Genetic characterization of Callosciurus (Rodentia: Sciuridae) Asiatic squirrels introduced in Argentina

Figures & data

Figure 1. (a) Location of the area of interest in Argentina (white square) and (b) study areas in the four invasion foci located next to the cities (black dots) of Luján and Escobar in Buenos Aires province, Cañada de Gómez in Santa Fé province, and La Cumbrecita in Córdoba province (lines divide provinces).

Figure 2. Bayesian inference trees of Callosciurus genus. Tree derived from D-loop. Numbers next to branches are Bayesian posterior probabilities, jackknife support values followed by bootstrap values, respectively. Numbers between brackets on a branch that defines a clade correspond to the groups obtained with the Automatic Barcode Gap Discovery (ABGD) method for the marker.

Figure 3. Bayesian inference trees of Callosciurus genus. Tree derived from cytochrome b (Cyt b). Numbers next to branches are Bayesian posterior probabilities, jackknife support values followed by bootstrap values, respectively. Numbers between brackets on a branch that defines a clade correspond to the groups obtained with the Automatic Barcode Gap Discovery (ABGD) method for the marker.

Figure 4. Bayesian inference trees of Callosciurus genus. Tree derived from citochrome oxidase c subunit I (COI). Numbers next to branches are Bayesian posterior probabilities, jackknife support values followed by bootstrap values, respectively. Numbers between brackets on a branch that defines a clade correspond to the groups obtained with the Automatic Barcode Gap Discovery (ABGD) method for the marker.

Figure 5. Bayesian inference trees of Callosciurus genus. Tree derived from recombination activating gene I (RAGI). Numbers next to branches are Bayesian posterior probabilities, jackknife support values followed by bootstrap values, respectively.

Table I. Percentage of sequence divergence (Kimura 1980) of Callosciurus species for the D-loop marker.

	C. erythraeus Arg.	C. Finlaysonii	C. erythraeus	C. prevostii
C. erythraeus Arg.	0
C. finlaysonii	5.88	6.80
C. erythraeus	13.59	13.13	6.87
C. prevostii	21.54	21.2	22.48	3.19

Table II. Percentage of sequence divergence (Kimura 1980) of Callosciurus species for the cytochrome b (Cyt b) marker.

	C. erythraeus Arg.	C. erythraeus	C.e. griseimanus	C. finlaysonii	C. prevostii	C. caniceps	C. inornatus	C. nigrovittatus	C. notatus
C. erythraeus Arg.	0
C. erythraeus	10.96	4.74
C.e. griseimanus	10.89	10.24	0.72
C. finlaysonii	5.39	9.85	9.7	2.46
C. prevostii	20.14	17.9	16.93	17.66	0.93
C. caniceps	18.29	17.13	16.87	16.22	18.72	0.72
C. inornatus	15.83	14.36	14.56	14.66	18.53	11.51	0
C. nigrovittatus	20.96	17.8	18.51	18.61	9.46	18.58	18.41	0.57
C. notatus	17.76	16.52	17.33	16.73	17.02	17.8	18.85	16.54	1

Table III. Percentage of sequence divergence (Kimura 1980) of Callosciurus species for the cytochrome oxidase c subunit I (COI) marker.

	C. erythraeus Arg.	C. erythraeus	C.e. flavimanus	C. prevostii	C. orestes	C. notatus
C. erythraeus Arg.	0
C. erythraeus	7.34	0.33
C.e. flavimanus	9.63	8.8	0
C. prevostii	19.06	18.18	18.87	2.38
C. orestes	19.21	18.23	19.58	7.67	0
C. notatus	18.6	17.53	18.07	13.41	13.51	0.94

Table IV. Percentage of sequence divergence (Kimura 1980) of Callosciurus species for the recombination activating gene I (RAGI) marker.

