Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Species and Sampling
2.2. DNA Extraction, Sequencing and Filtering
2.3. SNP Calling
2.4. Genetic Structure Analysis
2.5. Genetic Diversity and Inbreeding Analysis
2.6. Redundancy Analysis
3. Results
3.1. Genetic Structure Analysis
3.2. Genetic Diversity and Inbreeding
4. Discussion
4.1. Genetic Structure and Sources of Genetic Variation
4.2. Opportunistic Test of Admixture on Genetic Diversity
4.3. Genetic Diversity and Inbreeding
4.4. Management Recommendations
5. Concluding Remarks
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Appendix A
Collection Stand | Habitat Type | Census Count | n | Land Use History |
---|---|---|---|---|
Marshalls Road | Roadside vegetation. | 42 reveg. | 12 | Road reserve. Control burn in 2018 resulted in A. whibleyana plants emerging post fire. |
100+ seedlings | 44 | |||
Quarry | Post-disturbance regeneration in disused quarry, surrounded by remnant eucalypt woodland | 189 remnant | 15 | Council-owned land. Quarried up to 1950’s, stockpiling gravel then woodchips (to 1993). |
Southerns | Remnant eucalypt woodland. | 59 remnant | 39 | Private land. 40ha fenced to exclude stock in May 2012. |
8 reveg. | 5 | |||
Mount Liverpool | Remnant eucalypt woodland. | 50 remnant | 14 | Private land subdivided for rural living & stock removed 2005. |
Foothills Road | Roadside vegetation. | 17 remnant | 13 | Road reserve, burnt in 2005 bushfires. A. whibleyana plants emerged post fire. |
Sebs Patch | Remnant chenopod scrub along salt-scalded drainage line and salt lake. | 107 remnant | 24 | Private land under different land management regimes (grazed by sheep intermittently, a small portion fenced & revegetated) |
Salt Lake | Remnant chenopod scrub adjacent to salt lake. | 137 remnant | 14 | Council-owned land of road intersection, fenced in 1995 to exclude vehicles and rabbits. |
26 reveg. | 25 | |||
Moonlight Bay | Remnant mallee woodland on salt lake lunettes. | 557 remnant | 23 | Private land. Approx. one third of population fenced from stock. Remainder accessible to sheep on intermittent basis. Area around salt lake burnt in 2005 bushfires. |
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Collection Stand | Marshalls Rd | Marshalls Rd Seedlings | Quarry | Southerns Remnant | Southerns reveg. | Mt Liverpool | Foothills | Sebs Patch | Salt Lake remnant | Salt Lake reveg. | Moonlight Bay |
---|---|---|---|---|---|---|---|---|---|---|---|
Marshalls Rd | 0 | ||||||||||
Marshalls Rd seedlings | −0.008 | 0 | |||||||||
Quarry | 0.017 | 0.032 | 0 | ||||||||
Southerns remnant | 0.090 | 0.101 | 0.087 | 0 | |||||||
Southerns reveg. | 0.101 | 0.114 | 0.101 | 0.013 | 0 | ||||||
Mt Liverpool | 0.156 | 0.158 | 0.153 | 0.122 | 0.145 | 0 | |||||
Foothills | 0.192 | 0.193 | 0.189 | 0.147 | 0.176 | 0.185 | 0 | ||||
Sebs Patch | 0.109 | 0.117 | 0.111 | 0.083 | 0.090 | 0.104 | 0.134 | 0 | |||
Salt Lake remnant | 0.088 | 0.099 | 0.097 | 0.073 | 0.077 | 0.100 | 0.129 | 0.037 | 0 | ||
Salt Lake reveg. | 0.115 | 0.123 | 0.126 | 0.097 | 0.104 | 0.122 | 0.148 | 0.061 | 0.000 | 0 | |
Moonlight Bay | 0.136 | 0.145 | 0.137 | 0.111 | 0.116 | 0.135 | 0.161 | 0.084 | 0.075 | 0.097 | 0 |
Source of Variation | Nested in | %var | F-Value | SD | c.i.95% |
---|---|---|---|---|---|
Within Individual | - | 73.6 | 0.263 | 0.002 | ±0.004 |
