Summary of several approaches to obtaining genotypes, including what each method may measure, when it might be used, some potential drawbacks, and a few references for further study
| Genotyping approach . | What can best be measured? . | Why or when to use it? . | Key drawbacks . | Ref. . |
|---|---|---|---|---|
| Restriction site-associated DNA sequencing (RAD-seq) | Genetic diversity metrics (FST, He), individual inbreeding, relatedness, hybridization & introgression, DNA methylation for epigenetic studies (BsRAD-seq). | 1) When first establishing genome resources for a species and/or large genome size, or no or poor genome reference, 2) low budget but need 1000s of loci, 3) to screen 1000s of loci to identify 100–5k informative loci ideal for your question. | Not as useful for measures of linkage disequilibrium (LD), local adaptation (if LD is low), or variation in coding regions. Data filtering greatly influences downstream population genetic inferences. | 1–9 |
| RAD capture | Same as above but for targeted markers discovered from a RAD-seq experiment. | For establishing longer term monitoring programs or subsequent research where many individuals will be genotyped (e.g., annually for monitoring). | Expensive initial investment for marker discovery with array design and purchase (but pays off if genotyping thousands of individuals with ~500–50 000 loci). | 10–12 |
| Targeted capture | Individual-based genetic diversity metrics, population- level allele frequencies, coding region variants, etc. | For sequencing or re-sequencing candidate genes or other regions, when high coverage for a subset of the genome, or repeated use of markers is needed. | Can be expensive to design and generate probes (but see ExCapSeq and EecSeq); need a reference sequence for probe design. | 13–15 |
| Whole-genome sequencing- low depth of coverage (<10X), including Pool-Seq | Population-level allele frequencies, with individuals barcoded or not (Pool-Seq) | When individual genotypes are not important, e.g., measuring population-level variation, genome- wide signatures of selection, identifying runs of homozygosity and inversions. | Expensive when genome size is large (e.g., >1.5 Gb), requires large sample sizes (30–50 at a minimum), Pool-Seq has no individual barcodes or genotypes. | 16–21 |
| Whole-genome sequencing—high depth of coverage (>10X) | Individual genotypes with high genome contiguity and fidelity. | Many uses, including building reference genome, individual genotype- level analyses, and characterization of structural variants. | Cost prohibitive when reference genome size is large (e.g., >1.5 Gb) or complicated to sequence (e.g., highly repetitive, high heterozygosity). | 22–23 |
| Genotyping approach . | What can best be measured? . | Why or when to use it? . | Key drawbacks . | Ref. . |
|---|---|---|---|---|
| Restriction site-associated DNA sequencing (RAD-seq) | Genetic diversity metrics (FST, He), individual inbreeding, relatedness, hybridization & introgression, DNA methylation for epigenetic studies (BsRAD-seq). | 1) When first establishing genome resources for a species and/or large genome size, or no or poor genome reference, 2) low budget but need 1000s of loci, 3) to screen 1000s of loci to identify 100–5k informative loci ideal for your question. | Not as useful for measures of linkage disequilibrium (LD), local adaptation (if LD is low), or variation in coding regions. Data filtering greatly influences downstream population genetic inferences. | 1–9 |
| RAD capture | Same as above but for targeted markers discovered from a RAD-seq experiment. | For establishing longer term monitoring programs or subsequent research where many individuals will be genotyped (e.g., annually for monitoring). | Expensive initial investment for marker discovery with array design and purchase (but pays off if genotyping thousands of individuals with ~500–50 000 loci). | 10–12 |
| Targeted capture | Individual-based genetic diversity metrics, population- level allele frequencies, coding region variants, etc. | For sequencing or re-sequencing candidate genes or other regions, when high coverage for a subset of the genome, or repeated use of markers is needed. | Can be expensive to design and generate probes (but see ExCapSeq and EecSeq); need a reference sequence for probe design. | 13–15 |
| Whole-genome sequencing- low depth of coverage (<10X), including Pool-Seq | Population-level allele frequencies, with individuals barcoded or not (Pool-Seq) | When individual genotypes are not important, e.g., measuring population-level variation, genome- wide signatures of selection, identifying runs of homozygosity and inversions. | Expensive when genome size is large (e.g., >1.5 Gb), requires large sample sizes (30–50 at a minimum), Pool-Seq has no individual barcodes or genotypes. | 16–21 |
| Whole-genome sequencing—high depth of coverage (>10X) | Individual genotypes with high genome contiguity and fidelity. | Many uses, including building reference genome, individual genotype- level analyses, and characterization of structural variants. | Cost prohibitive when reference genome size is large (e.g., >1.5 Gb) or complicated to sequence (e.g., highly repetitive, high heterozygosity). | 22–23 |
Note that some methods (e.g., RNA-Seq, BsRAD-Seq, Methyl-Seq) are not discussed here. References: 1) Miller et al. 2007; 2) Baird et al. 2008; 3) Hohenlohe et al. 2010; 4) Hoffman et al. 2014; 5) Andrews et al. 2016; 6) Kovach et al. 2016; 7) McKinney et al. 2017; 8) Shafer et al. 2017; 9) Marconi et al. 2019; 10) Ali et al. 2016; 11) Hoffberg et al. 2016; 12) Kelson et al. 2020; 13) Jones & Good 2016; 14) Hendricks, et al. 2018b; 15) Puritz & Lotterhos 2018; 16) Ekblom & Wolf 2014; 17) Therkildsen & Palumbi 2017; 18) Kofler et al. 2011; 19) Schlötterer, et al. 2014; 20) Kardos et al. 2015; 21) Micheletti & Narum 2018; 22) Koepfli et al. 2019; and 23) Wright et al. 2020.
