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The genome complexity of papyrus baboons and the history of complex populations



RESULTS

We created an integral genome reference (Panu_3.0; GenBank adherence to GCA_000264685.2) for an olive spp.Papio anubis), baboon species most commonly used in biomedical research (S1 and Tables S1 and S2).7). In order to study the genetic separation of gender, we analyzed the complete genotypes sequences from 16 complementary individuals, from 2 to 4 individuals per six species Papyrus, and a frost (Thermophilus frozen), a closely related member as a foreign group (S2, and S3 table). This diversity panel produced 54.6 million nucleotides (SNV), of which> 42.4 million are variable Papyrus (Image S3 and Table S4). To develop an independent second independent genome differentiation, we have identified novels Alu Insertion, type of genetic variation that is fundamentally different from the mechanical mutation. Unexpectedly, we have found a very high number of last ones Alu Blisters (and rhesus macaques) with human and other primate genomes (inserting 2 images and S5 table). There are 192,889 lengths AluY elements P. anubis genome Line rate accumulation rate AluY insertion was four times higher (Figure 2) than hominoids (humans, chimpanzees or orangutans) than beans and rhesus macaques (than in African monkeys) (genus Chlorocebus), other OWM (22).

Figure 2 Comparison Alu mobilization rates in selected primates in genomes.

only Alu Items per line are included. The length of the circle corresponds to the full length length AluY elements of that species. At the right bars, the number of inscriptions per million in each line is calculated. Baboon (Panu_3.0), macaque rhesus (Mmul_8.0.1), African monkey green (chlSab2), chimpanzee (Pan_tro3) and human (GRCh38 / hg38), AluThe sequences of Y were recovered by means of cross-comparisons through some of the most recent available. Orangutan calculations are P_pygmaeus2.0.2.60). Line specifics AluY elements are similar to Rhesus macaque and baboon, and twice as much as Green African monkeys, although they are more independent of African monkeys.

Our phylogenetic analyzes provide new insights into genomic population and population protection. Maximum probability (ML) Combined SNV analyzes show that individual sponsored clusters are correctly compared to the different species of the six species in the northern and southern clades (Figure 3 and S4A image). On the other hand, SNSS suggests Bayesian analysis of the same data P. kindae It's the northernmost sister's sister P. cynocephalus and P. ursinus (S4B image). Multiple hybrid zones and documented discrepancies between relationships based on mtDNA and phenotypes (Figure 1) (12, 15) argued that the masculinised mixing and / or non-ordered oscillation lines (ILS) caused genetic relationships between these species. When polymorphism was aware, phylogenetic approach, PoMo (23, 24), once again we got to the south divine divine basal P. kindae Southern group. However, the relationship between the three southern species is the result of ML (Figure 3). PoMo offers much longer lengths of intelligent extensions P. ursinus and P. papio for other tribes. In simulations (S5 and Table S6), mixes of different lines can cross long branches and, as a result of the alleles, they will see long horns that are painfully artificially shorter. This suggests that the other four tribes may be more painful P. ursinus and P. papioIn fact, these two species are found in the southern and western ends of the baboon distribution (Figure 1).

Image 3 Phylogenetic relationships between baboon species.

(A) Phylogeny created using the phylogenetic method of polymorphism (PoMo)23, 24). The topology of the three northern species is also supported by the ML concentration of the ML concentration and 43.9% of the tree informant genes excluded from the codec sequences. [scaled concordance factor (CF) of 0.439, greater than the other two alternatives]. The topology that shows the three southern clad species is supported by PoMo analysis and has a 0.332 scaled CF score. (B) Alternative topology of the North American species, with a combined scaled 0.241 CF. (C) The alternative topology of the southern species, the analysis of the SN concentrations of the concentrated ML and the 0,513-point enlargement of the CF scale, that is, the proportion of the gene trees is greater than the other two genes that do not encode the genes.

