Search

Your search keyword '"Graphodatsky AS"' showing total 28 results
Start Over Author "Graphodatsky AS" Publication Type Electronic Resources
28 results on '"Graphodatsky AS"'

1. Widespread horse-based mobility arose around 2200 BCE in Eurasia.

Author

Librado, Pablo, Librado, Pablo, Tressières, Gaetan, Chauvey, Lorelei, Fages, Antoine, Khan, Naveed, Schiavinato, Stéphanie, Calvière-Tonasso, Laure, Kusliy, Mariya, Gaunitz, Charleen, Liu, Xuexue, Wagner, Stefanie, Der Sarkissian, Clio, Seguin-Orlando, Andaine, Perdereau, Aude, Aury, Jean-Marc, Southon, John, Shapiro, Beth, Bouchez, Olivier, Donnadieu, Cécile, Collin, Yvette, Gregersen, Kristian, Jessen, Mads, Christensen, Kirsten, Claudi-Hansen, Lone, Pruvost, Mélanie, Pucher, Erich, Vulic, Hrvoje, Novak, Mario, Rimpf, Andrea, Turk, Peter, Reiter, Simone, Brem, Gottfried, Schwall, Christoph, Barrey, Éric, Robert, Céline, Degueurce, Christophe, Horwitz, Liora, Klassen, Lutz, Rasmussen, Uffe, Kveiborg, Jacob, Johannsen, Niels, Makowiecki, Daniel, Makarowicz, Przemysław, Szeliga, Marcin, Ilchyshyn, Vasyl, Rud, Vitalii, Romaniszyn, Jan, Mullin, Victoria, Verdugo, Marta, Bradley, Daniel, Cardoso, João, Valente, Maria, Telles Antunes, Miguel, Ameen, Carly, Thomas, Richard, Ludwig, Arne, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Granado, José, Schlumbaum, Angela, Deschler-Erb, Sabine, Mráz, Monika, Boulbes, Nicolas, Gardeisen, Armelle, Mayer, Christian, Döhle, Hans-Jürgen, Vicze, Magdolna, Kosintsev, Pavel, Kyselý, René, Peške, Lubomír, OConnor, Terry, Ananyevskaya, Elina, Shevnina, Irina, Logvin, Andrey, Kovalev, Alexey, Iderkhangai, Tumur-Ochir, Sablin, Mikhail, Dashkovskiy, Petr, Graphodatsky, Alexander, Merts, Ilia, Merts, Viktor, Kasparov, Aleksei, Pitulko, Vladimir, Onar, Vedat, Öztan, Aliye, Arbuckle, Benjamin, McColl, Hugh, Renaud, Gabriel, Khaskhanov, Ruslan, Demidenko, Sergey, Kadieva, Anna, Atabiev, Biyaslan, Sundqvist, Marie, Lindgren, Gabriella, López-Cachero, F, Albizuri, Silvia, Trbojević Vukičević, Tajana, Rapan Papeša, Anita, Librado, Pablo, Librado, Pablo, Tressières, Gaetan, Chauvey, Lorelei, Fages, Antoine, Khan, Naveed, Schiavinato, Stéphanie, Calvière-Tonasso, Laure, Kusliy, Mariya, Gaunitz, Charleen, Liu, Xuexue, Wagner, Stefanie, Der Sarkissian, Clio, Seguin-Orlando, Andaine, Perdereau, Aude, Aury, Jean-Marc, Southon, John, Shapiro, Beth, Bouchez, Olivier, Donnadieu, Cécile, Collin, Yvette, Gregersen, Kristian, Jessen, Mads, Christensen, Kirsten, Claudi-Hansen, Lone, Pruvost, Mélanie, Pucher, Erich, Vulic, Hrvoje, Novak, Mario, Rimpf, Andrea, Turk, Peter, Reiter, Simone, Brem, Gottfried, Schwall, Christoph, Barrey, Éric, Robert, Céline, Degueurce, Christophe, Horwitz, Liora, Klassen, Lutz, Rasmussen, Uffe, Kveiborg, Jacob, Johannsen, Niels, Makowiecki, Daniel, Makarowicz, Przemysław, Szeliga, Marcin, Ilchyshyn, Vasyl, Rud, Vitalii, Romaniszyn, Jan, Mullin, Victoria, Verdugo, Marta, Bradley, Daniel, Cardoso, João, Valente, Maria, Telles Antunes, Miguel, Ameen, Carly, Thomas, Richard, Ludwig, Arne, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Granado, José, Schlumbaum, Angela, Deschler-Erb, Sabine, Mráz, Monika, Boulbes, Nicolas, Gardeisen, Armelle, Mayer, Christian, Döhle, Hans-Jürgen, Vicze, Magdolna, Kosintsev, Pavel, Kyselý, René, Peške, Lubomír, OConnor, Terry, Ananyevskaya, Elina, Shevnina, Irina, Logvin, Andrey, Kovalev, Alexey, Iderkhangai, Tumur-Ochir, Sablin, Mikhail, Dashkovskiy, Petr, Graphodatsky, Alexander, Merts, Ilia, Merts, Viktor, Kasparov, Aleksei, Pitulko, Vladimir, Onar, Vedat, Öztan, Aliye, Arbuckle, Benjamin, McColl, Hugh, Renaud, Gabriel, Khaskhanov, Ruslan, Demidenko, Sergey, Kadieva, Anna, Atabiev, Biyaslan, Sundqvist, Marie, Lindgren, Gabriella, López-Cachero, F, Albizuri, Silvia, Trbojević Vukičević, Tajana, and Rapan Papeša, Anita

Abstract

Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.

