Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. DNA Extraction
2.3. Chloroplast DNA Sequencing and Polymorphism Discovery
2.4. HRM Experiments
2.5. Chloroplast Microsatellites
2.6. Data Analysis
3. Results
3.1. Chloroplast DNA Variation
3.2. Sufficiency of Haplotype Capture in a European Context
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
References
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Population | Location | Provenance | Lat., Long. | Samples/Haplotypes | Gene Diversity ± S.D. | Species |
---|---|---|---|---|---|---|
Alberes, Pyrenees Orientales | France | Wild | 42.48, 2.95 | 1/NA | 0.0000 ± 0.0000 | |
Annamarron | Monaghan, Ireland | Wild | 53.93, −6.66 | 11/2 | 0.1640 ± 0.0334 | |
Glenbeg (Coillte) | Scotland | Breeding | 56.69, −5.94 | 13/5 | 0.1982 ± 0.0210 | |
Brownstown Wood | Kilkenny, Ireland | Wild | 52.42, −7.03 | 11/2 | 0.0826 ± 0.0313 | |
Carnpark | Westmeath, Ireland | Wild | 53.42, −7.82 | 10/3 | 0.1450 ± 0.0373 | |
Cork (Coillte) | Cork, Ireland | Breeding | 51.94, −8.73 | 11/3 | 0.2025 ± 0.0229 | |
Scariff (Coillte) | Clare, Ireland | Breeding | 52.71, −2.76 | 19/4 | 0.0727 ± 0.0248 | |
Scottish (Coillte) | Scotland | Breeding | 52.96, −8.58 | 2/2 | 0.0625 ± 0.0313 | |
Shropshire/Shrewsbury (Coillte) | England | Breeding | 56.49, −4.2 | 20/5 | 0.1836 ± 0.0222 | |
Crappagh | Monaghan, Ireland | Wild | 54.14, −7.1 | 12/3 | 0.1985 ± 0.0217 | |
Cronybyrne | Wicklow, Ireland | Wild | 52.97, −6.25 | 11/3 | 0.1010 ± 0.0333 | |
Deputy’s Pass | Wicklow, Ireland | Wild | 52.95, −6.16 | 10/2 | 0.0675 ± 0.0303 | |
Derrygoul | Clare, Ireland | Wild | 52.91, −8.85 | 5/1 | 0.0000 ± 0.0000 | |
Derrysheridan | Meath, Ireland | Wild | 53.78, -7.33 | 14/2 | 0.0546 ± 0.0252 | |
Killarney | Kerry, Ireland | Wild | 51.98, −9.57 | 7/1 | 0.0000 ± 0.0000 | |
Lac des Camboux, Lozere, | France | Wild | 44.49, 3.58 | 2/1 | 0.1250 ± 0.0431 | |
Lough Gill, Slishwood | Sligo, Ireland | Wild | 54.24, −8.4 | 14/3 | 0.2777 ± 0.0331 | |
Lough Slevin | Westmeath, Ireland | Wild | 53.56, −7.32 | 8/4 | 0.1832 ± 0.0437 | |
Moods | Kildare, Ireland | Wild | 53.27, −6.79 | 8/4 | 0.2305 ± 0.0426 | |
Norway | Norway | Wild | 60.47, 8.47 | 2/1 | 0.0625 ± 0.0312 | |
Ongenstown wood | Meath, Ireland | Wild | 53.64, −6.82 | 8/4 | 0.2653 ± 0.0377 | |
Rostrevor forest | Down, Ireland | Wild | 54.11, −6.18 | 5/2 | 0.3556 ± 0.0452 | |
Scragh Bog | Westmeath, Ireland | Wild | 53.58, −7.36 | 10/2 | 0.0225 ± 0.0172 | |
Spain | Spain | Wild | 40.46, 3.75 | 1/1 | 0.0000 ± 0.0000 | |
Stormanstown Bog | Louth, Ireland | Wild | 53.88, −6.62 | 12/5 | 0.3212 ± 0.0289 | |
Sylaun | Galway, Ireland | Wild | 53.53, −8.93 | 13/5 | 0.3113 ± 0.0320 |