To test a mixture of sexual baboon species, we have done an analysis fLocation links following the modeling of Markov's hidden co-calculation methods (image 4A, S7 table, and fig.S6). The best adaptation model (see Materials and methods) indicates history P. kindae It has an ancient mestization event P. ursinus (52% contribution P. kindae) and the northern clade (48% contribution) a nickname line (perhaps missing). The f-Estatists suggest that it exists P. papio It is closely linked P. anubis, but 10% of the genetic input was received in northern 10% language, although there is still no sample, perhaps missing.

Image 4 History of evolution and demography Papyrus baboons

(A) Used exams fThese conditions are stated P. kindae It was created through the tributaries of the South Clad lineage and the northern clan lineage, with contributions from 52 to 48 years. P. papio 10% introgresive insulin is due to the fact that ancient northern language is unknown to the population P. anubis. The data of divorce and crossbreeding data were derived from CoalHMM, and these nerve or mestizos events were labeled via node internal nodes A. K. He also analyzed the asymmetric sharing of our haplotype. P. cynocephalus Enter P. anubis just 21 generations ago. (B) Rebuild demographic history of Baboon using PSMC methods. There was a bottle of extension of Lottery Extension P. papio About 400 thousand years ago (ka), among the ancient population P. hamadryas and P. anubis enlarge ~ 280 ~ 160 ~ between. After diverging, P. anubis continued upward trend P. hamadryas decline ~ ~ 400k now, Ne to do it P. ursinus They vary according to the population according to estimates P. cynocephalus and P. kindae, and underwent a specific extension bottle. Du ~ 300 ka ago, the Ne Both have rebuilt P. cynocephalus and P. kindae It increased, ~ 150 ka before, before a fall. PSMC methods are not always reliable in recent times.

Our results increase the light of hybridization dynamics history P. anubis (northern clade species) and P. cynocephalus (southern clade species), which was first reported in southern Kenya on the Amboseli National Park (17). Observation observations and microsatellite analyzes support the last introgression P. anubis Enter P. cynocephalus From the 1980s onwards25, 26). Study of the broad genome distribution of the haplotype blocks P. anubis Kenya is also part of the Aberdare region, with more than 200 km north of Amboseli P. cynocephalus, ~ 546 MB of nuclear DNA derived P. cynocephalus (Image S7). If we believe that it is the result of a single-event event, it is estimated that it has occurred around 21 years (~ 220 years). However, more complex explanations are also possible. Second vertical person P. anubis It also makes Aberdare population P. cynocephalus Haplotypes, but these genomic segments are less and shorter, and perhaps due to introgressive antigens. In accordance with other studies (27), our findings suggest that several episodes of gene flow have been observed for some of these species for a long period of time, and the effects of permanent hybridization exceed the current hybrid field. This complexity may be representative of the complexity of other beans hybrid beans (10, 12, 15, 18, 19, 28).

Results motivated results fIn the discovery and sharing of haplotopes, we have done two complementary tests Papyrus Diversity panel using independent methods of analyzing hypothesis of ancient disorders. Alu Insertion polymorphisms are valuable phylogenetic characters because the polarity of specific mutations in mutations can be established for any specific genomic segment (SF image) (29). A novel haplotype Alu The insert consists of spelling haplotype Alu Repeating and rewriting are rare. A maximum rule by using the analogous Dolls parsimony using the novel baboons Alu The inserts again differed from north to south. However, the bottom lines are poorly resolved and they show apparent homoplasia (S8 image). In a well-defined phylogeny character defined polarity, it would not be expected that homoplasms have different types of ILS and / or gene flows between different species of radiation (30).

We analyzed the differences in evolution of different segments throughout the genome of the baboon genome. We distributed the reference genome into 808 genetic disorders (putatively neutral) in regions. Using BUCKy (31) and the SNV genotype from the diversity panel, we performed the Bayesian concordance analysis (BCA). Individual animals again, as expected, by clusters by species. Basal north-south divergence is allowed, but the factors of relations between each of these geographical codes (CFs) are small (Figure 3). P. hamadryas She is a sister for the most part Anubis-Papio Clade, but two other topologies are possible [(papio-(ham-anubis)) and (anubis-(ham-papio))] they are not displayed in the same frequency (SF image), as expected by the ILS. At the same time, P. kindae She is the sister in the majority cynocephalus-ursinus clade, ML results match but not f– Statistics or PoMo results. Again, two small BCA topologies are not found in the same proportion (SF image). Together, the Alu Inclusions and BCA results recognize that reticulation has been more effective than genotypic divergence (Table 1) with no ILS reticle.

