Presentation on theme: "FIGURE 1: INTRODUCTION Multiple lines of evidence suggest that forest and savanna elephants are distinct species. Measurements from 295 skulls demonstrated."— Presentation transcript:
FIGURE 1: INTRODUCTION Multiple lines of evidence suggest that forest and savanna elephants are distinct species. Measurements from 295 skulls demonstrated that forest and savanna elephants fall into two morphologically distinct groups (left panel; Groves and Grubb, 2000). Nuclear gene analyses using both slower-evolving nuclear gene sequences (center; Roca et al., 2001) and more rapidly evolving microsatellites (right; Comstock et al., 2002) demonstrated a deep genetic split between forest and savanna elephants, estimated at 3.5 million years. Only a few morphological intermediates and genetic hybrids were detected in a zone of mixed habitat that surrounds the tropical forests of Africa. In contrast to the distinctions between forest and savanna elephants detected by morphological and nuclear genetic studies, analyses using mitochondrial DNA (mtDNA) have detected genetic diversity in savanna elephants high enough to appear incongruent with nuclear DNA studies, and suggested greater mixing between forest and savanna elephants. To investigate this apparent disparity, we sampled wild elephant tissue from 21 African locations to determine the DNA sequences for 1642 biparentally inherited chromosomal segments in 3 X-linked genes, and 302 mtDNA and 128 Y chromosome sequences. Cyto-nuclear genomic dissociation in African elephant species Alfred L. Roca *, Nicholas Georgiadis ‡ and Stephen J. O’Brien † * Basic Research Program, SAIC-Frederick, and † Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA ‡ Mpala Research Center, PO Box 555, Nanyuki, Kenya References and Acknowledgments Comstock, K. E., Georgiadis, N., Pecon-Slattery, J., Roca, A. L., Ostrander, E. A., O'Brien, S. J. and Wasser, S. K. (2002) Patterns of molecular genetic variation among African elephant populations. Mol Ecol.11:2489-98. Groves, C. P. and Grubb, P. (2000) Do Loxodonta cyclotis and L. africana interbreed? Elephant 2(4):4-7. Roca, A. L., Georgiadis, N., Pecon-Slattery, J. and O'Brien, S. J. (2001) Genetic evidence for two species of elephant in Africa. Science 293(5534):1473-7. Roca, A. L., Georgiadis, N. and O'Brien, S. J. (2003) Male-driven genomic chimerization of elephant herds in Africa. In preparation. We thank R. Ruggiero, W. J. Murphy, E. Eizirik, A. Brandt, M. P. Gough, B. Gough, M. J. Malasky, J. Arthur, R. L. Hill, D. Munroe, S. Cevario, N. J. Crumpler, G. K. Pei, K. M. Helgen. For elephant samples, we thank A. Turkalo, J. M. Fay, R. Weladji, W. Karesh, M. Lindeque, W. Versvelt, K. Hillman Smith, F. Smith, M. Tchamba, S. Gartlan, P. Aarhaug, A. M. Austmyr, Bakari, Jibrila, J. Pelleteret, L. White, M. Habibou, M. W. Beskreo, D. Pierre, C. Tutin, M. Fernandez, R. Barnes, B. Powell, G. Doungoubé, M. Storey, M. Phillips, B. Mwasaga, A. Mackanga-Missandzou, B. York and A. Baker at the Burnet Park Zoo, and M. Bush at the National Zoological Park. We thank the governments of Botswana, Cameroon, the Central African Republic, Congo (Brazzaville), Congo (Kinshasa), Gabon, Kenya, Namibia, South Africa, Tanzania, and Zimbabwe for permission to collect samples. Tissues were obtained in full compliance with specific Federal Fish and Wildlife Permits (endangered/threatened species and CITES Permits US 750138 and US 756611 to N.G.). For funding we thank the U. S. Fish and Wildlife Service, National Geographic Society, and European Union (through the Wildlife Conservation Society). This publication has been funded in part with Federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. N01-CO-12400. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. African Forest Asian African Savanna BGN, 646 bp, n=556 PHKA2, 1012 bp, n=440 PLP, 479 bp, n=657 (A) (B) (C) Herd#2 Forest mtDNA, savanna nuclear DNA Herd#1 Forest habitat Savanna habitat Savanna mtDNA and nuclear DNA AA D C E B CH NA ZZ SA NG SE AB KE MK AM TA BE WA OD R SW MA KR HW 157 15 21 AMELYBGN PLP PHKA2 ND5 mtDNA biparental Y chro. AMELYBGN PLP PHKA2 ND5 GR 3 48 BE 1 26 WA 1 94 LO n=65 OD 7 DS 171 n=2 1 3 15 2 3 1 SE 447 NG 32 TA 67 11 7 n=11 3 26 1 11 5 1 5 4 9 1 4 3 1 6 mtDNA biparental Y chro. CH SA 154 HW 71 11 13 SW ZZ MA KR NA 46 56 170 2 2 1 AM 14917 35 8 11 8 4 10 5 4 37 AB KE MK n=280 n=15 n=58 (A) mtDNA ND5 319 bp AB (6), AM (34), CH (5), KE (16), KR (12) MA (1), MK (1), NA (21), NG (3), SE (1), SW (5), TA (6) 0.005 substitutions/site AB (1), AM (2), KE (4) CH (3), HW (4), KR (25), MA (3), SW (5) AB (1), KE (17), WA (4) GR (1) BE (1), WA (1) Elephas maximus (1) DS (1), LO (9), OD (1) BE (1), WA (1) LO (2) BE (1), WA (2) HW (2), NG (4), SA (2), SE (9), TA (1), ZZ (1) GR (10) CH (1), HW (6), SA (8), ZZ (4) DS (5) DS (8) DS (1), OD (2)BE (2), WA (1) GR (1) BE (1) DS (11) 100/100/100 64/64/63 70/66/63 90/91/87 89/92/97 94/96/98 62/74/78 I II IIA IIB (B) Y chromosome AMELY 1551 bp Ema006 0.001 substitutions/site AM0003 AM0005 AM0007 AM0015 AM0018 AM0019 AM0020 AM0021 AM0023 AM0030 AM0035 AM4551 AM4576 AM4583 AM4584 AM4585 AM4587 BE4035 BE4053 CH0882 CH0885 CH0895 CH0931 HW0062 HW0067 HW0076 HW0082 HW0086 HW0092 HW0112 HW0115 HW0117 HW0120 HW0122 HW0124 HW0151 KE4501 KE4509 KE4511 KE4516 KE4517 KE4549 KE4550 KE4601 KE4607 KE4609 KE4614 KE4617 KE4620 KE4621 KE4623 KR0114 MA0807 NA4653 NA4660 NA4665 NA4668 NA4669 NA4670 NA4671 NA4675 NA4678 NA4688 NA4697 NA4699 NA4702 NA4704 NA4710 NG2178 NG2180 NG2181 NG2182 NG2191 NG2192 NG2193 NG2194 NG2214 NG2215 NG2229 SA0972 SA0993 SA0994 SA1002 SA1004 SA1005 SA1009 SE2051 SE2098 SE2101 SE2103 SE2104 SE2106 SE2165 TA1144 TA1145 TA1431 TA1443 TA1450 TA1458 WA4020 WA4022 WA4027 ZZ0145 ZZ0148 DS1503 DS1505 DS1511 DS1527 DS1528 DS1530 DS1532 DS1543 LO3505 DS1537 DS1556 LO3517 BE4059 DS1504 DS1521 DS1523 DS1524 DS1555 GR0016 GR0022 OD0001 63/80/64 99/99/98 87/93/90 I II FIGURE 2 Haplotypes for three biparentally-inherited nuclear genes display almost complete separation among three elephant taxa. MP trees are shown. The length of each gene segment and number of chromosomes examined are indicated for each gene. Number of chromosomes per haplotype is proportional to the size of circles; differences between alleles are proportional to the distance between circles. Haplotypes/alleles found in Asian elephants are red; African forest haplotypes are green; and African savanna haplotypes are blue. (A) BGN haplotypes are completely distinct between forest and savanna populations. (B) PHKA2 proved to be the most diverse nuclear gene segment; the chromosomes examined were completely distinct between forest and savanna populations.