Filogen?mica do g?nero Panthera (mammalia, felidae)
Ano de defesa: | 2019 |
---|---|
Autor(a) principal: | |
Orientador(a): | |
Banca de defesa: | |
Tipo de documento: | Dissertação |
Tipo de acesso: | Acesso aberto |
Idioma: | por |
Instituição de defesa: |
Pontif?cia Universidade Cat?lica do Rio Grande do Sul
|
Programa de Pós-Graduação: |
Programa de P?s Gradua??o em Ecologia e Evolu??o da Biodiversidade
|
Departamento: |
Escola de Ci?ncias
|
País: |
Brasil
|
Palavras-chave em Português: | |
Palavras-chave em Inglês: | |
Área do conhecimento CNPq: | |
Link de acesso: | http://tede2.pucrs.br/tede2/handle/tede/8747 |
Resumo: | The evolutionary history of species, especially those derived from rapid and recent radiations, is often embedded in a complex network of past admixtures process. This complex history, associated with the stochastic nature of incomplete lineage sorting (ILS), poses challenges for reconstructing their phylogenetic relationships, even with the use of whole-genome-sequence (wgs) data. Several studies have addressed the evolutionary relationships among the five extant species of Panthera, and recent analyses have revealed extensive genealogical discordance in this group, making it difficult to discern which topology reflects the original sequence of speciation events. So far, phylogenomic studies of Panthera employing wgs data have included a single individual per species, which precludes an assessment of replicability of topological patterns when the species? representative is changed. Here we employ a Panthera-wide wgs dataset incorporating three jaguar genomes (two of which are novel), along with two representatives each of lions and leopards, to dissect the relationships among these three species. We tested the genome-wide monophyly of each of them, and then investigated their patterns of genealogical discordance. We initially assessed the frequency of each of the three alternative topologies along their genomes, by breaking up the alignment into windows of four different sizes (50 kb, 100 kb, 1 Mb and 5 Mb) and reconstructing the ML phylogeny (tested with nonparametric bootstrapping) for each window. Supported ML phylogenies were then plotted along the genome, and the frequency of each topology was assessed relative to the recombination rate of the respective genomic segment. Using 100-kb windows, we also estimated divergence times between the two sister-species defined by each topology, as well as a ?normalized age? in which the depth of the sisterspecies node was divided by that of the preceding (trio) node, to further correct for recombination-rate effects. We also employed 100-kb windows to identify and map introgression events along the genome, assuming different topologies as the ?species tree?. Genome-wide monophyly for all three tested species was strongly supported, and a clear pattern was observed with respect to their phylogenetic relationships: with all window sizes, the most frequent topology (76% ? 95%) united lion+leopard as sisterspecies (topology 1), followed by lion+jaguar (topology 2: 4% ? 8%) and leopard+jaguar (topology 3: 1% ? 6%). Topology 1 was strongly predominant in regions of high recombination, e.g. terminal chromosomal segments, whereas topologies 2 and 3 were strongly enriched in low-recombination regions, especially in centromeric segments. Absolute divergence times were younger for topologies 2 and 3 (relative to topology 1) on both autosomes and the X chromosome, but this pattern was reversed when we 19 ?normalized? the depth of the terminal node using the age of the preceding (trio) node. The introgression analyses indicated pervasive historical admixture among these species, regardless of the assumed species tree. For example, if topology 1 was assumed, 5% of the genome was inferred to derive from lion-jaguar hybridization, while if topology 2 or 3 were assumed, 35% of the genome was detected as introgressed between lion and leopard. Overall, our results indicate that topology 2 (lion+jaguar) most likely reflects the original speciation relationship, given its age, frequency and recombination profile. The jaguar+leopard topology did not differ significantly in age or recombination profile, and thus likely derives from ILS. Remarkably, these results imply that a large proportion of the genome has been overwritten by post-speciation admixture between lion and leopard, leading to a complex mosaic whose phylogenetic resolution requires integration among different approaches. |