Table 1 Summary of different data types and analytical analyzes used to study phylogeny of baboon species.

Differences between languages ​​and mestizaje events were calculated using Markov's hidden coil model (CoalHMM; Figs S10 and S15 and S8 and S9).32, 33). Using an estimated mutation rate of 0.9 × 10-8 for every single generation parent and for generational 11 years[seeMaterializationMethods([seeMaterialsandMethodsand([ikusiMaterialaketaMetodoaketa([seeMaterialsandMethodsand(11, 34)]We get the results shown in Figure 4A. In order to reconstruct the demographic history, divisions of Markovian divisions (PSMC) split into pairs (35), assuming the aforementioned generation and mutation rate (image 4B). As an exception P. papioWith a truncated soil, the other five species are very similar in population size (Ne) Du 4 Mai ago ~ 1.4 Du ago, deduced all baboon species before the same historical demography (ie, they were effectively a language) ~ 1.4 ago ago. all Ne Plots show a greater tendency after ~ 1.5 Ma, but specific species increases occur at different rates, perhaps due to population growth and dispersion, following the acceptance of the ecological condition after demographic expansion.14). Given the paleontological evidence of the genus south southern gender (36), we specify that the apparent decline stands out Ne In the southern clad species of north clade: links between 700,000 and 800,000 years of dispersal botulism can be seen as the geographical area of ​​the beans extends to the north. CoalHMM also suggests the existing North-East blend P. kindae It's been 100,000 years ago and PSMC's results suggest growth Ne to do it P. kindae at this moment.

To study the functional effects of the baboon mechanism, we analyzed 2201 appropriate gene regions (genomic genotypes, which have a genetic coding gene for each gene and a phylogenetic signal that is sufficient to protect a unique phylogenetic tree from all alternative trees). The phylogenetic relationships (gene trees) have been matched by individual loci, depending on the species that distinguish three northern northern species. The cluster has 1 1143 cell regions, and the phylogeny connects this result (S16 Image). The cluster has 629 genetic regions P. cynocephalus Haplotype hybaptop does not closely relate to other haplotypes (Figure 17). The ontology of these genes enriches the ontology of terms "learning and memory" (GO)P = 0.012), "knowledge" (P = 0.012), "head development" (P = 0.014), and "development development" (P = 0.017), as well as several GO categories related to the reproduction (see table S10). Chapter 3 of the cluster contains 429 genetic regions that show phylogenetic relationships among clade southern clade species, Fig. Figure 3. However, clapos of 3 haplotype northern Clada P. anubis Haplotypes are closer to the southern clade, haplotypes in the northern clade P. papio In general, the other baboon is the sister of all haplotypes (S18 image). The genes found in 3 regional clusters are related to the ontogenetic development of the various GO systems (kidney, heart, circulation and endocrine systems), especially enriched. P <0.03) (table S10). The differences between species belonging to specific genes are those that show the phylogeny of the species (that are, the species that transport the haplotypes that cross the species species). P. anubis and P. cynocephalus, a northern clade and southern clade, respectively, are hybridizing in southern Kenya (17) and DNA Nuclear Test (12).

