A genomic perspective on an old question: Salmo trouts or Salmo trutta (Teleostei: Salmonidae)? Author Hashemzadeh Segherloo, Iraj Author Freyhof, Jörg Author Berrebi, Patrick Author Ferchaud, Anne-Laure Author Geiger, Matthias Author Laroche, Jérôme Author Levin, Boris A. Author Normandeau, Eric Author Bernatchez, Louis text Molecular Phylogenetics and Evolution 2021 107204 2021-09-30 162 1 15 https://doi.org/10.1016/j.ympev.2021.107204 journal article 10.1016/j.ympev.2021.107204 15097488

Table 1 Results for Bayes Factor Delimitation (BFD) in different geographic and phylogenetic groups of trouts.

a. Models for the Caspian and Aral Sea basin trouts
Model			Species combinations				MLE	BF	Rank
CAS1	S. ciscaucasicus (I)	S. caspius (II)	Salmo sp. (III)	S. oxianus (IV)			̅ 18168.4		1
CAS5	I+III	S. caspius	–	S. oxianus			̅ 18788.1	1239.3	2
CAS3	I+II	–	Salmo sp.	S. oxianus			̅ 20175.5	4014.2	5
CAS4	S. ciscaucasicus	II+III	–	S. oxianus			̅ 20263.2	4189.6	6
CAS2	I+II+III	–	–	S. oxianus			̅ 20719.5	5102.1	8
CAS6	I+III+IV	S. caspius	–	–			̅ 19401.0	2465.2	4
CAS7	I+IV	S. caspius	Salmo sp.	–			̅ 18923.8	1510.8	3
CAS8	S. ciscaucasicus	II+IV	Salmo sp.	–			̅ 20415.4	4494	7
CAS9	I+II+IV		Salmo sp.	–			̅ 20959.3	5581.8	9
CAS10	S. ciscaucasicus	II+III+IV	–	–			̅ 21103.8	5870.8	10
CAS0	I+II+III+IV	–	–	–			̅ 21573.5	6810.2	11
b. Models for the Black Sea basin trouts
Model			Species combinations				MLE	BF	Rank
BL3	I+II+III	–	–	S. abanticus	Salmo sp.		̅ 18335.4	–	1
BL6	S. labrax	II+III	–	S. abanticus	Salmo sp.		̅ 18339	7.2	2
BL5	I+II+III+V	–	–	S. abanticus	–		̅ 18533.8	396.8	3
BL4	I+IV	II+III	–	–	Salmo sp.		̅ 18661.7	652.6	4
BL1	S. labrax (I)	S. rizeensis (II)	S. coruhensis (III)	S. abanticus (IV)	Salmo sp. (V)		̅ 21495.3	6319.8	5
BL2	I+II+III+IV	–	–	–	Salmo sp.		̅ 24395.3	12119.8	6
BL0	I+II+III+IV+V	–	–	–	–		̅ 25107.8	13544.8	7
c. Models for the Mediterranean basin trouts a*
Model			Species combinations				MLE	BF	Rank
MEa1	S. peristericus (I)	S. chilo (II)	S. lourosensis (III)	S. farioides (IV)	S. opimus (V)	S. carpio (VI)	̅ 28941.503	–	1
MEa2	S. peristericus	S. chilo	III+IV		S. opimus	S. carpio	̅ 30074.549	2266.092	2
MEa6	S. peristericus	II+III		S. farioides	S. opimus	S. carpio	̅ 30767.142	3651.278	3
MEa3	S. peristericus	II+V	S. lourosensis	S. farioides		S. carpio	̅ 31613.205	5343.404	4
MEa4	S. peristericus	II+V	III+IV			S. carpio	̅ 32784.702	7686.398	5
MEa9	S. peristericus	II+III		S. farioides	V+VI		̅ 33835.556	9788.106	6
MEa7	S. peristericus	II+III		IV+V+VI			̅ 35004.211	12125.42	7
MEa5	I+II+III+IV+V					S. carpio	̅ 36498.013	15113.02	8
MEa8	S. peristericus	II+III+IV+V+VI					̅ 36541.313	15199.62	9
MEa0	I+II+III+IV+V+VI						̅ 38698.408	19513.81	10
d. Models for the Moroccan and Mediterranean basin trouts b*
Model			Species combinations				MLE	BF	Rank
MEb1	S. carpio (I)	S. lumi (II)	Salmo sp. Sardinia (III)	S. platycephalus (IV)	S. pellegrini (V)		̅ 44621.128	–	1
MEb3	S. carpio	S. lumi	III+IV	–	S. pellegrini		̅ 48267.394	7292.532	3
MEb2	I+II	–	Salmo sp. Sardinia	S. platycephalus	S. pellegrini		̅ 48328.652	7415.048	2
MEb4	S. carpio	S. lumi	III+V	S. platycephalus	–		̅ 48403.802	7565.348	4
MEb7	S. carpio	II+III	–	S. platycephalus	S. pellegrini		̅ 48822.685	8403.114	5
MEb5	S. carpio	S. lumi	Salmo sp. Sardinia	IV+V	–		̅ 49422.185	9602.114	6
MEb8	I+II	–	III+IV	–	S. pellegrini		̅ 52031.647	14821.04	7
MEb10	I+II	–	III+V	S. platycephalus	–		̅ 52219.780	15197.3	8
MEb6	S. carpio	S. lumi	III+IV+V	–	–		̅ 52551.773	15861.29	9
MEb9	I+II	–	III+IV+V	–	–		̅ 56461.835	23681.41	10
MEb0	I+II+III+IV+V	–	–	–	–		̅ 61793.100	34343.94	11
* a and b denote models set for the members of the Mediterranean and the North African Clade (Clade II; Fig. 5) based on the clustering pattern of the phylogenetic tree, DPAC clusters,
and also	according to the taxonomy proposed by different authors (see the text).
e. Models for the Atlantic basin trouts
Model			Species combinations				MLE	BF	Rank
AT1	S. trutta 1 (I)	S. trutta 2 (II)	S. cettii (III)	S. marmoratus (IV)			̅ 30798.4	–	1
AT4	I+III	S. trutta 2	–	S. marmoratus			̅ 32872.5	4148.2	3
AT2	I+II	-	S. cettii	S. marmoratus			̅ 30873.3	149.8	2
AT5	S. trutta 1	II+III	–	S. marmoratus			̅ 32831.1	40.65.4
AT3	I+II+III	–	–	S. marmoratus			̅ 33231.1	4865.4	4
AT0	I+II+III+IV	–	–	-			̅ 37613.1	13629.4	5
f. Models for representatives from the respective trout clades
Model			Species combinations				MLE	BF	Rank
G1	S. labrax (I)	S. carpio (II)	S. pellegrini (III)	S. trutta (IV)	S. marmoratus (V)		̅ 37414.7	–	1
G6	S. labrax	S. carpio	S. pellegrini	IV+V			̅ 40213.1	5596.798	2
G4	I+II	–	S. pellegrini	S. trutta	S. marmoratus		̅ 41123.3	7417.186	3
G5	S. labrax	II+III		S. trutta	S. marmoratus		̅ 41366.2	7902.933	4
G3	I+II+III	–		S. trutta	S. marmoratus		̅ 45472.7	16116	5
G2	I+II+III+IV	–			S. marmoratus		̅ 49977.4	25125.48	6
G0	I+II+III+IV+V	–	–	–	–		̅ 53775.5	32721.67	7