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Eizirik, Eduardohttp://lattes.cnpq.br/3626004211018550http://lattes.cnpq.br/1235637399279833Santos, Sarah Helen Dias dos2019-06-25T12:08:16Z2019-03-27http://tede2.pucrs.br/tede2/handle/tede/8747The evolutionary history of species, especially those derived from rapid and recent radiations, is often embedded in a complex network of past admixtures process. This complex history, associated with the stochastic nature of incomplete lineage sorting (ILS), poses challenges for reconstructing their phylogenetic relationships, even with the use of whole-genome-sequence (wgs) data. Several studies have addressed the evolutionary relationships among the five extant species of Panthera, and recent analyses have revealed extensive genealogical discordance in this group, making it difficult to discern which topology reflects the original sequence of speciation events. So far, phylogenomic studies of Panthera employing wgs data have included a single individual per species, which precludes an assessment of replicability of topological patterns when the species? representative is changed. Here we employ a Panthera-wide wgs dataset incorporating three jaguar genomes (two of which are novel), along with two representatives each of lions and leopards, to dissect the relationships among these three species. We tested the genome-wide monophyly of each of them, and then investigated their patterns of genealogical discordance. We initially assessed the frequency of each of the three alternative topologies along their genomes, by breaking up the alignment into windows of four different sizes (50 kb, 100 kb, 1 Mb and 5 Mb) and reconstructing the ML phylogeny (tested with nonparametric bootstrapping) for each window. Supported ML phylogenies were then plotted along the genome, and the frequency of each topology was assessed relative to the recombination rate of the respective genomic segment. Using 100-kb windows, we also estimated divergence times between the two sister-species defined by each topology, as well as a ?normalized age? in which the depth of the sisterspecies node was divided by that of the preceding (trio) node, to further correct for recombination-rate effects. We also employed 100-kb windows to identify and map introgression events along the genome, assuming different topologies as the ?species tree?. Genome-wide monophyly for all three tested species was strongly supported, and a clear pattern was observed with respect to their phylogenetic relationships: with all window sizes, the most frequent topology (76% ? 95%) united lion+leopard as sisterspecies (topology 1), followed by lion+jaguar (topology 2: 4% ? 8%) and leopard+jaguar (topology 3: 1% ? 6%). Topology 1 was strongly predominant in regions of high recombination, e.g. terminal chromosomal segments, whereas topologies 2 and 3 were strongly enriched in low-recombination regions, especially in centromeric segments. Absolute divergence times were younger for topologies 2 and 3 (relative to topology 1) on both autosomes and the X chromosome, but this pattern was reversed when we 19 ?normalized? the depth of the terminal node using the age of the preceding (trio) node. The introgression analyses indicated pervasive historical admixture among these species, regardless of the assumed species tree. For example, if topology 1 was assumed, 5% of the genome was inferred to derive from lion-jaguar hybridization, while if topology 2 or 3 were assumed, 35% of the genome was detected as introgressed between lion and leopard. Overall, our results indicate that topology 2 (lion+jaguar) most likely reflects the original speciation relationship, given its age, frequency and recombination profile. The jaguar+leopard topology did not differ significantly in age or recombination profile, and thus likely derives from ILS. Remarkably, these results imply that a large proportion of the genome has been overwritten by post-speciation admixture between lion and leopard, leading to a complex mosaic whose phylogenetic resolution requires integration among different approaches.A hist?ria evolutiva das esp?cies, especialmente aquelas derivadas de radia??es r?pidas e recentes, ? frequentemente incorporada em uma complexa rede de processos de fluxo g?nico ancestral. Essa hist?ria complexa, associada ? natureza estoc?stica da segrega??o incompleta de linhagens (incomplete lineage sorting ? ILS), apresenta desafios para a reconstru??o de suas rela??es filogen?ticas, mesmo com o uso de dados de sequ?ncia de genoma completo (wgs). V?rios estudos abordaram as rela??es evolutivas entre as cinco esp?cies existentes de Panthera e an?lises recentes revelaram uma