Published
2024

2. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Author

Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, Kliver, Sergei, Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, and Kliver, Sergei

Abstract

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Published
2023

3. Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity

Author

Houck, Marlys L., Koepfli, Klaus-Peter, Hains, Taylor, Khan, Ruqayya, Charter, Suellen J., Fronczek, Julie A., Misuraca, Ann C., Kliver, Sergei, Perelman, Polina L., Beklemisheva, Violetta, Graphodatsky, Alexander, Luo, Shu-Jin, O'Brien, Stephen J., Lim, Norman T.-L., Chin, Jason S. C., Guerra, Vanessa, Tamazian, Gaik, Omer, Arina, Weisz, David, Kaemmerer, Kenneth, Sturgeon, Ginger, Gaspard, Joseph, Hahn, Alicia, McDonough, Mark, Garcia-Treviño, Isabel, Gentry, Jordan, Coke, Rob L., Janecka, Jan E., Harrigan, Ryan J., Tinsman, Jen, Smith, Thomas B., Aiden, Erez Lieberman, Dudchenko, Olga, Houck, Marlys L., Koepfli, Klaus-Peter, Hains, Taylor, Khan, Ruqayya, Charter, Suellen J., Fronczek, Julie A., Misuraca, Ann C., Kliver, Sergei, Perelman, Polina L., Beklemisheva, Violetta, Graphodatsky, Alexander, Luo, Shu-Jin, O'Brien, Stephen J., Lim, Norman T.-L., Chin, Jason S. C., Guerra, Vanessa, Tamazian, Gaik, Omer, Arina, Weisz, David, Kaemmerer, Kenneth, Sturgeon, Ginger, Gaspard, Joseph, Hahn, Alicia, McDonough, Mark, Garcia-Treviño, Isabel, Gentry, Jordan, Coke, Rob L., Janecka, Jan E., Harrigan, Ryan J., Tinsman, Jen, Smith, Thomas B., Aiden, Erez Lieberman, and Dudchenko, Olga

Abstract

We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.

Published
2023

4. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Author

Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, Kliver, Sergei, Yakupova, Aliya, Tomarovsky, Andrey, Totikov, Azamat, Beklemisheva, Violetta, Logacheva, Maria, Perelman, Polina L., Komissarov, Aleksey, Dobrynin, Pavel, Krasheninnikova, Ksenia, Tamazian, Gaik, Serdyukova, Natalia A., Rayko, Mike, Bulyonkova, Tatiana, Cherkasov, Nikolay, Pylev, Vladimir, Peterfeld, Vladimir, Penin, Aleksey, Balanovska, Elena, Lapidus, Alla, OBrien, Stephen J., Graphodatsky, Alexander, Koepfli, Klaus-Peter, and Kliver, Sergei

Abstract

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Published
2023

5. Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human

Author

Romanenko, Svetlana A., Kliver, Sergei F., Serdyukova, Natalia A., Perelman, Polina L., Trifonov, Vladimir A., Seluanov, Andrei, Gorbunova, Vera, Azpurua, Jorge, Pereira, Jorge C., Ferguson-Smith, Malcolm A., Graphodatsky, Alexander S., Romanenko, Svetlana A., Kliver, Sergei F., Serdyukova, Natalia A., Perelman, Polina L., Trifonov, Vladimir A., Seluanov, Andrei, Gorbunova, Vera, Azpurua, Jorge, Pereira, Jorge C., Ferguson-Smith, Malcolm A., and Graphodatsky, Alexander S.

Abstract

Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.

Published
2023

6. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes)

Author

Kliver, Sergei, Houck, Marlys L., Perelman, Polina L., Totikov, Azamat, Tomarovsky, Andrei, Dudchenko, Olga, Omer, Arina D., Colaric, Zane, Weisz, David, Aiden, Erez Lieberman, Chan, Saki, Hastie, Alex, Komissarov, Aleksey, Ryder, Oliver A., Graphodatsky, Alexander, Johnson, Warren E., Maldonado, Jesús E., Pukazhenthi, Budhan S., Marinari, Paul E., Wildt, David E., Koepfli, Klaus-Peter, Kliver, Sergei, Houck, Marlys L., Perelman, Polina L., Totikov, Azamat, Tomarovsky, Andrei, Dudchenko, Olga, Omer, Arina D., Colaric, Zane, Weisz, David, Aiden, Erez Lieberman, Chan, Saki, Hastie, Alex, Komissarov, Aleksey, Ryder, Oliver A., Graphodatsky, Alexander, Johnson, Warren E., Maldonado, Jesús E., Pukazhenthi, Budhan S., Marinari, Paul E., Wildt, David E., and Koepfli, Klaus-Peter

Abstract

The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 Kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million years ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.

Published
2023

7. Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human

Author

Romanenko, Svetlana A., Kliver, Sergei F., Serdyukova, Natalia A., Perelman, Polina L., Trifonov, Vladimir A., Seluanov, Andrei, Gorbunova, Vera, Azpurua, Jorge, Pereira, Jorge C., Ferguson-Smith, Malcolm A., Graphodatsky, Alexander S., Romanenko, Svetlana A., Kliver, Sergei F., Serdyukova, Natalia A., Perelman, Polina L., Trifonov, Vladimir A., Seluanov, Andrei, Gorbunova, Vera, Azpurua, Jorge, Pereira, Jorge C., Ferguson-Smith, Malcolm A., and Graphodatsky, Alexander S.

