2020
Kelson, Suzanne J.; Miller, Michael R.; Thompson, Tasha Q.; O’Rourke, Sean M.; Carlson, Stephanie M.
Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability Journal Article
In: Molecular Ecology, vol. 29, no. 5, pp. 870-885, 2020.
Abstract | Links | BibTeX | Tags: ecology, ERCZO, genetic variation, landscape genetics, life history, O. mykiss, Oncorhynchus mykiss, partial barrier, partial migration, river networks
@article{Kelson2020,
title = {Temporal dynamics of migration‐linked genetic variation are driven by streamflows and riverscape permeability},
author = {Suzanne J. Kelson and Michael R. Miller and Tasha Q. Thompson and Sean M. O'Rourke and Stephanie M. Carlson},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/mec.15367-1.pdf},
doi = {10.1111/mec.15367},
year = {2020},
date = {2020-02-03},
journal = {Molecular Ecology},
volume = {29},
number = {5},
pages = {870-885},
abstract = {Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.},
keywords = {ecology, ERCZO, genetic variation, landscape genetics, life history, O. mykiss, Oncorhynchus mykiss, partial barrier, partial migration, river networks},
pubstate = {published},
tppubtype = {article}
}
Landscape permeability is often explored spatially, but may also vary temporally. Landscape permeability, including partial barriers, influences migratory animals that move across the landscape. Partial barriers are common in rivers where barrier passage varies with streamflow. We explore the influence of partial barriers on the spatial and temporal distribution of migration‐linked genotypes of Oncorhynchus mykiss, a salmonid fish with co‐occurring resident and migratory forms, in tributaries to the South Fork Eel River, California, USA, Elder and Fox Creeks. We genotyped >4,000 individuals using RAD‐capture and classified individuals as resident, heterozygous or migratory genotypes using life history‐associated loci. Across four years of study (2014–2017), the permeability of partial barriers varied across dry and wet years. In Elder Creek, the largest waterfall was passable for adults migrating up‐river 4–39 days each year. In this stream, the overall spatial pattern, with fewer migratory genotypes above the waterfall, remained true across dry and wet years (67%–76% of migratory alleles were downstream of the waterfall). We also observed a strong relationship between distance upstream and proportion of migratory alleles. In Fox Creek, the primary barrier is at the mouth, and we found that the migratory allele frequency varied with the annual timing of high flow events. In years when rain events occurred during the peak breeding season, migratory allele frequency was high (60%–68%), but otherwise it was low (30% in two years). We highlight that partial barriers and landscape permeability can be temporally dynamic, and this effect can be observed through changing genotype frequencies in migratory animals.
2019
Kelson, Suzanne J.; Miller, Michael R.; Thompson, Tasha Q.; O’Rourke, Sean M.; Carlson, Stephanie M.
Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss? Journal Article
In: Canadian Journal of Fisheries and Aquatic Sciences, vol. 76, no. 11, pp. 2080-2088, 2019.
Abstract | Links | BibTeX | Tags: ERCZO, genetic variation, O. mykiss, partial migration
@article{Kelson2019b,
title = {Do genomics and sex predict migration in a partially migratory salmonid fish, Oncorhynchus mykiss?},
author = {Suzanne J. Kelson and Michael R. Miller and Tasha Q. Thompson and Sean M. O'Rourke and Stephanie M. Carlson},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/cjfas-2018-0394-1.pdf},
doi = {10.1139/cjfas-2018-0394},
year = {2019},
date = {2019-02-14},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
volume = {76},
number = {11},
pages = {2080-2088},
abstract = {Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.},
keywords = {ERCZO, genetic variation, O. mykiss, partial migration},
pubstate = {published},
tppubtype = {article}
}
Partial migration is a common phenomenon wherein populations include migratory and resident individuals. Whether an individual migrates or not has important ecological and management implications, particularly within protected populations. Within partially migratory populations of Oncorhynchus mykiss, migration is highly correlated with a specific genomic region, but it is unclear how well this region predicts migration at the individual level. Here, we relate sex and life history genotype, determined using >400 single nucleotide polymorphisms (SNPs) on the migratory-linked genomic region, to life history expression of marked juvenile O. mykiss from two tributaries to the South Fork Eel River, northern California. Most resident fish were resident genotypes (57% resident, 37% heterozygous, 6% migratory genotype) and male (78%). Most migratory fish were female (62%), but were a mixture of genotypes (30% resident, 45% heterozygous, 25% migratory genotype). Sex was more strongly correlated with life history expression than genotype, but the best-supported model included both. Resident genotypes regularly migrated, highlighting the importance of conserving the full suite of life history and genetic diversity in partially migratory populations.
