DOI: 10.5061/dryad.cvdncjtbh
title: Data from: Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish

description: Recent work has revealed the importance of contemporary evolution for
 shaping ecological outcomes. In particular, rapid evolutionary divergence
 between populations has been shown to impact the ecology of populations,
 communities, and ecosystems. While studies have focused largely on the
 role of adaptive divergence in generating ecologically-important variation
 among populations, much less is known about the role of gene flow in
 shaping ecological outcomes. After divergence, populations may continue to
 interact through gene flow, which may influence evolutionary and
 ecological processes. Here we investigate the role of gene flow in shaping
 the contemporary evolution and ecology of recently diverged populations of
 anadromous steelhead / resident rainbow trout (Oncorhynchus mykiss).
 Results show that resident rainbow trout introduced above waterfalls have
 diverged evolutionarily from downstream anadromous steelhead, which were
 the source of introductions. However, the movement of fish from above to
 below the waterfalls has facilitated gene flow, which has reshaped genetic
 and phenotypic variation in the anadromous source population. In
 particular, gene flow has led to an increased frequency of residency,
 which in turn has altered population density, size-structure, and sex
 ratio. This result establishes gene flow as a contemporary evolutionary
 process that can have important ecological outcomes. From a management
 perspective, anadromous steelhead are generally regarded as a higher
 conservation priority than resident rainbow trout, even when found within
 the same watershed. Our results show that anadromous and resident O.
 mykiss populations may be connected via gene flow, with important
 ecological consequences. Such eco-evolutionary processes should be
 considered when managing recently diverged populations connected by gene
 flow.
description: Our study used a historical translocation of anadromous O. mykiss
 above waterfalls on two tributaries of a coastal California watershed as
 the experimental basis for studying the effects of genetic divergence and
 one-way gene flow on a founding population. We integrated historical
 records and paired surveys above and below barriers on two tributaries to
 explore how variation in downstream dispersal and gene flow influence the
 distribution of genotypes, phenotypes, and population density and size
 structure. We sampled O. mykiss at a number of study sites distributed
 across the watershed, resulting in the datasets described in the following
 sections. <strong>Genetic
 Data</strong> We used single nucleotide
 polymorphism (SNP) data at both neutral and adaptive loci to analyze
 patterns of population differentiation and gene flow.
 Caudal fin tissue samples were extracted in 96-well plates using
 the DNeasy Blood and Tissue Kit following the manufacturer's
 specifications with the BioRobot 3000 (Qiagen Inc. Gaithersburg, MD, USA).
 Individuals were genotyped using a 95-SNP panel developed for performing
 genetic stock identification and parentage-based analysis in O. mykiss,
 following the methods of Abadía-Cardoso et al. (2011, 2013) and Pearse and
 Garza (2015). Two negative controls were included in each array, and
 genotypes were called using SNP Genotyping Analysis Software (Fluidigm,
 South San Francisco, CA, USA). Additionally, a Y chromosome-linked sex
 identification assay was used to categorize individuals as male or female
 (Brunelli et al., 2008). <strong>Mark/Recapture
 Data</strong> We used mark-recapture data,
 including a mixture of physical capture and PIT tag antenna detection
 data, to monitor fish movement and explore movement patterns for genotyped
 fish.  The initial marking of individuals occurred at
 each of the nine study sites, such that all captured individuals ≥ 65 mm
 FL were issued a 12 mm passive integrated transponder (PIT) tag (Oregon
 RFID Inc., Portland, OR, USA) via intraperitoneal injection. Recapture
 information was generated year-round through a variety of life cycle
 monitoring efforts, including passive detection events at two stationary
 PIT tag antenna arrays; electrofishing surveys, estuary/lagoon seining,
 and downstream migrant trapping. We recorded the geographic location of
 each observation, and for physical recaptures, we re-measured the
 individual for FL and mass. Additionally, we used data generated at two
 stationary PIT tag antenna arrays to infer the emigration of individuals
 out of the watershed. Our data set includes all fish
 that were (1) first captured and PIT tagged at one of our 8 study sites
 located in the upper watershed (i.e., above the confluence of Big Creek
 and the Mainstem) during our 2017-19 field seasons, and (2) genotyped for
 Omy05 and genetic sex. We used recapture histories to identify
 “migrants”—defined as individuals whose final encounter occurred in the
 lower watershed. Fish that were (1) detected repeatedly in the lower
 watershed for a period of &gt; 2 weeks (i.e., “milling”), or (2) at
 large for &gt; 1.5 years between initial and final encounter (i.e.,
 “too old”) were not considered migrants.
