Resumen
Las técnicas de secuenciación masiva o secuenciación de próxima generación han cambiado la forma de obtener datos genéticos para los estudios de conservación en aves, pasando del análisis de unos pocos loci ubicados en una pequeña porción del genoma a la obtención de información de cientos a miles de loci ubicados a lo largo de todo el genoma. Un mayor número de marcadores brinda más información para estudios filogenéticos, de introgresión y de estructuración poblacional, y permite una mejor estimación de los parámetros demográficos. Índices como la heterocigosis, el parentesco, la paternidad y la endogamia pueden ser estimados con mayor precisión. Además, uno de los mayores aportes de los estudios genómicos es la identificación de variación tanto adaptativa como neutra. En este trabajo se explica brevemente la base metodológica de la secuenciación masiva y se muestran ejemplos de la utilización de datos genómicos en estudios de conservación en aves.
Referencias
ALLENDORF FW (2017) Genetics and the conservationof natural populations: allozymes to genomes.Molecular Ecology 26:420–430
ANDERSEN MJ, MANTHEY JD, NAIKATINI A Y MOYLE RG(2017) Conservation genomics of the silktail (Aves:Lamprolia victoriae) suggests the need for increasedprotection of native forest on the Natewa Penin-sula, Fiji. Conservation Genetics 18:1277–1285
ANDREW SC, TAYLOR MP, LUNDREGAN S, LIEN S, JENSENH Y GRIFFITH SC (en prensa) Signs of adaptation totrace metal contamination in a common urban bird.Science of the Total Environment
AVISE JC (2010) Perspective: conservation genetics entersthe genomics era. Conservation Genetics 11:665–669
BAIRD NA, ETTER PD, ATWOOD TS, CURREY MC, SHIVERAL, LEWIS ZA, SELKER EU, CRESKO WA Y JOHNSONEA (2008) Rapid SNP discovery and genetic map-ping using sequenced RAD markers. PloS One3:e3376
BALL AD, STAPLEY J, DAWSON DA, BIRKHEAD TR, BURKET Y SLATE J (2010) A comparison of SNPs andmicrosatellites as linkage mapping markers: lessonsfrom the zebra finch (Taeniopygia guttata). BMCGenomics 11:art218
BATTEY CJ, LINCK EB, EPPERLY KL, FRENCH C, SLAGERDL, SYKES PW Y KLICKA J (2017) A migratory dividein the Painted Bunting (Passerina ciris). AmericanNaturalist 191:259–268
BIRDLIFE INTERNATIONAL (2018) Species factsheet:Gubernatrix cristata. BirdLife International, Cam-bridge (URL: http://datazone.birdlife.org/species/factsheet/yellow-cardinal-gubernatrix-cristata)
BOUZAT JL (2010) Conservation genetics of popula-tion bottlenecks: the role of chance, selection andhistory. Conservation Genetics 11:463–478
BULGARELLA M, KOPUCHIAN C, DI GIACOMO AS, MATUSR, BLANK O, WILSON RE Y MCCRACKEN KG (2014)Molecular phylogeny of the South Americansheldgeese with implications for conservation ofFalkland Islands (Malvinas) and continentalpopulations of the Ruddy-headed Goose Chloephagarubidiceps and Upland Goose C. picta. Bird Conser-vation International 24:59–71
CAMPAGNA L, GRONAU I, SILVEIRA LF, SIEPEL A Y LOVETTEIJ (2015) Distinguishing noise from signal in pat-terns of genomic divergence in a highly polymor-phic avian radiation. Molecular Ecology 24:4238–4251