Thanks: We recognize the Sequence Center for Genome Sequence for productive personnel contributions: KA Abraham, HA Akbar, SA Ali, UA Anosike, PA Aqrawi, FA Arias, TA Attaway, RA Awwad, CB Babu, DB Bandaranaike, PB Battles, AB Bell, BB Beltran, DB Berhane-Mersha, CB Bess, CB Bickham, TB Bolden, K. Cardenas, KC Carter, M. Cavazos, A. Chandrabose, S. Chao, DC Chau, AC Chavez, R. Chu, KC Clerc -Blankenburg, A. Cockrell , MC Coyle, A. Cree, MD Dao, ML Davila, LD Davy-Carroll, SD Denson, S. Dugan, V. Ebong, S. Elkadiri, SF Fernandez, Fernando PF, N. Flagg, LF Forbes, G.Fowler , CF Francis, LF Francisco, QF Fu, R. Gabisi, RG Garcia, T. Garner, TG Garrett, SG Gross, SG Gubbala, K. Hawkins, B. Hernandez, KH Hirani, MH Hogues, BH Hollins, LJ Jackson, MJ Javaid, JC Jayaseelan, AJ Johnson, BJ Johnson, JJ Jones, VJ Joshi, D. Kalra, JK Kalu, NK Khan, L. K Isamo, LL Lago, Y. Lai, FL Lara, T.-K. Le, F. L. Legall-Iii, S. L. Lemon, L. Lewis, J. L. Liu, Y.-S. Liu, DL Liyanage, P. London, JL Lopez, LL Lorensuhewa, E. Martinez, RM Mata, TM Mathew, T. Matskevitch, CM Mercado, IM Mercado, KM Morales, MM Morgan, MM Munidasa, LN Nazareth, IN Newsham, DN Ngo, LN Nguyen, P. Nguyen, TN Nguyen, NN Nguyen, M. Nwaokelemeh, MO Obregon, GO Okwuonu, FO Ongeri, CO Onwere, IO Osifeso, AP Parra, SP Patil, AP Perez, YP Pérez, CP Pham, E. Primus, L.-L. Pu, M. P. Puazo, J. Q. Quiroz, S. Richards, J. R. Rouhana, M. R. Ruiz, S.-J. Ruiz, N. S. Saada, J. S. Santibanez, M. S. Scheel, S. Scherer, B. S. Schneider, D. S. Simmons, I. S. Sisson, E. S. Skinner, N. Tabassum, L.-Y. Tang, A. Taylor, RT Thornton, JT Tisius, GT Toledanes, ZT Trejos, KU Usmani, RV Varghese, SV Vattathil, VV Vee, DW Walker, GW Weissenberger, CW White, K. Wilczek-Boney, AW Williams, K. Wilson, I. Woghiren, JW Woodworth, RW Wright, Y.-Q. Wu, Y. Xin, Y. Zhang, Y. Z. Zhu, and X. Zou. Biomaterials of reference DNA sequencing P. anubis Baboon and Baboons were multicultural panels at the Southwest National National Research Center (San Antonio, TX), with the collaboration of a NIH Research Infrastructures Program (P51-OD011133). The research that meets the Government and the IACUC guidelines and guidelines. J.R. It is also linked to the Wisconsin National Primate Research Center, Madison, WI. C.K. It also joins Institut für Populationsgen, Vetmeduni Vienna, Austria, and D.S. Eötvös works with Lorand University and Max Perutz Laboratories. Funding: Sequence and analysis of Sequence Center Sequencing Center, Baylor College of Medicine, NIH (NHGRI), U54-HG003273 and U54-HG006484, have been awarded R.A.G. and GAC gave 1 S10 RR026605 to J.G. Reidi. This research was also supported with NIH funding until R01-GM59290 M.A.B .; The Austrian Science Funds (FWF-P24551 and FWF-W1225) and the Vienna Science and Technology Fund (WWTF-MA16-061) help C.K. Wellcome Trust (WT108749 / Z / 15 / Z) and EMBL, B.A., F.J.M. and M.M. VEGA 1/0719/14 and APVV-14-0253 with T. Vinar (consortium member); Grant MINECO / FEDER, NIH U01-MH106874 scholarship, Howard Hughes International Career Award, and "La Caixa" Social Work T.M.-B.; The NSF grants will go BNS83-03506 to J.P.-C.; NSF1029302 J.P.-C., J.R. and C.J.J .; BNS96-15150: J.P.-C., C.J.J. and T.D .; and the National Geographic Society and Leakey Foundation J.P.