ABCMdb

PMID: 22768049

Hunemeier T, Amorim CE, Azevedo S, Contini V, Acuna-Alonzo V, Rothhammer F, Dugoujon JM, Mazieres S, Barrantes R, Villarreal-Molina MT, Paixao-Cortes VR, Salzano FM, Canizales-Quinteros S, Ruiz-Linares A, Bortolini MC
Evolutionary responses to a constructed niche: ancient Mesoamericans as a model of gene-culture coevolution.
PLoS One. 2012;7(6):e38862. Epub 2012 Jun 21., [PubMed]

Sentences

No. Mutations Sentence Comment

33 ABCA1 p.Arg230Cys Other examples are related to the coevolution of genes and languages [19,20], but only two more recently reported examples might be associated with positive selection: (1) Tovo-Rodrigues et al. [21] investigated the distribution of D4 dopamine receptor (DRD4) alleles in several South Amerindian populations and found a significant difference in the allelic distributions between hunter-gatherers and agriculturalists, with an increase of the 7R allele among the former; and (2) Acun˜a-Alonzo et al. [22] showed that the 230Cys allele (Arg230Cys, rs9282541) of the ATP-binding cassette transporter A1 (ABCA1) gene, which was previously associated with low HDL-cholesterol levels and obesity-related comorbidities, was exclusively present in Native American and mestizo individuals. Login to comment 34 ABCA1 p.Arg230Cys Other examples are related to the coevolution of genes and languages [19,20], but only two more recently reported examples might be associated with positive selection: (1) Tovo-Rodrigues et al. [21] investigated the distribution of D4 dopamine receptor (DRD4) alleles in several South Amerindian populations and found a significant difference in the allelic distributions between hunter-gatherers and agriculturalists, with an increase of the 7R allele among the former; and (2) Acun dc;a-Alonzo et al. [22] showed that the 230Cys allele (Arg230Cys, rs9282541) of the ATP-binding cassette transporter A1 (ABCA1) gene, which was previously associated with low HDL-cholesterol levels and obesity-related comorbidities, was exclusively present in Native American and mestizo individuals. Login to comment 40 ABCA1 p.Arg230Cys Here, we expand the investigations of the Arg230Cys polymorphism in Native Americans and integrate the thrifty genotype concept with the gene-culture coevolution process, considering the human ability to create new ecological niches that may lead to the selection of genetic variants. Login to comment 41 ABCA1 p.Arg230Cys ABCA1 p.Arg230Cys Materials and Methods (a) Populations New data for the Arg230Cys polymorphism were generated for 19 Amerindian populations (n = 229) from Meso/Central America and South America (Table 1). Login to comment 42 ABCA1 p.Arg230Cys Materials and Methods (a) Populations New data for the Arg230Cys polymorphism were generated for 19 Amerindian populations (n = 229) from Meso/Central America and South America (Table 1). Login to comment 43 ABCA1 p.Arg230Cys These new Arg230Cys data were then analyzed together with those