2008
McClure, T. J. Beechie S. M. Carlson M. M.
Evolutionary consequences of habitat loss for Pacific anadromous salmonids Journal Article
In: Evolutionary Applications, vol. 1, no. 2, pp. 300-18, 2008, ISSN: 1752-4571.
Abstract | Links | BibTeX | Tags: dams, differential habitat loss, evolutionary trajectory, genetic variation, Oncorhynchus
@article{doi:10.1111/j.1752-4571.2008.00030.x,
title = {Evolutionary consequences of habitat loss for Pacific anadromous salmonids},
author = {T. J. Beechie S. M. Carlson M. M. McClure},
url = {https://angelo.berkeley.edu/wp-content/uploads/sites/59/McClure_2008_EvoApp.pdf},
doi = {doi:10.1111/j.1752-4571.2008.00030.x},
issn = {1752-4571},
year = {2008},
date = {2008-00-00},
journal = {Evolutionary Applications},
volume = {1},
number = {2},
pages = {300-18},
abstract = {Large portions of anadromous salmonid habitat in the western United States
has been lost because of dams and other blockages. This loss has the potential
to affect salmonid evolution through natural selection if the loss is biased,
affecting certain types of habitat differentially, and if phenotypic traits correlated
with those habitat types are heritable. Habitat loss can also affect salmonid
evolution indirectly, by reducing genetic variation and changing its
distribution within and among populations. In this paper, we compare the
characteristics of lost habitats with currently accessible habitats and review the
heritability of traits which show correlations with habitat/environmental gradients.
We find that although there is some regional variation, inaccessible habitats
tend to be higher in elevation, wetter and both warmer in the summer and
colder in the winter than habitats currently available to anadromous salmonids.
We present several case studies that demonstrate either a change in phenotypic
or life history expression or an apparent reduction in genetic variation associated
with habitat blockages. These results suggest that loss of habitat will alter
evolutionary trajectories in salmonid populations and Evolutionarily Significant
Units. Changes in both selective regime and standing genetic diversity might
affect the ability of these taxa to respond to subsequent environmental perturbations.
Both natural and anthropogenic and should be considered seriously in
developing management and conservation strategies.},
keywords = {dams, differential habitat loss, evolutionary trajectory, genetic variation, Oncorhynchus},
pubstate = {published},
tppubtype = {article}
}
Large portions of anadromous salmonid habitat in the western United States
has been lost because of dams and other blockages. This loss has the potential
to affect salmonid evolution through natural selection if the loss is biased,
affecting certain types of habitat differentially, and if phenotypic traits correlated
with those habitat types are heritable. Habitat loss can also affect salmonid
evolution indirectly, by reducing genetic variation and changing its
distribution within and among populations. In this paper, we compare the
characteristics of lost habitats with currently accessible habitats and review the
heritability of traits which show correlations with habitat/environmental gradients.
We find that although there is some regional variation, inaccessible habitats
tend to be higher in elevation, wetter and both warmer in the summer and
colder in the winter than habitats currently available to anadromous salmonids.
We present several case studies that demonstrate either a change in phenotypic
or life history expression or an apparent reduction in genetic variation associated
with habitat blockages. These results suggest that loss of habitat will alter
evolutionary trajectories in salmonid populations and Evolutionarily Significant
Units. Changes in both selective regime and standing genetic diversity might
affect the ability of these taxa to respond to subsequent environmental perturbations.
Both natural and anthropogenic and should be considered seriously in
developing management and conservation strategies.
has been lost because of dams and other blockages. This loss has the potential
to affect salmonid evolution through natural selection if the loss is biased,
affecting certain types of habitat differentially, and if phenotypic traits correlated
with those habitat types are heritable. Habitat loss can also affect salmonid
evolution indirectly, by reducing genetic variation and changing its
distribution within and among populations. In this paper, we compare the
characteristics of lost habitats with currently accessible habitats and review the
heritability of traits which show correlations with habitat/environmental gradients.
We find that although there is some regional variation, inaccessible habitats
tend to be higher in elevation, wetter and both warmer in the summer and
colder in the winter than habitats currently available to anadromous salmonids.
We present several case studies that demonstrate either a change in phenotypic
or life history expression or an apparent reduction in genetic variation associated
with habitat blockages. These results suggest that loss of habitat will alter
evolutionary trajectories in salmonid populations and Evolutionarily Significant
Units. Changes in both selective regime and standing genetic diversity might
affect the ability of these taxa to respond to subsequent environmental perturbations.
Both natural and anthropogenic and should be considered seriously in
developing management and conservation strategies.