-C. and C.J.J. E.E.E. He is a researcher at Howard Hughes Medical Institute. This work, partly, U.S. The NIH grant was sent to HG002385 by E.E.E. Competitive interests: The author states that they did not confirm. Availability of data and materials: The raw information about the genome assembly project, sample metadata and other information are available at the BioJPG260523 Biography at www.ncbi.nlm.nih.gov. Additional information on RNA sequencing data is available from Nonhuman at the Primate Reference Transcriptome Project (http://nhprtr.org/). Additional information on SNV and indel variation is the follow-up of the UCSC browser (https://hgsc.bcm.edu/non-human-primates/baboon-genome-project). Additional data associated with this document may require authors.Members of the Baboon Genome Analysis Consortium:Bronwen Aken1Nicoletta Archidiacono2, Georgios Athanasiadis3, Mark A. Batzer4, Thomas O. Beckstrom4Christina Bergey5.6, Konstantinos Billis1, Andrew Burrell5, Oronzo Capozzi2, Claudia R. Catacchio2, Jade Cheng3, Laura A. Cox7.8, Huyen H. Dinh9, Todd Disotell5, HarshaVardhan Doddapaneni9, Evan E. Eichler10.11, James Else12, Richard A. Gibbs9,13, Matthew W. Hahn14, Yi Han9, R. Alan Harris9,13, John Huddleston10, Shalini N. Jhangiani9, Clifford J. Jolly5, Vallmer E. Jordan4, Anis Karimpour-Fard15, Miriam K. Konkel32, Gisela H. Kopp16.17, Viktoriya Korchina9, Carolin Kosiol18, Maximillian Kothe19, Christie L. Kovar9, Lukas Kuderna20, Sandra L. Lee9, Kalle Leppälä3, Xiaoming Liu21, Yue Liu9, Thomas Mailund3, Tomas Marques-Bonet20,22,23,33, Alessia Marra-Campanale2, Fergal J. Martin1, Christopher E. Mason24, Marc de Manuel Montero20, Matthieu Muffato1Kasper Munch3, Shwetha Murali9, Donna M. Muzny9,13, Angela Noll19, Kymberleigh A. Pagel25, Antonio Palazzo2, Jera Pecotte7, Vikas Pejaver25, Jane Phillips-Conroy26, Lenore Pipes24, Veronica Searles Quick15, Predrag Radivojac25, Archana Raja10, Brian J. Raney27, Muthuswamy Raveendran9, Karen Rice7, Mariano Rocchi2, Jeffrey Rogers9,13, Christian Roos19, Mikkel Heide Schierup3, Dominik Schrempf28, James M. Sikela15, Roscoe Stanyon29, Cody J. Steely4, Gregg W. C. Thomas14, Jenny Tung30, Mario Ventura2, Tauras P. Vilgalys30, Tomás Vinar31, Jerilyn A. Walker4, Lutz Walter19, Kim C. Worley9,13, and Dietmar Zinner16.1European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom. 2Bariology, Bari, Italy, Department of Biology. 3Bioinformatic Research Center, Aarhus University, Aarhus, Denmark. 4Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA. 5Department of Anthropology, New York University, New York, NY, USA. 6Department of Biological Sciences, Notre Dame University, South Bend, IN, USA. 7Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA. 8Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA. 9Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA. 10Genomics Faculty, Washington University, Seattle, WA, USA. 11Howard Hughes Medical Institute, Washington University, Seattle, WA, USA. 12Department of Pathology and Laboratory of Medicine and Yerkes Primate Research Center, Emory University, Atlanta, GA, USA. 13Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. 14Department of Biology, Indiana University, Bloomington, IN, USA. 15Biochemistry and Molecular Genetics Department, Anschutz Medical Campus University of Colorado, Denver, CO, USA. 16Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany. 17Konstanz University, Konstanz, Germany, Department of Biology. 18Biological Diversity Center, Biology School, St. Andrews, United Kingdom. 19Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany. 20Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, ​​Spain. 