Abstract

Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.

Published
2023

8. The Origins and Spread of Domestic Horses from the Western Eurasian Steppes

Author

Librado, P., Khan, N., Fages, A., Kusliy, M. A., Suchan, T., Tonasso-Calvière, L., Schiavinato, S., Alioglu, D., Fromentier, A., Perdereau, A., Aury, J. -M., Gaunitz, C., Chauvey, L., Seguin-Orlando, A., Der Sarkissian, C., Southon, J., Shapiro, B., Tishkin, A. A., Kovalev, A. A., Alquraishi, S., Alfarhan, A. H., Al-Rasheid, K. A. S., Seregély, T., Klassen, L., Iversen, R., Bignon-Lau, O., Bodu, P., Olive, M., Castel, J. -C., Boudadi-Maligne, M., Alvarez, N., Germonpré, M., Moskal-del Hoyo, M., Wilczyński, J., Pospuła, S., Lasota-Kuś, A., Tunia, K., Nowak, M., Rannamäe, E., Saarma, U., Boeskorov, G., Lōugas, L., Kyselý, R., Peške, L., Bălășescu, A., Dumitrașcu, V., Dobrescu, R., Gerber, D., Kiss, V., Szécsényi-Nagy, A., Mende, B. G., Gallina, Z., Somogyi, K., Kulcsár, G., Gál, E., Bendrey, R., Allentoft, M. E., Sirbu, G., Dergachev, V., Shephard, H., Tomadini, N., Grouard, S., Kasparov, A., Basilyan, A. E., Anisimov, M. A., Nikolskiy, P. A., Pavlova, E. Y., Pitulko, V., Brem, G., Wallner, B., Schwall, C., Keller, M., Kitagawa, K., Bessudnov, A. N., Bessudnov, A., Taylor, W., Magail, J., Gantulga, J. -O., Bayarsaikhan, J., Erdenebaatar, D., Tabaldiev, K., Mijiddorj, E., Boldgiv, B., Tsagaan, T., Pruvost, M., Olsen, S., Makarewicz, C. A., Valenzuela Lamas, S., Albizuri Canadell, S., Nieto Espinet, A., Iborra, M. P., Lira Garrido, J., Rodríguez González, E., Celestino, S., Olària, C., Arsuaga, J. L., Kotova, N., Pryor, A., Crabtree, P., Zhumatayev, R., Toleubaev, A., Morgunova, N. L., Kuznetsova, T., Lordkipanize, D., Marzullo, M., Prato, O., Bagnasco Gianni, G., Tecchiati, U., Clavel, B., Lepetz, S., Davoudi, H., Mashkour, M., Berezina, N. Y., Stockhammer, P. W., Krause, J., Haak, W., Morales-Muñiz, A., Benecke, N., Hofreiter, M., Ludwig, A., Graphodatsky, A. S., Peters, J., Kiryushin, K. Y., Iderkhangai, T. -O., Bokovenko, N. A., Vasiliev, S. K., Seregin, N. N., Chugunov, K. V., Plasteeva, N. A., Baryshnikov, G. F., Petrova, E., Sablin, M., Ananyevskaya, E., Logvin, A., Shevnina, I., Logvin, V., Kalieva, S., Loman, V., Kukushkin, I., Merz, I., Merz, V., Sakenov, S., Varfolomeyev, V., Usmanova, E., Zaibert, V., Arbuckle, B., Belinskiy, A. B., Kalmykov, A., Reinhold, S., Hansen, S., Yudin, A. I., Vybornov, A. A., Epimakhov, A., Berezina, N. S., Roslyakova, N., Kosintsev, P. A., Kuznetsov, P. F., Anthony, D., Kroonen, G. J., Kristiansen, K., Wincker, P., Outram, A., Orlando, L., Librado, P., Khan, N., Fages, A., Kusliy, M. A., Suchan, T., Tonasso-Calvière, L., Schiavinato, S., Alioglu, D., Fromentier, A., Perdereau, A., Aury, J. -M., Gaunitz, C., Chauvey, L., Seguin-Orlando, A., Der Sarkissian, C., Southon, J., Shapiro, B., Tishkin, A. A., Kovalev, A. A., Alquraishi, S., Alfarhan, A. H., Al-Rasheid, K. A. S., Seregély, T., Klassen, L., Iversen, R., Bignon-Lau, O., Bodu, P., Olive, M., Castel, J. -C., Boudadi-Maligne, M., Alvarez, N., Germonpré, M., Moskal-del Hoyo, M., Wilczyński, J., Pospuła, S., Lasota-Kuś, A., Tunia, K., Nowak, M., Rannamäe, E., Saarma, U., Boeskorov, G., Lōugas, L., Kyselý, R., Peške, L., Bălășescu, A., Dumitrașcu, V., Dobrescu, R., Gerber, D., Kiss, V., Szécsényi-Nagy, A., Mende, B. G., Gallina, Z., Somogyi, K., Kulcsár, G., Gál, E., Bendrey, R., Allentoft, M. E., Sirbu, G., Dergachev, V., Shephard, H., Tomadini, N., Grouard, S., Kasparov, A., Basilyan, A. E., Anisimov, M. A., Nikolskiy, P. A., Pavlova, E. Y., Pitulko, V., Brem, G., Wallner, B., Schwall, C., Keller, M., Kitagawa, K., Bessudnov, A. N., Bessudnov, A., Taylor, W., Magail, J., Gantulga, J. -O., Bayarsaikhan, J., Erdenebaatar, D., Tabaldiev, K., Mijiddorj, E., Boldgiv, B., Tsagaan, T., Pruvost, M., Olsen, S., Makarewicz, C. A., Valenzuela Lamas, S., Albizuri Canadell, S., Nieto Espinet, A., Iborra, M. P., Lira Garrido, J., Rodríguez González, E., Celestino, S., Olària, C., Arsuaga, J. L., Kotova, N., Pryor, A., Crabtree, P., Zhumatayev, R., Toleubaev, A., Morgunova, N. L., Kuznetsova, T., Lordkipanize, D., Marzullo, M., Prato, O., Bagnasco Gianni, G., Tecchiati, U., Clavel, B., Lepetz, S., Davoudi, H., Mashkour, M., Berezina, N. Y., Stockhammer, P. W., Krause, J., Haak, W., Morales-Muñiz, A., Benecke, N., Hofreiter, M., Ludwig, A., Graphodatsky, A. S., Peters, J., Kiryushin, K. Y., Iderkhangai, T. -O., Bokovenko, N. A., Vasiliev, S. K., Seregin, N. N., Chugunov, K. V., Plasteeva, N. A., Baryshnikov, G. F., Petrova, E., Sablin, M., Ananyevskaya, E., Logvin, A., Shevnina, I., Logvin, V., Kalieva, S., Loman, V., Kukushkin, I., Merz, I., Merz, V., Sakenov, S., Varfolomeyev, V., Usmanova, E., Zaibert, V., Arbuckle, B., Belinskiy, A. B., Kalmykov, A., Reinhold, S., Hansen, S., Yudin, A. I., Vybornov, A. A., Epimakhov, A., Berezina, N. S., Roslyakova, N., Kosintsev, P. A., Kuznetsov, P. F., Anthony, D., Kroonen, G. J., Kristiansen, K., Wincker, P., Outram, A., and Orlando, L.

