Research Article
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Year 2020, Volume: 3 Issue: 3, 76 - 80, 01.07.2020

Hasan Onder Levent Mercan

https://doi.org/10.34248/bsengineering.682950

Abstract

References

  • Anderson MJ. 2006. Distance-Based tests for homogeneity of multivariate dispersions. Biometrics, 62: 245 – 253.
  • Beier S, Mohit V, Ettema TJG, Östman Ö, Tranvik LJ, Bertilsson S. 2012. Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing. Environmental Microbiology, 14(9): 2467 – 2479.
  • Bennett AB, Gratton C. 2013. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition. Ecological Applications, 23: 86–95.
  • Blum MJ, Bagley MJ, Walters DM, Jackson SA, Daniel FB, Chaloud DJ, Cade BS. 2012. Genetic diversity and species diversity of stream fishes covary across a land-use gradient. Oecologia, 168: 83–95.
  • Bonnet, E, Van de Peer Y. 2002. ZT: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 7: 1–12.
  • Cordier T, Robin C, Capdevielle X, Desprez-Loustau ML, Vacher C. 2012. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecology, 5: 509 – 520.
  • Costa D, Bouchon D, Van Straalen NM, Sousa JP, Riberio R. 2013. Copper tolerance and genetic diversity of porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat. Environmental Toxicology and Chemistry, 32(4): 884–888.
  • Eckholm BJ, Anderson KE, Weiss M, DeGrandi-Hoffman G. 2011. Intracolonial genetic diversity in honeybee (Apis mellifera) colonies increases pollen foraging efficiency. Behav Ecol Sociobiol, 65: 1037 – 1044.
  • Hillis DM. 1984. Misuse and Modification of Nei’s genetic distance. Systematic Zoology, 33(2): 238 – 240.
  • İkinci N, Oberprieler C. 2010. Genetic relationships among NE Turkish Lilium L. (Liliaceae) species based on a random amplified polymorphic DNA analysis. Plant Syst Evol, 284: 41 – 48.
  • Kokare M, Chatterji BN, Biswas PK. 2003. Comparison of similarity metrics for texture image retrieval, TENCON 2003. Conference on Convergent Technologies for the Asia-Pacific Region, Vol. 2: 571 – 575, 15-17 October 2003, Bangalore, India.
  • Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RR. 2013. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLOS Computational Biology, 9(1): 1 – 16.
  • Legendre P, Fortin MJ. 2010. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Molecular Ecology Resources, 10: 831–844.
  • Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res, 27: 209 – 220.
  • Mason KL, Erb Downward JR, Mason KD, Falkowski NR, Eaton KA, Kao JY, Young VB, Huffnagle GB. 2012. Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun, 80(10): 3371 – 3380.
  • Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell, 152(1-2): 39 – 50.
  • Mercan L. 2010. Analysis of genetic dissimilarity between native and commercial chicken genotypes by SSR (Simple sequence repeats) method. PhD Thesis, 155p. Ondokuz Mayis University Natural Science Institute, Samsun.
  • Mercan L, Okumuş A. 2015. Genetic diversity of village chickens in Central Black Sea Region and commercial chickens in Turkey by using microsatellite markers. Turkish Journal of Veterinary and Animal Sciences, 39: 134 – 140.
  • Møller AK, Søborg DA, Al-Soud WA, Sørensen SJ, Kroer N. 2013. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation. Polar Research, 32: 1 – 11.
  • Nei M. 1972. Genetic distance between populations. The American Naturalist, 106(949): 283 – 292.
  • Odat N, Jetschke G, Hellwig FH. 2004. Genetic diversity of Ranunculus acris L. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities. Molecular Ecology, 13: 1251 – 1257.
  • Papadopoulou A, Anastasiou I, Spagopoulou F, Stalimerou M, Terzopoulou S, Legakis A, Vogler AP. 2011. Testing the species–genetic diversity correlation in the Aegean archipelago: Toward a haplotype-based macroecology? The American Naturalist, 178(2): 241 – 255.
  • Parker KA, Anderson MJ, Jenkins PF, Brunton DH. 2012. The effects of translocation-induced isolation and fragmentation on the cultural evolution of bird song. Ecology Letters, 15: 778 – 785.
  • Peres-Neto PR, Legendre P, Dray S, Borcard D. 2006. Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology, 87(10): 2614 – 2625.
  • Procházka P, Stokke BG, Jensen H, Fáinova D, Bellinvia E, Fossøy F, Vikan JR, Bryja J, Soler M. 2011. Low genetic differentiation among reed warbler Acrocephalus scirpaceus populations across Europe. J Avian Biol, 42: 103-113.
  • Sahoo PK, Mohanty J, Garnayak SK, Mohanty BR, Kar B, Jena J, Prasanth H. 2013. Genetic diversity and species identification of Argulus parasites collected from major aquaculture regions of India using RAPD-PCR. Aquaculture Research, 44: 220–230.
  • Sharma A, Dutt G, Jayakumar S, Saroha V, Verma NK, Dixit SP. 2013. Genetic structuring of nine indian domestic goat breeds based on SNPs identified in IGF-1 gene. Animal Biotechnology, 24(2): 148 – 157.
  • Shiro S, Matsuura S, Saiki R, Sigua GC, Yamamoto A, Umehara Y, Hayashi M, Saeki Y. 2013. Genetic diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in the United States. Appl Environ Microbiol, 79(12): 3610 – 3618.

Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data

Year 2020, Volume: 3 Issue: 3, 76 - 80, 01.07.2020

Hasan Onder Levent Mercan

https://doi.org/10.34248/bsengineering.682950

Abstract

In this study we aimed to examine the effects of both Nei’s genetic distance and Bray Curtis distance versus geographical distance for Mantel test on chicken diversity data. Many researchers used Nei’s genetic distance which measure that genetic differences arise due to mutations and genetic drift but some researchers used Bray Curtis distance which used to quantify the compositional dissimilarity between two different locations. We used molecular data from 28 microsatellite loci with the sample size of 364 local chicken from 45 locations and Euclidean distance of this locations using Google Earth v.4. Mantel test results suggest that relationship between genetic differentiations and geographic distance between populations using Bray Curtis distance could be substituted for Nei’s genetic distance with great reliability on chicken diversity data.

Keywords

Mantel test Bray Curtis distance Nei’s genetic distance Chicken

References

  • Anderson MJ. 2006. Distance-Based tests for homogeneity of multivariate dispersions. Biometrics, 62: 245 – 253.
  • Beier S, Mohit V, Ettema TJG, Östman Ö, Tranvik LJ, Bertilsson S. 2012. Pronounced seasonal dynamics of freshwater chitinase genes and chitin processing. Environmental Microbiology, 14(9): 2467 – 2479.
  • Bennett AB, Gratton C. 2013. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition. Ecological Applications, 23: 86–95.
  • Blum MJ, Bagley MJ, Walters DM, Jackson SA, Daniel FB, Chaloud DJ, Cade BS. 2012. Genetic diversity and species diversity of stream fishes covary across a land-use gradient. Oecologia, 168: 83–95.
  • Bonnet, E, Van de Peer Y. 2002. ZT: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 7: 1–12.
  • Cordier T, Robin C, Capdevielle X, Desprez-Loustau ML, Vacher C. 2012. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecology, 5: 509 – 520.
  • Costa D, Bouchon D, Van Straalen NM, Sousa JP, Riberio R. 2013. Copper tolerance and genetic diversity of porcellionides sexfasciatus (ISOPODA) in a highly contaminated mine habitat. Environmental Toxicology and Chemistry, 32(4): 884–888.
  • Eckholm BJ, Anderson KE, Weiss M, DeGrandi-Hoffman G. 2011. Intracolonial genetic diversity in honeybee (Apis mellifera) colonies increases pollen foraging efficiency. Behav Ecol Sociobiol, 65: 1037 – 1044.
  • Hillis DM. 1984. Misuse and Modification of Nei’s genetic distance. Systematic Zoology, 33(2): 238 – 240.
  • İkinci N, Oberprieler C. 2010. Genetic relationships among NE Turkish Lilium L. (Liliaceae) species based on a random amplified polymorphic DNA analysis. Plant Syst Evol, 284: 41 – 48.
  • Kokare M, Chatterji BN, Biswas PK. 2003. Comparison of similarity metrics for texture image retrieval, TENCON 2003. Conference on Convergent Technologies for the Asia-Pacific Region, Vol. 2: 571 – 575, 15-17 October 2003, Bangalore, India.
  • Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RR. 2013. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLOS Computational Biology, 9(1): 1 – 16.
  • Legendre P, Fortin MJ. 2010. Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Molecular Ecology Resources, 10: 831–844.
  • Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res, 27: 209 – 220.
  • Mason KL, Erb Downward JR, Mason KD, Falkowski NR, Eaton KA, Kao JY, Young VB, Huffnagle GB. 2012. Candida albicans and bacterial microbiota interactions in the cecum during recolonization following broad-spectrum antibiotic therapy. Infect Immun, 80(10): 3371 – 3380.
  • Maurice CF, Haiser HJ, Turnbaugh PJ. 2013. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell, 152(1-2): 39 – 50.
  • Mercan L. 2010. Analysis of genetic dissimilarity between native and commercial chicken genotypes by SSR (Simple sequence repeats) method. PhD Thesis, 155p. Ondokuz Mayis University Natural Science Institute, Samsun.
  • Mercan L, Okumuş A. 2015. Genetic diversity of village chickens in Central Black Sea Region and commercial chickens in Turkey by using microsatellite markers. Turkish Journal of Veterinary and Animal Sciences, 39: 134 – 140.
  • Møller AK, Søborg DA, Al-Soud WA, Sørensen SJ, Kroer N. 2013. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation. Polar Research, 32: 1 – 11.
  • Nei M. 1972. Genetic distance between populations. The American Naturalist, 106(949): 283 – 292.
  • Odat N, Jetschke G, Hellwig FH. 2004. Genetic diversity of Ranunculus acris L. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities. Molecular Ecology, 13: 1251 – 1257.
  • Papadopoulou A, Anastasiou I, Spagopoulou F, Stalimerou M, Terzopoulou S, Legakis A, Vogler AP. 2011. Testing the species–genetic diversity correlation in the Aegean archipelago: Toward a haplotype-based macroecology? The American Naturalist, 178(2): 241 – 255.
  • Parker KA, Anderson MJ, Jenkins PF, Brunton DH. 2012. The effects of translocation-induced isolation and fragmentation on the cultural evolution of bird song. Ecology Letters, 15: 778 – 785.
  • Peres-Neto PR, Legendre P, Dray S, Borcard D. 2006. Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology, 87(10): 2614 – 2625.
  • Procházka P, Stokke BG, Jensen H, Fáinova D, Bellinvia E, Fossøy F, Vikan JR, Bryja J, Soler M. 2011. Low genetic differentiation among reed warbler Acrocephalus scirpaceus populations across Europe. J Avian Biol, 42: 103-113.
  • Sahoo PK, Mohanty J, Garnayak SK, Mohanty BR, Kar B, Jena J, Prasanth H. 2013. Genetic diversity and species identification of Argulus parasites collected from major aquaculture regions of India using RAPD-PCR. Aquaculture Research, 44: 220–230.
  • Sharma A, Dutt G, Jayakumar S, Saroha V, Verma NK, Dixit SP. 2013. Genetic structuring of nine indian domestic goat breeds based on SNPs identified in IGF-1 gene. Animal Biotechnology, 24(2): 148 – 157.
  • Shiro S, Matsuura S, Saiki R, Sigua GC, Yamamoto A, Umehara Y, Hayashi M, Saeki Y. 2013. Genetic diversity and geographical distribution of indigenous soybean-nodulating bradyrhizobia in the United States. Appl Environ Microbiol, 79(12): 3610 – 3618.
There are 28 citations in total.