 <strong>Demographic Data</strong>
 We used population survey data to estimate density and population
 size structure over three consecutive years (2017–2019). Sampling took
 place within a two-week window during low (base) flow conditions
 (August/September) to minimize the potential for individuals to disperse
 among sampling sites. Environmental and hydrological conditions remained
 fairly constant throughout each annual sampling period. During each fish
 sampling event, we installed block nets (6 mm mesh) at the upstream and
 downstream ends of the site and collected fish from the area between the
 nets using a backpack electrofisher (Model LR-24; Smith-Root Inc.,
 Vancouver, WA, USA). To quantify fish abundance and size distribution at
 each site, we employed multiple-pass depletion (removal) methods,
 completing three passes of equal effort by time in most cases. However,
 additional passes were completed when cumulative catch increased by more
 than 50% between the previous two passes. Following capture, we
 anesthetized O. mykiss with tricaine methanesulphonate (MS-222; Western
 Chemical Inc., Ferndale, WA, USA), measured for fork length (FL; ± 1.0 mm)
 and wet mass (± 0.1 g).
description: # Genetic divergence and one-way gene flow influence contemporary
 evolution and ecology of a partially migratory fish
 [https://doi.org/10.5061/dryad.cvdncjtbh](https://doi.org/10.5061/dryad.cvdncjtbh) Our study used a historical translocation of anadromous *O. mykiss* above waterfalls on two tributaries of a coastal California watershed as the experimental basis for studying the effects of genetic divergence and one-way gene flow on a founding population. We integrated historical records and paired surveys above and below barriers on two tributaries to explore how variation in downstream dispersal and gene flow influence the distribution of genotypes, phenotypes, and population density and size structure. We sampled *O. mykiss* at a number of study sites distributed across the watershed, resulting in the datasets described in the following sections. ## Genetic Data | `/snps.csv` We used single nucleotide polymorphism (SNP) data at both neutral and adaptive loci to analyze patterns of population differentiation and gene flow. Caudal fin tissue samples were extracted in 96-well plates using the DNeasy Blood and Tissue Kit following the manufacturer's specifications with the BioRobot 3000 (Qiagen Inc. Gaithersburg, MD, USA). Individuals were genotyped using a 95-SNP panel developed for performing genetic stock identification and parentage-based analysis in O. mykiss, following the methods of Abadía-Cardoso et al. (2011, 2013) and Pearse and Garza (2015). Two negative controls were included in each array, and genotypes were called using SNP Genotyping Analysis Software (Fluidigm, South San Francisco, CA, USA). Additionally, a Y chromosome-linked sex identification assay was used to categorize individuals as male or female (Brunelli et al., 2008).  The resulting data set includes the following variables, where each row represents an *individual* *sample*: | Variable(s) | Description | | :-------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `sample_id` | **Master Identification Code.** Primary unique identifier for each sample, used as a key to relate our genetic dataset (`/snps.csv`) and field dataset (`/field.csv`). | | `date` | **Sampling Date.** Date of sample collection.  | | `site_code` | **Site Code.** 3-digit code denoting sampling location. Can be cross referenced with additional site metadata provided in our field dataset (`/field.csv`). | | `sexid` and `sexid.1` | **Sex Identification Markers.** Genotypes are provided in two-column format, where `7` `6`  = male, `6` `6`  = female. | | | *The remaining variables (N = 190) represent 95 SNP loci reported in two-column format, with both columns containing the corresponding assay name, one of which is contains the suffix* `".1"`. *Additional details are detailed in Abadía-Cardoso et al. (2011, 2013) and Pearse and Garza (2015). Data are provided in two-column format.* | ## Mark-Recapture Data | `/mark-recap.csv` We used mark-recapture data, including a mixture of physical capture and PIT tag antenna detection data, to monitor fish movement and explore movement patterns for genotyped fish.  The initial marking of individuals occurred at each of the nine study sites, such that all captured individuals ≥ 65 mm FL were issued a 12 mm passive integrated transponder (PIT) tag (Oregon RFID Inc., Portland, OR, USA) via intraperitoneal injection. Recapture information was generated year-round through a variety of life cycle monitoring efforts, including passive detection events at two stationary PIT tag antenna arrays; electrofishing surveys, estuary/lagoon seining, and downstream migrant trapping. We recorded the geographic location of each observation, and for physical recaptures, we re-measured the individual for FL and mass. Additionally, we used data generated at two stationary PIT tag antenna arrays to infer the emigration of individuals out of the watershed. Our data set includes all fish that were (1) first captured and PIT tagged at one of our 8 study sites located in the upper watershed (i.e., above the confluence of Big Creek and the Mainstem) during our 2017-19 field seasons, and (2) genotyped for Omy05 and genetic sex. We used recapture histories to identify “migrants”—defined as individuals whose final encounter occurred in the lower watershed. Fish that were (1) detected repeatedly in the lower watershed for a period of &gt; 2 weeks (i.e., “milling”), or (2) at large for &gt; 1.5 years between initial and final encounter (i.e., “too old”) were not considered migrants.  