How many species of giraffe are there in Africa? David M. Brown 1 and Nicholas J. Georgiadis 2 1. University of California, Los Angeles; 2. Mpala Research Centre RATIONALE • The genus Giraffa in Africa is comprised of phenotypically distinct groups, currently classified as nine ‘subspecies’. • Are the different groups reproductively isolated, and perhaps different species? • Or do the different groups interbreed, and will their distinctiveness disappear over time? • Arguments have surrounded these questions for over 100 years. • The different giraffe groups have hybridized in captivity. • What does this variation mean in evolutionary terms? • What are the evolutionary dynamics of giraffes in the wild? APPROACH We examined genetic variation in the mitochondrial and nuclear genomes of free-ranging individual giraffes from six taxonomic giraffe subspecies. We are tested whether the giraffe subspecies: • Are genetically isolated from each other: Is genetic isolation recent or deep in evolutionary time? • Are hybridizing with each other: Is hybridization rare or common? • Biopsy-dart samples were collected from 397 free-ranging individual giraffes representing six subspecies: * Giraffa camelopardalis peralta (W) from Niger * G.c. rothschildi (N) from Uganda and Western Kenya * G.c. reticulata (R) from Kenya * G.c. tippelskirchi (M) from Kenya and Tanzania * G.c. angolensis (S) from Namibia * G.c. capensis (S) from South Africa Mitochondrial DNA: MATERNAL HISTORY Mitochondrial DNA is maternally inherited and does not capture the genetic history of males in a species. • 656 nucleotide fragment starting in cytochrome b extending through tRNAs to control region. • Okapi was used as the ‘outgroup’ for reconstruction of the phylogenetic tree. • There were 37 unique mtDNA sequences (haplotypes) found in 266 individuals. Peralta Rothschildi Reticulata Tippelskirchi Capensis A ngolensis H aplotypes N iger M urchison Falls W estern Kenya Sam buru Meru O lJogi A thi Chyulu N aivasha Tara M anyara S erengeti Kruger Etosha H oanib 1PeraltaA 7 2PeraltaB 15 3R othsA 25 16 4R othsB 8 5R othsC 2 6R eticA 2 7R eticB 1 1 11 8R eticC 7 8 9R eticD 1 10R eticE 1 11R eticF 5 6 12R eticG 2 5 13 13M asaiA 9 14M asaiB 4 13 4 7 5 15M asaiC 1 16M asaiD 2 17M asaiE 2 18M asaiF 1 19M asaiG 2 2 1 2 20M asaiH 1 21M asaiI 2 22M asaiJ 1 23M asaiK 2 14 24M asaiL 1 25M asaiM 3 26M asaiN 1 27M asaiO 3 28C apensisA 11 29C apensisB 1 30A ngolensisA 3 31A ngolensisB 7 32A ngolensisC 2 33A ngolensisD 2 34A ngolensisE 1 1 35A ngolensisF 1 36A ngolensisG 17 37A ngolensisH 1 Okapi 17MasaiE 19MasaiG 20MasaiH 15MasaiC 18MasaiF 14MasaiB 21MasaiI 16MasaiD 22MasaiJ 24MasaiL 23MasaiK 25MasaiM 26MasaiN 27MasaiO 13MasaiA 12ReticG OlJogi10Hap15 10ReticE 8ReticC 9ReticD 7ReticB 1PeraltaA 2PeraltaB 3RothsA 5RothsC 4RothsB 32AngolensisC 33AngolensisD 35AngolensisF 31AngolensisB 30AngolensisA 37AngolensisH 36AngolensisG 34AngolensisE 28CapensisA 29CapensisB 1 change NJ tippelskirchi 6ReticA reticul peralta rothsch angolensis capensis Fig. 2. (right) Phylogenetic tree of mitochondrial haplotypes • Each group is monophyletic with exception of one Masai haplotype grouping with reticulated giraffes. • In general, giraffes of different morphotypes are not interbreeding in the wild. Table 1. Distribution of mtDNA haplotypes by sampling location • peralta (W) N=22; rothschildi (N) N=51; reticulata (R) N=63; tippelskirchi (M) N=83; capensis (S) N=12, angolensis (S) N=35 • Each taxonomic subspecies has a unique set of mtDNA haplotypes • No haplotypes were shared between groups Nuclear DNA: THE GENETIC HISTORY OF POPULATIONS AND SPECIES Fig. 3. FES: cladogram of single-copy nuclear intron