Gene Flow Dependent Introgression and Species Delimitation

doi:10.3724/SP.J.1143.2012.11187

Abstract

Abstract:

Species delimitation is one of the most fundamental issues in biology and has recently drawn significant interest. A main reason for the increasing interests was the barcoding initiative associated rapid development of molecular techniques. One of the most important principles to diagnose species or species groups is to choose appropriate markers. However, incomplete linkage sorting and introgression, which are widespread phenomena in plants, present major obstacles in species delimitation. Recently, significant progress in our understanding of gene flow dependent introgression and species delimitation has been made both theoretically and empirically. In this paper, we reviewed the gene flow mediated speciation; evaluated the difference of introgression and incomplete linkage sorting; and finally concluded that species delimitation should be more effective with markers experiencing high levels of gene flow.

Key words: Species delimitation, Molecular Marker, DNA barcoding, Species introgression, Incomplete linkage sorting, Gene flow

CLC Number:

Q 949
Q 943

DU Fang, XU Fang. Gene Flow Dependent Introgression and Species Delimitation[J]. Plant Diversity, 2012, 34(3): 257-262.

References

Anderson E, Hubricht L, 1938. Hybridization in tradescantia. III. The evidence for introgressive hybridization［J］. American Journal of Botany, 25 (6): 396—402
Anderson E, 1953. Introgressive hybridization［J］. Biological Reviews, 28 (3): 280—307
Anderson E, Stebbins GLJ, 1954. Hybridization as an evolutionary stimulus［J］. Evolution, 8 (4): 378—388
Arnold ML, Tang SX, Knapp SJ et al., 2010. Asymmetric introgressive hybridization among louisiana iris species［J］. Genes, 1: 9—22
Bessey CE, 1906. Crop improvement by utilizing wild species［J］. Journal of Heredity, os2 (1): 112—118
Briggs D, Walters SM, 1997. Plant Variation and Evolution［M］. Cambridge: Cambridge University Press
Burgess R, Yang ZH, 2008. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors［J］. Molecular Biology Evolution, 25 (9): 1979—1994
China Plant BOL Group, Li DZ, Gao LM et al., 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants［J］. Proceedings of the National Academy of Science, 108 (49): 19641—19646
Coyne JA, Orr HA, 1997. “Patterns of speciation in Drosophila” revisited［J］. Evolution, 51 (1): 295—303
Currat M, Ruedi M, Petit RJ et al., 2008. The hidden side of invasions: massive introgression by local genes［J］. Evolution, 62 (8): 1908—1920
De Queiroz K, 2007. Species concepts and species delimitation［J］. Systematic Biology, 56 (6): 879—886
Dobzhansky T, 1937. Genetics and the Origin of Species［M］. New York: Columbia University Press, 364
Du FK, Petit RJ, Liu JQ, 2009. More introgression with less gene flow: chloroplast vs. mitochondrial DNA in the Picea asperata complex in China, and comparison with other Conifers［J］. Molecular Ecology, 18 (7): 1396—1407
Du FK, Peng XL, Liu JQ et al., 2011. Direction and extent of organelle DNA introgression between two spruce species in the QinghaiTibetan Plateau［J］. New Phytologist, 192 (4): 1024—1033
Ehrlich PR, Raven P, 1969. Differentiation of populations［J］. Science, 165 (3899): 1228—1232
Flexner SB, Hauck LC, 1993. Random House Webster′s Unabridged Dictionary［M］. German: Random House
Gay L, Neubauer G, ZagalskaNeubauer M et al., 2007. Molecular and morphological patterns of introgression between two large whiteheaded gull species in a zone of recent secondary contact［J］. Molecular Ecology, 16 (15): 3215—3227
Gilpin M, 1991. The genetic effective size of a metapopulation［J］. Biological Journal of the Linnean Society, 42 (1-2): 165—175
Gur A, Zamir D, 2004. Unused natural variation can lift yield barriers in plant breeding［J］. Plos Biology, 2 (10): e245
