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Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus

Allison Black, Rachel Breyta, Trevor Bedford, Gael Kurath
DOI: http://dx.doi.org/10.1093/ve/vew034 vew034 First published online: 26 December 2016

Figures

  • Figure 1.

    (A) Distribution of numbers of genotyped U genogroup IHNV isolates, by year, collected between 1971 and 2013 (n = 1219). (B) Distribution of numbers of genotyped U genogroup IHNV detection events that occurred between 1971 and 2013 (n = 619). (C) Numbers of genotyped U genogroup events that occurred by year in either the Columbia River Basin (purple) or in coastal watersheds (green) between 1971 and 2013 (n = 619). (D) Numbers of genotyped U genogroup events that occurred by year in Chinook salmon (red), sockeye salmon (including kokanee) (yellow), or steelhead trout (including rainbow trout) (blue) between 1971 and 2013 (n = 581).

  • Figure 2.

    Analysis of UC and UP subgroups. (A) Maximum likelihood tree of all 114 U genotypes detected within the study geographic range between 1971 and 2013. Blue branches indicate genotypes within the UP subgroup and orange branches indicate genotypes within the UC subgroup. Numbers of events attributable to each genotype are indicated as the last argument in the taxon name. Bolded numbers indicate bootstrap support values based on 1,000 replicates. Black bars represent clade defining mutations, whereby site number (s. no.) corresponds to the alignment figure in panel B, and the nucleotide substitution is stated. (B) Alignment of 113 UP and UC genotypes against the earliest genotype in the dataset, a UP subgroup virus. Black sites indicate a nucleotide difference between the analyzed genotype and the reference genotype. Coloring indicates which subgroup each genotype belongs to. Genotypes are arranged chronologically within their respective subgroups from earliest to most recent detection. (C) Root-to-tip divergence (phylogeny not shown) plotted against sampling date for all 619 U genogroup events occurring within the study region between 1971 and 2013. Orange indicates UC events and blue indicates UP events. Linear regression lines approximate the observed rate of evolution over the study time period. For UP events: slope = 2.22 × 10−4 subs per site per year, R2 = 0.2093, P < 0.001. For UC events: slope = 1.79 × 10−4 subs per site per year, R2 = 0.2184, P < 0.001.

  • Figure 3.

    Coalescent phylogenetic tree showing U genogroup topology. UC viruses are shown in orange and UP viruses are shown in blue. Posterior support values are given at key nodes. Scale represents number of substitutions per site per year.

  • Figure 4.

    UC and UP coalescent phylogenetic trees showing ancestral geographic range and ancestral host species. (A) Separate UC and UP trees showing inferred ancestral geographic states. Inferred detection in the Columbia River Basin is indicated in purple and inferred detection in coastal watersheds is indicated in green. Rarely, the ancestral state had the same probability of occurring in both ranges; these branches are indicated as unresolved and are colored grey. Line thickness indicates the probability of being in the colored state; thicker lines indicate higher probabilities. (B) Separate UC and UP trees showing inferred ancestral host states. Red denotes Chinook salmon, yellow denotes sockeye/kokanee salmon, and light blue denotes steelhead/rainbow trout. Only rarely ancestral states had equal probability of detection in multiple host species. These are indicated as unresolved and colored grey. Non-dominant hosts for IHNV such as coho salmon, chum salmon, and Atlantic salmon are all indicated by maroon. As in panel A, line thickness correlates with probability of being in a state.

  • Figure 5.

    Changes in effective population size over time for UP and UC subgroup viruses. The median effective population size is indicated in black and the shaded area represents the 95% HPD around the estimate.

  • Figure 6.

    Maps indicating sampling locations and event counts. (A) Location of sample collection sites where one or more events occurred within this study. WA, Washington; OR, Oregon; ID, Idaho. (B) Locations of all events that occurred in either sockeye salmon (including kokanee salmon) or in Chinook salmon. Circle scale indicates the number of events that occurred. This host delineation also represents the partitions used in the by-host analysis of population structure. (C) Locations of all events occurring in either the Columbia River Basin or in coastal watersheds. Circles scale according to numbers of events. These event counts correspond to the partitions defined for tests of population structure due to geographic subdivision.

Tables

  • Table 1.

    Descriptive analysis of U genogroup events occurring in Washington, Oregon, and Idaho between 1971 and 2013.

    All U Events (n = 619)UC Events (n = 475)UP Events (n = 144)
    Geography
    Coastal watersheds (37 sites)131 (21.2%)15 (3.2%)116 (80.6%)
    Columbia River Basin (77 sites)488 (78.8%)460 (96.8%)28 (19.4%)
    Host
    Sockeye Salmon92 (14.9%)9 (1.9%)83 (57.6%)
    Kokanee Salmon131 (5.0%)22 (4.6%)9 (6.3%)
    Chinook Salmon295 (47.7%)282 (59.4%)13 (9.0%)
    Steelhead Trout153 (24.7%)141 (29.7%)12 (8.3%)
    Rainbow Trout210 (1.6%)6 (1.3%)4 (2.8%)
    Coho Salmon20 (3.2%)12 (2.5%)8 (5.6%)
    Chum Salmon14 (2.3%)3 (0.6%)11 (7.6%)
    Atlantic Salmon4 (0.6%)N/A4 (2.8%)
    Lifestage
    Juveniles119 (19.2%)86 (18.1%)33 (22.9%)
    Adults491 (79.3%)386 (81.3%)105 (72.9%)
    Unknown Age9 (1.5%)3 (0.6%)6 (4.2%)
    • 1 Kokanee salmon are a freshwater form of sockeye salmon, O. nerka.

    • 2 Rainbow trout are a freshwater form of steelhead trout, O. mykiss.

  • Table 2.

    Detection of population structure by host and by geography.

    By Host: Chinook salmon and sockeye salmon3
    Mean interpopulation diversity0.0161
    Mean subpopulation diversity0.00608
    Metapopulation diversity0.0102
    FST (95% CI), P-value0.406 (0.358–0.458), P < 0.001
    By Geography: Columbia River Basin and coastal watersheds
    Mean interpopulation diversity0.0171
    Mean subpopulation diversity0.00606
    Metapopulation diversity0.00975
    FST (95% CI), P-value0.379 (0.334–0.422), P < 0.001
    • 3 Sockeye includes both sockeye and kokanee salmon (both O. nerka)

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