Details

Primary Language English
Subjects Engineering
Journal Section Research Articles
Authors

Hasan Onder 0000-0002-8404-8700

Levent Mercan 0000-0002-6790-1458

Publication Date July 1, 2020
Submission Date January 31, 2020
Acceptance Date March 3, 2020
Published in Issue Year 2020 Volume: 3 Issue: 3

Cite

APA Onder, H., & Mercan, L. (2020). Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data. Black Sea Journal of Engineering and Science, 3(3), 76-80. https://doi.org/10.34248/bsengineering.682950
AMA Onder H, Mercan L. Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data. BSJ Eng. Sci. July 2020;3(3):76-80. doi:10.34248/bsengineering.682950
Chicago Onder, Hasan, and Levent Mercan. “Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data”. Black Sea Journal of Engineering and Science 3, no. 3 (July 2020): 76-80. https://doi.org/10.34248/bsengineering.682950.
EndNote Onder H, Mercan L (July 1, 2020) Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data. Black Sea Journal of Engineering and Science 3 3 76–80.
IEEE H. Onder and L. Mercan, “Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data”, BSJ Eng. Sci., vol. 3, no. 3, pp. 76–80, 2020, doi: 10.34248/bsengineering.682950.
ISNAD Onder, Hasan - Mercan, Levent. “Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data”. Black Sea Journal of Engineering and Science 3/3 (July 2020), 76-80. https://doi.org/10.34248/bsengineering.682950.
JAMA Onder H, Mercan L. Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data. BSJ Eng. Sci. 2020;3:76–80.
MLA Onder, Hasan and Levent Mercan. “Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data”. Black Sea Journal of Engineering and Science, vol. 3, no. 3, 2020, pp. 76-80, doi:10.34248/bsengineering.682950.
Vancouver Onder H, Mercan L. Comparison of Bray Curtis and Nei’s Genetic Distance on Mantel Test for Chicken Diversity Data. BSJ Eng. Sci. 2020;3(3):76-80.
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