	C. erythraeus Arg.	C. erythraeus	C. prevostii
C. erythraeus Arg.	0.64
C. erythraeus	1.53	0.51
C. prevostii	2.75	2.01	0

Polymerase chain reaction thermal cycling amplification profiles.^a

Locus^b	Number of cycles	Denaturation		Annealing		Extension
		Time (min)	Temperature (ºC)	Time (min)	Temperature (ºC)	Time (min)	Temperature (ºC)
RAG1	40	0,75	94	1	55	1.5	72
D-loop	40	0.75	94	0.5	56	0.75	72
COI	40	0.75	94	0.5	54	1	72
cyt-b	40	0,75	94	1.5	55	2	72

^aEach thermal cycling profile includes a beginning denaturation of 94˚C for 5 min, 30–40 cycles of amplifications and a final extension of 72˚C for 5 or 10 min.

^bLocus: RAG1, recombination activating gene 1; D-loop, the control region of DNA mitochondrial; COI, mitochondrial cytochrome oxidase c subunit I gene; cyt-b, mitochondrial cytochrome b gene.

Species name; locality of collection; GenBank accession numbers of markers; pelage colouration: of the belly (red, orange or creamy), other underparts such as chest, groins or genital area (red, orange or creamy), and the back (black stripe, faint black stripe or no stripe) of the squirrels captured in Argentina, and references of samples used in this study.

