Phylogeography of Lanius senator in its breeding range: conflicts between alpha taxonomy, subspecies distribution and genetics

Figures & data

Figure 1. Breeding range of Lanius senator. Coloured areas delimit the distribution of subspecies L. s. senator, L. s. badius, L. s. niloticus, as shown in the legend. Black dots define the samples size for each locality (specific details on sampling sites are reported in Table I & Figure S2). Wintering range is not shown, although we included a Genbank sequence from Gambia in the analysis. The map was made with QGIS 3.16.10 (https://qgis.org) and it was based on BirdLife international and Handbook of the Birds of the World (2020).

Table I. List of specimens investigated in this study with voucher/accession number, subspecies, sex, sampling locality and origin.

Voucher specimen/accession number	Subspecies	Sex	Country	Locality	Museums
IT 0813	L. s. badius	F	Italy	Sardinia, Telti	W.I.N.E.S.
IT 0820	L. s. badius	M	Italy	Sardinia, Telti	W.I.N.E.S.
IT 1090	L. s. senator	M	Italy	Calabria, Caccuri	W.I.N.E.S.
IT 1092	L. s. senator	M	Italy	Calabria, Caccuri	W.I.N.E.S.
IT2867	L. s. senator	M	Italy	Abruzzo, Volpe	W.I.N.E.S.
IT2868	L. s. senator	M	Italy	Abruzzo, Volpe	W.I.N.E.S.
MNCN6732	L. s. senator	F	Spain	Madrid, Alcalá de Henares	MNCN
MNCN10812	L. s. senator	M	Spain	Ciudad Real, Pueblonuevo del Bullaque	MNCN
woodchat 1	L. s. niloticus	M	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
woodchat 2	L. s. niloticus	F	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
MNCN19119	L. s. senator	F	Spain	Madrid, Villavieja de Lozoya	MNCN
MNCN19513	L. s. senator	F	Spain	Madrid, Manjirón	MNCN
MNCN19601	L. s. senator	F	Spain	Madrid, Puentes Viejas	MNCN
MNCN41114	L. s. senator	F	Spain	Madrid, Horcajo de la Sierra	MNCN
woodchat 3	L. s. niloticus	M	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
woodchat 4	L. s. niloticus	M	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
woodchat 5	L. s. niloticus	M	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
woodchat 6	L. s. niloticus	M	Iran	Kohgiluyeh and Boyer-Ahmad Province, Yasuj	Yasouj University
IT2085	L. s. badius	M	Italy	Sardinia, Cardedu	W.I.N.E.S.
IT2086	L. s. badius	F	Italy	Sardinia, Cardedu	W.I.N.E.S.
IT2087	L. s. badius	F	Italy	Sardinia, Ilbono-Elini	W.I.N.E.S.
NHMO-BI-15168/2	L. s. niloticus	M	Israel	Eilat	NHMO
NHMO-BI-15169/2	L. s. niloticus	F	Israel	Eilat	NHMO
NHMO-BI-15277/1	L. s. niloticus	M	Israel	Eilat	NHMO
NHMO-BI-15274/2	L. s. niloticus	F	Israel	Eilat	NHMO
MZB 2003-1092	L. s. senator	M	Spain	Cervià de les Garrigues, Lleida - Les Garrigues	MZB
MZB 2011-0953	L. s. senator	F	Spain	Catalunya	MZB
MZB 2011-1010	L. s. senator	M	Spain	\	MZB
MZB 2005-0946	L. s. senator	M	Spain	Balaguer, Lleida - La Noguera	MZB
MCCI 3114	L. s. badius	F	Italy	Sicily, Marettimo - Isola	MCC
MCCI 4629	L. s. senator	M	Italy	Liguria, Savona	MCC
MCCI 4107	L. s. niloticus	M	Armenia	Meghri	MCC
MCCI 4113	L. s. niloticus	F	Armenia	Meghri	MCC
MCCI 4227	L. s. niloticus	M	Armenia	Meghri	MCC
AY599852	L. s. senator	\	Italy	_	GenBank
AY599853	L. s. senator	\	Italy	_	GenBank
AY599854	L. s. niloticus	\	Israel	_	GenBank
AY599855	L. s. badius	\	Italy	_	GenBank
IPMB 10541*	L. s. senator	\	France	southern France	GenBank
IPMB 12701*	L. s. niloticus	\	Israel	_	GenBank
IPMB 8644*	L. s. senator	\	Greece	Crete	GenBank
HQ996787	L. s. niloticus	\	Israel	_	GenBank
JF498788	L. s. niloticus	\	Iraq	Muhafazat Salah ad Din, Joint Base Balad	GenBank
JQ175216	L. s. senator		Grecee	Lesvos	GenBank
JQ175217	L. s. senator	\	Grecee	Lesvos	GenBank
JQ175218	L. s. senator		Grecee	Lesvos	GenBank

MZB: Museu de Ciències Naturals de Barcelona.

MCC: Museum of Naturali History of Carmagnola.

W.I.N.E.S.: collection from TAMU/UNIUPO/MusNatHist Carmagnola.

NHMO: Natural History Museum University of Oslo.

MNCN: Museo Nacional de Ciencias Naturales Madrid.

*Voucher specimens.

Figure 2. Haplotype median-joining networks of the concatenated mtDNA dataset. (a) shows haplotypes network based on putative subspecies designations (see inset), while (b) is based on sampling locality (see inset).

