelic data. PCA separated most samples from Tiandong, Guangxi (GX-td), and Linzhi, Tibet (Tibet-lz), from the remaining isolates. However, both maximum likelihood and Bayesian inference supported the close relationship between Xiangfan, Hubei (HB-xf), and GX-td. The molecular dating analysis suggested that the Chinese isolates started to diverge during the Late Pleistocene (0.69 Mya). Generally, T. spiralis was observed to harbor low genetic variation, and further investigation with deeper sampling is needed to elucidate the population structure.
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Affiliation(s)
| | | | | | | | | | - Zhong Quan Wang
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jing Cui
- Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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Kánainé Sipos D, Bakos K, Ősz Á, Hegyi Á, Müller T, Urbányi B, Kovács B. Development and characterization of 49 novel microsatellite markers in the African catfish, Clarias gariepinus (Burchell, 1822). Mol Biol Rep 2019; 46:6599-6608. [PMID: 31535323 DOI: 10.1007/s11033-019-05062-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
The African catfish or sharp tooth catfish (Clarias gariepinus) is one of the important species (due to its high environmental tolerance and easily controllable breeding habits) that can significantly contribute to reducing hunger in many countries. It is farmed in numerous African, Asian, and European countries. Moreover, during the last decades its production has grown significantly worldwide. Currently, following the carp, this species is produced in the second largest volume in Hungary. Despite its economic importance, the stocks have been maintained without genetic control or guided breeding. Molecular genetic data on bred populations or strains are very limited. In order to investigate the genetic structure of the stocks, 49 new microsatellite markers were characterized and tested on 32 individuals from a Hungarian farmed stock. All these markers were polymorph. The number of alleles per locus ranged from 2 to 11. The observed and expected overall heterozygosities were between 0.519 and 0.544 respectively and the overall inbreeding coefficient (Fis: 0.063) does not reveal the presence of inbreeding. However, 63% of the markers showed significant deviations from HWE. The results suggest that the maintenance of genetic variation within the stock require high attention in closed bred populations. These new markers provide a useful tool for population and conservation genetics of natural and bred African catfish populations.
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Affiliation(s)
- Dóra Kánainé Sipos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Katalin Bakos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Ágnes Ősz
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Árpád Hegyi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Tamás Müller
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Páter K. u. 1, 2100, Gödöllő, Hungary.
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Baroudy F, Putman AI, Habib W, Puri KD, Subbarao KV, Nigro F. Genetic Diversity of Verticillium dahliae Populations From Olive and Potato in Lebanon. PLANT DISEASE 2019; 103:656-667. [PMID: 30823856 DOI: 10.1094/pdis-03-18-0420-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Verticillium dahliae is widely distributed in potato and olive fields in Lebanon, causing serious economic losses. However, little is known about the inoculum source, population structure, and genetic diversity of the pathogen or the mechanisms of dissemination within Lebanon. To understand the population structure, a total of 203 isolates sampled from olive (n = 78) and potato (n = 125) were characterized for species, mating type, and race, and the genetic relationships were delineated using 13 microsatellite markers. All isolates except one from potato were V. dahliae, with 55.1 and 12.1% race 1, and 43.6 and 83.1% race 2 in olive and potato, respectively. The genetic structure of the studied population was best described by two large and two small clusters. Membership in the two large clusters was determined by the presence or absence of the effector gene Ave1. Furthermore, genetic structure was moderately associated with the host of origin but was weakly associated with the geographic origin. All but four isolates represented by three multilocus haploid genotypes were MAT1-2. This study identified a clear lack of gene flow between virulence genotypes of V. dahliae despite the proximity of these cropping systems and the wide distribution of genetic diversity among hosts and geographic regions in Lebanon.