of an earlier published report [22], providing a total of 1905 investigated individuals. Login to comment 44 ABCA1 p.Arg230Cys These new Arg230Cys data were then analyzed together with those of an earlier published report [22], providing a total of 1905 investigated individuals. Login to comment 52 ABCA1 p.Arg230Cys (b) SNP Genotyping and Intra-and Inter-subdivision Structures The Arg230Cys polymorphism was genotyped using TaqMan assays (ABI Prism 7900HT Sequence Detection System; Applied Biosystems). Login to comment 53 ABCA1 p.Arg230Cys (b) SNP Genotyping and Intra-and Inter-subdivision Structures The Arg230Cys polymorphism was genotyped using TaqMan assays (ABI Prism 7900HT Sequence Detection System; Applied Biosystems). Login to comment 58 ABCA1 p.Arg230Cys Population N1 Genotype frequency Allele frequency Country Geographical coordinates References Arg 230 Arg Arg 230 Cys Cys 230 Cys Arg230 230Cys Mesoamerican agriculturalist2 (1218) Yaqui 45 30 11 4 0.79 0.21 Mexico 27u 299 N 110u 409 W Acun˜a-Alonzo et al. (2010) Tarahumara 109 81 23 5 0.85 0.15 Mexico 26u 499 N 107u 049 W Acun˜a-Alonzo et al. (2010) Teenek 67 45 20 2 0.82 0.18 Mexico 21u 369 N 98u 589 W Acun˜a-Alonzo et al. (2010) Cora 123 62 51 10 0.71 0.29 Mexico 22u 39 N 104u 559 W Acun˜a-Alonzo et al. (2010) Purepecha 35 22 11 2 0.79 0.21 Mexico 19u 369 N 102u 149 W Acun˜a-Alonzo et al. (2010) Mazahua 83 68 15 0 0.91 0.09 Mexico 19u 269 N 100u 009 W Acun˜a-Alonzo et al. (2010) Mixe 19 15 4 0 0.89 0.11 Mexico 17u N 96uW Present study Mixtec 4 4 0 0 1.00 0.00 Mexico 17u N 97uW Present study Nahuatl 267 185 73 9 0.83 0.17 Mexico 19u 589 N 97u 379 W Acun˜a-Alonzo et al. (2010) Totonaco 113 86 24 3 0.87 0.13 Mexico 19u 579 N 97u 449 W Acun˜a-Alonzo et al. (2010) Otomı´es 42 35 7 0 0.92 0.08 Mexico 20u 289 N 99u 139 W Acun˜a-Alonzo et al. (2010) Zapotec 125 71 50 4 0.76 0.24 Mexico 17u149 N 96u149 W Present study; Acun˜a-Alonzo et al. (2010) Mayan 110 68 39 3 0.80 0.20 Mexico 20u139 N 90u289 W Acun˜a-Alonzo et al. (2010) Kaqchikel-Quiche 17 13 3 1 0.85 0.15 Guatemala 15u N 91uW Present study Cabecar 24 19 5 0 0.90 0.10 Costa Rica 9u 309 N 84uW Present study Guaymı´ 35 26 8 1 0.85 0.15 Costa Rica/ Panama´ 8u309 N 82u W Present study South American hunter-gatherer/forager2 (572) Parkatejeˆ (Gavia˜o) 78 65 12 1 0.91 0.09 Brazil 05u 039 S 48u 369 W Acun˜a-Alonzo et al. (2010) Jamamadi 26 26 0 0 1.00 0.00 Brazil 07u 159 S 66u 419 W Acun˜a-Alonzo et al. (2010) Mekranoti (Kayapo´) 25 24 1 0 0.98 0.02 Brazil 08u 409 S 54u W Acun˜a-Alonzo et al. (2010) Mura (Piraha˜) 18 11 6 1 0.78 0.22 Brazil 03u349 S 59u 129 W Acun˜a-Alonzo et al. (2010) Pacaa´s-Novos (Wari) 25 23 2 0 0.96 0.04 Brazil 11u 089 S 65u 059 W Acun˜a-Alonzo et al. (2010) Satere´-Mawe´ 25 20 4 1 0.88 0.12 Brazil 03u S 57u W Acun˜a-Alonzo et al. (2010) Apalaı´ 22 15 7 0 0.84 0.16 Brazil 01u209 N 54u409 W Acun˜a-Alonzo et al. (2010) Arara 24 15 9 0 0.81 0.19 Brazil 03u 309 S 54u109 W Acun˜a-Alonzo et