Species name	Locality	GenBank accession number				Pelage colour (belly/other underparts/back)	References
		Cyt b	D-loop	RAG1	COI
C. erythraeus	Argentina: Luján, Buenos Aires		KF786012	KF786040	KF856233	red/red/black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786013		KF856231	red/red/black stripe	present study
C. erythraeus.	Argentina: Luján, Buenos Aires		KF786014		KF856219	red/red/black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786015		KF856232	red/creamy/no stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires				KF856211	orange/red/no stripe	present study
C. erythraeus	Argentina: Cañada de Gómez, Santa Fe.		KF786011	KF786037	KF856212	red/creamy/black stripe	present study
C. erythraeus	Argentina: Cañada de Gómez, Santa Fe.		KF786010		KF856228	red/red/light black stripe	present study
C. erythraeus	Argentina: Cañada de Gómez, Santa Fe.	KF786041	KF786009		KF856227	red/creamy/black stripe	present study
C. erythraeus	Argentina: Cañada de Gómez, Santa Fe.		KF786008		KF856226	red/creamy/black stripe	present study
C. erythraeus	Argentina: Cañada de Gómez, Santa Fe.		KF786007		KF856225	red/creamy/black stripe	present study
C. erythraeus.	Argentina: La Cumbrecita, Córdoba.				KF856213	red/creamy/black stripe	present study
C. erythraeus	Argentina: La Cumbrecita, Córdoba.		KF786006		KF856214	creamy/creamy/no stripe	present study
C. erythraeus	Argentina: La Cumbrecita, Córdoba.		KF786005	KF786038	KF856229	red/creamy/black stripe	present study
C. erythraeus	Argentina: La Cumbrecita, Córdoba.				KF856230	red/orange/black stripe	present study
C. erythraeus	Argentina: La Cumbrecita, Córdoba.		KF786004	KF786039	KF856215	red/creamy/faint black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786016		KF856216	red/creamy/faint black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786017			red/creamy/faint black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786018		KF856217	red/creamy/black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786019			red/orange/black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786020		KF856224	red/orange/black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires		KF786021		KF856223	red/red/black stripe	present study
C. erythraeus	Argentina: Escobar, Buenos Aires				KF856218	red/red/black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires.				KF856220	creamy/creamy/no stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires.				KF856221	red/creamy/no stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires				KF856222	creamy/red/faint black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786022			red/creamy/black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786023			red/creamy/black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786024			creamy/orange/faint black stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786025			creamy/creamy/no stripe	present study
C. erythraeus	Argentina: Luján, Buenos Aires		KF786026			red/creamy/faint black stripe	present study
C. erythraeus	Taiwan: Kaohsiung: Tianchi	HQ698358		HQ698438			Chang et al. (2011)
C. erythraeus	Taiwan: Nantou: Zhongxingxincun	HQ698359		HQ698439			Chang et al. (2011)
C. erythraeus	Taiwan: Nantou: Shishan	HQ698360		HQ698440			Chang et al. (2011)
C. erythraeus	China,Yunnan, Jingdong, Wuliangshan, Raomalu			AY241479			Steppan et al. (2004)
C. erythraeus	China		GU474432				Guo et al. (2011)
C. erythraeus	China		GU474433				Guo et al. (2011)
C. erythraeus	China		GU474434				Guo et al. (2011)
C. erythraeus	China		GU474435				Guo et al. (2011)
C. erythraeus	China		GU474436				Guo et al. (2011)
C. erythraeus	China		GU474437				Guo et al. (2011)
C. erythraeus	China		GU474438				Guo et al. (2011)
C. erythraeus	China		GU474439				Guo et al. (2011)
C. erythraeus	China		GU474440				Guo et al. (2011)
C. erythraeus	China		GU474441				Guo et al. (2011)
C. erythraeus	China		GU474442				Guo et al. (2011)
C. erythraeus	China		GU474443				Guo et al. (2011)
C. erythraeus	China		GU474444				Guo et al. (2011)
C. erythraeus	China		GU474445				Guo et al. (2011)
C. erythraeus	China		GU474446				Guo et al. (2011)
C. erythraeus	China		GU474447				Guo et al. (2011)
C. erythraeus	China		GU474448				Guo et al. (2011)
C. erythraeus	China		GU474449				Guo et al. (2011)
C. erythraeus	Taiwan		AB181249				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181250				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181251				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181252				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181253				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181254				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181255				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181256				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181257				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181258				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181259				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181260				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181261				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181262				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181263				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181264				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181265				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181266				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181267				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181268				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181269				