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Affiliation(s)
- Farah Baroudy
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Alexander I Putman
- 3 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A.; and
| | - Wassim Habib
- 2 Lebanese Agricultural Research Institute, Laboratory of Mycology, Department of Plant Protection, Fanar, Jdeidet El Metn, Lebanon
| | - Krishna D Puri
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Krishna V Subbarao
- 4 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905, U.S.A
| | - Franco Nigro
- 1 Dipartimento di Scienze del Suolo, Università degli Studi di Bari - Aldo Moro, Bari, 70126 Bari, Italy
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Development of EST-derived microsatellite markers to investigate the population structure of sparganum - the causative agent of zoonotic sparganosis. Parasitology 2019; 146:947-955. [PMID: 30859932 DOI: 10.1017/s0031182019000222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The plerocercoid (sparganum) of Spirometra erinaceieuropaei is the main aetiological agent of human sparganosis. To improve the current knowledge on S. erinaceieuropaei evolution, we performed multi-locus microsatellite typing of sparganum isolates from China for the first time. All available expressed sequence tag (EST) sequences for the Spirometra were downloaded from the GenBank. The identification and localization of microsatellites in ESTs was accomplished by MISA. Based on the selected microsatellites, the genetic structure of 64 sparganum isolates collected from 11 geographical locations in southwest China were investigated through principal component analysis, STRUCTURE analysis and neighbour-joining clustering. A total of 522 non-redundant ESTs containing 915 simple sequence repeats were identified from 12 481 ESTs screened. Five primer pairs were finally selected. Using these loci, a total of 12 alleles were detected in 64 sparganum isolates. Little variability was observed within each of geographical population, especially among isolates derived from Kunming of Yunnan (YN-KM) province. Both STRUCTURE analysis and the clustering analysis supported that two genotypes existed among the sparganum isolates from southwest China. In conclusion, five microsatellite markers were successfully developed, and sparganum population was observed to harbour low genetic variation, further investigation with deeper sampling was needed to elucidate the population structure.
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Karlin EF, Smouse PE. Holantarctic diversity varies widely among genetic loci within the gametophytically allotriploid peat moss Sphagnum × falcatulum. AMERICAN JOURNAL OF BOTANY 2019; 106:137-144. [PMID: 30644542 DOI: 10.1002/ajb2.1220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY The traditional approach used in analyses of population genetic data for historical inference is to average across multiple marker loci, but averaging conflates the different evolutionary signals provided by stable vs. labile markers. METHODS We used a battery of microsatellites with a wide range of mutation/substitution rates, grouping them into two sets (stable and hypervariable) to provide a more nuanced reconstruction of the population genetics and evolutionary history of the allotriploid peat moss Sphagnum × falcatulum across three disjunct regions. KEY RESULTS Shannon diversity translation analyses show that the relative apportionment of total within-species allelic diversity (∆WS ) within and among strata ranges widely, both between the two sets and within and among regions. The majority of diversity in the stable set was inherited directly from the ancestors of this genetically complex allopolyploid, but most of the diversity in the hypervariable set has developed post-hybrid-origin. CONCLUSIONS It is useful to group markers into sets having similar evolutionary lability, with each set being analyzed separately, particularly for allopolyploids. A methodology for determining how to group markers into such sets is presented, which can be applied to the requirements of other studies. Within-individual allelic diversity (ΔWI ) should be addressed in genetic studies on allopolyploids. Allotriploid haplotypes based on a set of nine highly stable microsatellites appear to serve as a clonal-detection set for S. × falcatulum. An additive "allele-metric" diversity approach is introduced, which facilitates a direct comparison of within- and among-stratum diversity components at all levels of diversity.
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Affiliation(s)
- Eric F Karlin
- Department of Environmental Science, School of Theoretical and Applied Science, Ramapo College, Mahwah, New Jersey, 07430-1680, USA
| | - Peter E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, 08901-8551, USA
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Gaggiotti OE, Chao A, Peres‐Neto P, Chiu C, Edwards C, Fortin M, Jost L, Richards CM, Selkoe KA. Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evol Appl 2018; 11:1176-1193. [PMID: 30026805 PMCID: PMC6050189 DOI: 10.1111/eva.12593] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/21/2017] [Indexed: 02/03/2023] Open
Abstract
Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organization (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap, we present a unifying framework for the measurement of biodiversity across hierarchical levels of organization. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon's entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.), we applied the framework to a real data set on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics and eco-evolutionary dynamics.