extensa discord?ncia geneal?gica neste grupo, tornando dif?cil discernir qual topologia reflete a sequ?ncia original dos eventos de especia??o. At? o momento, estudos filogen?micos de Panthera empregando dados de wgs inclu?ram um ?nico indiv?duo por esp?cie, o que impede uma avalia??o da replicabilidade de padr?es topol?gicos quando o representante ? alterado. Nesse estudo, empregamos um conjunto de dados wgs de Panthera, incorporando tr?s genomas de on?a-pintada (dois dos quais s?o novos), juntamente com dois representantes de le?es e leopardos, para dissecar as rela??es entre essas tr?s esp?cies. N?s testamos a monofilia de cada um deles e investigamos seus padr?es de discord?ncia geneal?gica. Avaliamos inicialmente a frequ?ncia de cada uma das tr?s topologias alternativas ao longo de seus genomas, dividindo o alinhamento em janelas de quatro tamanhos diferentes (50 kb, 100 kb, 1 Mb e 5 Mb) e reconstruindo a filogenia de m?xima verossimilhan?a (maximum likelihood ? ML) (testada com bootstrapping n?o param?trico) para cada janela. As filogenias de ML apoiadas foram ent?o plotadas ao longo do genoma e a frequ?ncia de cada topologia foi avaliada em rela??o ? taxa de recombina??o do respectivo segmento gen?mico. Usando janelas de 100 kb, tamb?m estimamos tempos de diverg?ncia entre as duas esp?cies-irm?s definidas por cada topologia, bem como uma 'idade normalizada' em que a profundidade do n? de esp?ciesirm?s foi dividida pela do n? anterior (trio), para corrigir ainda mais poss?veis efeitos da taxa de recombina??o. Essas mesmas janelas foram utilizadas para identificar e mapear eventos de introgress?o ao longo do genoma, assumindo topologias diferentes como a "?rvore de esp?cies". A monofilia em n?vel gen?mico para todas as tr?s esp?cies testadas foi fortemente apoiada e um padr?o claro foi observado quanto ?s suas rela??es filogen?ticas: com todos os tamanhos de janela, a topologia mais frequente ? le?o+leopardo como esp?cies-irm? (topologia 1: 76% - 95%), seguida de le?o+on?apintada (topologia 2: 4% - 8%) e leopardo+on?a-pintada (topologia 3: 1% - 6%). A topologia 1 foi fortemente predominante em regi?es de alta recombina??o, i.e. segmentos cromoss?micos terminais, enquanto as topologias 2 e 3 foram fortemente enriquecidas 3 em regi?es de baixa recombina??o, especialmente em segmentos centrom?ricos. Os tempos de diverg?ncia absoluta foram menores para as topologias 2 e 3 (em rela??o ? topologia 1) tanto em autossomos como no cromossomo X, mas esse padr?o foi revertido quando "normalizamos" a profundidade do n? terminal usando a idade do n? anterior (trio). As an?lises de introgress?o indicaram uma extensa miscigena??o hist?rica entre essas esp?cies, independentemente da ?rvore de esp?cies assumida. Por exemplo, sendo a topologia 1 assumida, 5% do genoma apresenta sinal de hibridiza??o le?o-on?a, enquanto que se a topologia 2 ou 3 for assumida, 35% do genoma ? detectado como sendo introgredido entre le?o e leopardo. De forma geral, nossos resultados indicam que a topologia 2 (le?o+on?a) provavelmente reflete a rela??o de especia??o original, dada sua idade, frequ?ncia e perfil de recombina??o. A topologia leopardo+on?a n?o diferiu significativamente em idade ou perfil de recombina??o e, portanto, provavelmente deriva de ILS. Notavelmente, estes resultados implicam que uma grande propor??o do genoma foi sobrescrita pela miscigena??o p?s-especia??o entre le?o e leopardo, levando a um mosaico complexo cuja resolu??o filogen?tica requer integra??o entre diferentes abordagens.Submitted by PPG Ecologia e Evolu??o da Biodiversidade (eebpg.ciencias@pucrs.br) on 2019-06-12T12:32:45Z No. of bitstreams: 1 Sarah_Santos_Dissertacao_de_Mestrado.pdf: 7773050 bytes, checksum: a92ea4bd170c4699327b7c193681528e (MD5)Approved for entry into archive by Caroline Xavier (caroline.xavier@pucrs.br) on 2019-06-25T12:02:55Z (GMT) No. of bitstreams: 1 Sarah_Santos_Dissertacao_de_Mestrado.pdf: 7773050 bytes, checksum: a92ea4bd170c4699327b7c193681528e (MD5)Made available in DSpace on 2019-06-25T12:08:16Z (GMT). No. of bitstreams: 1 Sarah_Santos_Dissertacao_de_Mestrado.pdf: 7773050 bytes, checksum: a92ea4bd170c4699327b7c193681528e (MD5) Previous issue date: 2019-03-27Conselho Nacional de Pesquisa e Desenvolvimento Cient?fico e Tecnol?gico - CNPqapplication/pdfhttp://tede2.pucrs.br:80/tede2/retrieve/175699/DIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.jpgporPontif?cia Universidade Cat?lica do Rio Grande do SulPrograma de P?s Gradua??o em Ecologia e Evolu??o da BiodiversidadePUCRSBrasilEscola de Ci?nciasFilogen?micaHibrida??oIntrogress?oEspecia??oFelidaePhylogenomicsHybridizationIntrogressionSpeciationCIENCIAS