Sampling data, colony runfiles, VCFs, and Rscripts for: genomic determination of reproductive mode in facultatively parthenogenetic Opiliones
Data files
Oct 29, 2020 version files 18.96 MB
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                Brownetal_Sampling.xlsx
                100.10 KB
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                globo_error.txt
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                globo_ExclMat.txt
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                globo_ExclSib.txt
                3.78 KB
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                globo_Matsibships.txt
                266 B
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                Globo211.txt
                50.46 KB
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                Globo422.txt
                58.76 KB
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                Globo423.txt
                49.99 KB
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                globoAlleleFreq.txt
                7.77 KB
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                heterozygheredity.R
                28.04 KB
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                Hsglobo.csv
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                HsLm1_named.csv
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                HsLm2_named.csv
                6.28 KB
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                HsLm3_named.csv
                960 B
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                HsLm4_named.csv
                1.05 KB
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                HsLm5_named.csv
                1.88 KB
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                HsLm6_named.csv
                729 B
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                HsLm7_named.csv
                1.71 KB
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                HsLm8_named.csv
                5.22 KB
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                HsLmGBS_named.csv
                1.49 KB
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                Hstoho.csv
                8.19 KB
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                Lg25_Jheredity.snps.vcf
                134.74 KB
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                Lm_80_2015.vcf
                2.88 MB
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                Lm103-115.snps.vcf
                654.35 KB
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                Lm116.snps.vcf
                353.59 KB
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                Lm118-120.snps.vcf
                321.80 KB
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                Lm119clutch.txt
                44.34 KB
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                Lm201-507.snps.vcf
                1.04 MB
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                Lm511-513.snps.vcf
                619.57 KB
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                Lm514-515.snps.vcf
                95.26 KB
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                Lm518-520.snps.vcf
                374.54 KB
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                LmGBS1.txt
                410.40 KB
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                LmGBS13.txt
                155.94 KB
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                LmGBS17.txt
                137.05 KB
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                LmGBS20.txt
                120.69 KB
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                LmGBS3.txt
                721.54 KB
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                LmGBS4.txt
                501.22 KB
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                LmGBS5.txt
                575.01 KB
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                LmGBS6.txt
                933.48 KB
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                Lt_80p3_MatGenotypes.txt
                14.79 KB
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                Lt_80p3_Offspring.txt
                498.49 KB
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                Lt80p3_Jheredity.snps.vcf
                1.31 MB
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                matLg.txt
                10.40 KB
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                offLg.txt
                45.83 KB
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                populations103.snps.vcf
                43.96 KB
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                populations108.snps.vcf
                150.86 KB
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                populations109.snps.vcf
                108.55 KB
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                populations110.snps.vcf
                96.61 KB
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                populations111.snps.vcf
                99.89 KB
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                populations112.snps.vcf
                48.64 KB
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                populations114.snps.vcf
                128.84 KB
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                populations115.snps.vcf
                111.99 KB
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                populations116.snps.vcf
                211.29 KB
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                populations118.snps.vcf
                214.73 KB
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                populations119.snps.vcf
                45.06 KB
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                populations120.snps.vcf
                85.67 KB
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                populations201.snps.vcf
                148.37 KB
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                populations202.snps.vcf
                121 KB
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                populations203.snps.vcf
                187.42 KB
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                populations204.snps.vcf
                98.26 KB
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                populations205.snps.vcf
                105.82 KB
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                populations206.snps.vcf
                143.16 KB
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                populations208.snps.vcf
                108.12 KB
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                populations504.snps.vcf
                153.04 KB
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                populations507.snps.vcf
                310.29 KB
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                populations511.snps.vcf
                251.66 KB
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                populations513.snps.vcf
                369.51 KB
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                populations514.snps.vcf
                38.57 KB
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                populations515.snps.vcf
                64.43 KB
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                populations518.snps.vcf
                282.50 KB
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                populations520.snps.vcf
                105.10 KB
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                populations521.snps.vcf
                457.35 KB
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                populations524.snps.vcf