Figure 3. Bayesian Inference and Neighbor-Joining phylogenetic tree of the concatenated mtDNA haplotypes. Numbers on the nodes refer to BI posterior probabilities (left) and to bootstrap support values of the NJ analysis (right) using the p-distance substitution model. Thresholds for both BI posterior probabilities and bootstrap support values were set at ≥50%; dashes represent values below that threshold. The colours shown here mimic those used in Figure 1, such that the orange-blue background corresponds to the badius/senator (BS) haplogroup, while the yellow background represents the niloticus (N) haplogroup. Squares to the right of each individual define the putative subspecies attributed to the individual, based on geography and morphology.

Table II. Genetic distances (p-distance) dataset between and within different groups: within Lanius senator, between and within L. senator haplogroups N and L. senator haplogroups BS; Lanius spp. (excluding L. senator). Distances were estimated for all the mtDNA loci dataset (Table S4). Column S(n) includes the number of considered group/species and, within brackets, the overall number of considered sequences.

	Group	S(n)	Avg. between groups p-dist (S.D.)	Range	Avg. within groups p-dist (S.D.)	Range
ND2	Lanius senator	1(35)	_	_	0.0154 (0.0167)	0–0.0395
	L. senator N - L.senator BS	2(35)	0.0361 (0.0058)	0.0317–0.0395	0.0021 (0.0012)	0–0.0058
	Lanius spp (excluding L. senator)	12(34)	0.0960 (0.0333)	0.0058–0.1423	0.007 (0.0049)	0–0.0173
COI	Lanius senator	1(36)	_	_	0.0079 (0.0076)	0–0.0233
	L. senator N - L. senator BS	2(36)	0.0171 (0.0052)	0.0149–0.0233	0.0020 (0.0018)	0–0.0083
	Lanius spp (excluding L. senator)	13(286)	0.0724 (0.0218)	0–0.1111	0.0103 (0.0110)	0–0.0365
cytb	Lanius senator	1(37)	_	_	0.0088 (0.0074)	0–0.0235
	L. senator N - L. senator BS	2(37)	0.0181 (0.0022)	0.0138–0.0235	0.0033 (0.0020)	0–0.0083
	Lanius spp (excluding L. senator)	21(305)	0.0831 (0.0204)	0–0.1259	0.0117 (0.0108)	0–0.0443
CR	Lanius senator	1(38)	_	_	0.0071 (0.0074)	0–0.0218
	L. senator N - L. senator BS	2(38)	0.0165 (0.0016)	0–0.0218	0.0016 (0.0020)	0–0.0063
	Lanius spp (excluding L. senator)	11(25)	0.0925 (0.0390)	0–0.1506	0.0056 (0.0076)	0–0.0255

Table III. Genetic diversity indices calculated on mtDNA loci, concatenated mtDNA dataset, and nuDNA loci. * (p < 0.05), ** (p < 0.01).

	Haplogroup	N	N haplotypes	Haplotype diversity	Nucleotide diversity	Number of polymorphic sites	Tajima D’s	Fu’s Fs
ND2	N	9	8	0.972 ± 0.064	0.00290 ± 0.00045	9	−0.58727	−4.47939 **
	BS	26	16	0.926 ± 0.035	0.00190 ± 0.00026	18	−2.12117 *	−13.91433 **
	TOT	35	24	0.958 ± 0.021	0.01588 ± 0.00259	58	0.30932	−3.23459
COI	N	10	6	0.778 ± 0.137	0.00219 ± 0.00059	6	−1.49289	−2.92289 **
	BS	26	9	0.726 ± 0.083	0.00200 ± 0.00044	10	−1.72790 *	−4.68477 **
	TOT	36	15	0.843 ± 0.049	0.00809 ± 0,00109	24	−0.45872	−2.44501
cytb	N	9	5	0.722 ± 0.159	0.00219 ± 0.00065	8	−1.28352	−0.72729
	BS	28	18	0.960 ± 0.20	0.00306 ± 0.00032	24	−1.91354 *	−14.27295 **
	TOT	37	23	0.962 ± 0.016	0.00869 ± 0.00113	44	−0.77977	−7.36222 *
CR	N	9	2	0.222 ± 0.166	0.00069 ± 0.00051	1	−1.08823	−0.26348
	BS	29	9	0.483 ± 0.115	0.00170 ± 0.00048	8	− 2.23273 **	− 8.92803 **
	TOT	38	11	0.661 ± 0.075	0.00714 ± 0.00113	12	−0.58991	−2.77910 *
Concatenated	N	9	9	1.00 ± 0.0274	0.00223 ± 0.00037	23	−1.14918	−4.01016 *
	BS	23	22	0.996 ± 0.014	0.00216 ± 0.00017	51	−2.13204 *	−17.55270 **
	TOT	32	31	0.998 ± 0.008	0.01126 ± 0.00158	130	0.05467	− 9.01335 **
ODC	TOT	32	10	0.831 ± 0.045	0.00564 ± 0.00059	9	0.71448	−1.62233
MYO	TOT	36	8	0.613 ± 0.088	0.00132 ± 0.00027	8	−1.53902 *	−3.99708 **

NS p > 0.10, *p < 0.05, **p < 0.01.

Data availability statement

All specimen data are accessible on GenBank (Accession numbers OD991865-OD992005).