BIOLOGICAS::ZOOLOGIAFilogen?mica do g?nero Panthera (mammalia, felidae)info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisTrabalho ser? publicado como artigo ou livro36 meses25/06/2024-64826523806012675585006001802873727776104890info:eu-repo/semantics/openAccessreponame:Biblioteca Digital de Teses e Dissertações da PUC_RSinstname:Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)instacron:PUC_RSORIGINALDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdfDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdfapplication/pdf263083https://tede2.pucrs.br/tede2/bitstream/tede/8747/5/DIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdfb3f961354cce1bf459d2efe9317a2d8fMD55THUMBNAILDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.jpgDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.jpgimage/jpeg4078https://tede2.pucrs.br/tede2/bitstream/tede/8747/4/DIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.jpg6c8852c023ea3bb3bbde5f95bc4b69d0MD54TEXTDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.txtDIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.txttext/plain1334https://tede2.pucrs.br/tede2/bitstream/tede/8747/3/DIS_SARAH_HELEN_DIAS_DOS_SANTOS_CONFIDENCIAL.pdf.txt8d5d2801c91278b45b4d97becc0571e1MD53LICENSElicense.txtlicense.txttext/plain; charset=utf-8590https://tede2.pucrs.br/tede2/bitstream/tede/8747/1/license.txt220e11f2d3ba5354f917c7035aadef24MD51tede/87472022-05-26 09:33:33.3oai:tede2.pucrs.br:tede/8747QXV0b3JpemE/P28gcGFyYSBQdWJsaWNhPz9vIEVsZXRyP25pY2E6IENvbSBiYXNlIG5vIGRpc3Bvc3RvIG5hIExlaSBGZWRlcmFsIG4/OS42MTAsIGRlIDE5IGRlIGZldmVyZWlybyBkZSAxOTk4LCBvIGF1dG9yIEFVVE9SSVpBIGEgcHVibGljYT8/byBlbGV0cj9uaWNhIGRhIHByZXNlbnRlIG9icmEgbm8gYWNlcnZvIGRhIEJpYmxpb3RlY2EgRGlnaXRhbCBkYSBQb250aWY/Y2lhIFVuaXZlcnNpZGFkZSBDYXQ/bGljYSBkbyBSaW8gR3JhbmRlIGRvIFN1bCwgc2VkaWFkYSBhIEF2LiBJcGlyYW5nYSA2NjgxLCBQb3J0byBBbGVncmUsIFJpbyBHcmFuZGUgZG8gU3VsLCBjb20gcmVnaXN0cm8gZGUgQ05QSiA4ODYzMDQxMzAwMDItODEgYmVtIGNvbW8gZW0gb3V0cmFzIGJpYmxpb3RlY2FzIGRpZ2l0YWlzLCBuYWNpb25haXMgZSBpbnRlcm5hY2lvbmFpcywgY29ucz9yY2lvcyBlIHJlZGVzID9zIHF1YWlzIGEgYmlibGlvdGVjYSBkYSBQVUNSUyBwb3NzYSBhIHZpciBwYXJ0aWNpcGFyLCBzZW0gP251cyBhbHVzaXZvIGFvcyBkaXJlaXRvcyBhdXRvcmFpcywgYSB0P3R1bG8gZGUgZGl2dWxnYT8/byBkYSBwcm9kdT8/byBjaWVudD9maWNhLgo=Biblioteca Digital de Teses e Dissertaçõeshttp://tede2.pucrs.br/tede2/PRIhttps://tede2.pucrs.br/oai/requestbiblioteca.central@pucrs.br||opendoar:2022-05-26T12:33:33Biblioteca Digital de Teses e Dissertações da PUC_RS - Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)false |
dc.title.por.fl_str_mv |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
title |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
spellingShingle |
Filogen?mica do g?nero Panthera (mammalia, felidae) Santos, Sarah Helen Dias dos Filogen?mica Hibrida??o Introgress?o Especia??o Felidae Phylogenomics Hybridization Introgression Speciation CIENCIAS BIOLOGICAS::ZOOLOGIA |
title_short |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
title_full |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
title_fullStr |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
title_full_unstemmed |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
title_sort |
Filogen?mica do g?nero Panthera (mammalia, felidae) |
author |
Santos, Sarah Helen Dias dos |
author_facet |
Santos, Sarah Helen Dias dos |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Eizirik, Eduardo |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/3626004211018550 |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/1235637399279833 |
dc.contributor.author.fl_str_mv |
Santos, Sarah Helen Dias dos |
contributor_str_mv |
Eizirik, Eduardo |
dc.subject.por.fl_str_mv |
Filogen?mica Hibrida??o Introgress?o Especia??o |
topic |
Filogen?mica Hibrida??o Introgress?o Especia??o Felidae Phylogenomics Hybridization Introgression Speciation CIENCIAS BIOLOGICAS::ZOOLOGIA |
dc.subject.eng.fl_str_mv |
Felidae Phylogenomics Hybridization Introgression Speciation |
dc.subject.cnpq.fl_str_mv |
CIENCIAS BIOLOGICAS::ZOOLOGIA |
description |