Primer | Region | Location a | Sequence (5′-3′) | Reference |
---|---|---|---|---|
trnC-f | trnC-D | 1–20 bp | CCAGTTCAAATCTGGGTGTC | [21] |
trnC_int_F | trnC-D | 708–734 bp | TCCAGGGGTGTATCTACGTATTTTGCT | This work |
CD_int_birch_seq1 | trnC-D | 1617–1590 bp | CTTACAATTCGAATTCCTAGAATTTCTG | This work |
psbMF_Shaw | trnC-D | 2068–2097bp | AGCAATAAATGCGAGAATATTTACTTCCAT | [22] |
Ag_trnC-D_indel_R | trnC-D | 2237–2215 bp | TCATGATATTGCTCCGATTCGAT | [19] |
CD_int_birch_seq2 | trnC-D | 3009–2985 bp | CTATACGTTTACAGGAGGCTATACA | This work |
trnD-M | trnC-D | 3408–3389 bp | GGGATTGTAGTTCAATTGGT | [21] |
psaA-f | psaA-trnS | 1-22 bp | ACTTCTGGTTCCGGCGAACGAA | [21] |
Birch_AS_indel1_b-F | psaA-trnS | 892–872 bp | TGGTTGAAGATCACAAGGCGT | This work |
Birch_AS_SNP3_R | psaA-trnS | 1076–1095 bp | CGGCTCAGCAGTCAATTCTT | This work |
Birch_AS_SNP3_F | psaA-trnS | 1275–1252 bp | GCTTTATTCTTCTAAAGGTGGGAA | This work |
Birch_AS_SNP2_F | psaA-trnS | 1845–1826 bp | AGGGCACTAGAACGAAACCC | This work |
Birch_AS_SNP1_F | psaA-trnS | 2292–2272 bp | TCCTGGAAATTAAGGGGTGCT | This work |
AS_int_birch_seq_1 | psaA-trnS | 2840–2816 bp | CCCAGATCTCGGATAAATGGAAATT | This work |
Tab_a | trnT-F | 1–20 bp | CATTACAAATGCGATGCTCT | [23] |
TF11_Rv | trnT-F | 633–610 bp | GTGTAATTTGAGATACTCGAACGG | This work |
Tab_b | trnT-F | 968–949 bp | TCTACCGATTTCGCCATATC | [23] |
trnL(UAA)h | trnT-F | 1155–1134 bp | CCATTGAGTCTCTGCACCTATC | [24] |
Tab_d | trnT-F | 1399–1380 bp | GGGGATAGAGGGACTTGAAC | [23] |
Tab_f | trnT-F | 1855–1836 bp | ATTTGAACTGGTGACACGAG | [23] |
Birch_AS_indel1_F b | psaA-trnS | 885–866 bp | AGATCACAAGGCGTTTCGAA | This work |
Birch_AS_indel1_R b | psaA-trnS | 693–712 bp | TGGGGACAACAAACAAAACT | This work |
Birch_CD_indel1_b-F b | trnC-D | 2575–2595 bp | AAGGAGAGTCCGGGTATAAAA | This work |
Birch_CD_indel1_b-R b | trnC-D | 2746–2725 bp | TCCAAAGAACAAAGAAATGGGA | This work |
trnC-D | psaA-trnS | ccmp5 | ccmp10 | ccmp6 | ccmp2 | ccmp4 | ccmp7 | Found in: | Frequency a | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
All | Pb | Pn | Un | ||||||||||
H1 | 1 | 1 | 105 | 118 | 100 | 205 | 117 | 147 | Ireland, England, Scotland, France, Norway | 115 | 94 | 20 | 1 |
H2 | 2 | 2 | 106 | 118 | 100 | 205 | 117 | 147 | Ireland, England, Scotland | 40 | 35 | 3 | 2 |
H3 | 1 | 1 | 105 | 118 | 100 | 205 | 118 | 147 | Ireland | 24 | 24 | 0 | 0 |
H4 | 2 | 2 | 108 | 118 | 100 | 205 | 117 | 154 | Ireland | 11 | 11 | 0 | 0 |
H5 | 2 | 1 | 106 | 118 | 100 | 205 | 117 | 147 | England, Scotland | 7 | 7 | 0 | 0 |
H6 | 2 | 1 | 105 | 118 | 100 | 205 | 118 | 147 | Ireland, England, Scotland | 5 | 2 | 3 | 0 |
