Complex phylogeographic history of central African forest elephants and its implications for taxonomy

Johnson, Mireille B; Clifford, Stephen L; Goossens, Benoît; Nyakaana, Silvester; Curran, Bryan; White, Lee JT; Wickings, E Jean; Bruford, Michael W

doi:10.1186/1471-2148-7-244

BMC Ecology and Evolution

Table 1 HVR1 haplotypes used in the Figure 2. Haplotype frequency is indicated in brackets when there is more than one.

From: Complex phylogeographic history of central African forest elephants and its implications for taxonomy

Haplotype	Taxon	Designation*	Geographic origin	Genbank accession numbers	Author
H01	Loxodonta africana africana	Angola1	Angola	AY741072	Debruyne 2005
H02 (2)	L. a. africana	Botswana1, BOT4	Botswana	AY741074, AF106230	Debruyne 2005, Nyakaana et al. 2002
H03 (3)	L. a. africana, L. a. cyclotis	BOT2, BOT21, DRC4	Botswana, DRC	AF106228, AF106234, AY359275	Nyakaana et al. 2002, Debruyne 2005
H04 (2)	L. a. africana	BOT9, Zimbabwe2	Botswana, Zimbabwe	AF106231, AY741329	Nyakaana et al. 2002, Debruyne 2005
H05	L. a. africana	BOT15	Botswana	AF106232	Nyakaana et al. 2002
H06 (3)	L. a. africana, L. a. cyclotis	BOT16, DRC1, Zimbabwe4	Botswana, DRC, Zimbabwe	AF106233, AY359277, AY742799	Nyakaana et al. 2002, Debruyne 2005
H07 (4)	L. a. cyclotis	Bmbo6, Dja39, CAR3214, CAR394	Cameroon, CAR	AF527653, AF527647	Eggert et al. 2002, this study
H08	L. a. cyclotis	Cameroon1	Cameroon	AY359267	Debruyne 2005
H09 (4)	L. a. cyclotis	Cameroon2, Bmbo1, Bmbo37, NYO0310	Cameroon, Gabon	AY359269, AF527646, AF527649	Debruyne 2005, Eggert et al. 2002, this study
H10 (7)	L. a. cyclotis	Bmbo16, Bmbo43, CAR274, CAR297, Congo2, NN0713, NN2911	Cameroon, CAR, CR	AF527648, AF527650, AY359268	Eggert et al. 2002, Debruyne 2005, this study
H11	L. a. cyclotis	Dja34	Cameroon	AF527651	Eggert et al. 2002
H12 (3)	L. africana, L.a. fricana, L. a. cyclotis	DRC13**, B1, DRC9	DRC, Cameroon	AY741081, AY359279, AF527654,	Debruyne 2005, Eggert et al. 2002
H13 (2)	L. a. africana	B7, Waza15	Cameroon	AF527655, AF527659	Eggert et al. 2002
H14 (3)	L. a. africana	B8, Waza10, Sudan1	Cameroon, Sudan	AF527656, AF527658, AY741073	Eggert et al. 2002, Debruyne 2005
H15 (2)	L. a. africana	Waza27, Mali2	Cameroon, Mali	AF527660, AF527666	Eggert et al. 2002
H16 (4)	L. a. cyclotis	CAR3622, NN059, NN279, NN3014	CAR, CR		This study
H17 (2)	L. a. cyclotis	CAR3315, CAR381	CAR		This study
H18 (4)	L. a. cyclotis	CAR5712, AFE82lan, MDC012, NOG053,	CAR, Gabon		This study
H19	L. a. cyclotis	CAR1	CAR	AY359272	Debruyne 2005
H20	L. a. cyclotis	CAR309	CAR		This study
H21	L. a. cyclotis	CAR3519	CAR		This study
H22 (5)	L. a. africana	Chad1, K68, RVV15, Mole13, WA6	Chad, Ghana	AY741080, AF527643, AF527641, AF527676, AF106243	Eggert et al. 2002, Debruyne 2005, Nyakaana et al. 2002