Abstract

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12. © 2021, The Author(s).

Published
2021

9. The origins and spread of domestic horses from the Western Eurasian steppes

Author

Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, Orlando, Ludovic, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, and Orlando, Ludovic

Abstract

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12., Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.

Published
2021

10. Performance and automation of ancient DNA capture with RNA hyRAD probes

Author

Université Toulouse III Paul Sabatier, Centre National de la Recherche Scientifique (France), European Research Council, Russian Foundation for Basic Research, Suchan, Tomas, Kusliy, Mariya A., Khan, Naveed, Chauvey, Loreleï, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Southon, John, Keller, Marcel, Kitagawa, Keiko, Krause, Johannes, Bessudnov, Alexander N., Bessudnov, Alexander A., Graphodatsky, Alexander S., Valenzuela-Lamas, Silvia, Wilczyński, Jarosław, Pospuła, Sylwia, Tunia, Krzysztof, Nowak, Marek, Moskal-del Hoyo, Magdalena, Tishkin, Alexey A., Pryor, Alexander J. E., Outram, Alan K., Orlando, Ludovic, Université Toulouse III Paul Sabatier, Centre National de la Recherche Scientifique (France), European Research Council, Russian Foundation for Basic Research, Suchan, Tomas, Kusliy, Mariya A., Khan, Naveed, Chauvey, Loreleï, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Southon, John, Keller, Marcel, Kitagawa, Keiko, Krause, Johannes, Bessudnov, Alexander N., Bessudnov, Alexander A., Graphodatsky, Alexander S., Valenzuela-Lamas, Silvia, Wilczyński, Jarosław, Pospuła, Sylwia, Tunia, Krzysztof, Nowak, Marek, Moskal-del Hoyo, Magdalena, Tishkin, Alexey A., Pryor, Alexander J. E., Outram, Alan K., and Orlando, Ludovic

Abstract

DNA hybridization-capture techniques allow researchers to focus their sequencing efforts on preselected genomic regions. This feature is especially useful when analys- ing ancient DNA (aDNA) extracts, which are often dominated by exogenous environ- mental sources. Here, we assessed, for the first time, the performance of hyRAD as an inexpensive and design-free alternative to commercial capture protocols to obtain authentic aDNA data from osseous remains. HyRAD relies on double enzymatic re- striction of fresh DNA extracts to produce RNA probes that cover only a fraction ofthe genome and can serve as baits for capturing homologous fragments from aDNA li- braries. We found that this approach could retrieve sequence data from horse remains coming from a range of preservation environments, including beyond radiocarbon range, yielding up to 146.5-fold on-target enrichment for aDNA extracts showing ex- tremely low endogenous content (<1%). Performance was, however, more limited for those samples already characterized by good DNA preservation (>20%¿30%), while the fraction of endogenous reads mapping on- and off-target was relatively insensi- tive to the original endogenous DNA content. Procedures based on two instead of a single round of capture increased on-target coverage up to 3.6-fold. Additionally, we used methylation-sensitive restriction enzymes to produce probes targeting hypo- methylated regions, which improved data quality by reducing post-mortem DNA dam- age and mapping within multicopy regions. Finally, we developed a fully automated hyRAD protocol utilizing inexpensive robotic platforms to facilitate capture process- ing. Overall, our work establishes hyRAD as a cost-effective strategy to recover a set of shared orthologous variants across multiple ancient samples.