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Affiliation(s)
- Oscar E. Gaggiotti
- School of BiologyScottish Oceans InstituteUniversity of St AndrewsSt AndrewsUK
| | - Anne Chao
- Institute of StatisticsNational Tsing Hua UniversityHsin‐ChuTaiwan
| | | | - Chun‐Huo Chiu
- Department of AgronomyNational Taiwan UniversityTaipeiTaiwan
| | - Christine Edwards
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSaint LouisMOUSA
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Lou Jost
- Ecominga FundationBanosTungurahuaEcuador
| | | | - Kimberly A. Selkoe
- National Center for Ecological Analysis and SynthesisUniversity of California Santa BarbaraSanta BarbaraCAUSA
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i at MānoaKaneoheHIUSA
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Timme NM, Lapish C. A Tutorial for Information Theory in Neuroscience. eNeuro 2018; 5:ENEURO.0052-18.2018. [PMID: 30211307 PMCID: PMC6131830 DOI: 10.1523/eneuro.0052-18.2018] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/10/2018] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Understanding how neural systems integrate, encode, and compute information is central to understanding brain function. Frequently, data from neuroscience experiments are multivariate, the interactions between the variables are nonlinear, and the landscape of hypothesized or possible interactions between variables is extremely broad. Information theory is well suited to address these types of data, as it possesses multivariate analysis tools, it can be applied to many different types of data, it can capture nonlinear interactions, and it does not require assumptions about the structure of the underlying data (i.e., it is model independent). In this article, we walk through the mathematics of information theory along with common logistical problems associated with data type, data binning, data quantity requirements, bias, and significance testing. Next, we analyze models inspired by canonical neuroscience experiments to improve understanding and demonstrate the strengths of information theory analyses. To facilitate the use of information theory analyses, and an understanding of how these analyses are implemented, we also provide a free MATLAB software package that can be applied to a wide range of data from neuroscience experiments, as well as from other fields of study.
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Affiliation(s)
- Nicholas M Timme
- Department of Psychology, Indiana University - Purdue University Indianapolis, 402 N. Blackford St, Indianapolis, IN 46202
| | - Christopher Lapish
- Department of Psychology, Indiana University - Purdue University Indianapolis, 402 N. Blackford St, Indianapolis, IN 46202
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Sahu PK, Mondal S, Sharma D, Vishwakarma G, Kumar V, Das BK. InDel marker based genetic differentiation and genetic diversity in traditional rice (Oryza sativa L.) landraces of Chhattisgarh, India. PLoS One 2017; 12:e0188864. [PMID: 29190790 PMCID: PMC5708757 DOI: 10.1371/journal.pone.0188864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/14/2017] [Indexed: 11/28/2022] Open
Abstract
Rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. The significant indica–japonica differentiation in rice provides great opportunities for its genetic improvement. In the present investigation, a total of 42 polymorphic InDel markers were used for differentiating 188 rice landraces and two local varieties of Chhattisgarh, India into indica and japonica related genotypes based on ‘InDel molecular index’. Frequency of japonica alleles varied from 0.11 to 0.89 among landraces. Results revealed that 104 rice landraces have indica type genetic architecture along with three tested indica cultivars Swarna, Mahamaya and Rajeshwari. Another 60 landraces were placed under ‘close to indica’ type. It was found that three rice landraces i.e. Kalajeera, Kapri, Tulsimala were ‘close to japonica’ type and 21 landraces were ‘intermediate’ type. The result from the calculation of ‘InDel molecular index’ was further verified with STRUCTURE, AMOVA, PCA and cluster analysis. Population structure analysis revealed two genetically distinct populations within the 190 rice landraces/genotypes. Based on AMOVA, ‘intermediate’ type, ‘close to japonica’ type and Dongjinbyeo (a japonica cultivar from Republic of Korea) displayed significant genetic differentiation (ɸPT = 0.642, P = 0.000) from ‘indica’ and ‘close to indica’ groups. The PCA scatter plot and dendrogram demonstrated a clear pattern of two major group differentiations. ‘Close to japonica’ type and ‘intermediate’ type landraces/genotypes were grouped with Dongjinbyeo and formed a separate cluster at 30% Jaccard’s similarity level from rest of the landraces/genotypes which were ‘close to indica’ or ‘indica’ type. Such a significant genetic differentiation among the locally adapted landraces could be exploited for the development of rice varieties introgressing higher yield potential and better plant types of japonica type as per the need of consumers and rice traders.
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Affiliation(s)
- Parmeshwar Kumar Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- * E-mail: (SM); (DS)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
- * E-mail: (SM); (DS)
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Vikash Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
| | - Bikram Kishore Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
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Sherwin WB, Chao A, Jost L, Smouse PE. Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. Trends Ecol Evol 2017; 32:948-963. [PMID: 29126564 DOI: 10.1016/j.tree.2017.09.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 01/18/2023]
Abstract
Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.