al. (2010) Guarani 31 30 1 0 0.98 0.02 Brazil 25u 209 S 52u 309 W Present study; Acun˜a-Alonzo et al. (2010) Gorotire (Kayapo) 7 6 0 1 0.86 0.14 Brazil 07u 449 S 51u 109 W Acun˜a-Alonzo et al. (2010) Karitiana 20 20 0 0 1.00 0.00 Brazil 08u 459 S 63u 519 W Acun˜a-Alonzo et al. (2010) Xavante 21 10 9 2 0.69 0.31 Brazil 13u 209 S 51u 409 W Acun˜a-Alonzo et al. (2010) Xikrin (Kayapo) 17 16 1 0 0.97 0.03 Brazil 05u559 S 51u119 W Acun˜a-Alonzo et al. (2010) Yanomama 25 20 4 1 0.88 0.12 Brazil 02u30 9-04u309 N 64u W Acun˜a-Alonzo et al. (2010) Txukahamae (Kayapo) 30 26 4 0 0.93 0.07 Brazil 10u 209 S 53u 59 W Acun˜a-Alonzo et al. (2010) Tiriyo´ (Trio) 25 21 4 0 0.92 0.08 Brazil 01u 579 N 55u499 W Acun˜a-Alonzo et al. (2010) Ic¸ana River (Baniwa) 19 13 3 3 0.76 0.24 Brazil 01u N 67u 509 W Acun˜a-Alonzo et al. (2010) Kuben Kran Keng (Kayapo) 17 13 4 0 0.88 0.12 Brazil 08u109 S 58u89 W Acun˜a-Alonzo et al. (2010) Lengua 29 29 0 0 1.00 0.00 Paraguay 23u S 56u W Acun˜a-Alonzo et al. (2010) Ache (Guayaki) 23 23 0 0 1.00 0.00 Paraguay 23u S 58u W Acun˜a-Alonzo et al. (2010) Ayoreo 30 30 0 0 1.00 0.00 Paraguay 16-22u S 58-63u W Acun˜a-Alonzo et al. (2010) Zenu 4 4 0 0 1.00 0.00 Colombia 9u N 75u W Present study Kogi 7 7 0 0 1.00 0.00 Colombia 11u N 74u W Present study Ticuna 1 1 0 0 1.00 0.00 Colombia 3u 539 S 70uW Present study Embera 3 3 0 0 1.00 0.00 Colombia 7u N 76u W Present study Wayuu 17 15 2 0 0.94 0.06 Colombia 11u N 73u W Present study Palikur 3 1 2 0 0.67 0.33 French Guiana 4u N 51u 459 W Present study ,680,000 SNPs (Ruiz-Linares et al., unpublished data). Login to comment 59 ABCA1 p.Arg230Cys Population N1 Genotype frequency Allele frequency Country Geographical coordinates References Arg 230 Arg Arg 230 Cys Cys 230 Cys Arg230 230Cys Mesoamerican agriculturalist2 (1218) Yaqui 45 30 11 4 0.79 0.21 Mexico 27u 299 N 110u 409 W Acun dc;a-Alonzo et al. (2010) Tarahumara 109 81 23 5 0.85 0.15 Mexico 26u 499 N 107u 049 W Acun dc;a-Alonzo et al. (2010) Teenek 67 45 20 2 0.82 0.18 Mexico 21u 369 N 98u 589 W Acun dc;a-Alonzo et al. (2010) Cora 123 62 51 10 0.71 0.29 Mexico 22u 39 N 104u 559 W Acun dc;a-Alonzo et al. (2010) Purepecha 35 22 11 2 0.79 0.21 Mexico 19u 369 N 102u 149 W Acun dc;a-Alonzo et al. (2010) Mazahua 83 68 15 0 0.91 0.09 Mexico 19u 269 N 100u 009 W Acun dc;a-Alonzo et al. (2010) Mixe 19 15 4 0 0.89 0.11 Mexico 17u N 96uW Present study Mixtec 4 4 0 0 1.00 0.00 Mexico 17u N 97uW Present study Nahuatl 267 185 73 9 0.83 0.17 Mexico 19u 589 N 97u 379 W Acun dc;a-Alonzo et al. (2010) Totonaco 113 86 24 3 0.87 0.13 Mexico 19u 579 N 97u 449 W Acun dc;a-Alonzo et al. (2010) Otom &#b4;es 42 35 7 0 0.92 0.08 Mexico 20u 289 N 99u 139 W Acun dc;a-Alonzo et al. (2010) Zapotec 125 71 50 4 0.76 0.24 Mexico 17u149 N 96u149 W Present study; Acun dc;a-Alonzo et al. (2010) Mayan 110 68 39 3 0.80 0.20 Mexico 20u139 N 90u289 W Acun dc;a-Alonzo et al. (2010) Kaqchikel-Quiche 17 13 3 1 0.85 0.15 Guatemala 15u N 91uW Present study Cabecar 