H7 | 1 | 1 | 105 | 118 | 100 | 205 | 118 | 148 | Ireland | 4 | 4 | 0 | 0 |
H8 | 2 | 2 | 106 | 118 | 100 | 205 | 118 | 147 | Ireland | 2 | 2 | 0 | 0 |
H9 | 1 | 1 | 105 | 118 | 100 | 205 | 119 | 147 | Ireland | 2 | 2 | 0 | 0 |
H10 | 1 | 1 | 104 | 118 | 100 | 205 | 117 | 147 | Ireland | 1 | 0 | 1 | 0 |
H11 | 2 | 2 | 106 | 118 | 100 | 205 | 119 | 147 | Scotland | 1 | 0 | 1 | 0 |
H12 | 2 | 2 | 106 | 118 | 100 | 205 | 116 | 147 | England | 1 | 0 | 1 | 0 |
H13 | 2 | 2 | 105 | 118 | 100 | 205 | 117 | 154 | Spain | 1 | 0 | 0 | 1 |
H14 | 1 | 1 | 105 | 118 | 100 | 205 | 119 | 148 | Ireland | 1 | 1 | 0 | 0 |
H15 | 1 | 1 | 105 | 118 | 98 | 205 | 118 | 147 | Ireland | 1 | 1 | 0 | 0 |
H16 | 1 | 2 | 105 | 118 | 100 | 205 | 117 | 147 | Scotland | 1 | 1 | 0 | 0 |
hS | hT | GST | GST | |
---|---|---|---|---|
All species (n = 236/228 a) | 0.173 | 0.236 | 0.268 [0.214, 0.324] | 0.336 [0.276, 0.397] |
B. pubescens (n = 193/192 a) | 0.160 | 0.217 | 0.261 [0.205, 0.320] | 0.323 [0.259, 0.387] |
B. pendula (n = 29/20 a) | 0.136 | 0.144 | 0.056 [−0.042, 0.198] | 0.122 [−0.071, 0.356] |
Putative hybrid (n = 6/0 a) | NA | NA | NA | NA |
All Sites. | d.f. | SSD | Variance | Variance (%) | p value | |||||
Between sites | 20 | 98.56 | 0.33 | 19.16 | 0.015 | |||||
Species within sites | 8 | 11.94 | 0.03 | 1.58 | 0.301 | |||||
Within all | 183 | 251.07 | 1.37 | 79.25 | <0.001 | |||||
Total a | 211 | 361.57 | 1.73 | 100.00 | ||||||
Irish only | d.f. | SSD | Variance | Variance (%) | p value | |||||
N-S | E-W | N-S | E-W | N-S | E-W | N-S | E-W | N-S | E-W | |
Between | 1 | 1 | 15.82 | 0.65 | 0.13 | 0.00 | 7.03 | 0.00 | 0.034 | 1.000 |
Sites within | 17 | 17 | 74.50 | 89.66 | 0.33 | 0.42 | 18.18 | 23.92 | <0.001 | <0.001 |
Within all | 162 | 162 | 216.73 | 216.73 | 1.34 | 1.34 | 74.79 | 76.08 | <0.001 | <0.001 |
Total a | 180 | 180 | 307.04 | 307.04 | 1.79 | 1.76 | 100.00 | 100.00 |
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Belton, S.; Cubry, P.; Fox, E.; Kelleher, C.T. Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation. Forests 2021, 12, 1246. https://doi.org/10.3390/f12091246
Belton S, Cubry P, Fox E, Kelleher CT. Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation. Forests. 2021; 12(9):1246. https://doi.org/10.3390/f12091246
Chicago/Turabian StyleBelton, Samuel, Philippe Cubry, Erica Fox, and Colin T. Kelleher. 2021. "Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation" Forests 12, no. 9: 1246. https://doi.org/10.3390/f12091246
APA StyleBelton, S., Cubry, P., Fox, E., & Kelleher, C. T. (2021). Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation. Forests, 12(9), 1246. https://doi.org/10.3390/f12091246