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Affiliation(s)
- W B Sherwin
- Evolution and Ecology Research Centre, School of Biological Earth and Environmental Science, University of New South Wales, Sydney, NSW 2052, Australia; Murdoch University Cetacean Research Unit, Murdoch University, South Road, Murdoch, WA 6150, Australia.
| | - A Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - L Jost
- EcoMinga Foundation, Via a Runtun, Baños, Tungurahua, Ecuador
| | - P E Smouse
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8551, USA
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Smouse PE, Banks SC, Peakall R. Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others. PLoS One 2017; 12:e0185499. [PMID: 29088229 PMCID: PMC5663342 DOI: 10.1371/journal.pone.0185499] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
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Affiliation(s)
- Peter E. Smouse
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sam C. Banks
- The Fenner School of Environment and Society, The Australian National University, Acton, ACT, Australia
- * E-mail:
| | - Rod Peakall
- Research School of Biology, The Australian National University, Acton, ACT, Australia
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Karlin EF, Smouse PE. Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers. ANNALS OF BOTANY 2017; 120:221-231. [PMID: 28088765 PMCID: PMC5737827 DOI: 10.1093/aob/mcw269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/28/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. METHODS Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. KEY RESULTS The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. CONCLUSIONS Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.
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Affiliation(s)
- Eric F. Karlin
- Environmental Science, School of Theoretical & Applied Science, Ramapo College, Mahwah, NJ 07430-1680, USA
| | - Peter E. Smouse
- Department of Ecology, Evolution, and Natural Resources, School of Environmental & Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8551, USA
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Piaggio AJ, Russell AL, Osorio IA, Jiménez Ramírez A, Fischer JW, Neuwald JL, Tibbels AE, Lecuona L, McCracken GF. Genetic demography at the leading edge of the distribution of a rabies virus vector. Ecol Evol 2017; 7:5343-5351. [PMID: 28770072 PMCID: PMC5528231 DOI: 10.1002/ece3.3087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/21/2017] [Accepted: 05/02/2017] [Indexed: 11/21/2022] Open
Abstract
The common vampire bat, Desmodus rotundus, ranges from South America into northern Mexico in North America. This sanguivorous species of bat feeds primarily on medium to large-sized mammals and is known to rely on livestock as primary prey. Each year, there are hotspot areas of D. rotundus-specific rabies virus outbreaks that lead to the deaths of livestock and economic losses. Based on incidental captures in our study area, which is an area of high cattle mortality from D. rotundus transmitted rabies, it appears that D. rotundus are being caught regularly in areas and elevations where they previously were thought to be uncommon. Our goal was to investigate demographic processes and genetic diversity at the north eastern edge of the range of D. rotundus in Mexico. We generated control region sequences (441 bp) and 12-locus microsatellite genotypes for 602 individuals of D. rotundus. These data were analyzed using network analyses, Bayesian clustering approaches, and standard population genetic statistical analyses. Our results demonstrate panmixia across our sampling area with low genetic diversity, low population differentiation, loss of intermediate frequency alleles at microsatellite loci, and very low mtDNA haplotype diversity with all haplotypes being very closely related. Our study also revealed strong signals of population expansion. These results follow predictions from the leading-edge model of expanding populations and supports conclusions from another study that climate change may allow this species to find suitable habitat within the U.S. border.