H23 (10)	L. a. cyclotis	NN3218, Lan027, LOP067, LOP51a14, NOG014, NOG025, NOG026, Mpa01, Mpa028, RAB0113	RC, Gabon		This study
H24	L. a. cyclotis	Congo1	RC	AY359266	Debruyne 2005
H25 (2)	L. a. cyclotis	CKT04a14, RAB275	RC, Gabon		This study
H26	L. a. cyclotis	DRC2	DRC	AY359270	Debruyne 2005
H27 (4)	L. a. africana and L. a. cyclotis	KV8, MF1, MF5, DRC3	Uganda, DRC	AF106206, AF106209, AF106210, AY359271	Nyakaana et al. 2002, Debruyne 2005
H28 (2)	L. a. cyclotis	DRC6, DRC8	DRC	AY359273, AY359274	Debruyne 2005
H29	L. a. cyclotis	DRC5	DRC	AY359276	Debruyne 2005
H30 (2)	L. a. africana	DRC11, AM1	DRC, Kenya	AY741078, AF106217	Nyakaana et al. 2002, Debruyne 2005
H31 (2)	L. africana and L. a. africana	DRC17**, QE13	DRC, Uganda	AY742802, AF106213	Nyakaana et al. 2002, Debruyne 2005
H32 (2)	L. a. cyclotis	IVI1011, RAB067	Gabon		This study
H33 (11)	L. a. cyclotis	Igl032, AFE85Igl, AFE86Igl, AFE88Igl, IVI1012, IVI043, LOA0310, LOP146, Mpa0319, RAB0215, WAK0410	Gabon		This study
H34 (3)	L. a. cyclotis	Lan015, Lan15911, RAB131	Gabon		This study
H35 (5)	L. a. cyclotis	Lan1566, IVI05a6, IVI05b8, RAB032, WAK0817	Gabon		This study
H36	L. a. cyclotis	Lan16014	Gabon		This study
H37 (3)	L. a. cyclotis	Gabon2, LOP0710, PBA023	Gabon	AY359265	Debruyne 2005, this study
H38 (8)	L. a. cyclotis	IVI06b2, Kes0721, Kes0819, LOA068, AFE79LOP, PBA0510, RAB044, RAB1118	Gabon		This study
H39 (4)	L. a. cyclotis	Kes0211, Kes0314, Kes0517, PBA0714	Gabon		This study
H40	L. a. cyclotis	Gabon1	Gabon	AY359278	Debruyne 2005
H41	L. a. cyclotis	NOG0810	Gabon		This study
H42	L. a. cyclotis	PBA0612	Gabon		This study
H43	L. a. cyclotis	IVI05a5	Gabon		This study
H44 (3)	L. a. cyclotis	Bia3, Bia69, Liberia1	Ghana, Liberia	AF527677, AF527680, AY741079	Eggert et al 2002, Debruyne 2005
H45	L. a. cyclotis	Bia48	Ghana	AF527678	Eggert et al 2002
H46 (6)	L. a. cyclotis and L. a. africana	Bia64, RVV22, Mole9, WA3, WA14, Mali7	Ghana, Mali	AF527679, AF527642, AF527675, AF106242, AF106245, AF527667	Eggert et al 2002, Nyakaana et al 2002
H47 (2)	L. a. africana	Mole3, Mali14	Ghana, Mali	AF527674, AF527668	Eggert et al 2002
H48	L. a. africana	Mole33	Ghana	AF527683	Eggert et al 2002
H49 (2)	L. a. cyclotis	Tai6, Tai17	Ivory Coast	AF527670, AF527671	Eggert et al 2002
H50 (2)	L. a. cyclotis	Tai19, Tai29	Ivory Coast	AF527672, AF527673	Eggert et al 2002
H51	L. a. africana	IvoryCoast1	Ivory Coast	AY741327	Debruyne 2005
H52 (2)	L. a. africana	SouthAfrica3, Zimbabwe1	South Africa, Zimbabwe	AY741320, AY741321	Debruyne 2005
H53	L. a. africana	MM4	Kenya	AF106214	Nyakaana et al 2002
H54	L. a. africana	MM19	Kenya	AF106215	Nyakaana et al 2002
