Detecting and quantifying introgression in hybridized populations: simplifying assumptions yield overconfidence and uncertainty

被引:9
作者
Della Croce, Patrick [1 ]
Poole, Geoffrey C. [1 ,2 ]
Luikart, Gordon [3 ]
机构
[1] Montana State Univ, Dept Land Resources & Environm Sci, POB 173120, Bozeman, MT 59717 USA
[2] Montana State Univ, Montana Univ Syst, Inst Ecosyst, 106 AJM Johnson Hall, Bozeman, MT 59717 USA
[3] Univ Montana, Div Biol Sci, Fish & Wildlife Genom Grp, Flathead Lake Biol Stn, Missoula, MT 59812 USA
基金
瑞士国家科学基金会; 美国国家科学基金会;
关键词
admixture; genetic monitoring; introgression; invasive species; non-native species; power analysis; simplifying assumptions; simulation model; WESTSLOPE CUTTHROAT TROUT; ONCORHYNCHUS-CLARKII-LEWISI; INTRODUCED RAINBOW-TROUT; LANDSCAPE GENETICS; RIVER DRAINAGE; LIFE-HISTORY; MYKISS; SPREAD; THOUSANDS; INFERENCE;
D O I
10.1111/1755-0998.12520
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
A growing threat to the conservation of many native species worldwide is genetic introgression from non-native species. Although improved molecular genetic techniques are increasing the availability of species-diagnostic markers for many species, efficient field sampling design and reliable data interpretation require accurate estimates of uncertainty associated with the detection of non-native alleles and the quantification of introgression in native populations. Using fish populations as examples, we developed a simulation model of an age-structured population that tracks the introduction and inheritance of non-native alleles across generations by simulating stochastic mating and survival of individual fish and the resulting transmission of diagnostic markers. To simulate detection and quantification of introgression, we sampled varying combinations of n fish and m diagnostic markers to detect and quantify introgression from thousands of virtual, independent fish populations for a wide range of hybridization scenarios. Using the results of simulated sampling, we quantified the extent to which common simplifying assumptions regarding population structure and inheritance mechanisms can lead to the following: (i) overconfidence in our ability to detect non-native alleles and (ii) unrealistically narrow confidence intervals for estimates of the proportion of non-native alleles present. Under many circumstances, commonly used simplifying assumptions underestimate the probability of failing to detect ongoing introgression and the uncertainty associated with estimates of introgression by orders of magnitude. Such overconfidence in our ability to detect and quantify introgression can affect critical conservation and management decisions regarding native species undergoing or at risk of introgression from non-native species.
引用
收藏
页码:1287 / 1302
页数:16
相关论文
共 36 条
  • [1] Ali OA, 2015, GENETICS, V115, P28837
  • [2] Intercrosses and the US Endangered Species Act: Should hybridized populations be included as Westslope cutthroat trout?
    Allendorf, FW
    Leary, RF
    Hitt, NP
    Knudsen, KL
    Lundquist, LL
    Spruell, P
    [J]. CONSERVATION BIOLOGY, 2004, 18 (05) : 1203 - 1213
  • [3] The problems with hybrids: setting conservation guidelines
    Allendorf, FW
    Leary, RF
    Spruell, P
    Wenburg, JK
    [J]. TRENDS IN ECOLOGY & EVOLUTION, 2001, 16 (11) : 613 - 622
  • [4] RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays
    Amish, Stephen J.
    Hohenlohe, Paul A.
    Painter, Sally
    Leary, Robb F.
    Muhlfeld, Clint
    Allendorf, Fred W.
    Luikart, Gordon
    [J]. MOLECULAR ECOLOGY RESOURCES, 2012, 12 (04) : 653 - 660
  • [5] [Anonymous], 2015, pracma: practical numerical math functions.-R package ver. 1.6.4
  • [6] [Anonymous], 2017, Miscellaneous functions for Grid Graphics R package gridExtra version 2.3
  • [7] Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms
    Araki, Hitoshi
    Waples, Robin S.
    Ardren, William R.
    Cooper, Becky
    Blouin, Michael S.
    [J]. MOLECULAR ECOLOGY, 2007, 16 (05) : 953 - 966
  • [8] Behnke R.T., 2002, Trout and salmon of North America
  • [9] Levels of Introgression in Westslope Cutthroat Trout Populations Nine Years after Changes to Rainbow Trout Stocking Programs in Southeastern British Columbia
    Bennett, Stephen N.
    Kershner, Jeffrey L.
    [J]. NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT, 2009, 29 (05) : 1271 - 1282
  • [10] Rainbow trout (Oncorhynchus mykiss) invasion and the spread of hybridization with native westslope cutthroat trout (Oncorhynchus clarkii lewisi)
    Boyer, Matthew C.
    Muhlfeld, Clint C.
    Allendorf, Fred W.
    [J]. CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, 2008, 65 (04) : 658 - 669