Harrison RG, 1986. Pattern and process in a narrow hybrid zone［J］. Heredity, 56 (3): 337—349
Hebert PDN, Ratnasingham S, deWaard JR, 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species［J］. Proceedings of the Royal Society B: Biological Sciences, 270(Suppl 1): S96—S99
Hebert PDN, Stoeckle MY, Zemlak TS et al., 2004. Identification of birds through DNA barcodes［J］. Plos Biology, 2 (10): e312
Heckman KL, Mariani CL, Rasoloarison R et al., 2007. Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus) ［J］. Molecular Phylogenetics and Evolution, 43 (2): 353—367
Hey J, 2001. The mind of the species problem［J］. Trends in Ecology & Evolution, 16 (7): 326—329
Hollingsworth PM, Graham SW, Little DP, 2011. Choosing and using a plant DNA barcode［J］. Plos One, 6 (5): e19254. doi:10.1371/journal.pone.0019254
Joly S, McLenachan PA, Lockhart PJ, 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting［J］. American Naturalist, 174 (2): E54—E70
Key KHL, 1968. The concept of stasipatric speciation［J］. Systematic Zoology, 17 (1): 14—22
Liston A, Robinson WA, Piero D et al., 1999. Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences［J］. Molecular Phylogenetics and Evolution, 11 (1): 95—109
Mayden RL, 1997. “A hierarchy of species concepts: the denouement in the saga of the species problem”［J］. Species the Units of Biodiversity, 54: 381—424
Mayr E, 1942. Systematics and the Origin of Species［M］. New York: Columbia University Press
Mayr E, 1963. Animal Species and Evolution［M］. Cambridge MA: Harvard University Press
McGuire JA, Linkem CW, Koo MS et al., 2007. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards［J］. Evolution, 61 (12): 2879—2897
Morjan CL, Rieseberg LH, 2004. How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles［J］. Molecular Ecology, 13 (6): 1341—1356
Niklas KJ, 1997. The Evolutionary Biology of Plants［M］. Chicago: The University of Chicago Press
Palmasilva C, Wendt T, Pinheiro F et al., 2011. Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs［J］. Molecular Ecology, 20 (15): 3185—3201
Petit RJ, Excoffier L, 2009. Gene flow and species delimitation［J］. Trends in Ecology & Evolution, 24 (7): 386—393
Rannala B, Yang ZH, 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci［J］. Genetics, 164 (4): 1645—1656
Rieseberg LH, Brunsfeld SJ, 1992. Molecular evidence and plant introgression［A］. In: Soltis DE, Soltis PS, Doyle JJ (eds). Molecular Systematics of Plants［M］. New York: Chapman and Hall Inc., 151—176
Rieseberg LH, Wood TE, Baack EJ, 2006. The nature of plant species［J］. Nature, 440 (7083): 524—527
Sites JW, Marshall JC, 2004. Operational criteria for delimiting species［J］. Annual Review of Ecology, Evolution, and Systematics, 35 (1): 199—227
Smith CI, Farrell BD, 2005. Phylogeography of the longhorn cactus beetle Moneilema appressum Lecont (Coleoptera: Cerambycidae) was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?［J］. Molecular Ecology, 14 (10): 3049—3065
Wang J, Wu YX, Ren GP et al., 2011a. Genetic Differentiation and Delimitation between Ecologically Diverged Populus euphratica and P.pruinosa［J］. PLoS One, 6 (10): e26530. doi:10.1371/journal.pone.0026530
Wang Q, Yu QS, Liu JQ, 2011b. Are nuclear loci ideal for barcoding plants? A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals［J］. Journal of Systematics and Evolution, 49 (3): 182—188
Wiens JJ, 2004. What is speciation and how should we study it? ［J］. The American Naturalist, 163 (6): 914—923
Wilyard A, Cronn R, Liston A, 2009. Reticulate evolution and incomplete lineage sorting among the Ponderosa pines［J］. Molecular Phylogenetics and Evolution, 52: 498—511
Wright S, 1943. Isolation by distance［J］. Genetics, 28 (2): 114—138
Zhou YF, Abbott RJ, Jiang ZY et al., 2010. Gene flow and species delimitation: a case study of two pine species with overlapping distributions in southeast China［J］. Evolution, 64 (8): 2342—2352