CAMPAGNA L, REPENNING M, SILVEIRA LF, SUERTEGARAYFONTANA C, TUBARO PL & LOVETTE IJ (2017) Repeateddivergent selection on pigmentation genes in arapid finch radiation. Science Advances 3:art1602404
CHARLESWORTH B (2001) The effect of life-history andmode of inheritance on neutral genetic variability.Genetical Research 77:153–166
DAVEY JW, HOHENLOHE PA, ETTER PD, BOONE JQ,CATCHEN JM Y BLAXTER ML (2011) Genome-widegenetic marker discovery and genotyping usingnext-generation sequencing. Nature Reviews Genetics12:499–510
DESAIX MG, BULLUCK LP, ECKERT AJ, VIVERETTE CB,BOVES TJ, REESE JA, TONRA CM Y DYER RJ (en prensa)Population assignment reveals low migratory connecti-vity in a weakly structured songbird. Molecular Ecology
DOMÍNGUEZ M, PIZZARELLO G, ATENCIO M, SCARDA-MAGLIA R Y MAHLER B (en prensa) Genetic assign-ment and monitoring of yellow cardinals. Journal ofWildlife Management
DOYLE JM, BELL DA, BLOOM PH, EMMONS G, FESNOCKA, KATZNER TE, LAPRÉ L, LEONARD K, SANMIGUEL P,WESTERMAN R Y DEWOODY JA (2018) New insights intothe phylogenetics and population structure of theprairie falcon (Falco mexicanus). BMC Genomics 19:art233
ELGVIN TO, TRIER CN, TØRRESEN OK, HAGEN IJ, LIENS, NEDERBRAGT AJ, RAVINET M, JENSEN H Y SÆTRE GP(2017) The genomic mosaicism of hybrid speciation.Science Advances 3:art1602996
ELLEGREN H (2010) Evolutionary stasis: the stablechromosomes of birds. Trends in Ecology and Evolu-tion 25:283–291
ELLEGREN H (2013) The evolutionary genomics ofbirds. Annual Review of Ecology, Evolution and Sys-tematics 44:239–259
ELLEGREN H (2014) Genome sequencing and popula-tion genomics in non-model organisms. Trends inEcology and Evolution 29:51–63
ELSHIRE RJ, GLAUBITZ JC, SUN Q, POLAND JA, KAWA-MOTO K, BUCKLER ES Y MITCHELL SE (2011) A robust,simple genotyping-by-sequencing (GBS) approachfor high diversity species. PLoS One 6:e19379
EÖRY L, GILBERT MT, LI C, LI B, ARCHIBALD A, AKENBL, ZHANG G, JARVIS E, FLICEK P Y BURT DW (2015)Avianbase: a community resource for bird geno-mics. Genome Biology 16:art21
FEDER JL, EGAN SP Y NOSIL P (2012) The genomics ofspeciation-with-gene-flow. Trends in Genetics28:342–350
FERNANDES G Y CAPARROZ R (2013) DNA sequenceanalysis to guide the release of blue and yellowmacaws (Ara ararauna, Psittaciformes, Aves) fromthe illegal trade back to the wild. Molecular BiologyReports 40:2757–2762
FRANKEL OH (1974) Genetic conservation: our evo-lutionary responsibility. Genetics 78:53–65
FRANKHAM R (1995) Conservation genetics. AnnualReview of Genetics 29:305–327
FRANKHAM R (2005) Stress and adaptation in conser-vation genetics. Journal of Evolutionary Biology18:750–755
FRANKHAM R (2010) Challenges and opportunities ofgenetic approaches to biological conservation. Bio-logical Conservation 143:1919–1927
FRANKHAM R, BALLOU JD, ELDRIDGE MDB, LACY RC,RALLS K, DUDASH MR Y FENSTER CB (2011) Predict-ing the probability of outbreeding depression. Con-servation Biology 25:465–475