The evolutionary history of species, especially those derived from rapid and recent radiations, is often embedded in a complex network of past admixtures process. This complex history, associated with the stochastic nature of incomplete lineage sorting (ILS), poses challenges for reconstructing their phylogenetic relationships, even with the use of whole-genome-sequence (wgs) data. Several studies have addressed the evolutionary relationships among the five extant species of Panthera, and recent analyses have revealed extensive genealogical discordance in this group, making it difficult to discern which topology reflects the original sequence of speciation events. So far, phylogenomic studies of Panthera employing wgs data have included a single individual per species, which precludes an assessment of replicability of topological patterns when the species? representative is changed. Here we employ a Panthera-wide wgs dataset incorporating three jaguar genomes (two of which are novel), along with two representatives each of lions and leopards, to dissect the relationships among these three species. We tested the genome-wide monophyly of each of them, and then investigated their patterns of genealogical discordance. We initially assessed the frequency of each of the three alternative topologies along their genomes, by breaking up the alignment into windows of four different sizes (50 kb, 100 kb, 1 Mb and 5 Mb) and reconstructing the ML phylogeny (tested with nonparametric bootstrapping) for each window. Supported ML phylogenies were then plotted along the genome, and the frequency of each topology was assessed relative to the recombination rate of the respective genomic segment. Using 100-kb windows, we also estimated divergence times between the two sister-species defined by each topology, as well as a ?normalized age? in which the depth of the sisterspecies node was divided by that of the preceding (trio) node, to further correct for recombination-rate effects. We also employed 100-kb windows to identify and map introgression events along the genome, assuming different topologies as the ?species tree?. Genome-wide monophyly for all three tested species was strongly supported, and a clear pattern was observed with respect to their phylogenetic relationships: with all window sizes, the most frequent topology (76% ? 95%) united lion+leopard as sisterspecies (topology 1), followed by lion+jaguar (topology 2: 4% ? 8%) and leopard+jaguar (topology 3: 1% ? 6%). Topology 1 was strongly predominant in regions of high recombination, e.g. terminal chromosomal segments, whereas topologies 2 and 3 were strongly enriched in low-recombination regions, especially in centromeric segments. Absolute divergence times were younger for topologies 2 and 3 (relative to topology 1) on both autosomes and the X chromosome, but this pattern was reversed when we 19 ?normalized? the depth of the terminal node using the age of the preceding (trio) node. The introgression analyses indicated pervasive historical admixture among these species, regardless of the assumed species tree. For example, if topology 1 was assumed, 5% of the genome was inferred to derive from lion-jaguar hybridization, while if topology 2 or 3 were assumed, 35% of the genome was detected as introgressed between lion and leopard. Overall, our results indicate that topology 2 (lion+jaguar) most likely reflects the original speciation relationship, given its age, frequency and recombination profile. The jaguar+leopard topology did not differ significantly in age or recombination profile, and thus likely derives from ILS. Remarkably, these results imply that a large proportion of the genome has been overwritten by post-speciation admixture between lion and leopard, leading to a complex mosaic whose phylogenetic resolution requires integration among different approaches. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-06-25T12:08:16Z |
dc.date.issued.fl_str_mv |
2019-03-27 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/masterThesis |
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masterThesis |
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publishedVersion |
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http://tede2.pucrs.br/tede2/handle/tede/8747 |
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http://tede2.pucrs.br/tede2/handle/tede/8747 |
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por |
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application/pdf |
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Pontif?cia Universidade Cat?lica do Rio Grande do Sul |
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Programa de P?s Gradua??o em Ecologia e Evolu??o da Biodiversidade |
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PUCRS |
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Brasil |
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Escola de Ci?ncias |
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Pontif?cia Universidade Cat?lica do Rio Grande do Sul |
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