[1]	Hai-Su Hu, Jiu-Yang Mao, Xue Wang, Yu-Ze Liang, Bei Jiang, De-Quan Zhang. Plastid phylogenomics and species discrimination in the “Chinese” clade of Roscoea (Zingiberaceae) [J]. Plant Diversity, 2023, 45(05): 523-534.
[2]	Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li. Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia [J]. Plant Diversity, 2023, 45(02): 147-155.
[3]	Jin-Feng Wu, Dong-Rui Jia, Rui-Juan Liu, Zhi-Li Zhou, Lin-Lin Wang, Min-Yu Chen, Li-Hua Meng, Yuan-Wen Duan. Multiple lines of evidence supports the two varieties of Halenia elliptica (Gentianaceae) as two species [J]. Plant Diversity, 2022, 44(03): 290-299.
[4]	Lei Huang, Fang-Dong Geng, Jing-Jing Fan, Wei Zhai, Cheng Xue, Xiao-Hui Zhang, Yi Ren, Ju-Qing Kang. Evidence for two types of Aquilegia ecalcarata and its implications for adaptation to new environments [J]. Plant Diversity, 2022, 44(02): 153-162.
[5]	Meng-Jiao Fu, Hai-Yang Wu, Dong-Rui Jia, Bin Tian. Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow [J]. Plant Diversity, 2021, 43(06): 462-471.
[6]	Kai-Wen Jiang, Rong Zhang, Zhong-Fu Zhang, Bo Pan, Bin Tian. DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage [J]. Plant Diversity, 2020, 42(05): 376-385.
[7]	Sergei Volis*, Danara Ormanbekova , Irina Shulgina. Fine-scale spatial genetic structure in predominantly selfing plants with limited seed dispersal: a rule or exception? [J]. Plant Diversity, 2016, 38(02): 75-81.
[8]	HE Wei-Ying-, PAN Yue-Zhi. Study on the DNA Barcoding of Genus Ligularia Cass. (Asteraceae) [J]. Plant Diversity, 2015, 37(06): 693-703.
[9]	HUANG Ju, XU Yan-Fu, XIE Mi-Xue, LI Jian-Yue. Genotypes Analyses of Ten Genes Related to Eating Quality of Twenty-three Fragrant Rice Cultivars by Molecular Marker [J]. Plant Diversity, 2014, 36(03): 381-387.
[10]	LIU Min-Lu-, YU Wen-Bin-, Wang-Hong. Rapid Identification of Plant Species and iFlora: Application of DNA Barcoding in a Large Temperate Genus Pedicularis (Orobanchaceae) [J]. Plant Diversity, 2013, 35(6): 707-714.
[11]	ZENG Chun-Xia, HE Zheng-Shan, YANG Jun-Bei. DNA Barcoding for Plant Specimen Identification* [J]. Plant Diversity, 2013, 35(6): 693-700.
[12]	CHEN Zhi-Duan-**, LI De-Zhu. On Barcode of Life and Tree of Life [J]. Plant Diversity, 2013, 35(6): 675-681.
[13]	JIAO Li-Juan-, SHUI Yu-Min. Evaluating Candidate DNA Barcodes among Chinese Begonia (Begoniaceae) Species [J]. Plant Diversity, 2013, 35(6): 715-724.
[14]	LI Yan-Chun, WU Gang, YANG Zhu-Liang. DNA Barcoding of Edible Boletes (Boletaceae) from Yunnan, China [J]. Plant Diversity, 2013, 35(6): 725-732.
[15]	ZHANG Yu-Xiao-, HU Yu-Xing-, MA Peng-Fei-, ZHANG Li-Na-, LI De-Zhu. Selection of Potential Plastid DNA Barcodes for Bambusoideae (Poaceae) [J]. Plant Diversity, 2013, 35(6): 743-750.