Published
2021

11. The origins and spread of domestic horses from the Western Eurasian steppes

Author

Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, Orlando, Ludovic, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan, Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean-Marc, Gaunitz, Charleen, Chauvey, Lorelei, Seguin-Orlando, Andaine, Der Sarkissian, Clio, Southon, John, Shapiro, Beth, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A. S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Alvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lōugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Gerber, Daniel, Kiss, Viktória, Szécsényi-Nagy, Anna, Mende, Balázs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Valenzuela Lamas, Silvia, Albizuri Canadell, Silvia, Nieto Espinet, Ariadna, Iborra, Ma Pilar, Lira Garrido, Jaime, Rodríguez González, Esther, Celestino, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Toleubaev, Abdesh, Morgunova, Nina L., Kuznetsova, Tatiana, Lordkipanize, David, Marzullo, Matilde, Prato, Ornella, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus J., Kristiansen, Kristian, Wincker, Patrick, Outram, Alan, and Orlando, Ludovic

Abstract

Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12., Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture11,12.

Published
2021

12. The origins and spread of domestic horses from the Western Eurasian steppes

Author

Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan,Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean‐Marc, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lõugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Toleubaev, Abdesh, Gerber, Daniel, Kiss, Viktória, Anna Szécsényi-Nagy, Mende, Balazs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Morgunova, Nina L., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Kuznetsova, Tatyana V., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Lordkipanidze, David, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Marzullo, Matilde, Valenzuela-Lamas, Silvia, Albizuri, Silvia, Nieto-Espinet, Ariadna, Iborra Eres, María Pilar, Lira, Jaime, Rodríguez González, Esther, Celestino Pérez, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Prato, Ornella, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Gaunitz, Charleen, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Chauvey, Lorelei, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Seguin-Orlando, Andaine, Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Sarkissian, Clio Der, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Southon, John, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus, Kristiansen, Kristian, Shapiro, Beth, Wincker, Patrick, Outram, Alan K., Orlando, Ludovic, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A.S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Álvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, Tunia, Krzysztof, Librado, Pablo, Khan, Naveed, Fages, Antoine, Kusliy, Mariya A., Suchan,Tomasz, Tonasso-Calvière, Laure, Schiavinato, Stéphanie, Alioglu, Duha, Fromentier, Aurore, Perdereau, Aude, Aury, Jean‐Marc, Nowak, Marek, Rannamäe, Eve, Saarma, Urmas, Boeskorov, Gennady, Lõugas, Lembi, Kyselý, René, Peške, Lubomír, Bălășescu, Adrian, Dumitrașcu, Valentin, Dobrescu, Roxana, Toleubaev, Abdesh, Gerber, Daniel, Kiss, Viktória, Anna Szécsényi-Nagy, Mende, Balazs G., Gallina, Zsolt, Somogyi, Krisztina, Kulcsár, Gabriella, Gál, Erika, Bendrey, Robin, Allentoft, Morten E., Morgunova, Nina L., Sirbu, Ghenadie, Dergachev, Valentin, Shephard, Henry, Tomadini, Noémie, Grouard, Sandrine, Kasparov, Aleksei, Basilyan, Alexander E., Anisimov, Mikhail A., Nikolskiy, Pavel A., Pavlova, Elena Y., Kuznetsova, Tatyana V., Pitulko, Vladimir, Brem, Gottfried, Wallner, Barbara, Schwall, Christoph, Keller, Marcel, Kitagawa, Keiko, Bessudnov, Alexander N., Bessudnov, Alexander, Taylor, William, Magail, Jérome, Lordkipanidze, David, Gantulga, Jamiyan-Ombo, Bayarsaikhan, Jamsranjav, Erdenebaatar, Diimaajav, Tabaldiev, Kubatbeek, Mijiddorj, Enkhbayar, Boldgiv, Bazartseren, Tsagaan, Turbat, Pruvost, Mélanie, Olsen, Sandra, Makarewicz, Cheryl A., Marzullo, Matilde, Valenzuela-Lamas, Silvia, Albizuri, Silvia, Nieto-Espinet, Ariadna, Iborra Eres, María Pilar, Lira, Jaime, Rodríguez González, Esther, Celestino Pérez, Sebastián, Olària, Carmen, Arsuaga, Juan Luis, Kotova, Nadiia, Prato, Ornella, Pryor, Alexander, Crabtree, Pam, Zhumatayev, Rinat, Bagnasco Gianni, Giovanna, Tecchiati, Umberto, Clavel, Benoit, Lepetz, Sébastien, Gaunitz, Charleen, Davoudi, Hossein, Mashkour, Marjan, Berezina, Natalia Ya., Stockhammer, Philipp W., Krause, Johannes, Haak, Wolfgang, Morales-Muñiz, Arturo, Benecke, Norbert, Hofreiter, Michael, Ludwig, Arne, Chauvey, Lorelei, Graphodatsky, Alexander S., Peters, Joris, Kiryushin, Kirill Yu., Iderkhangai, Tumur-Ochir, Bokovenko, Nikolay A., Vasiliev, Sergey K., Seregin, Nikolai N., Chugunov, Konstantin V., Plasteeva, Natalya A., Baryshnikov, Gennady F., Seguin-Orlando, Andaine, Petrova, Ekaterina, Sablin, Mikhail, Ananyevskaya, Elina, Logvin, Andrey, Shevnina, Irina, Logvin, Victor, Kalieva, Saule, Loman, Valeriy, Kukushkin, Igor, Merz, Ilya, Sarkissian, Clio Der, Merz, Victor, Sakenov, Sergazy, Varfolomeyev, Victor, Usmanova, Emma, Zaibert, Viktor, Arbuckle, Benjamin, Belinskiy, Andrey B., Kalmykov, Alexej, Reinhold, Sabine, Hansen, Svend, Southon, John, Yudin, Aleksandr I., Vybornov, Alekandr A., Epimakhov, Andrey, Berezina, Natalia S., Roslyakova, Natalia, Kosintsev, Pavel A., Kuznetsov, Pavel F., Anthony, David, Kroonen, Guus, Kristiansen, Kristian, Shapiro, Beth, Wincker, Patrick, Outram, Alan K., Orlando, Ludovic, Tishkin, Alexey A., Kovalev, Alexey A., Alquraishi, Saleh, Alfarhan, Ahmed H., Al-Rasheid, Khaled A.S., Seregély, Timo, Klassen, Lutz, Iversen, Rune, Bignon-Lau, Olivier, Bodu, Pierre, Olive, Monique, Castel, Jean-Christophe, Boudadi-Maligne, Myriam, Álvarez, Nadir, Germonpré, Mietje, Moskal-del Hoyo, Magdalena, Wilczyński, Jarosław, Pospuła, Sylwia, Lasota-Kuś, Anna, and Tunia, Krzysztof