FRASER DJ Y BERNATCHEZ L (2001) Adaptive evolution-ary conservation: towards a unified concept fordefining conservation units. Molecular Ecology10:2741–2752
FUENTES-PARDO AP Y RUZZANTE DE (2017) Whole-genome sequencing approaches for conservationbiology: advantages, limitations and practical rec-ommendations. Molecular Ecology 26:5369–5406
FUNK WC, MCKAY JK, HOHENLOHE PA Y ALLENDORFFW (2012) Harnessing genomics for delineatingconservation units. Trends in Ecology and Evolution27:489–496
GALLA SJ, FORSDICK NJ, BROWN L, HOEPPNER MP, KNAPPM, MALONEY RF, MORAGA R, SANTURE AW Y STEEVESTE (en prensa) Reference genomes from distantlyrelated species can be used for discovery of singlenucleotide polymorphisms to inform conservationmanagement. Genes
GILLIGAN DM, BRISCOE DA Y FRANKHAM R (2005) Com-parative losses of quantitative and molecular geneticvariation in finite populations of Drosophilamelanogaster. Genetical Research 85:47–55
GOMULKIEWICZ R Y HOLT RD (2006) When does evo-lution by natural selection prevent extinction? Evo-lution 49:201–207
GOODWIN S, MCPHERSON JD Y MCCOMBIE WR (2016)Coming of age: ten years of next-generation sequen-cing technologies. Nature Reviews Genetics 17:333–351
GREGORY TR (2005) Synergy between sequence andsize in large-scale genomics. Nature Reviews Genet-ics 6:699–708
GROHME MA, FRIAS SOLER R, WINK M Y FROHME M(2013) Microsatellite marker discovery using singlemolecule real-time circular consensus sequencingon the Pacific Biosciences RS. BioTechniques55:253–256
HARTMANN SA, SCHAEFER HM Y SEGELBACHER G (2014)Development of 12 microsatellite loci for the endan-gered Pale-headed Brushfinch (Atlapetes pallidiceps)and their cross-amplification in two co-occurringbrushfinches. Journal of Ornithology 155:835–839
HARVEY MG, SMITH BT, GLENN TC, FAIRCLOTH BC YBRUMFIELD RT (2016) Sequence capture versusrestriction site associated DNA sequencing for shal-low systematics. Systematic Biology 65:910–924
HEDRICK PW (2001) Conservation genetics: where arewe now? Trends in Ecology and Evolution 16:629–636HOBAN S, KELLEY JL, LOTTERHOS KE, ANTOLIN MF,BRADBURD G, LOWRY DB, POSS ML, REED LK, STORFERA Y WHITLOCK MC (2016) Finding the genomic basisof local adaptation: pitfalls, practical solutions andfuture directions. American Naturalist 188:379–397
IUCN (2018) The IUCN Red List of threatened species.IUCN, Gland (URL: http://www.iucnredlist.org/)
IUCN SPECIES SURVIVAL COMMISSION (2013) Guidelinesfor reintroductions and other conservation translocations.Version 1.0. IUCN, Gland
KAISER SA, TAYLOR SA, CHEN N, SILLETT TS, BONDRAER Y WEBSTER MS (2017) A comparative assessmentof SNP and microsatellite markers for assigningparentage in a socially monogamous bird. Molecu-lar Ecology Resources 17:183–193
KAWECKI TJ Y EBERT D (2004) Conceptual issues in localadaptation. Ecology Letters 7:1225–1241
KIIALAINEN A, KARLBERG O, AHLFORD A, SIGURDSSON S,LINDBLAD-TOH K Y SYVÄNEN AC (2011) Performanceof microarray and liquid based capture methods fortarget enrichment for massively parallel sequencingand SNP discovery. PLoS One 6:e16486