(C) PLP haplotypes were distinct between forest and savanna elephants except for one haplotype, indicated by the arrow. This common forest elephant haplotype is present in two individuals from Cameroon. FIGURE 3 Maternally and paternally inherited markers demonstrate cytonuclear dissociation. Phylogenetic relationships for Asian, African forest, and African savanna elephants inferred from (A) 319 bp of the maternally inherited mitochondrial ND5 gene (number of individuals with identical haplotypes indicated by location), and from (B) 1551 bp of the paternally inherited Y chromosome gene AMELY (each individual shown separately). Forest populations or individuals are indicated in green; savanna in blue; Asian elephants in red. Garamba (GR) is a mixed habitat zone and is not colored. FIGURE 4 Distribution of cytonuclear disequilibrium. Pie charts indicate by locale the distribution of genetic markers that are inherited maternally (left pie chart in each set of three), paternally (right), or biparentally (center). Totals indicate the number of individuals (mtDNA, Y chromosomes) or combined number of chromosome segments (biparental genes) examined. Map indicates locations of sampled elephant populations in Africa. Green circles are forest locations. Blue circles are savanna locations. Garamba (GR) includes both habitats. Orange indicates current African elephant range; historic range includes entire land area shown. (A) Male-mediated gene flow occurs between adjacent forest elephant herds, and between adjacent savanna elephant herds; however (B) interbreeding between savanna and forest elephants at the contact zone between forest and savanna habitats is rare. (C) As forest habitat retreats (or when forest herds move into savanna habitats), larger male savanna elephants have increased opportunity to hybridize with forest female elephants. However, (D) the smaller forest and hybrid males do not reproduce due either to outbreeding depression or to reproductive dominance by larger unhybridized savanna males. (E) After multiple generations of unidirectional hybridization, nuclear genes alleles are those of savanna elephants, although a forest mitochondrial haplotype is retained in the now-savanna herds. 16 microsatellite loci Comstock et al. 2002 Forest elephants DS-Dzanga Sangha LO-Lope GA-Garamba Savannah elephants NORTH-CENTRAL BE-Benoue WA-Waza Savannah elephants EASTERN AB-Aberdares AM-Amboseli MK-Mount Kenya KE-Central Kenya NG-Ngorongoro SE-Serengeti TA-Tarangire Savannah elephants SOUTHERN CH-Chobe HW-Hwange KR-Kruger NA-Namibia MA-Mashatu SA-Savuti SW-Sengwa ZZ-Zambezi Asian elephants METHODS DNA was extracted from samples from wild African elephants and captive Asian elephants (Elephas maximus). Three nuclear gene segments (BGN, PHKA2 and PLP); a portion of the mitochondrial gene ND5, and a Y-chromosome gene fragment (AMELY) were amplified and sequenced. Sequences were aligned using CLUSTALX. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor joining (NJ), and maximum likelihood (ML) methods implemented in PAUP*4.0b10. FIGURE 5: CONCLUSIONS Cytonuclear disequilibrium suggests historic unidirectional hybridization (i.e., savanna males and forest females) with subsequent unidirectional backcrossing to larger reproductively successful savanna males, swamping the forest nuclear genomic contribution. The interactions between forest and savanna elephants inferred from differing patterns detected by maternally-inherited versus paternally- or biparentally-inherited genes are as follows: DS-Dzanga Sangha, LO-Lope, OD-Odzala, GR-Garamba, AB-Aberdares, AM- Amboseli, BE-Benoue, CH-Chobe, HW-Hwange, KE-Central Kenya, KR-Kruger, MA-Mashatu, MK-Mount Kenya, NA-Namibia, NG-Ngorongoro, SA-Savuti, SE- Serengeti, SW-Sengwa, TA-Tarangire, WA-Waza, ZZ-Zambezi.