Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes

Nie, Wenhui; O’Brien, Patricia C. M.; Fu, Beiyuan; Wang, Jinghuan; Su, Weiting; He, Kai; Bed’Hom, Bertrand; Volobouev, Vitaly; Ferguson-Smith, Malcolm A.; Dobigny, Gauthier; Yang, Fengtang

doi:10.1186/s12862-015-0484-0

Table 1 Data matrix used in the PAUP analysis

From: Multidirectional chromosome painting substantiates the occurrence of extensive genomic reshuffling within Accipitriformes

Character no.	Character (GGA)	GGA (2n = 78)	Falconiformes			Accipitriformes
			Falconiformes			Cathartidae	Pandiondae	Accipitridae
			FTI (2n = 52)	FPE (2n = 50)	FCO (2n = 40)	GCA CAU (2n = 80)	PHA (2n = 74)	GBA (2n = 60)	GFU GHI GRU (2n = 66)	HHA (2n = 58)	NNI (2n = 66)	BNI BME RMA (2n = 68)	PAL (2n = 66)	BBU (2n = 68)
1	1p/1q	0	1	1	0	0	1	1	1	1	1	1	1	1
2	2p/2q	0	1	1	1	0	1	1	1	1	1	1	1	1
3	3qprx/3qmed	0	0	0	0	0	1	1	1	1	1	1	1	1
4	5qprx/5qdis	0	1	1	1	0	1	1	1	1	1	1	1	1
5	5qprx/mic1	0	1	1	1	0	1	1	1	0	1	1	1	1
6	2p/mic2	0	1	1	1	0	0	0	0	0	0	0	0	0
7	2q/mic3	0	1	1	1	0	0	0	0	0	0	0	0	0
8	4p/mic4	0	1	1	1	0	0	0	0	0	0	0	0	0
9	4q/mic5	0	1	1	1	0	0	0	0	0	0	0	0	0
10	5qmed/mic6	0	1	1	1	0	0	0	0	0	0	0	0	0
11	6/mic7	0	1	1	1	0	0	0	0	0	0	0	0	0
12	7/mic8	0	1	1	1	0	0	0	0	0	0	0	0	0
13	(5qdis + mic6)/(7 + mic8)	0	0	1	1	0	0	0	0	0	0	0	0	0
14	3qdis-1/(4q + mic5)	0	0	0	1	0	0	0	0	0	0	0	0	0
15	3qprx-1/(2p + mic2)	0	0	0	1	0	0	0	0	0	0	0	0	0
16	(2q + mic3)/(5qprx + mic1)	0	0	0	1	0	0	0	0	0	0	0	0	0
17	8/(6 + mic7)	0	0	0	1	0	0	0	0	0	0	0	0	0
18	1pdis/1pmed	0	0	0	0	0	1	0	1	1	1	1	1	1
19	1pmed/1pprx	0	0	0	0	0	1	0	1	0	1	0	0	1
20	1qprx/1qmed	0	0	0	0	0	1	1	1	1	1	1	1	1
21	1qmed/1qdis	0	0	0	0	0	1	1	1	1	1	1	1	1
22	1qdis-a/1qdis-b	0	0	0	0	0	1	0	1	1	1	0	0	1
23	1pdis-a/1pdis-b	0	0	0	0	0	0	0	0	0	0	0	0	1
24	1seg-n1/mic9	0	0	0	0	0	0	0	0	1	0	0	0	0
25	1seg-n2/mic10	0	0	0	0	0	0	0	0	1	0	0	0	0
26	(1seg-n1 + mic9)/(1seg-n2 + mic10)	0	0	0	0	0	0	0	0	1	0	0	0	0
27	3qmed-1/3qmed-2	0	0	0	0	0	1	1	1	1	1	1	1	1
28	3qmed-2/3qdis	0	0	0	0	0	1	1	1	1	1	1	1	1
29	3qprx/mic11	0	0	0	0	0	1	1	1	0	1	0	0	1
30	3qmed-1/mic12	0	0	0	0	0	1	0	1	0	1	0	0	1
31	7/mic13	0	0	0	0	0	1	1	1	1	1	1	1	1
32	8/mic14	0	0	0	0	0	1	0	1	0	1	0	0	1
33	2qprx/mic15	0	0	0	0	0	0	1	1	0	1	0	0	1
34	2p/mic16	0	0	0	0	0	0	0	0	1	0	0	0	0
35	6qprx/6qdis	0	0	0	0	0	1	0	0	0	0	0	0	0
36	1seg-na/9	0	0	0	0	0	1	0	0	0	0	0	0	0
37	1seg-nb/4p	0	0	0	0	0	1	0	0	0	0	0	0	0
38	1seg-nc/6qprx	0	0	0	0	0	1	0	0	0	0	0	0	0
39	1seg-nd/mic16	0	0	0	0	0	1	0	0	0	0	0	0	0
40	1seg-ne/mic17	0	0	0	0	0	1	0	0	0	0	0	0	0
41	9/mic18	0	0	0	0	0	0	1	1	1	1	0	0	1
42	2qprx/2qdis	0	0	0	0	0	0	1	1	0	1	1	1	1
43	2qdis-a/2qdis-b	0	0	0	0	0	0	1	0	0	0	0	0	0
44	1seg-nA/1seg-nB	0	0	0	0	0	0	1	0	0	0	0	0	0
45	1seg-nC/3qmed-1	0	0	0	0	0	0	1	0	0	0	0	0	0
46	6/mic-NOR	0	0	0	0	0	0	0	0	1	0	0	0	0
47	(3q-n + mic19)/5 dis	0	0	0	0	0	0	0	0	1	0	0	0	0
48	6/mic20	0	0	0	0	0	0	1	0	0	1	0	0	0
49	1pdis/6	0	0	0	0	0	0	0	0	0	0	1	1	0
50	mic21-a/mic21-b	0	0	0	0	0	0	0	0	0	0	0	0	1
51	1pdis-2/6	0	0	0	0	0	0	0	0	0	0	0	0	1
52	2p/mic22	0	0	0	0	0	1	0	0	0	0	0	0	0
53	2qprx/mic23	0	0	0	0	0	0	0	0	0	1	0	0	0
54	3qprx-1/3qdis-1	0	1	1	1	0	0	0	0	0	0	0	0	0
55	3qmed-2/mic24	0	0	0	0	0	0	0	0	0	1	0	0	0
56	3q-n/mic25	0	0	0	0	0	0	0	0	1	0	0	0	0
57	5qdis/mic26	0	0	0	0	0	1	0	0	0	0	0	0	0
58	6qdis/mic27	0	0	0	0	0	1	0	0	0	0	0	0	0
59	4p/4q	1	0	0	0	0	0	0	0	0	0	0	0	0