KLICKA LB, KUS BE, TITLE PO Y BURNS KJ (2016) Con-servation genomics reveals multiple evolutionaryunits within Bell’s Vireo (Vireo bellii). ConservationGenetics 17:455–471
KOHN MH, MURPHY WJ, OSTRANDER EA Y WAYNE RK(2006) Genomics and conservation genetics. Trendsin Ecology and Evolution 21:629–637
KOPUCHIAN C, CAMPAGNA L, DI GIACOMO AS, WILSONRE, BULGARELLA M, PETRACCI P, MAZAR BARNETT J,MATUS R, BLANK O Y MCCRACKEN KG (2016) Demo-graphic history inferred from genome-wide datareveals two lineages of sheldgeese endemic to a gla-cial refugium in the southern Atlantic. Journal of Bio-geography 43:1979–1989
LABUSCHAGNE C, NUPEN L, KOTZÉ A, GROBLER PJ YDALTON DL (2015) Assessment of microsatellite andSNP markers for parentage assignment in ex situAfrican Penguin (Spheniscus demersus) populations.Ecology and Evolution 5:4389–4399
LACY RC (1994) Managing genetic diversity in cap-tive populations of animals. Pp. 63–89 en: BOWLESML Y WHELAN CJ (eds) Restoration and recovery ofendangered plants and animals. Cambridge Univer-sity Press, Cambridge
LACY RC (2013) Achieving true sustainability of zoopopulations. Zoo Biology 32:19–26
LANGIN KM, ALDRIDGE CL, FIKE JA, CORNMAN RS,MARTIN K, WANN GT, SEGLUND AE, SCHROEDER MA,BRAUN CE, BENSON DP, FEDY BC, YOUNG JR,WILSON S, WOLFE DH Y OYLER-MCCANCE SJ (2018)Characterizing range-wide divergence in analpine-endemic bird: a comparison of genetic andgenomic approaches. Conservation Genetics19:1471–1485
LEE L, TIRRELL N, BURRELL C, CHAMBERS S, VOGEL S YDOMYAN ET (2018) Genetic tests reveal extra-pairpaternity among Gentoo penguins (Pyogoscelispapua ellsworthii) at Loveland Living PlanetAquarium: implications for ex situ colony manage-ment. Zoo Biology 37:236–244
MACE GM (2004) The role of taxonomy in species con-servation. Philosophical Transactions of the Royal Soci-ety of London B 359:711–719
MARRA PP, COHEN EB, LOSS SR, RUTTER JE Y TONRACM (2015) A call for full annual cycle research inanimal ecology. Biology Letters 11:art20150552
MARTIN-WINTLE MS, WINTLE NJP, DÍEZ-LEÓN M,SWAISGOOD RR Y ASA CS (en prensa) Improving thesustainability of ex situ populations with matechoice. Zoo Biology
MCMAHON BJ, TEELING EC Y HÖGLUND J (2014) Howand why should we implement genomics into con-servation? Evolutionary Applications 7:999–1007MEIRMANS PG (2015) Seven common mistakes inpopulation genetics and how to avoid them.Molecular Ecology 24:3223–3231
NARUM SR, BUERKLE CA, DAVEY JW, MILLER MR YHOHENLOHE PA (2013) Genotyping-by-sequencingin ecological and conservation genomics. MolecularEcology 22:2841–2847
NG EYX, GARG KM, LOW GW, CHATTOPADHYAY B, OHRRY, LEE JGH Y RHEINDT FE (2017) Conservationgenomics identifies impact of trade in a threatenedsongbird. Biological Conservation 214:101–108
NOOR MAF Y BENNETT SM (2009) Islands of speciationor mirages in the desert: examining the role ofrestricted recombination in maintaining species.Heredity 103:439–444
OUBORG NJ, PERTOLDI C, LOESCHCKE V, BIJLSMA RK YHEDRICK PW (2010) Conservation genetics in tran-sition to conservation genomics. Trends in Genetics26:177–187