Abstract

Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture.

Published
2021

13. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Author

Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., Lewin, Harris A., Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., and Lewin, Harris A.

Abstract

BACKGROUND: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. FINDINGS: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. CONCLUSIONS: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population

Published
2019

14. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi).

Author

Farré, Marta, Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A, Kulemzina, Anastasia I, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Graphodatsky, Alexander S, Zhang, Guoije, Larkin, Denis M, Lewin, Harris A, Farré, Marta, Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A, Kulemzina, Anastasia I, Chemnick, Leona G, Kim, Jaebum, Ryder, Oliver A, Ma, Jian, Graphodatsky, Alexander S, Zhang, Guoije, Larkin, Denis M, and Lewin, Harris A

Abstract

The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population size has declined by 52% in recent ye

Published
2019

15. Precision nomenclature for the new genomics.

Author

Lewin, Harris A, Lewin, Harris A, Graves, Jennifer A Marshall, Ryder, Oliver A, Graphodatsky, Alexander S, O'Brien, Stephen J, Lewin, Harris A, Lewin, Harris A, Graves, Jennifer A Marshall, Ryder, Oliver A, Graphodatsky, Alexander S, and O'Brien, Stephen J

Abstract

The confluence of two scientific disciplines may lead to nomenclature conflicts that require new terms while respecting historical definitions. This is the situation with the current state of cytology and genomics, which offer examples of distinct nomenclature and vocabularies that require reconciliation. In this article, we propose the new terms C-scaffold (for chromosome-scale assemblies of sequenced DNA fragments, commonly named scaffolds) and scaffotype (the resulting collection of C-scaffolds that represent an organism's genome). This nomenclature avoids conflict with the historical definitions of the terms chromosome (a microscopic body made of DNA and protein) and karyotype (the collection of images of all chromosomes of an organism or species). As large-scale sequencing projects progress, adoption of this nomenclature will assist end users to properly classify genome assemblies, thus facilitating genomic analysis.

Published
2019

16. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks.

Author

Farré, Marta, Farré, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna V, Zhang, Guojie, O'Brien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, Larkin, Denis M, Farré, Marta, Farré, Marta, Kim, Jaebum, Proskuryakova, Anastasia A, Zhang, Yang, Kulemzina, Anastasia I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L, Perelman, Polina L, Johnson, Warren E, Warren, Wesley C, Kukekova, Anna V, Zhang, Guojie, O'Brien, Stephen J, Ryder, Oliver A, Graphodatsky, Alexander S, Ma, Jian, Lewin, Harris A, and Larkin, Denis M

Abstract

The role of chromosome rearrangements in driving evolution has been a long-standing question of evolutionary biology. Here we focused on ruminants as a model to assess how rearrangements may have contributed to the evolution of gene regulation. Using reconstructed ancestral karyotypes of Cetartiodactyls, Ruminants, Pecorans, and Bovids, we traced patterns of gross chromosome changes. We found that the lineage leading to the ruminant ancestor after the split from other cetartiodactyls was characterized by mostly intrachromosomal changes, whereas the lineage leading to the pecoran ancestor (including all livestock ruminants) included multiple interchromosomal changes. We observed that the liver cell putative enhancers in the ruminant evolutionary breakpoint regions are highly enriched for DNA sequences under selective constraint acting on lineage-specific transposable elements (TEs) and a set of 25 specific transcription factor (TF) binding motifs associated with recently active TEs. Coupled with gene expression data, we found that genes near ruminant breakpoint regions exhibit more divergent expression profiles among species, particularly in cattle, which is consistent with the phylogenetic origin of these breakpoint regions. This divergence was significantly greater in genes with enhancers that contain at least one of the 25 specific TF binding motifs and located near bovidae-to-cattle lineage breakpoint regions. Taken together, by combining ancestral karyotype reconstructions with analysis of cis regulatory element and gene expression evolution, our work demonstrated that lineage-specific regulatory elements colocalized with gross chromosome rearrangements may have provided valuable functional modifications that helped to shape ruminant evolution.