                614.50 KB
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                Toho_80p3_allelefreq.txt
                10.31 KB
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                Toho_80p3_error.txt
                9.11 KB
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                Toho_80p3_ExclMat.txt
                10.69 KB
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                Toho_80p3_Exclsibs.txt
                362.93 KB
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                Toho_80p3_matsibships.txt
                2.35 KB
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                Toho301.vcf
                340.07 KB
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                Toho302.txt
                94.86 KB
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                Toho303.txt
                146.58 KB
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                Toho306.txt
                247.93 KB
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                Toho307.txt
                274.60 KB
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                Toho312.txt
                265.41 KB
Nov 02, 2020 version files 21.86 MB
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                Brownetal_Sampling.xlsx
                100.10 KB
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                DamsFor511-513_518-524.txt
                210.16 KB
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                DamsFor516.txt
                14.08 KB
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                globo_error.txt
                10.75 KB
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                globo_ExclMat.txt
                1 KB
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                globo_ExclSib.txt
                3.78 KB
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                globo_Matsibships.txt
                266 B
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                Globo211.txt
                50.46 KB
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                Globo422.txt
                58.76 KB
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                Globo423.txt
                49.99 KB
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                globoAlleleFreq.txt
                7.77 KB
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                heterozygheredity.R
                28.04 KB
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                Hsglobo.csv
                1.03 KB
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                HsLm1_named.csv
                2.08 KB
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                HsLm2_named.csv
                6.28 KB
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                HsLm3_named.csv
                960 B
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                HsLm4_named.csv
                1.05 KB
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                HsLm5_named.csv
                1.88 KB
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                HsLm6_named.csv
                729 B
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                HsLm7_named.csv
                1.71 KB
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                HsLm8_named.csv
                5.22 KB
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                HsLmGBS_named.csv
                1.49 KB
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                Hstoho.csv
                8.19 KB
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                Lg25_Jheredity.snps.vcf
                134.74 KB
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                Lm_80_2015.vcf
                2.88 MB
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                Lm103-115.snps.vcf
                654.35 KB
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                Lm116.snps.vcf
                353.59 KB
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                Lm118-120.snps.vcf
                321.80 KB
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                Lm119clutch.txt
                44.34 KB
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                Lm201-507.snps.vcf
                1.04 MB
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                Lm511-513.snps.vcf
                619.57 KB
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                Lm514-515.snps.vcf
                95.26 KB
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                Lm518-520.snps.vcf
                374.54 KB
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                LmGBS1.txt
                410.40 KB
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                LmGBS13.txt
                155.94 KB
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                LmGBS17.txt
                137.05 KB
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                LmGBS20.txt
                120.69 KB
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                LmGBS3.txt
                721.54 KB
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                LmGBS4.txt
                501.22 KB
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                LmGBS5.txt
                575.01 KB
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                LmGBS6.txt
                933.48 KB
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                Lt_80p3_MatGenotypes.txt
                14.79 KB
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                Lt_80p3_Offspring.txt
                498.49 KB
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                Lt80p3_Jheredity.snps.vcf
                1.31 MB
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                markers.error.103-115.txt
                11.22 KB
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                markers.error.118-120.txt
                3.50 KB
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                markers.error.201-507.txt
                18.98 KB
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                markers.error.511-513.txt
                31.34 KB
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                markers.error.514-515.txt
                2.62 KB
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                markers.error.516.txt
                2.46 KB
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                markers.error.518-520.txt
                4.70 KB
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                markers.error.521-524.txt
                27.27 KB
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                markers.error.all.combined.txt
                78.44 KB
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                markers.error.total.511-513_518-524.txt
                38.25 KB
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                matLg.txt
                10.40 KB
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                offLg.txt
                45.83 KB
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                populations103.snps.vcf
                43.96 KB
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                populations108.snps.vcf
                150.86 KB
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                populations109.snps.vcf
                108.55 KB
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                populations110.snps.vcf
                96.61 KB
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                populations111.snps.vcf
                99.89 KB
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                populations112.snps.vcf
                48.64 KB