sequences, representing: * peralta (W) N=5 * rothschildi (N) N=10 * reticulata (R) N=14 * tippelskirchi (M) N=27 * capensis (S) N=10 * angolensis (S) N=11 Microsatellites: hypervariable sections of DNA *17 different microsatellite markers *397 individual giraffes from six taxonomic groups: * peralta (W) N=28 * tippelskirchi (M) N=142 * rothschildi (N) N=81 * capensis (S) N=27 * reticulata (R) N=80 *angolensis (S) N=38 Athi18 Athi23 ChyuluM2 TarangireM2264 LoboM2081 TarangireM2235 TarangireM2249 Athi3 Athi5 Athi6 Athi21 Athi13 Athi2 Chyulu17 Chyulu25 4868 4856 5017 Chyulu5 Chyulu4 Chyulu1 Athi25 2271 5016 5026 Chyulu20 Athi8 SamburuRe4812 Niger10 Niger18 RumaRoGR40 OlJogiRe2 OlJogiRe15 OlJogiRe26 OlJogiRe3 OlJogiRe8 Samburu3 OlJogi2 MFNPF3 MFNPM2 MFNPM5 Kruger12 Kruger2 Kruger4 Niger13 GN30 Kruger3 Niger5 Niger14 Samburu4 GN16 GN22 MFNPM3 MFNPF2 MFNPF1 4814 4812 4810 ENPF8 Kruger1 Kruger11 OlJogi16 OlJogi18 Kruger15 Kruger7 Kruger13 ENPF1 ENPF2 ENPF3 ENPM1 ENPM5 ENPM6 KHBM1 HSBM2 ENPM3 HNBF3 Kruger8 Okapi1 NJ tippelski peralta reticula rothschi angolens capensis capensis angolensis Masai (tippelskirchi ) giraffes have a unique SNP (single nucleotide polymorphism) in the FES intron sequence, distinguishing them from all others. Southern Africa capensis+angolensis Masai (tippelskirchi) Reticulated (reticulata) Western Africa peralta+rothschildi Population clusters of composite microsatellite genotyp CONCLUSIONS Mitochondrial DNA • Each of the sampled groups has a unique set of haplotypes (Reticulated, Rothschilds, Peralta, Masai, Angolensis, Capensis). • Exceptions to monophyly may be due to retention of ancestral polymorphism, or hybridization at range boundaries, for example, between tippelskirchi females and reticulata males in the Athi Plains region. • Since there is no evidence for nuclear DNA hybridization between them, it is likely that recurrent backcrossing of hybrid females to tippelskirchi males replaced the reticulata genome in hybrid individuals over many generations. Nuclear DNA: Microsatellites • Microsatellite genotypes cluster into 4 major nuclear DNA pools: Reticulated, Rothschilds + Peralta, Masai, Angolensis + Capensis • Each gene pool is equivalent of a monophyletic group (no interbreeding between them) • Some evolutionary force has kept reticulata and tippleskirchi reproductively isolated from each other: *Ecological selection for climate or some other factor? *Sexual selection? • The population genetic structure of giraffes in the wild conflicts with the
How many species of giraffe are there in Africa? David M. Brown 1 and Nicholas J. Georgiadis 2
Mar 14, 2016
Masai ( tippelskirchi ). Southern Africa capensis + angolensis. Reticulated ( reticulata ). Western Africa peralta+rothschildi. Population clusters of composite microsatellite genotypes. How many species of giraffe are there in Africa? David M. Brown 1 and Nicholas J. Georgiadis 2 - PowerPoint PPT Presentation
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How many species of giraffe are there in Africa?David M. Brown1 and Nicholas J. Georgiadis2
1. University of California, Los Angeles; 2. Mpala Research Centre
RATIONALE• The genus Giraffa in Africa is comprised of phenotypically distinct groups, currently classified as nine ‘subspecies’.• Are the different groups reproductively isolated, and perhaps different species?• Or do the different groups interbreed, and will their distinctiveness disappear over time?• Arguments have surrounded these questions for over 100 years.• The different giraffe groups have hybridized in captivity.• What does this variation mean in evolutionary terms?• What are the evolutionary dynamics of giraffes in the wild?