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181270				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181271				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181272				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181273				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181274				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181275				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181276				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181277				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181278				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181279				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181280				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181281				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181282				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181283				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181284				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181285				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181286				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181287				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181288				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181289				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181290				Oshida et al. (2006)
C. erythraeus	Taiwan		AB181291				Oshida et al. (2006)
C. erythraeus	Izu-ohshima Island, Japan		AB259592				Oshida et al. (2007)
C. erythraeus	Izu-ohshima Island / Fukue Island, Japan		AB259593				Oshida et al. (2007)
C. erythraeus	Izu-ohshima Island, Japan		AB259594				Oshida et al. (2007)
C. erythraeus	Hamamatsu, Japan		AB259596				Oshida et al. (2007)
C. erythraeus	Izu Peninsular, Japan		AB259598				Oshida et al. (2007)
C. erythraeus	Miyazaki, Japan		AB259599				Oshida et al. (2007)
C.e.cf. hendeei	Tam Dao, Vietnam	AB499908					Oshida et al. (2011)
C.e.cf. hendeei	Tam Dao, Vietnam	AB499909					Oshida et al. (2011)
C. erythraeus	Ohshima, Tokyo, Japan	AB043876					Oshida et al. (2001b)
C. erythraeus	?	AB043877					Oshida et al. (2001b)
C. erythraeus	Qiongzhong, China				HM031932		Lu et al. (2012)
C. erythraeus	Qiongzhong, China				HM031933		Lu et al. (2012)
C. erythraeus	Qiongzhong, China				HM031934		Lu et al. (2012)
C. erythraeus	Qiongzhong, China				HM031935		Lu et al. (2012)
C.e. flavimanus	Vietnam				SKMZM949-10*		BOLD
C.e. griseimanus	Cat Tien National Park, Vietnam	AB716958					Oshida et al. (2013)
C.e. griseimanus	Cat Tien National Park, Vietnam	AB716959					Oshida et al. (2013)
C.e. griseimanus	Cat Tien National Park, Vietnam	AB716960					Oshida et al. (2013)
C.e. griseimanus	Vinh Cuu Nature Reserve, Vinh Cuu, Vietnam	AB716961					Oshida et al. (2013)
C.e. griseimanus	Vinh Cuu Nature Reserve, Vinh Cuu, Vietnam	AB716962					Oshida et al. (2013)
C. finlaysonii	Hamamatsu, Japan		AB259595				Oshida et al. (2007)
C. finlaysonii	Hamamatsu, Japan		AB259597				Oshida et al. (2007)
C. f. menamicus	nearby Vientianne, Laos		AB181242/AB259600				Oshida et al. (2007)
C. f. menamicus	nearby Vientianne, Laos		AB181243/AB259601				Oshida et al. (2007)
C. f. boonsongi	Thailand		AB621590				Kuramoto et al. (2012)
C. finlaysonii	Thailand	AB499910					Oshida et al. (2011)
C. finlaysonii	Thailand	AB499911					Oshida et al. (2011)
C. finlaysonii	near Vientianne, Laos	AB043878					Oshida et al. (2001b)
C. prevostii	Sumatra Island, Indonesia		AB259602				Oshida et al. (2007)
C. prevostii	Sumatra Island, Indonesia		AB259603				Oshida et al. (2007)
C. prevostii	Palembang, Indonesia	AB499914					Oshida et al. (2011)
C. prevostii	Palembang, Indonesia	AB499915					Oshida et al. (2011)
C. prevostii	?	AB043879					Oshida et al. (2001b)
C. prevostii	?	AB043880					Oshida et al. (2001b)
C. prevostii	Indonesia, Kayan Mentarang Nature Reserve				JF459623		BARCODE 2011
C. prevostii	Indonesia, Kayan Mentarang Nature Reserve				JF444288		BARCODE 2011
C. prevostii	Zoo captive			AY241480			Steppan et al. (2004)
C. caniceps	Negeri Sembilan, Malaysia	AB499918					Oshida et al. (2011)
C. caniceps	Negeri Sembilan, Malaysia	AB499919					Oshida et al. (2011)
C. caniceps	Negeri Sembilan, Malaysia	AB043875					Oshida et al. (2001b)
C. inornatus	Co Ma, Thuan, Chau, Son La, Vietnam	AB499905					Oshida et al. (2011)
C. inornatus	Hon, Phu Yen, Son La, Vietnam	AB499906					Oshida et al. (2011)
C. inornatus	Hon, Phu Yen, Son La, Vietnam	AB499907					Oshida et al. (2011)
C. nigrovittatus	Negeri Sembilan, Malaysia	AB499916					Oshida et al. (2011)
C. nigrovittatus	Negeri Sembilan, Malaysia	AB499917					Oshida et al. (2011)
C. nigrovittatus	Negeri Sembilan, Malaysia	AB043882					Oshida et al. (2011)
C. notatus	Negeri Sembilan, Malaysia	AB499912					Oshida et al. (2001b)
C. notatus	Negeri Sembilan, Malaysia	AB499913					Oshida et al. (2011)
C. notatus	USA				HM102291		Cooper et al. (2007)
C. notatus	Indonesia, Kayan Mentarang Nature Reserve				JF444286		BARCODE 2011
C. orestes	Indonesia, Kayan Mentarang Nature Reserve				JF444287		BARCODE 2011
Dremomys rufigenis	Viet Nam: Quang Nam, Tra Giac				JQ601436		BARCODE 2012
Lariscus insignis	Negeri Sembilan, Malaysia	AB499904					Oshida et al. (2011)
Sciurus lis	Fukui Pref., Japan	AB043881					Oshida et al. (2001b)
Petaurista albiventer			AB100913				Oshida et al. (2004)
P. albiventer			AB100904				Oshida et al. (2004)
P. philippensis			AB239458				Oshida et al. (2011)
P. leucogenys			AB043805				Oshida et al. (2001a)
Sundasciurus philippinensis				AY241483			Steppan et al. (2004)

*Sequence retrieved from Barcode of Life Data Systems.

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