Published
2019

17. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Author

Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., Lewin, Harris A., Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., and Lewin, Harris A.

Abstract

BACKGROUND: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. FINDINGS: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. CONCLUSIONS: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population

Published
2019

18. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Author

Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A., Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L., Perelman, Polina L., Johnson, Warren E., Warren, Wesley C., Kukekova, Anna, V, Zhang, Guojie, O'Brien, Stephen J., Ryder, Oliver A, Graphodatsky, Alexander S., Ma, Jian, Lewin, Harris A., Larkin, Denis M., Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A., Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L., Perelman, Polina L., Johnson, Warren E., Warren, Wesley C., Kukekova, Anna, V, Zhang, Guojie, O'Brien, Stephen J., Ryder, Oliver A, Graphodatsky, Alexander S., Ma, Jian, Lewin, Harris A., and Larkin, Denis M.

Published
2019

19. Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks

Author

Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A., Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L., Perelman, Polina L., Johnson, Warren E., Warren, Wesley C., Kukekova, Anna, V, Zhang, Guojie, O'Brien, Stephen J., Ryder, Oliver A, Graphodatsky, Alexander S., Ma, Jian, Lewin, Harris A., Larkin, Denis M., Farre, Marta, Kim, Jaebum, Proskuryakova, Anastasia A., Zhang, Yang, Kulemzina, Anastasia, I, Li, Qiye, Zhou, Yang, Xiong, Yingqi, Johnson, Jennifer L., Perelman, Polina L., Johnson, Warren E., Warren, Wesley C., Kukekova, Anna, V, Zhang, Guojie, O'Brien, Stephen J., Ryder, Oliver A, Graphodatsky, Alexander S., Ma, Jian, Lewin, Harris A., and Larkin, Denis M.

Published
2019

20. An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi)

Author

Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., Lewin, Harris A., Farré, Marta, Li, Qiye, Darolti, Iulia, Zhou, Yang, Damas, Joana, Proskuryakova, Anastasia A., Kulemzina, Anastasia I., Chemnick, Leona G., Kim, Jaebum, Ryder, Oliver A., Ma, Jian, Graphodatsky, Alexander S., Zhang, Guoije, Larkin, Denis M., and Lewin, Harris A.

Abstract

BACKGROUND: The Masai giraffe (Giraffa camelopardalis tippelskirchi) is the largest-bodied giraffe and the world's tallest terrestrial animal. With its extreme size and height, the giraffe's unique anatomical and physiological adaptations have long been of interest to diverse research fields. Giraffes are also critical to ecosystems of sub-Saharan Africa, with their long neck serving as a conduit to food sources not shared by other herbivores. Although the genome of a Masai giraffe has been sequenced, the assembly was highly fragmented and suboptimal for genome analysis. Herein we report an improved giraffe genome assembly to facilitate evolutionary analysis of the giraffe and other ruminant genomes. FINDINGS: Using SOAPdenovo2 and 170 Gbp of Illumina paired-end and mate-pair reads, we generated a 2.6-Gbp male Masai giraffe genome assembly, with a scaffold N50 of 3 Mbp. The incorporation of 114.6 Gbp of Chicago library sequencing data resulted in a HiRise SOAPdenovo + Chicago assembly with an N50 of 48 Mbp and containing 95% of expected genes according to BUSCO analysis. Using the Reference-Assisted Chromosome Assembly tool, we were able to order and orient scaffolds into 42 predicted chromosome fragments (PCFs). Using fluorescence in situ hybridization, we placed 153 cattle bacterial artificial chromosomes onto giraffe metaphase spreads to assess and assign the PCFs on 14 giraffe autosomes and the X chromosome resulting in the final assembly with an N50 of 177.94 Mbp. In this assembly, 21,621 protein-coding genes were identified using both de novo and homology-based predictions. CONCLUSIONS: We have produced the first chromosome-scale genome assembly for a Giraffidae species. This assembly provides a valuable resource for the study of artiodactyl evolution and for understanding the molecular basis of the unique adaptive traits of giraffes. In addition, the assembly will provide a powerful resource to assist conservation efforts of Masai giraffe, whose population

Published
2019

21. B chromosomes of the Asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations

Author

Komissarov, A., Vij, S., Yurchenko, A., Trifonov, V., Thevasagayam, N., Saju, J., Sridatta, P., Purushothaman, K., Graphodatsky, A., Orbán, L., Kuznetsova, I., Komissarov, A., Vij, S., Yurchenko, A., Trifonov, V., Thevasagayam, N., Saju, J., Sridatta, P., Purushothaman, K., Graphodatsky, A., Orbán, L., and Kuznetsova, I.

Abstract

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT-and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.

