Table 1.

Collection sites and genetic diversity for mitochondrial (mtDNA) cytochrome c oxidase subunit 3–NADH dehydrogenase subunit 1 (COX3-ND1) and microsatellites in two highly invasive species Ciona intestinalis spA (west coast) and spB (east coast) in North America. The first letter of the haplotype name denotes mtDNA (COX3-ND1) and the second letter indicates species affiliation: a, spA; b, spB. N, number of individuals tested; n, number of haplotypes; h, haplotypic diversity; π, nucleotide diversity; A, mean number of alleles; A_r, mean allelic richness; H_O, mean observed heterozygosity; H_E, mean expected heterozygosity. The major ports are ranked based on shipping and other purposes such as cruise and local delivery

Sampling location	Habitat type	ID	mtDNA					Microsatellite
			N	N	Haplotype	H	π	N	A	Ar	HO	HE
West coast (C. intestinalis spA)
Tomales Bay, CA, USA	Semi-enclosed bay	TB	13	4	Ca1, Ca6, Ca11, Ca20	0.679	0.0034	26	6.5	5.3	0.302	0.565
San Francisco Estuary, CA, USA	Estuary, port (major)	SF	9	3	Ca11, Ca20, Ca21	0.861	0.0036	32	7.4	5.8	0.231	0.622
Monterey Bay, CA, USA	Open sea shore	MO	8	2	C6, Ca11	0.429	0.0015	20	3.6	3.4	0.124	0.699
Santa Barbara, CA, USA	Marina	SB	16	6	Ca6, Ca7, Ca11, Ca15, Ca22, Ca23	0.783	0.0019	30	8.8	6.2	0.399	0.619
Channel Islands, CA, USA	Semi-enclosed port	CI	27	8	Ca1, Ca6–Ca12	0.772	0.0026	22	4.9	4.1	0.253	0.610
Port Hueneme, CA, USA	Semi-enclosed port (major)	PH	21	8	Ca6, Ca7, Ca10, Ca11, Ca16–Ca19	0.752	0.0028	20	4.1	3.9	0.219	0.563
Los Angeles, CA, USA	Port (major)	LA	31	5	Ca6, Ca7, Ca10, Ca11, Ca13	0.710	0.0016	34	7.0	5.5	0.245	0.576
Newport Bay, CA, USA	Semi-enclosed estuary, port	NB	21	5	Ca6, Ca7, Ca10, Ca13, Ca14	0.719	0.0016	24	6.6	5.2	0.310	0.702
Oceanside Estuary, CA, USA	Estuary, marina	OE	23	8	Ca6, Ca7, Ca10–Ca15	0.802	0.0027	30	8.5	6.7	0.377	0.703
Mission Bay, CA, USA	Semi-enclosed bay	MI	8	3	Ca6, Ca7, Ca10	0.714	0.0015	25	7.4	5.7	0.345	0.691
San Diego, CA, USA	Semi-enclosed bay, port (major)	SD	26	8	Ca1, Ca6, Ca7, Ca10, Ca12–Ca14	0.714	0.0022	38	10.4	7.0	0.397	0.692
Sub-total (West coast)		11	203	20		0.721	0.0023	301	183	5.3	0.291	0.640
East coast (C. intestinalis spB)
Cardigan River, PE, Canada	Estuary, aquaculture farm	CR	30	8	Cb4, Cb9, Cb13, Cb24–Cb28	0.556	0.0019	30	9.4	7.4	0.299	0.823
Brudenell River, PE, Canada	Estuary, aquaculture farm	BR	30	3	Cb4, Cb10, Cb11	0.191	0.0004	29	9.1	7.2	0.337	0.810
Murray River, PE, Canada	Estuary, aquaculture farm	MR	30	3	Cb4, Cb12, Cb13	0.191	0.0004	30	8.9	7.1	0.309	0.805
Sydney, NS, Canada	Port (major)	SN	42	5	Cb2, Cb4, Cb9, Cb13, Cb18	0.577	0.0020	23	8.5	7.2	0.268	0.812
Point Tupper, NS, Canada	Port (major)	PT	21	3	Cb4, Cb10, Cb13	0.267	0.0005	33	10.1	6.9	0.363	0.771
Halifax, NS, Canada	Port (major)	HF	28	4	Cb4, Cb13, Cb18, Cb29	0.429	0.0031	21	10.1	7.9	0.314	0.826
Chester, NS, Canada	Marina	CT	28	4	Cb4, Cb13–Cb15	0.418	0.0012	25	11.1	8.2	0.357	0.832
Martin's River, NS, Canada	Estuary	MA	46	6	Cb4, Cb9, Cb10, Cb13, Cb30, Cb31	0.592	0.0015	24	4.1	3.7	0.196	0.510
Mahone Bay, NS, Canada	Bay	MB	28	3	Cb4, Cb9, Cb13	0.569	0.0012	24	5.4	4.3	0.242	0.611
Stone Hurst, NS, Canada	Bay	ST	28	7	Cb4, Cb9, Cb13, Cb24, Cb31–Cb33	0.798	0.0019	20	5.9	5.0	0.201	0.653
Lunenburg, NS, Canada	Open sea shore	LU	21	3	Cb4, Cb13, Cb29	0.338	0.0008	31	6.8	5.3	0.236	0.674
Shelburne, NS, Canada	Port	SH	39	7	Cb2, Cb4, Cb9, Cb13, Cb18, Cb26, Cb34	0.547	0.0039	25	8.6	6.6	0.279	0.755
Port La Tour, NS, Canada	Marina	LT	21	3	Cb4, Cb9, Cb13	0.292	0.0006	21	8.6	6.8	0.297	0.794
Yarmouth, NS, Canada	Port	YM	20	8	Cb4, Cb9, Cb13, Cb18, Cb35–Cb38	0.821	0.0062	24	12.6	9.3	0.355	0.875
Groton, CT, USA	Estuary, port	GT	48	6	Cb4, Cb9, Cb13, Cb17–Cb19	0.688	0.0043	48	15.0	8.9	0.416	0.849
Sub-total (East coast)		15	460	27		0.485	0.0020	408	239	6.8	0.298	0.760
Total		26	663	46		0.603	0.0022	709	422	6.1	0.295	0.700