A comprehensive genomic history of extinct and living elephants

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 11, 2018, Pages E2566-E2574

  Palkopoulou, Eleftheria ^a,b   Lipson, Mark ^a   Mallick, Swapan ^a,b   Nielsen, Svend ^c   Rohland, Nadin ^a   Baleka, Sina ^d   Karpinski, Emil ^e,f,g   Ivancevic, Atma M ^h   To, Thu Hien ^h   Daniel Kortschak, R ^h   Raison, Joy M ^h   Qu, Zhipeng ^h   Chin, Tat Jun ^h   Alt, Kurt W ^i,j,k   Claesson, Stefan ^l   Dalén, Love ^m   MacPhee, Ross D E ⁿ   Meller, Harald ^o   Roca, Alfred L ^p   Ryder, Oliver A ^q   Heiman, David ^b   Young, Sarah ^b   Breen, Matthew ^r   Williams, Christina ^r   Aken, Bronwen L ^s,t   Ruffier, Magali ^s,t   Karlsson, Elinor ^b,u   Johnson, Jeremy ^b   Palma, Federica Di ^v   Alfoldi, Jessica ^b   Adelson, David L ^h   Mailund, Thomas ^c   Munch, Kasper ^c   Lindblad Toh, Kerstin ^b,w   Hofreiter, Michael ^d   Poinar, Hendrik ^e,f,g   Reich, David ^a,b,x   more..

^a HARVARD MEDICAL SCHOOL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c AARHUS UNIVERSITY   (Denmark)

^d UNIVERSITY OF POTSDAM   (Germany)

^e MCMASTER UNIVERSITY   (Canada)

^f MCMASTER UNIVERSITY   (Canada)

^g MCMASTER UNIVERSITY   (Canada)

^h UNIVERSITY OF ADELAIDE   (Australia)

ⁱ Austria   (Austria)

^j UNIVERSITY HOSPITAL BASEL   (Switzerland)

^k UNIVERSITY OF BASEL   (Switzerland)

^l Institute of Maritime History   (United States)

^m SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

ⁿ DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^o Archaeology Saxony Anhalt   (Germany)

^p UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^q Institute for Conservation Research   (United States)

^r NORTH CAROLINA STATE UNIVERSITY   (United States)

^s EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^t WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^u UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^v EARLHAM INSTITUTE   (United Kingdom)

^w UPPSALA UNIVERSITY   (Sweden)

^x HOWARD HUGHES MEDICAL INSTITUTE   (United States)

more..

Author keywords

Admixture; Elephantid evolution; Mammoth; Paleogenomics; Species divergence

Indexed keywords

ARTICLE; ELEPHANT; EVOLUTION; EXTINCT SPECIES; GENE FLOW; GENOMICS; HEREDITY; INTERBREEDING; INTERSPECIFIC HYBRIDIZATION; LOXODONTA AFRICANA; LOXODONTA CYCLOTIS; MAMMUTHUS COLUMBI; MASTODON; NONHUMAN; PALAEOLOXODON ANTIQUUS; PHYLOGENY; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; SPECIES DIVERSITY; WOOLLY MAMMOTH; ANIMAL; CLASSIFICATION; FOSSIL; GENETICS; GENOME; HISTORY; MAMMOTH; MOLECULAR EVOLUTION; SPECIES EXTINCTION;

ANIMALS; ELEPHANTS; EVOLUTION, MOLECULAR; EXTINCTION, BIOLOGICAL; FOSSILS; GENE FLOW; GENOME; GENOMICS; HISTORY, ANCIENT; MAMMOTHS; MASTODONS; PHYLOGENY;

EID: 85043762317     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1720554115     Document Type: Article

References (61)