21Public Health School, University of the Health Sciences Center, Houston, TX, USA. 22The Catalan Institute for Advanced Research and Studies (ICREA), Barcelona, ​​Spain. 23CNAG-CRG, Center for Genomic Regulation, Barcelona Science and Technology Institute, Barcelona, ​​Spain. 24Physiology and Biophysics Department, Weill Cornell Medical College, New York, NY, USA, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Biomedicine Computation Institute, Weill Cornell Medicine, New York, NY, USA. 25Computer and Computer Department, Indiana University, Bloomington, IN, USA. 26Department of Neuroscience, Washington University School of Medicine, St. Louis. MO, USA, and Department of Anthropology, Washington University, Seattle, WA, USA. 27Institute of Genomics, University of California, Santa Cruz, CA, USA. 28Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Vienna, Austria. 29Department of Biology, University of Florence, Florence, Italy. 30Evolutionary Anthropology Department, Duke University, Durham, NC, USA. 31Mathematics, Physics and Computer Science Faculty, Comenius University, Bratislava, Slovakia. 32Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA. 33Catalan Institute of Palaeontology Miquel Crusafont, Autonomous University of Barcelona, ​​Barcelona, ​​Spain.Contributions from members of the Consortium:Designed research and directed study: J. Rogers *, K. C. Worley and R. Gibbs. Manage or monitor sex production: D. M. Muzny *, C. L. Kovar, H. H. Dinh and Y. Han. Direction or supervision of sequencing libraries: H. Doddapaneni *, S. Lee and D.M. Muzny. This assembly was produced: K. C. Worley *, Y. Liu, S. Murali and R. A. Harris. Project and data management: D. M. Muzny *, M. Raveendran, R. A. Harris, K. C. Worley, S. N. Jhangiani, V. Korchina, C. Kovar. Genome Annotation: B. Aken *, F. J. Martin, M. Muffato, K. Billis and X. Liu. Alu A repetitive study: M. A. Batzer *, J. A. Walker, M. K. Konkel, V. E. Jordan, C. J. Steely, and T. O. Beckstrom. SNV and Indel Analysis: R. A. Harris and M. Raveendran. Admixture and phylogenetic analysis: T. Mailund, M. H. Schierup, K. Leppälä, J. Cheng, K. Munch and G. Athanasiadis. Philogenetics and population analysis: C. Bergey, A. Burrell, A. Noll, D. Schrempf, C. Kosiol, GH Kopp, G. Athanasiadis, K. Munch, J. Phillips-Conroy, M. Kothe, T. Disotell, J. Tung, J. Rogers, CJ Jolly, D. Zinner and C. Roos. Validation of cytogenetics and assembly: M. Rocchi *, R. Stanyon, E. E. Eichler, N. Archidiacono, A. Palazzo, and O. Capozzi. Gene family analysis: M. W. Hahn *, J. Sikela *, G. W. C. Thomas, V. Searles Quick, A. Karimpour-Fard, and L. Walter. Methylation Analysis: J. Tung * and T. P. Vilgalys. Positive selection selection: C. Kosiol *, T. Vinar *, and B. J. Raney. Submission changes: P. Radivojac *, K. A. Pagel and V. Pejaver. Analysis of double segmentation: E. E. Eichler *, M. Ventura, A. Raja, C. Catacchio, A. Marra-Campanale and J. Huddleston. Copy the number change: T. Marques-Bonet *, L. Kuderna, and M. d. M. Montero. Transcriptome analysis: C. E. Mason * and L. Pipes. Basic Biomaterials: K. Rice, J. Pecotte, J. Phillips-Conroy, C. J. Jolly, J. Rogers, J. Else and L. A. Cox. Texts and / or figures provided: D. Zinner, C. Roos, T. Mailund, K. Leppälä, E. Eichler, G. Athanasiadis, J. Cheng, K. Munch, C. Kosiol, C. Bergey, A. Burrell, MK Konkel, JA Walker, MA Batzer and J. Tung. Writing Papers: J. Rogers *, C. J. Jolly, J. Tung, M. Hahn, D. Zinner, C. Roos, T. Marques-Bonet and K. C. Worley. * Group leader.

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