24 19 5 0 0.90 0.10 Costa Rica 9u 309 N 84uW Present study Guaym &#b4; 35 26 8 1 0.85 0.15 Costa Rica/ Panama &#b4; 8u309 N 82u W Present study South American hunter-gatherer/forager2 (572) Parkateje c6; (Gavia dc;o) 78 65 12 1 0.91 0.09 Brazil 05u 039 S 48u 369 W Acun dc;a-Alonzo et al. (2010) Jamamadi 26 26 0 0 1.00 0.00 Brazil 07u 159 S 66u 419 W Acun dc;a-Alonzo et al. (2010) Mekranoti (Kayapo &#b4;) 25 24 1 0 0.98 0.02 Brazil 08u 409 S 54u W Acun dc;a-Alonzo et al. (2010) Mura (Piraha dc;) 18 11 6 1 0.78 0.22 Brazil 03u349 S 59u 129 W Acun dc;a-Alonzo et al. (2010) Pacaa &#b4;s-Novos (Wari) 25 23 2 0 0.96 0.04 Brazil 11u 089 S 65u 059 W Acun dc;a-Alonzo et al. (2010) Satere &#b4;-Mawe &#b4; 25 20 4 1 0.88 0.12 Brazil 03u S 57u W Acun dc;a-Alonzo et al. (2010) Apala &#b4; 22 15 7 0 0.84 0.16 Brazil 01u209 N 54u409 W Acun dc;a-Alonzo et al. (2010) Arara 24 15 9 0 0.81 0.19 Brazil 03u 309 S 54u109 W Acun dc;a-Alonzo et al. (2010) Guarani 31 30 1 0 0.98 0.02 Brazil 25u 209 S 52u 309 W Present study; Acun dc;a-Alonzo et al. (2010) Gorotire (Kayapo) 7 6 0 1 0.86 0.14 Brazil 07u 449 S 51u 109 W Acun dc;a-Alonzo et al. (2010) Karitiana 20 20 0 0 1.00 0.00 Brazil 08u 459 S 63u 519 W Acun dc;a-Alonzo et al. (2010) Xavante 21 10 9 2 0.69 0.31 Brazil 13u 209 S 51u 409 W Acun dc;a-Alonzo et al. (2010) Xikrin (Kayapo) 17 16 1 0 0.97 0.03 Brazil 05u559 S 51u119 W Acun dc;a-Alonzo et al. (2010) Yanomama 25 20 4 1 0.88 0.12 Brazil 02u30 9-04u309 N 64u W Acun dc;a-Alonzo et al. (2010) Txukahamae (Kayapo) 30 26 4 0 0.93 0.07 Brazil 10u 209 S 53u 59 W Acun dc;a-Alonzo et al. (2010) Tiriyo &#b4; (Trio) 25 21 4 0 0.92 0.08 Brazil 01u 579 N 55u499 W Acun dc;a-Alonzo et al. (2010) Ic &#b8;ana River (Baniwa) 19 13 3 3 0.76 0.24 Brazil 01u N 67u 509 W Acun dc;a-Alonzo et al. (2010) Kuben Kran Keng (Kayapo) 17 13 4 0 0.88 0.12 Brazil 08u109 S 58u89 W Acun dc;a-Alonzo et al. (2010) Lengua 29 29 0 0 1.00 0.00 Paraguay 23u S 56u W Acun dc;a-Alonzo et al. (2010) Ache (Guayaki) 23 23 0 0 1.00 0.00 Paraguay 23u S 58u W Acun dc;a-Alonzo et al. (2010) Ayoreo 30 30 0 0 1.00 0.00 Paraguay 16-22u S 58-63u W Acun dc;a-Alonzo et al. (2010) Zenu 4 4 0 0 1.00 0.00 Colombia 9u N 75u W Present study Kogi 7 7 0 0 1.00 0.00 Colombia 11u N 74u W Present study Ticuna 1 1 0 0 1.00 0.00 Colombia 3u 539 S 70uW Present study Embera 3 3 0 0 1.00 0.00 Colombia 7u N 76u W Present study Wayuu 17 15 2 0 0.94 0.06 Colombia 11u N 73u W Present study Palikur 3 1 2 0 0.67 0.33 French Guiana 4u N 51u 459 W Present study ,680,000 SNPs (Ruiz-Linares et al., unpublished data). Login to comment 83 ABCA1 p.Arg230Cys Population N1 Genotype frequency Allele frequency Country Geographical coordinates References Arg 230 Arg Arg 230 Cys Cys 230 Cys Arg230 230Cys Andean agriculturalist2 (115) Mapuche 40 40 0 0 1.00 0.00 Chile 40u 309 S 69u 209 W Acun˜a-Alonzo et al. (2010) Aymara 16 16 0 0 1.00 0.00 Bolivia 16u309 S 68u99 W Present study Quechua 16 15 1 0 0.97 0.03 Bolivia 14u309 S 69u