BNI, Buteo nitida (= Asturina nitida); BBU, Buteo buteo; BME, Buteogallus meridionalis; CAU, Cathartes aura; FCO, Falco columbarius; FPE, Falco peregrinus; FTI, Falco tinnunculus; GBA, Gypaetus barbatus; GCA, Gymnogyps californianus; GFU, Gyps fulvus; GHI, Gyps himalayensis; GRU, Gyps rueppellii; HHA, Harpia harpyja; PAL, Pseudastur albicollis (= Leucopternis albicollis); NNI, Nisaetus nipalensis orientialis; PHA, Pandion haliaetus; RMA, Rupornis magnirostris
Note: Chromosomal rearrangement characters used in this table were from previous published data and current study (see the section of materials for details). In the column of “Character (GGA)”, the individual numbers or the numbers before alphabets represent the numbers of homologous GGA chromosomes or chromosomal segments. “p”: the short arm of a given chromosome; “q”: the long arm of a given chromosome; “seg”: a segment on a given chromosome; “prx”: the part which is near to the centromere of a given chromosome or its arm; “med”: the part which is in the medial of a given chromosome or its arm; “dis”: the part which is distal to the centromere of a given chromosome or its arm; “mic”: the homologous GGA microchromosome. The chromosomal rearrangements in the diurnal birds of prey involved many homologous GGA microchromosomes. However, it is impossible to identify each homologous GGA microchromosomes due to the lack of single GGA microchromosome-specific probes. The numbers after “mic” are arbitrary numbers assigned for GGA microchromosomes involved in different species. GGA 1 is homologous to 4–8 pairs of chromosomes in different Accipitriformes species. Whereby the homologues of GGA 1 segments involved in chromosome arrangements could not be identified unambiguously based chromosome banding and painting data, different symbols were used to represent the homologues of GGA 1 segments in different species, such as 1 seg-n1 and 1seg-n2 in HHA, 1seg-nA, 1seg-nB and 1seg-nC in GBA, and 1seg-na to 1seg-ne in PHA

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