OYLER-MCCANCE SJ, OH KP, LANGIN KM Y ALDRIDGECL (2016) A field ornithologist’s guide to genomics:practical considerations for ecology and conserva-tion. Auk 133:626–64
8OZSOLAK F Y MILOS PM (2011) RNA sequencing:advances, challenges and opportunities. NatureReviews Genetics 12:87–98
PARIS JR, STEVENS JR Y CATCHEN JM (2017) Lost inparameter space: a road map for STACKS. Methodsin Ecology and Evolution 8:1360–1373
PERTOLDI C, BIJLSMA R Y LOESCHCKE V (2007) Conser-vation genetics in a globally changing environment:present problems, paradoxes and future challenges.Biodiversity and Conservation 16:4147–4163
PETERS JL, LAVRETSKY P, DACOSTA JM, BIELEFELD RR,FEDDERSEN JC Y SORENSON MD (2016) Populationgenomic data delineate conservation units in mot-tled ducks (Anas fulvigula). Biological Conservation203:272–281
PETERSON BK, WEBER JN, KAY EH, FISHER HS YHOEKSTRA HE (2012) Double digest RADseq: aninexpensive method for de novo SNP discovery andgenotyping in model and non-model species. PLoSOne 7:e37135
POELSTRA JW, VIJAY N, BOSSU CM, LANTZ H, RYLL B,MULLER I, BAGLIONE V, UNNEBERG P, WIKELSKI M,GRABHERR MG, UNNEBERG P & WOLF JBW (2014) Thegenomic landscape underlying phenotypic integ-rity in the face of gene flow in crows. Science344:1410–1414
PRATT D Y MITTERMEIER JC (2016) Notes on the natu-ral history, taxonomy and conservation of theendemic avifauna of the Samoan Archipelago.Wilson Journal of Ornithology 128:217–241
PRIMMER CR, PAINTER JN, KOSKINEN MT, PALO JU YMERILÄ J (2005) Factors affecting avian cross-speciesmicrosatellite amplification. Journal of Avian Biology36:348–360
RUEGG KC, ANDERSON EC, PAXTON KL, APKENAS V, LAOS, SIEGEL RB, DESANTE DF, MOORE F Y SMITH TB (2014)Mapping migration in a songbird using high-resolution genetic markers. Molecular Ecology23:5726–5739
RUEGG KC, BAY RA, ANDERSON EC, SARACCO JF,HARRIGAN RJ, WHITFIELD M, PAXTON EH Y SMITH TB(2018) Ecological genomics predicts climate vulner-ability in an endangered southwestern songbird.Ecology Letters 21:1085–1096
RUNGE CA, MARTIN TG, POSSINGHAM HP, WILLIS SG YFULLER RA (2014) Conserving mobile species. Fron-tiers in Ecology and the Environment 12:395–402
SANGER F, NICKLEN S Y COULSON AR (1977) DNAsequencing with chain-terminating inhibitors. Pro-ceedings of the National Academy of Sciences74:5463–5467
SAVOLAINEN O, LASCOUX M Y MERILÄ J (2013) Ecologi-cal genomics of local adaptation. Nature ReviewsGenetics 14:807–820
SHAFER ABA, WOLF JBW, ALVES PC, BERGSTRÖM L,BRUFORD MW, BRÄNNSTRÖM I, COLLING G, DALÉN L,DE MEESTER L, EKBLOM R, FAWCETT KD, FIOR S,HAJIBABAEI M, HILL JA, HOEZEL AR, HÖGLUND J,JENSEN EL, KRAUSE J, KRISTENSEN TN, KRÜTZEN M,MCKAY JK, NORMAN AJ, OGDEN R, ÖSTERLING EM,OUBORG NJ, PICCOLO J, POPOVIC D, PRIMMER CR,REED FA, ROUMET M, SALMONA J, SCHENEKAR T,SCHWARTZ MK, SEGELBACHER G, SENN H, THAULOW J,VALTONEN M, VEALE A, VERGEER P, VIJAY N, VILÀ C,WEISSENSTEINER M, WENNERSTRÖM L, WHEAT CW YZIELINSKI P (2015) Genomics and the challengingtranslation into conservation practice. Trends in Ecol-ogy and Evolution 30:78–87