APPROACHWe examined genetic variation in the mitochondrial and nuclear genomes of free-ranging individual giraffes from six taxonomic giraffe subspecies.
We are tested whether the giraffe subspecies:• Are genetically isolated from each other: Is genetic isolation recent or deep in evolutionary time?• Are hybridizing with each other: Is hybridization rare or common?
• Biopsy-dart samples were collected from 397 free-ranging individual giraffes representing six subspecies: * Giraffa camelopardalis peralta (W) from Niger * G.c. rothschildi (N) from Uganda and Western Kenya * G.c. reticulata (R) from Kenya * G.c. tippelskirchi (M) from Kenya and Tanzania * G.c. angolensis (S) from Namibia * G.c. capensis (S) from South Africa
Mitochondrial DNA: MATERNAL HISTORY
Mitochondrial DNA is maternally inherited and does not capture the genetic history of males in a species.• 656 nucleotide fragment starting in cytochrome b extending through tRNAs to control region.• Okapi was used as the ‘outgroup’ for reconstruction of the phylogenetic tree.• There were 37 unique mtDNA sequences (haplotypes) found in 266 individuals.
Peralta Rothschildi Reticulata Tippelskirchi Capensis Angolensis Haplotypes Niger Murchison
Falls Western Kenya
Samburu Meru Ol J ogi Athi Chyulu Naivasha Tarangire
Manyara Serengeti Kruger Etosha Hoanib
1PeraltaA 7 2PeraltaB 15 3RothsA 25 16 4RothsB 8 5RothsC 2 6ReticA 2 7ReticB 1 1 11 8ReticC 7 8 9ReticD 1 10ReticE 1 11ReticF 5 6 12ReticG 2 5 13 13MasaiA 9 14MasaiB 4 13 4 7 5 15MasaiC 1 16MasaiD 2 17MasaiE 2 18MasaiF 1 19MasaiG 2 2 1 2 20MasaiH 1 21MasaiI 2 22MasaiJ 1 23MasaiK 2 14 24MasaiL 1 25MasaiM 3 26MasaiN 1 27MasaiO 3 28CapensisA 11 29CapensisB 1 30AngolensisA 3 31AngolensisB 7 32AngolensisC 2 33AngolensisD 2 34AngolensisE 1 1 35AngolensisF 1 36AngolensisG 17 37AngolensisH 1
Okapi17MasaiE
19MasaiG20MasaiH15MasaiC18MasaiF
14MasaiB21MasaiI
16MasaiD22MasaiJ
24MasaiL23MasaiK25MasaiM
26MasaiN27MasaiO
13MasaiA12ReticG
OlJogi10Hap1510ReticE8ReticC
9ReticD7ReticB
1PeraltaA2PeraltaB
3RothsA5RothsC
4RothsB
32AngolensisC33AngolensisD35AngolensisF31AngolensisB30AngolensisA37AngolensisH
36AngolensisG34AngolensisE
28CapensisA29CapensisB
1 change
NJ
tippelskirchi
6ReticA
reticulata
peralta
rothschildi
angolensis
capensis
Fig. 2. (right) Phylogenetic tree of mitochondrial haplotypes • Each group is monophyletic with exception of one Masai haplotype grouping with reticulated giraffes.• In general, giraffes of different morphotypes are not interbreeding in the wild.