Among Individual | Collection stand | 15.7 | 0.175 | 0.002 | ±0.004 |
Among Population | 10.7 | 0.107 | 0.001 | ±0.002 |
Collection Stand | Status | n | HO | HE | F | Kinship |
---|---|---|---|---|---|---|
All stands | ||||||
Marshalls Rd | Translocation | 12 | 0.114 (0.111 to 0.116) b,c | 0.137 (0.135 to 0.140) c,d | 0.173 (0.163 to 0.182) b | −0.008 (0.018 to −0.027) a,b |
Marshalls Rd seedlings (all) | Seedlings | 44 | 0.107 (0.105 to 0.109) a,b | 0.131 (0.128 to 0.133) b | 0.183 (0.176 to 0.189) b | 0.001 (0.003 to −0.002) a |
Quarry | Remnant | 15 | 0.111 (0.109 to 0.114) b | 0.136 (0.134 to 0.139) c,d | 0.183 (0.174 to 0.192) b | 0.004 (0.011 to −0.003) a |
Southerns remnant | Remnant | 39 | 0.118 (0.116 to 0.121) c | 0.145 (0.142 to 0.147) d | 0.183 (0.177 to 0.189) b | 0.000 (0.003 to −0.003) a |
Southerns reveg. | Revegetation | 5 | 0.118 (0.115 to 0.121) c | 0.140 (0.137 to 0.143) c,d | 0.157 (0.143 to 0.170) b | 0.006 (0.043 to −0.031) a,b |
Mt Liverpool | Remnant | 14 | 0.109 (0.107 to 0.112) b | 0.123 (0.120 to 0.126) a | 0.110 (0.100 to 0.121) a | 0.009 (0.026 to −0.007) a |
Foothills | Remnant | 13 | 0.102 (0.099 to 0.105) a | 0.117 (0.114 to 0.120) a | 0.130 (0.119 to 0.141) a | 0.008 (0.023 to −0.006) a |
Sebs Patch | Remnant | 24 | 0.109 (0.107 to 0.111) b | 0.138 (0.136 to 0.141) c,d | 0.211 (0.204 to 0.218) c | 0.001 (0.006 to −0.003) a |
Salt Lake remnant | Remnant | 14 | 0.110 (0.108 to 0.112) b | 0.141 (0.139 to 0.144) d | 0.221 (0.212 to 0.229) c | −0.011 (−0.008 to −0.014) b |
Salt Lake reveg. | Revegetation | 25 | 0.117 (0.115 to 0.120) b,c | 0.138 (0.136 to 0.141) c,d | 0.151 (0.144 to 0.159) b | 0.001 (0.009 to −0.006) a |
Moonlight Bay | Remnant | 23 | 0.104 (0.102 to 0.106) a | 0.135 (0.132 to 0.137) b,c | 0.226 (0.219 to 0.234) c | −0.004 (0.000 to −0.008) a,b |
Marshalls Rd focus | ||||||
Marshalls Rd adults | Translocation | 12 | 0.114 (0.111 to 0.116) b | 0.137 (0.135 to 0.140) b | 0.173 (0.163 to 0.182) b | −0.008 (0.018 to −0.027) a |
Marshalls Rd seedlings (non-admixed only) | Seedlings | 34 | 0.103 (0.101 to 0.106) a | 0.126 (0.124 to 0.129) a | 0.181 (0.173 to 0.188) b | 0.008 (0.010 to −0.002) a |
Marshalls Rd seedlings (admixed only) | Seedlings | 10 | 0.120 (0.117 to 0.123) c | 0.125 (0.122 to 0.127) a | 0.036 (0.023 to 0.049) a | 0.117 (0.122 to −0.005) a |
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Share and Cite
Blyth, C.; Christmas, M.J.; Bickerton, D.C.; Faast, R.; Packer, J.G.; Lowe, A.J.; Breed, M.F. Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction. Diversity 2020, 12, 299. https://doi.org/10.3390/d12080299
Blyth C, Christmas MJ, Bickerton DC, Faast R, Packer JG, Lowe AJ, Breed MF. Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction. Diversity. 2020; 12(8):299. https://doi.org/10.3390/d12080299
Chicago/Turabian StyleBlyth, Colette, Matthew J. Christmas, Doug C. Bickerton, Renate Faast, Jasmin G. Packer, Andrew J. Lowe, and Martin F. Breed. 2020. "Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction" Diversity 12, no. 8: 299. https://doi.org/10.3390/d12080299
APA StyleBlyth, C., Christmas, M. J., Bickerton, D. C., Faast, R., Packer, J. G., Lowe, A. J., & Breed, M. F. (2020). Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction. Diversity, 12(8), 299. https://doi.org/10.3390/d12080299