H55	L. a. africana	MM20	Kenya	AF106216	Nyakaana et al 2002
H56	L. a. africana	AM2	Kenya	AF106218	Nyakaana et al 2002
H57	L. a. africana	AM10	Kenya	AF106219	Nyakaana et al 2002
H58	L. a. africana	AM12	Kenya	AF106220	Nyakaana et al 2002
H59	L. a. africana	SA8	Kenya	AF106221	Nyakaana et al 2002
H60	L. a. africana	Mali28	Mali	AF527669	Eggert et al 2002
H61	L. a. africana	Mozambique1	Mozambic	AY741076	Debruyne 2005
H62 (5)	L. a. africana	Namibia1, Addo5, Uganda1, QE1, Zimbabwe10	Namibia, South Africa, Uganda, Zimbabwe	AY741325, AF527682, AF106211, AY741323, AY742800	Nyakaana et al 2002, Eggert et al 2002, Debruyne 2005
H63	L. a. africana	KH2	Namibia	AF106239	Nyakaana et al 2002
H64	L. a. africana	Addo1	South Africa	AF527681	Eggert et al 2002
H65	L. a. africana	KG1	South Africa	AF106240	Nyakaana et al 2002
H66 (3)	L. a. africana	KG2, Tanzania2, Zimbabwe7	South Africa, Tanzania, Zimbabwe	AF106241, AY741070, AY741067	Nyakaana et al 2002, Debruyne 2005
H67	L. a. africana	Tanzania1	Tanzania	AY742801	Debruyne 2005
H68 (4)	L. a. africana	QE4, Zambia1, Af9, Af10	Uganda, Zambia, Kenya	AF106212, AY741328, AF527639, AF527640	Nyakaana et al 2002, Eggert et al 2002, Debruyne 2005
H69 (2)	L. a. africana	Uganda2, KV1	Uganda	AY741077, AF106203	Nyakaana et al 2002, Debruyne 2005
H70	L. a. africana	KV2	Uganda	AF106204	Nyakaana et al 2002
H71	L. a. africana	KV7	Uganda	AF106205	Nyakaana et al 2002
H72	L. a. africana	KV17	Uganda	AF106207	Nyakaana et al 2002
H73	L. a. africana	KV28	Uganda	AF106208	Nyakaana et al 2002
H74	L. a. africana	WC2	Namibia	AF106235	Nyakaana et al 2002
H75	L. a. africana	WC4	Namibia	AF106236	Nyakaana et al 2002
H76	L. a. africana	WC6	Namibia	AF106237	Nyakaana et al 2002
H77	L. a. africana	WC13	Namibia	AF106238	Nyakaana et al 2002
H78	L. a. africana	WA11	Ghana	AF106244	Nyakaana et al 2002
H79	L. a. africana	AF8	Kenya	AF527638	Eggert et al 2002
H80	L. a. africana	ZBE1	Zimbabwe	AF106222	Nyakaana et al. 2002
H81	L. a. africana	ZBE2	Zimbabwe	AF106223	Nyakaana et al. 2002
H82	L. a. africana	ZBE3	Zimbabwe	AF106224	Nyakaana et al. 2002
H83	L. a. africana	ZBE4	Zimbabwe	AF106225	Nyakaana et al. 2002
H84	L. a. africana	ZBE5	Zimbabwe	AF106226	Nyakaana et al. 2002
H85	L. a. africana	ZBE6	Zimbabwe	AF106227	Nyakaana et al. 2002
H86	L. a. africana	Zimbabwe3	Zimbabwe	AY741069	Debruyne 2005
H87	L. a. africana	Zimbabwe6	Zimbabwe	AY741071	Debruyne 2005
H88	L. a. africana	Zimbabwe5	Zimbabwe	AY741322	Debruyne 2005

* Original name from each author (Debruyne, 2005; Eggert et al. 2002; Nyakaana et al. 2002; and this study. ** Sample sharing both, forest and savannah haplotypes, according to the author (Debruyne, 2005).

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