Summary of several approaches to obtaining genotypes, including what each method may measure, when it might be used, some potential drawbacks, and a few references for further study
| Genotyping approach . | What can best be measured? . | Why or when to use it? . | Key drawbacks . | Ref. . |
|---|---|---|---|---|
| Restriction site-associated DNA sequencing (RAD-seq) | Genetic diversity metrics (FST, He), individual inbreeding, relatedness, hybridization & introgression, DNA methylation for epigenetic studies (BsRAD-seq). | 1) When first establishing genome resources for a species and/or large genome size, or no or poor genome reference, 2) low budget but need 1000s of loci, 3) to screen 1000s of loci to identify 100–5k informative loci ideal for your question. | Not as useful for measures of linkage disequilibrium (LD), local adaptation (if LD is low), or variation in coding regions. Data filtering greatly influences downstream population genetic inferences. | 1–9 |
| RAD capture | Same as above but for targeted markers discovered from a RAD-seq experiment. | For establishing longer term monitoring programs or subsequent research where many individuals will be genotyped (e.g., annually for monitoring). | Expensive initial investment for marker discovery with array design and purchase (but pays off if genotyping thousands of individuals with ~500–50 000 loci). | 10–12 |
| Targeted capture | Individual-based genetic diversity metrics, population- level allele frequencies, coding region variants, etc. | For sequencing or re-sequencing candidate genes or other regions, when high coverage for a subset of the genome, or repeated use of markers is needed. | Can be expensive to design and generate probes (but see ExCapSeq and EecSeq); need a reference sequence for probe design. | 13–15 |
| Whole-genome sequencing- low depth of coverage (<10X), including Pool-Seq | Population-level allele frequencies, with individuals barcoded or not (Pool-Seq) | When individual genotypes are not important, e.g., measuring population-level variation, genome- wide signatures of selection, identifying runs of homozygosity and inversions. | Expensive when genome size is large (e.g., >1.5 Gb), requires large sample sizes (30–50 at a minimum), Pool-Seq has no individual barcodes or genotypes. | 16–21 |
| Whole-genome sequencing—high depth of coverage (>10X) | Individual genotypes with high genome contiguity and fidelity. | Many uses, including building reference genome, individual genotype- level analyses, and characterization of structural variants. | Cost prohibitive when reference genome size is large (e.g., >1.5 Gb) or complicated to sequence (e.g., highly repetitive, high heterozygosity). | 22–23 |
| Genotyping approach . | What can best be measured? . | Why or when to use it? . | Key drawbacks . | Ref. . |
|---|---|---|---|---|
| Restriction site-associated DNA sequencing (RAD-seq) | Genetic diversity metrics (FST, He), individual inbreeding, relatedness, hybridization & introgression, DNA methylation for epigenetic studies (BsRAD-seq). | 1) When first establishing genome resources for a species and/or large genome size, or no or poor genome reference, 2) low budget but need 1000s of loci, 3) to screen 1000s of loci to identify 100–5k informative loci ideal for your question. | Not as useful for measures of linkage disequilibrium (LD), local adaptation (if LD is low), or variation in coding regions. Data filtering greatly influences downstream population genetic inferences. | 1–9 |
| RAD capture | Same as above but for targeted markers discovered from a RAD-seq experiment. | For establishing longer term monitoring programs or subsequent research where many individuals will be genotyped (e.g., annually for monitoring). | Expensive initial investment for marker discovery with array design and purchase (but pays off if genotyping thousands of individuals with ~500–50 000 loci). | 10–12 |
| Targeted capture | Individual-based genetic diversity metrics, population- level allele frequencies, coding region variants, etc. | For sequencing or re-sequencing candidate genes or other regions, when high coverage for a subset of the genome, or repeated use of markers is needed. | Can be expensive to design and generate probes (but see ExCapSeq and EecSeq); need a reference sequence for probe design. | 13–15 |
| Whole-genome sequencing- low depth of coverage (<10X), including Pool-Seq | Population-level allele frequencies, with individuals barcoded or not (Pool-Seq) | When individual genotypes are not important, e.g., measuring population-level variation, genome- wide signatures of selection, identifying runs of homozygosity and inversions. | Expensive when genome size is large (e.g., >1.5 Gb), requires large sample sizes (30–50 at a minimum), Pool-Seq has no individual barcodes or genotypes. | 16–21 |
| Whole-genome sequencing—high depth of coverage (>10X) | Individual genotypes with high genome contiguity and fidelity. | Many uses, including building reference genome, individual genotype- level analyses, and characterization of structural variants. | Cost prohibitive when reference genome size is large (e.g., >1.5 Gb) or complicated to sequence (e.g., highly repetitive, high heterozygosity). | 22–23 |
Note that some methods (e.g., RNA-Seq, BsRAD-Seq, Methyl-Seq) are not discussed here. References: 1) Miller et al. 2007; 2) Baird et al. 2008; 3) Hohenlohe et al. 2010; 4) Hoffman et al. 2014; 5) Andrews et al. 2016; 6) Kovach et al. 2016; 7) McKinney et al. 2017; 8) Shafer et al. 2017; 9) Marconi et al. 2019; 10) Ali et al. 2016; 11) Hoffberg et al. 2016; 12) Kelson et al. 2020; 13) Jones & Good 2016; 14) Hendricks, et al. 2018b; 15) Puritz & Lotterhos 2018; 16) Ekblom & Wolf 2014; 17) Therkildsen & Palumbi 2017; 18) Kofler et al. 2011; 19) Schlötterer, et al. 2014; 20) Kardos et al. 2015; 21) Micheletti & Narum 2018; 22) Koepfli et al. 2019; and 23) Wright et al. 2020.
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