Published
2018

22. B chromosomes of the Asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations

Author

Komissarov, A., Vij, S., Yurchenko, A., Trifonov, V., Thevasagayam, N., Saju, J., Sridatta, P., Purushothaman, K., Graphodatsky, A., Orbán, L., Kuznetsova, I., Komissarov, A., Vij, S., Yurchenko, A., Trifonov, V., Thevasagayam, N., Saju, J., Sridatta, P., Purushothaman, K., Graphodatsky, A., Orbán, L., and Kuznetsova, I.

Abstract

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT-and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.

Published
2018

23. Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours

Author

Kukekova, Anna V., Johnson, Jennifer L., Xiang, Xueyan, Feng, Shaohong, Liu, Shiping, Rando, Halie M., Kharlamova, Anastasiya V., Herbeck, Yury, Serdyukova, Natalya A., Xiong, Zijun, Beklemischeva, Violetta, Koepfli, Klaus-Peter, Gulevich, Rimma G., Vladimirova, Anastasiya V., Hekman, Jessica P., Perelman, Polina L., Graphodatsky, Aleksander S., O'Brien, Stephen J., Wang, Xu, Clark, Andrew G., Acland, Gregory M., Trut, Lyudmila N., Zhang, Guojie, Kukekova, Anna V., Johnson, Jennifer L., Xiang, Xueyan, Feng, Shaohong, Liu, Shiping, Rando, Halie M., Kharlamova, Anastasiya V., Herbeck, Yury, Serdyukova, Natalya A., Xiong, Zijun, Beklemischeva, Violetta, Koepfli, Klaus-Peter, Gulevich, Rimma G., Vladimirova, Anastasiya V., Hekman, Jessica P., Perelman, Polina L., Graphodatsky, Aleksander S., O'Brien, Stephen J., Wang, Xu, Clark, Andrew G., Acland, Gregory M., Trut, Lyudmila N., and Zhang, Guojie

Published
2018

24. Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group

Author

Basset, Patrick, Yannic, Glenn, Yang, Fengtang, O'Brien, Patricia, Graphodatsky, Alexander, Ferguson-Smith, Malcolm, Balmus, Gabriel, Volobouev, Vitaly, Hausser, Jacques, Basset, Patrick, Yannic, Glenn, Yang, Fengtang, O'Brien, Patricia, Graphodatsky, Alexander, Ferguson-Smith, Malcolm, Balmus, Gabriel, Volobouev, Vitaly, and Hausser, Jacques

Abstract

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group

Published
2018

25. Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog

Author

Druzhkova, A.S., Thalmann, O., Trifonov, V.A., Leonard, Jennifer A., Vorobieva, N.A., Ovodov, N.D., Graphodatsky, A.S., Wayne, Robert K., Druzhkova, A.S., Thalmann, O., Trifonov, V.A., Leonard, Jennifer A., Vorobieva, N.A., Ovodov, N.D., Graphodatsky, A.S., and Wayne, Robert K.

Abstract

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication. © 2013 Druzhkova et al.

Published
2013

26. Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

Author

Froenicke, Lutz, Froenicke, Lutz, Caldés, Montserrat Garcia, Graphodatsky, Alexander, Müller, Stefan, Lyons, Leslie A, Robinson, Terence J, Volleth, Marianne, Yang, Fengtang, Wienberg, Johannes, Froenicke, Lutz, Froenicke, Lutz, Caldés, Montserrat Garcia, Graphodatsky, Alexander, Müller, Stefan, Lyons, Leslie A, Robinson, Terence J, Volleth, Marianne, Yang, Fengtang, and Wienberg, Johannes

Abstract

"Excavating" ancestral genomes The recent release of the chicken genome sequence (Hillier et al. 2004Go) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004Go; Bourque et al. 2005Go). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003Go; Yang et al. 2003Go; Robinson et al. 2004Go; Svartman et al. 2004Go; Wienberg 2004Go; Froenicke 2005Go) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005Go). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.

Published
2006

27. Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

Author

Froenicke, Lutz, Froenicke, Lutz, Caldés, Montserrat Garcia, Graphodatsky, Alexander, Müller, Stefan, Lyons, Leslie A, Robinson, Terence J, Volleth, Marianne, Yang, Fengtang, Wienberg, Johannes, Froenicke, Lutz, Froenicke, Lutz, Caldés, Montserrat Garcia, Graphodatsky, Alexander, Müller, Stefan, Lyons, Leslie A, Robinson, Terence J, Volleth, Marianne, Yang, Fengtang, and Wienberg, Johannes

Abstract

"Excavating" ancestral genomes The recent release of the chicken genome sequence (Hillier et al. 2004Go) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004Go; Bourque et al. 2005Go). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003Go; Yang et al. 2003Go; Robinson et al. 2004Go; Svartman et al. 2004Go; Wienberg 2004Go; Froenicke 2005Go) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005Go). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.

Published
2006

28. Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group

Author

Basset, Patrick, Yannic, Glenn, Yang, Fengtang, O'Brien, Patricia, Graphodatsky, Alexander, Ferguson-Smith, Malcolm, Balmus, Gabriel, Volobouev, Vitaly, Hausser, Jacques, Basset, Patrick, Yannic, Glenn, Yang, Fengtang, O'Brien, Patricia, Graphodatsky, Alexander, Ferguson-Smith, Malcolm, Balmus, Gabriel, Volobouev, Vitaly, and Hausser, Jacques

Abstract

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group

Catalog

Books, media, physical & digital resources
See catalog results