The resulting data set includes the following variables, where each row represents a *unique* *individual*: | Variable(s) | Description | | :------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `pit` | **PIT-Tag Code.** 15-digit code associated with a unique passive integrated transponder (PIT) tag. This code is used as a unique identifier for tagged individuals. Can be used as a relational key for genetic (`/snps.csv`) and field (`/field.csv`) datasets. *Note that genetic and field datasets include multiple entries for some individuals, as well as individuals that were not assigned a PIT tag.* | | `fl_last` | **Fork Length at Last Handling (mm).** Length of a fish as measured from the tip of its snout to the fork of the tail, recorded at the time of the most recent capture prior to emigrating. Values are recorded in millimeters. Derived from field dataset (`/field.csv`) (see below). | | `omy05` | **Omy05 Genotype.** Inferred genotype for *Omy05* inversion, where: `AA` = homozygous ancestral, `AR` = heterozygous, and `RR` = homozygous rearranged. Derived from genetic dataset (`/snps.csv`) (see above). | | `genetic_sex` | **Genetic Sex.** Inferred sex, where:  `M` = male, and  `F` = female. Derived from genetic dataset (`/snps.csv`) (see above). | | `detect` | **Emigration Detection.** Binary variable indicating whether an was detected emigrating through the lower watershed, per the definition provided in our methods. Values are coded as: `1` = detected (migrant), and `0` = not detected (non-migrant). | ## Field Data | `/field.csv` We used population survey data to estimate density and population size structure over three consecutive years (2017–2019). Sampling took place within a two-week window during low (base) flow conditions (August/September) to minimize the potential for individuals to disperse among sampling sites. Environmental and hydrological conditions remained fairly constant throughout each annual sampling period. During each fish sampling event, we installed block nets (6 mm mesh) at the upstream and downstream ends of the site and collected fish from the area between the nets using a backpack electrofisher (Model LR-24; Smith-Root Inc., Vancouver, WA, USA). To quantify fish abundance and size distribution at each site, we employed multiple-pass depletion (removal) methods, completing three passes of equal effort by time in most cases. However, additional passes were completed when cumulative catch increased by more than 50% between the previous two passes. Following capture, we anesthetized O. mykiss with tricaine methanesulphonate (MS-222; Western Chemical Inc., Ferndale, WA, USA), measured for fork length (FL; ± 1.0 mm) and wet mass (± 0.1 g). The resulting data set includes the following variables, where each row represents a *unique* *sampling event*: | Variable(s) | Description | | :------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | `sample_id` | **Master Identification Code.** Primary unique identifier for each sample, used as a key to relate our genetic dataset (`/snps.csv`) and field dataset (`/field.csv`). | | `date` | **Sampling Date.** Date of sample collection.  | | `site_code` | **Site Code.** 3-digit code denoting sampling location. Can be cross referenced with additional site metadata provided in our field dataset (`/field.csv`). | | `trib` | **Tributary Name.** Indicates whether the study site was located on Mainstem Scott Creek (`Mainstem`), or `Big Creek`.  | | `prox` | **Barrier Proximity.** Categorical variable indicating whether the study site is located `Above` or `Below` the waterfall barrier on its respective tributary.  | | `census_site` | **Census Site Name.** Name used to identify study sites in manuscript and figures. | | `mean_width` | **Mean Wetted Stream Width.** Mean width of wetted channel, derived from 11 transect measurements distributed evenly along the 100-m study site. Units are in meters.  | | `pass` | **Electrofishing Pass Number.** Integer variable indicating the pass number in which an individual was captured during multi-pass depletion electrofishing efforts.  | | `event` | **Sampling Event Type.** Categorical variable indicating the type of sampling event, where: `CAP` = capture only, `TAG` = issued a PIT-tag, `REC` = recapture of a previously tagged fish, and `MOR` = mortality.  | | `pit` | **PIT-Tag Code.** 15-digit code associated with a unique passive integrated transponder (PIT) tag. This code is used as a unique identifier for tagged individuals. Can be used as a relational key for genetic (`/snps.csv`) and field (`/field.csv`) datasets. *Note that genetic and field datasets include multiple entries for some individuals, as well as individuals that were not assigned a PIT tag.* | | `fl` | **Fork Length (mm).** Length of a fish as measured from the tip of its snout to the fork of the tail, recorded at the time of the most recent capture prior to emigrating. Values are recorded in millimeters (± 1.0 mm). | | `mass` | **Mass (g).** Wet mass recorded in grams (± 0.1 g). | | `omy05` | **Omy05 Genotype.** Inferred genotype for *Omy05* inversion, where: `AA` = homozygous ancestral, `AR` = heterozygous, and `RR` = homozygous rearranged. Derived from genetic dataset (`/snps.csv`) (see above). | | `genetic_sex` | **Genetic Sex.** Inferred sex, where:  `M` = male, and  `F` = female. Derived from genetic dataset (`/snps.csv`) (see above). | Missing data code : NA ## Additional information For additional questions regarding these data, including additional sharing/access information, please contact the corresponding author(s).