1. Shoshani J (1998) Understanding proboscidean evolution: A formidable task. Trends Ecol Evol 13:480–487.
2. Maglio V (1973) Origin and evolution of the Elephantidae. Trans Am Philos Soc 63:1–149.
3. Todd NE (2010) New phylogenetic analysis of the family Elephantidae based on cranial-dental morphology. Anat Rec (Hoboken) 293:74–90.
4. Vartanyan SL, Arslanov KA, Karhu JA, Possnert G, Sulerzhitsky LD (2008) Collection of radiocarbon dates on the mammoths (Mammuthus primigenius) and other genera of Wrangel Island, northeast Siberia, Russia. Quat Res 70:51–59.
5. Veltre DW, Yesner DR, Crossen KJ, Graham RW, Coltrain JB (2008) Patterns of faunal extinction and paleoclimatic change from mid-Holocene mammoth and polar bear remains, Pribilof Islands, Alaska. Quat Res 70:40–50.
6. Enk J, et al. (2011) Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biol 12:R51.
7. Lister AM, Sher AV (2015) Evolution and dispersal of mammoths across the Northern Hemisphere. Science 350:805–809.
8. Stuart AJ (2005) The extinction of woolly mammoth (Mammuthus primigenius) and straight-tusked elephant (Palaeoloxodon antiquus) in Europe. Quat Int 126–128:171–177.
9. Shoshani J, et al. (2007) Relationships within the Elephantinae using hyoid characters. Quat Int 169–170:174–185.
10. Meyer M, et al. (2017) Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. eLife 6:e25413.
11. Shoshani J, et al. (2006) A proboscidean from the late Oligocene of Eritrea, a “missing link” between early Elephantiformes and Elephantimorpha, and biogeographic implications. Proc Natl Acad Sci USA 103:17296–17301.
12. Palkopoulou E, et al. (2015) Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol 25:1395–1400.
13. Lynch VJ, et al. (2015) Elephantid genomes reveal the molecular bases of woolly mammoth adaptations to the Arctic. Cell Rep 12:217–228.
14. Reddy PC, et al. (2015) Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus. J Biosci 40:891–907.
15. Rohland N, et al. (2010) Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biol 8:e1000564.
16. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494.
17. Green RE, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710–722.
18. Patterson N, et al. (2012) Ancient admixture in human history. Genetics 192:1065–1093.
19. Sanders WJGE, Harris JM, Saegusa H, Delmer C (2010) Proboscidea. Cenozoic Mammals of Africa, eds Werdelin L, Sanders WJ (Univ of California Press, Berkeley, CA).
20. Parmentier I, et al. (2007) The odd man out? Might climate explain the lower tree α-diversity of African rain forests relative to Amazonian rain forests? J Ecol 95: 1058–1071.
21. Enk J, et al. (2016) Mammuthus population dynamics in Late Pleistocene North America: Divergence, phylogeography, and introgression. Front Ecol Evol 4:42.
22. Roca AL, Georgiadis N, O’Brien SJ (2005) Cytonuclear genomic dissociation in African elephant species. Nat Genet 37:96–100.
23. Ishida Y, Georgiadis NJ, Hondo T, Roca AL (2013) Triangulating the provenance of African elephants using mitochondrial DNA. Evol Appl 6:253–265.
24. Backhaus D (1958) Zur Variabilität der äusseren systematischen Merkmale des afrikanischen Elefanten (Loxodonta Cuvier, 1825), Säugetierkd. Mitt 6:166–173.
25. Debruyne R (2005) A case study of apparent conflict between molecular phylogenies: The interrelationships of African elephants. Cladistics 21:31–50.
26. Johnson MB, et al. (2007) Complex phylogeographic history of central African forest elephants and its implications for taxonomy. BMC Evol Biol 7:244.
27. Mondol S, et al. (2015) New evidence for hybrid zones of forest and savanna elephants in Central and West Africa. Mol Ecol 24:6134–6147.
28. Blanc J (2008) Loxodonta africana. The IUCN Red List of Threatened Species 2008 (International Union for Conservation of Nature, Gland, Switzerland), e. T12392A3339343.
29. Mayr E (1942) Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Harvard Univ Press, Cambridge, MA).
30. Rasmussen M, et al. (2011) An Aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94–98.
31. Agenbroad LD (2005) North American Proboscideans: Mammoths: The state of knowledge, 2003. Quat Int 126–128:73–92.
32. Dutheil JY, et al. (2009) Ancestral population genomics: The coalescent hidden Markov model approach. Genetics 183:259–274.
33. Rohland N, et al. (2007) Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol 5:e207.
34. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2:e190.
35. Roca AL, et al. (2015) Elephant natural history: A genomic perspective. Annu Rev Anim Biosci 3:139–167.
36. Brandt AL, Ishida Y, Georgiadis NJ, Roca AL (2012) Forest elephant mitochondrial genomes reveal that elephantid diversification in Africa tracked climate transitions. Mol Ecol 21:1175–1189.
37. Aquadro CF, Begun DJ, Kindahl EC (1994) Selection, recombination, and DNA polymorphism in Drosophila. Non-Neutral Evolution: Theories and Molecular Data, ed Golding B (Springer, Boston), pp 46–56.
38. Laporte V, Charlesworth B (2002) Effective population size and population subdivision in demographically structured populations. Genetics 162:501–519.
39. Mailund T, et al. (2012) A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 8:e1003125.
40. Roca AL, Georgiadis N, Pecon-Slattery J, O’Brien SJ (2001) Genetic evidence for two species of elephant in Africa. Science 293:1473–1477.
41. Comstock KE, et al. (2002) Patterns of molecular genetic variation among African elephant populations. Mol Ecol 11:2489–2498.
42. Ishida Y, et al. (2011) Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. PLoS One 6:e20642.
43. Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475:493–496.
44. Sukumar R (2003) The Living Elephants: Evolutionary Ecology, Behavior, and Conservation (Oxford Univ Press, Oxford).
45. Fleischer RC, Perry EA, Muralidharan K, Stevens EE, Wemmer CM (2001) Phylogeography of the Asian elephant (Elephas maximus) based on mitochondrial DNA. Evolution 55: 1882–1892.
46. Vidya TNC, Sukumar R, Melnick DJ (2009) Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants. Proc Biol Sci 276:893–902.
47. Cahill JA, et al. (2015) Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol 24:1205–1217.
48. vonHoldt BM, Kays R, Pollinger JP, Wayne RK (2016) Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol 25:2443–2453.
49. Koepfli K-P, et al. (2015) Genome-wide evidence reveals that African and Eurasian golden jackals are distinct species. Curr Biol 25:2158–2165.
50. de Manuel M, et al. (2016) Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354:477–481.
51. Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103–1108.
52. Figueiró HV, et al. (2017) Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Sci Adv 3:e1700299.
53. Lister AM (2013) The role of behaviour in adaptive morphological evolution of African proboscideans. Nature 500:331–334.
54. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010:pdb. prot5448.
55. Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40:e3.
56. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
57. Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.
58. Felsenstein J (1989) PHYLIP–Phylogeny Inference Package (version 3.2). Cladistics 5: 164–166.
59. Staab PR, Zhu S, Metzler D, Lunter G (2015) scrm: Efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics 31: 1680–1682.
60. Csillery K, Francois O, Blum MGB (2012) abc: An R package for approximate Bayesian computation (ABC). Methods Ecol Evol 3:475–479.
61. Haubold B, Pfaffelhuber P, Lynch M (2010) mlRho–A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Mol Ecol 19:277–284.