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                populations114.snps.vcf
                128.84 KB
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                populations115.snps.vcf
                111.99 KB
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                populations116.snps.vcf
                211.29 KB
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                populations118.snps.vcf
                214.73 KB
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                populations119.snps.vcf
                45.06 KB
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                populations120.snps.vcf
                85.67 KB
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                populations201.snps.vcf
                148.37 KB
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                populations202.snps.vcf
                121 KB
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                populations203.snps.vcf
                187.42 KB
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                populations204.snps.vcf
                98.26 KB
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                populations205.snps.vcf
                105.82 KB
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                populations206.snps.vcf
                143.16 KB
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                populations208.snps.vcf
                108.12 KB
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                populations504.snps.vcf
                153.04 KB
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                populations507.snps.vcf
                310.29 KB
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                populations511.snps.vcf
                251.66 KB
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                populations513.snps.vcf
                369.51 KB
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                populations514.snps.vcf
                38.57 KB
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                populations515.snps.vcf
                64.43 KB
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                populations518.snps.vcf
                282.50 KB
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                populations520.snps.vcf
                105.10 KB
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                populations521.snps.vcf
                457.35 KB
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                populations524.snps.vcf
                614.50 KB
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                Toho_80p3_allelefreq.txt
                10.31 KB
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                Toho_80p3_error.txt
                9.11 KB
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                Toho_80p3_ExclMat.txt
                10.69 KB
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                Toho_80p3_Exclsibs.txt
                362.93 KB
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                Toho_80p3_matsibships.txt
                2.35 KB
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                Toho301.vcf
                340.07 KB
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                Toho302.txt
                94.86 KB
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                Toho303.txt
                146.58 KB
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                Toho306.txt
                247.93 KB
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                Toho307.txt
                274.60 KB
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                Toho312.txt
                265.41 KB
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                VCF_converted_all_dams.txt
                409.36 KB
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                VCF_convertedmatpopulation518.txt
                969 B
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                VCF_convertedmatpopulation518.xlsx
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                vcf_convertedmatpopulations103-115.snps.txt
                15.91 KB
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                vcf_convertedmatpopulations118-120.snps.txt
                2.19 KB
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                vcf_convertedmatpopulations201-507.snps.txt
                42.08 KB
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                vcf_convertedmatpopulations511-513.snps.txt
                12.38 KB
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                vcf_convertedmatpopulations514-515.snps.txt
                1.11 KB
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                vcf_convertedmatpopulations516.snps.txt
                521 B
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                vcf_convertedmatpopulations518-520.snps.txt
                969 B
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                vcf_convertedmatpopulations521-524.snps.txt
                16.24 KB
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                vcf_convertedoffpopulations103-116.snps.txt
                245.77 KB
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                vcf_convertedoffpopulations118-120.snps.txt
                125.19 KB
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                vcf_convertedoffpopulations201-507.snps.txt
                512.88 KB
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                vcf_convertedoffpopulations511-513.snps.txt
                359.11 KB
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                vcf_convertedoffpopulations514-515.snps.txt
                35.57 KB
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                vcf_convertedoffpopulations516.snps.txt
                60.27 KB
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                vcf_convertedoffpopulations518-520.snps.txt
                42.76 KB
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                vcf_convertedoffpopulations521-524.snps.txt
                563.25 KB
Abstract
Sexual reproduction may pose myriad short-term costs to females. Despite these costs, sexual reproduction is near ubiquitous. Facultative parthenogenesis is theorized to mitigate some of the costs of sex, as individuals can participate in occasional sex to limit costs while obtaining many benefits. However, most theoretical models assume sexual reproduction is fixed following mating, with no possibility of clutches of mixed reproductive ontogeny. Therefore, we asked: if coercive males are present at high frequency in a population of facultative parthenogens, will their clutches be solely sexually produced, or will there be evidence of sexually and asexually-produced offspring? How will their offspring production compare to conspecifics in low frequency male populations? We addressed our questions by collecting females and egg clutches of the facultatively parthenogenetic Opiliones species Leiobunum manubriatum and L. globosum. In L. manubriatum, females from populations with few males were not significantly more fecund than females from populations with higher male relative frequency, despite the potential release of the former from sexual conflict. We used three genotyping methods along with a custom set of DNA capture probes to reveal that offspring of L. manubriatum from these high male populations were primarily produced via asexual reproduction. This is surprising because sex ratios in these southern populations approach equality, increasing the probability for females to encounter mates and produce offspring sexually. We additionally found evidence for reproductive polymorphisms within populations. Rapid and accurate SNP genotyping data will continue to allow us to address broader evolutionary questions regarding the role of facultative reproductive modes in the maintenance of sex.