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Affiliation(s)
| | - Amy L. Russell
- Department of BiologyGrand Valley State UniversityAllendaleMIUSA
| | - Ignacio A. Osorio
- Committee of Promotion and Animal Health ProtectionRabies Campaign, San Luis Potosi CitySan Luis PotosiMéxico
| | - Alejandro Jiménez Ramírez
- Former State Chief of the National Campaign of Bovine Paralytic Rabies SENASICA/SAGARPAMéxico CityMéxico
- Present address:
MVZ.Marcelino Champagnat 505 Colonia Guadalupe Tepatitlán de MorelosJaliscoMexico
| | | | | | | | - Luis Lecuona
- USDA/APHIS/International ServicesDistrito FederalMéxico
| | - Gary F. McCracken
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTNUSA
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In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 2017; 107:455-465. [DOI: 10.1016/j.ympev.2016.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022]
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Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham M, Breen J, Metcalfe A, Stephen JR, De Bei R, Collins C, Lopez CMR. Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine ( Vitis vinifera cv. Shiraz). FRONTIERS IN PLANT SCIENCE 2017; 8:1860. [PMID: 29163587 PMCID: PMC5670326 DOI: 10.3389/fpls.2017.01860] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/11/2017] [Indexed: 05/21/2023]
Abstract
Understanding how grapevines perceive and adapt to different environments will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant's phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. To study the genetic and epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six wine sub-regions of the Barossa, South Australia. Methylation sensitive amplified polymorphisms (MSAPs) were used to obtain global patterns of DNA methylation. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Pairwise epigenetic distances between vineyards indicate that the main contributor (23-24%) to the detected variability is associated to the distribution of the vineyards on the N-S axis. Analysis of the methylation profiles of vineyards pruned with the same system increased the positive correlation observed between geographic distance and epigenetic distance suggesting that pruning system affects inter-vineyard epigenetic differentiation. Finally, methylation sensitive genotyping by sequencing identified 3,598 differentially methylated genes in grapevine leaves that were assigned to 1,144 unique gene ontology terms of which 8.6% were associated with response to environmental stimulus. Our results suggest that DNA methylation differences between vineyards and sub-regions within The Barossa are influenced both by the geographic location and, to a lesser extent, by pruning system. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
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Affiliation(s)
- Huahan Xie
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Moumouni Konate
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Na Sai
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - Kiflu G. Tesfamicael
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Cavagnaro
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- The ARC Centre of Excellence in Plant Energy Biology, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Andrew Metcalfe
- School of Mathematical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - John R. Stephen
- Plant Genomics Centre, Australian Genome Research Facility Ltd., Adelaide, SA, Australia
| | - Roberta De Bei
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Cassandra Collins
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M. R. Lopez
- Environmental Epigenetics and Genetics Group, University of Adelaide, Adelaide, SA, Australia
- The Waite Research Institute and The School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Carlos M. R. Lopez,
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Mandel JR, Ramsey AJ, Iorizzo M, Simon PW. Patterns of Gene Flow between Crop and Wild Carrot, Daucus carota (Apiaceae) in the United States. PLoS One 2016; 11:e0161971. [PMID: 27603516 PMCID: PMC5014312 DOI: 10.1371/journal.pone.0161971] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Studies of gene flow between crops and their wild relatives have implications for both management practices for cultivation and understanding the risk of transgene escape. These types of studies may also yield insight into population dynamics and the evolutionary consequences of gene flow for wild relatives of crop species. Moreover, the comparison of genetic markers with different modes of inheritance, or transmission, such as those of the nuclear and chloroplast genomes, can inform the relative risk of transgene escape via pollen versus seed. Here we investigate patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in two regions of the United States. We employed 15 nuclear simple sequence repeat (SSR) markers and one polymorphic chloroplast marker. Further, we utilized both conventional population genetic metrics along with Shannon diversity indices as the latter have been proposed to be more sensitive to allele frequency changes and differentiation. We found that populations in both regions that were proximal to crop fields showed lower levels of differentiation to the crops than populations that were located farther away. We also found that Shannon measures were more sensitive to differences in both genetic diversity and differentiation in our study. Finally, we found indirect evidence of paternal transmission of chloroplast DNA and accompanying lower than expected levels of chloroplast genetic structure amongst populations as might be expected if chloroplast DNA genes flow through both seed and pollen. Our findings of substantial gene flow for both nuclear and chloroplast markers demonstrate the efficiency of both pollen and seed to transfer genetic information amongst populations of carrot.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
- W. Harry Feinstone Center for Genomic Research, The University of Memphis, Memphis, Tennessee, United States of America
- * E-mail:
| | - Adam J. Ramsey
- Department of Biological Sciences, The University of Memphis, Memphis, Tennessee, United States of America
| | - Massimo Iorizzo
- Plants for Human Health Institute, Department of Horticultural Science, North Carolina State University, Kannapolis, North Carolina, United States of America
| | - Philipp W. Simon
- USDA-Agricultural Research Service, Vegetable Crops Unit, University of Wisconsin-Madison, Wisconsin, United States of America
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Validation of non-invasive genetic tagging in two large macaw species (Ara macao and A. chloropterus) of the Peruvian Amazon. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0573-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops. BMC Evol Biol 2016; 16:101. [PMID: 27176034 PMCID: PMC4866072 DOI: 10.1186/s12862-016-0680-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 11/11/2022] Open
Abstract
Background The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. Results The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Conclusions Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0680-6) contains supplementary material, which is available to authorized users.
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