Table 1. Distribution of mtDNA haplotypes by sampling location • peralta (W) N=22; rothschildi (N) N=51; reticulata (R) N=63; tippelskirchi (M) N=83; capensis (S) N=12, angolensis (S) N=35 • Each taxonomic subspecies has a unique set of mtDNA haplotypes• No haplotypes were shared between groups
Nuclear DNA: THE GENETIC HISTORY OF POPULATIONS AND SPECIES
Fig. 3. FES: cladogram of single-copy nuclear intron sequences, representing:
* peralta (W) N=5* rothschildi (N) N=10* reticulata (R) N=14 * tippelskirchi (M) N=27 * capensis (S) N=10 * angolensis (S) N=11
Microsatellites: hypervariable sections of DNA*17 different microsatellite markers *397 individual giraffes from six taxonomic groups: * peralta (W) N=28 * tippelskirchi (M) N=142* rothschildi (N) N=81 * capensis (S) N=27* reticulata (R) N=80 *angolensis (S) N=38
Athi18Athi23ChyuluM2TarangireM2264LoboM2081TarangireM2235TarangireM2249Athi3Athi5Athi6Athi21Athi13Athi2Chyulu17Chyulu25486848565017Chyulu5Chyulu4Chyulu1Athi25227150165026Chyulu20Athi8SamburuRe4812Niger10Niger18RumaRoGR40OlJogiRe2OlJogiRe15OlJogiRe26OlJogiRe3OlJogiRe8Samburu3OlJogi2MFNPF3MFNPM2MFNPM5Kruger12Kruger2Kruger4Niger13GN30Kruger3Niger5Niger14Samburu4GN16GN22MFNPM3MFNPF2MFNPF1481448124810ENPF8Kruger1Kruger11OlJogi16OlJogi18Kruger15Kruger7Kruger13ENPF1ENPF2ENPF3ENPM1ENPM5ENPM6KHBM1HSBM2ENPM3HNBF3Kruger8Okapi1
NJ
tippelskirchi
peralta reticulata rothschildi angolensis capensis
capensis angolensis
Masai (tippelskirchi) giraffes have a unique SNP (single nucleotide polymorphism) in the FES intron sequence, distinguishing them from all others.
Southern Africa capensis+angolensis
Masai(tippelskirchi)
Reticulated (reticulata)
Western Africaperalta+rothschildi
Population clusters of composite microsatellite genotypes
CONCLUSIONSMitochondrial DNA • Each of the sampled groups has a unique set of haplotypes (Reticulated, Rothschilds, Peralta, Masai, Angolensis, Capensis).• Exceptions to monophyly may be due to retention of ancestral polymorphism, or hybridization at range boundaries, for example, between tippelskirchi females and reticulata males in the Athi Plains region.• Since there is no evidence for nuclear DNA hybridization between them, it is likely that recurrent backcrossing of hybrid females to tippelskirchi males replaced the reticulata genome in hybrid individuals over many generations.
Nuclear DNA: Microsatellites• Microsatellite genotypes cluster into 4 major nuclear DNA pools: Reticulated, Rothschilds + Peralta, Masai, Angolensis + Capensis• Each gene pool is equivalent of a monophyletic group (no interbreeding between them)• Some evolutionary force has kept reticulata and tippleskirchi reproductively isolated from each other: *Ecological selection for climate or some other factor? *Sexual selection?• The population genetic structure of giraffes in the wild conflicts with the currently held classification of ‘9 subspecies’.• There are at least four distinct groups of giraffes that, based on genetic evidence, appear to be reproductively isolated from each other in the wild.• These groups may correspond with different species of giraffe.
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