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4 results on '"Samaniego Castruita, J. A."'

1. Dire Wolves Were the Last of an Ancient New World Canid Lineage

Author

Perri, A. R., Mitchell, K. J., Mouton, A., Álvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., dos Reis, M., Evin, A., Gaubert, P., Gopalakrishnan, S., Gower, G., Heiniger, H., Helgen, K. M., Kapp, J., Kosintsev, P. A., Linderholm, A., Ozga, A. T., Presslee, S., Salis, A. T., Saremi, N. F., Shew, C., Skerry, K., Taranenko, D. E., Thompson, M., Sablin, M. V., Kuzmin, Y. V., Collins, M. J., Sinding, M. -H. S., Gilbert, M. T. P., Stone, A. C., Shapiro, B., Van Valkenburgh, B., Wayne, R. K., Larson, G., Cooper, A., Frantz, L. A. F., Perri, A. R., Mitchell, K. J., Mouton, A., Álvarez-Carretero, S., Hulme-Beaman, A., Haile, J., Jamieson, A., Meachen, J., Lin, A. T., Schubert, B. W., Ameen, C., Antipina, E. E., Bover, P., Brace, S., Carmagnini, A., Carøe, C., Samaniego Castruita, J. A., Chatters, J. C., Dobney, K., dos Reis, M., Evin, A., Gaubert, P., Gopalakrishnan, S., Gower, G., Heiniger, H., Helgen, K. M., Kapp, J., Kosintsev, P. A., Linderholm, A., Ozga, A. T., Presslee, S., Salis, A. T., Saremi, N. F., Shew, C., Skerry, K., Taranenko, D. E., Thompson, M., Sablin, M. V., Kuzmin, Y. V., Collins, M. J., Sinding, M. -H. S., Gilbert, M. T. P., Stone, A. C., Shapiro, B., Van Valkenburgh, B., Wayne, R. K., Larson, G., Cooper, A., and Frantz, L. A. F.

Abstract

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.

Published
2021

2. Modern wolves trace their origin to a late Pleistocene expansion from Beringia

Author

Loog, L., Thalmann, O., Sinding, M., Schuenemann, V., Perri, A., Germonpre, M., Bocherens, H., Witt, K., Samaniego Castruita, J., Velasco, M., Lundstrom, I., Wales, N., Sonet, G., Frantz, L., Schroeder, H., Budd, J., Jimenez, E., Fedorov, S., Gasparyan, B., Kandel, A., Lazni{ˇ c}kova-Galetova, M., Napierala, H., Uerpmann, H., Nikolskiy, P., Pavlova, E., Pitulko, V., Herzig, K., Malhi, R., Willerslev, E., Hansen, A., Dobney, K., Gilbert, M., Krause, J., Larson, G., Eriksson, A., and Manica, A.

Abstract

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

Published
2018

3. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.

Author

Zepeda Mendoza, M., Xiong, Z., Escalera-Zamudio, M., Runge, A., Thézé, J., Streicker, D., Frank, H., Loza-Rubio, E., Liu, S., Ryder, O., Samaniego Castruita, J., Katzourakis, A., Pacheco, G., Taboada, B., Löber, U., Pybus, O., Li, Y., Rojas-Anaya, E., Bohmann, K., Carmona Baez, A., Arias, C., Greenwood, A., Bertelsen, M., White, Nicole, Bunce, Michael, Zhang, G., Sicheritz-Pontén, T., Gilbert, M., Zepeda Mendoza, M., Xiong, Z., Escalera-Zamudio, M., Runge, A., Thézé, J., Streicker, D., Frank, H., Loza-Rubio, E., Liu, S., Ryder, O., Samaniego Castruita, J., Katzourakis, A., Pacheco, G., Taboada, B., Löber, U., Pybus, O., Li, Y., Rojas-Anaya, E., Bohmann, K., Carmona Baez, A., Arias, C., Greenwood, A., Bertelsen, M., White, Nicole, Bunce, Michael, Zhang, G., Sicheritz-Pontén, T., and Gilbert, M.

Abstract

Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50?=?26.9?Mb, contig N50?=?36.6?kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.

Published
2018

4. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

Author

Gopalakrishnan, S., Samaniego Castruita, J., Sinding, M., Kuderna, L., Raikkonen, J., Petersen, B., Sicheritz-Ponten, T., Larson, G., Orlando, L., Marques-Bonet, T., Hansen, A., Dalen, L., Gilbert, Thomas, Gopalakrishnan, S., Samaniego Castruita, J., Sinding, M., Kuderna, L., Raikkonen, J., Petersen, B., Sicheritz-Ponten, T., Larson, G., Orlando, L., Marques-Bonet, T., Hansen, A., Dalen, L., and Gilbert, Thomas

Abstract

Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference. Results: Reassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples. Conclusion: In conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome

Published
2017

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