STAPLEY J, REGER J, FEULNER PGD, SMADJA C, GALINDOJ, EKBLOM R, BENNISON C, BALL AD, BECKERMAN APY SLATE J (2010) Adaptation genomics: the next gen-eration. Trends in Ecology and Evolution 25:705–712
VA N STRAALEN NM Y ROELOFS D (2006) An introduction toecological genomics. Oxford University Press, Oxford
TEER JK, BONNYCASTLE LL, CHINES PS, HANSEN NF,AOYAMA N, SWIFT AJ, ABAAN HO, ALBERT TJ, MARGU-LIES EH, GREEN ED, COLLINS FS, MULLIKIN JC YBIESECKER LG (2010) Systematic comparison of threegenomic enrichment methods for massively paral-lel DNA sequencing. Genome Research 20:1420–1431
THRASHER DJ, BUTCHER BG, CAMPAGNA L, WEBSTER MSY LOVETTE IJ (2018) Double-digest RAD sequencingoutperforms microsatellite loci at assigning pater-nity and estimating relatedness: a proof of conceptin a highly promiscuous bird. Molecular EcologyResources 18:953–965
TOEWS DPL, CAMPAGNA L, TAYLOR SA, BALAKRISHNANCN, BALDASSARRE DT, DEANE-COE PE, HARVEY MG,HOOPER DM, IRWIN DE, JUDY CD, MASON NA,MCCORMACK JE, MCCRACKEN KG, OLIVEROS CH,SAFRAN RJ, SCORDATO ESC, STRYJEWSKI KF, TIGANO A,UY JAK Y WINGER BM (2015) Genomic approachesto understanding population divergence andspeciation in birds. Auk 133:13–30
WEINMAN LR, SOLOMON JW Y RUBENSTEIN DR (2015)A comparison of single nucleotide polymorphismand microsatellite markers for analysis of parent-age and kinship in a cooperatively breeding bird.Molecular Ecology Resources 15:502–511
WU CI (2001) The genic view of the process ofspeciation. Journal of Evolutionary Biology14:851–865
ZHANG G, LI B, LI C, GILBERT MTP, JARVIS ED Y WANG J(2014a) Comparative genomic data of the AvianPhylogenomics Project. GigaScience 3:art26
ZHANG G, LI C, LI Q, LI B, LARKIN DM, LEE C, STORZJF, ANTUNES A, GREENWOLD MJ, MEREDITH RW, ÖDEENA, CUI J, ZHOU Q, XU L, PAN H, WANG Z, JIN L, ZHANGP, HU H, YANG W, HU J, XIAO J, YANG Z, LIU Y, XIE Q,YU H, LIAN J, WEN P, ZHANG F, LI H, ZENG Y, XIONGZ, LIU S, ZHOU L, HUANG Z, AN N, WANG J, ZHENGQ, XIONG Y, WANG G, WANG B, WANG J, FAN Y, DAFONSECA RR, ALFARO-NÚÑEZ A, SCHUBERT M,ORLANDO L, MOURIER T, HOWARD JT, GANAPATHY G,PFENNING A, WHITNEY O, RIVAS MV, HARA E, SMITH J,FARRÉ M, NARAYAN J, SLAVOV G, ROMANOV MN,BORGES R, MACHADO JP, KHAN I, SPRINGER MS, GATESYJ, HOFFMANN FG, OPAZO JC, HÅSTAD O, SAWYER RH,KIM H, KIM KW, KIM HJ, CHO S, LI N, HUANG Y,BRUFORD MW, ZHAN X, DIXON A, BERTELSEN MF,DERRYBERRY E, WARREN W, WILSON RK, LI S, RAYDA, GREEN RE, O’BRIEN SJ, GRIFFIN D, JOHNSONWE, HAUSSLER D, RYDER OA, WILLERSLEV E, GRAVESGR, ALSTRÖM P, FJELDSÅ J, MINDELL DP, EDWARDSSV, BRAUN EL, RAHBEK C, BURT DW, HOUDE P,ZHANG Y, YANG H, WANG J, AVIAN GENOME CON-SORTIUM, JARVIS ED, GILBERT MTP Y WANG J (2014b)Comparative genomics reveals insights into aviangenome evolution and adaptation. Science346:1311–1320
ZINK RM (2004) The role of subspecies in obscuringavian biological diversity and misleading conser-vation policy. Proceedings of the Royal Society B, Bio-logical Sciences 271:561–564

Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial 4.0.