W Present study Aymara 22 20 2 0 0.95 0.05 Chile 22u S 70u W Present study Chilote 2 2 0 0 1.00 0.00 Chile 42u309 S 73u559 W Present study Hulliche 13 10 3 0 0.89 0.11 Chile 41u S 73u W Present study Ingano 6 5 1 0 0.92 0.08 Colombia 1u N 77u W Present study 1 Samples genotyped in present study = 229; 2 Caution is needed regarding the classification of these modes of subsistence, since they are not stable over time and may not be unique. Login to comment 84 ABCA1 p.Arg230Cys Population N1 Genotype frequency Allele frequency Country Geographical coordinates References Arg 230 Arg Arg 230 Cys Cys 230 Cys Arg230 230Cys Andean agriculturalist2 (115) Mapuche 40 40 0 0 1.00 0.00 Chile 40u 309 S 69u 209 W Acun dc;a-Alonzo et al. (2010) Aymara 16 16 0 0 1.00 0.00 Bolivia 16u309 S 68u99 W Present study Quechua 16 15 1 0 0.97 0.03 Bolivia 14u309 S 69u W Present study Aymara 22 20 2 0 0.95 0.05 Chile 22u S 70u W Present study Chilote 2 2 0 0 1.00 0.00 Chile 42u309 S 73u559 W Present study Hulliche 13 10 3 0 0.89 0.11 Chile 41u S 73u W Present study Ingano 6 5 1 0 0.92 0.08 Colombia 1u N 77u W Present study 1 Samples genotyped in present study = 229; 2 Caution is needed regarding the classification of these modes of subsistence, since they are not stable over time and may not be unique. Login to comment 140 ABCA1 p.Arg230Cys Discussion We can now examine some hypotheses in an attempt to explain the results and to draw the evolutionary scenario associated with the pattern of diversity of the ABCA1* Arg230Cys polymorphism. Login to comment 141 ABCA1 p.Arg230Cys Discussion We can now examine some hypotheses in an attempt to explain the results and to draw the evolutionary scenario associated with the pattern of diversity of the ABCA1* Arg230Cys polymorphism. Login to comment 167 ABCA1 p.Arg230Cys ABCA1 p.Arg230Cys In agreement with this historical scenario, the genetic variation in Arg230Cys presented a worse fit to neutrality than loci known to be neutral, indicating that selective mechanisms are necessary to explain the genetic diversity of Arg230Cys, especially when the Mesoamerican agriculturalist subdivision is considered in the analysis. Login to comment 177 ABCA1 p.Arg230Cys Therefore, the significant role of random processes and/or more heterogeneous cultural and ecological scenarios makes it difficult to define a particular pattern associated with the Arg230Cys polymorphism in South American groups, a situation different from that in Mesoamerica. In conclusion, our analyses demonstrate for the first time a robust correlation between a constructed niche and a selected Native American autochthonous allele. Login to comment 259 ABCA1 p.Arg230Cys ABCA1 p.Arg230Cys Romero-Hidalgo S, Villarreal-Molina T, Gonza´lez-Barrios JA, Canizales- Quinteros S, Rodrı´guez-Arellano ME, et al. (2012) Carbohydrate intake modulates the effect of the ABCA1-R230C variant on HDL cholesterol concentrations in premenopausal women. Login to comment