Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales)

Figures & data

Table I.  DNA barcoding in species of Zamia occurring in Megamexico: comparative assessment of the number of diagnostic sites for four chloroplast coding and non-coding genome regions and one nuclear region.

		Diagnostic sites
Zamia species	Country of distribution	psbK-I	atpF-H	ITS2	rpoC1	matK
Zamia cremnophila Vovides, Schutzman & Dehgan*	Mexico	>1	–	–	–	5
Z. fischeri Miq.*	Mexico	–	2	–	–	–
Z. furfuracea L. f.*	Mexico	–	–	4	–	–
Z. herrerae Calderón & Standl.*	Mexico	–	1	–	–	–
Z. inermis Vovides, Rees & Vázq. Torres*	Mexico	1	–	–	–	2
Z. katzeriana (Regel) Rettig	Mexico	–	–	–	–	–
Z. lacandona Schutzman & Vovides*	Mexico	–	1	–	–	–
Z. loddigesii Miq.*	Mexico	2	–	–	1	–
Z. paucijuga Wieland	Mexico	–	–	–	–	–
Z. polymorpha Stevenson, Moretti & Vázq. Torres*	Mexico	3	–	–	–	–
Z. prasina W. Bull*	Belize	1	1	–	–	–
Z. purpurea Vovides, Rees & Vázq. Torres*	Mexico	–	–	–	1	–
Z. soconuscensis Schutzman, Vovides & Dehgan*	Mexico	1	1	–	–	–
Z. spartea A. DC.	Mexico	–	–	–	–	–
Z. standleyi Schutzman*	Honduras	2	–	3	–	–
Z. tuerckheimii Donn. Sm.*	Guatemala	–	–	1	–	–
Z. variegata Warsz.*	Mexico	–	–	1	–	–
Z. vazquezii Stevenson, Sabato, Moretti & De Luca	Mexico	–	–	–	–	–
Z. cunaria Dressler & Stevenson*	Panama	–	4	–	1	–
Z. elegantissima Schutzman, Vovides & Adams*	Panama	–	–	–	1	–
Z. integrifolia L. f.*	USA	1	–	3	–	–
Z. manicata Linden ex Regel*	Colombia	4	1	1	1	–
Z. pseudoparasitica Yates in Seem*	Panama	>50	–	–	–	–
Z. pygmea Sims	Cuba	–	–	–	–	–

The intergenic spacer psbK-psbI displays the best single-locus performance. Information compiled from Nicolalde-Morejón et al. (2010).

* The Zamia species diagnosable with these loci.

Table II.  Sequence data and geographical origin characteristics of sampled Zamia species.

			Number of sequences per collection locality and haplotypes
Zamia species	Number of populations	Distribution (state, country)	psbk-psbI	Haplotype and GenBank accession numbers
Z. paucijuga	13	1. Nayarit, Mexico	9	H1: HQ454120
		2. Jalisco, Mexico	9	H1
		3. Jalisco, Mexico	10	H1
		4. Jalisco, Mexico	9	H1
		5. Jalisco, Mexico	10	H1
		6. Michoacán, Mexico	10	H1
		7. Guerrero, Mexico	5	H1
		8. Guerrero, Mexico	10	H1
		9. Guerrero, Mexico	9	H1
		10. Guerrero, Mexico	8	H11: HQ454130
		11. Oaxaca, Mexico	8	H11
		12. Oaxaca, Mexico	10	H11
		13. Oaxaca, Mexico	10	H1
Z. soconuscensis	1	1. Chiapas, Mexico	10	H1
Z. herrerae	2	1. Chiapas, Mexico	9	H4: HQ454123
		2. Chiapas, Mexico	7	H4
Z. loddigesii	7	1. Tabasco, Mexico	10	H1 (Ind. 1–3, 5–8, 10); H4 (Ind. 4, 9)
		2. Tamaulipas, Mexico	10	H4
		3. Veracruz, Mexico	4	H1 (Ind. 1, 3, 4); H4 (Ind. 2)
		4. Veracruz, Mexico	3	H1
		5. Veracruz, Mexico	3	H1
		6. Veracuz, Mexico	2	H1
		7. Oaxaca, Mexico	4	H4 (Ind. 3); H9: HQ454128 (Ind. 1, 2); H10: HQ454129 (Ind. 4)
Z. fischeri	2	1. San Luis Potosí, Mexico	10	H2: HQ454121
		2. San Luis Potosí, Mexico	8	H2 (Ind. 1, 4, 5, 6, 7); H3: HQ454122 (Ind. 2, 3, 8)
Z. vazquezii	1	1. Veracruz, Mexico	9	H8: HQ454127
Z. inermis	1	1. Veracruz, Mexico	8	H2 (Ind. 1, 3–8); H5: HQ454124 (Ind. 2)
Z. furfuracea	6	1. Veracruz, Mexico	10	H1
		2. Veracruz, Mexico	10	H1
		3. Veracruz, Mexico	8	H1
		4. Veracruz, Mexico	7	H1 (Ind. 1, 2, 4–7); H4 (Ind. 3)
		5. Veracruz, Mexico	9	H1
		6. Veracruz, Mexico	10	H1
Z. katzeriana	4	1. Chiapas, Mexico	7	H1
		2. Chiapas, Mexico	7	H4
		3. Chiapas, Mexico	2	H1
		4. Veracruz, Mexico	4	H1 (Ind. 1, 3); H4 (Ind. 2, 4)
Z. spartea	3	1. Oaxaca, Mexico	9	H1 (Ind. 1–3, 5–8); H4 (Ind. 4, 9)
		2. Oaxaca, Mexico	9	H1
		3. Oaxaca, Mexico	3	H1 (Ind. 3); H4 (Ind. 1, 2)
Z. purpurea	2	1. Veracruz, Mexico	8	H1
		2. Oaxaca, Mexico	10	H1
Z. cremnophila	1	1. Tabasco, Mexico	10	H1
Z. lacandona	3	1. Chiapas, Mexico	5	H1
		2. Chiapas, Mexico	1	H1
Z. polymorpha	11	1. Yucatán, Mexico	3	H12 (Ind. 1); H13 (Ind. 2, 3)
		2. Yucatán, Mexico	4	H12: HQ454131
		3. Yucatán, Mexico	4	H12
		4. Campeche, Mexico	3	H12
		5. Campeche, Mexico	4	H13: HQ454132
		6. Quintana Roo, Mexico	2	H12
		7. Quintana Roo, Mexico	2	H1 (Ind. 1); H12 (Ind. 2)
		8. Quintana Roo, Mexico	2	H12
		9. Quintana Roo, Mexico	2	H12
		10. Chiapas, Mexico	3	H12
		11. Tabasco, Mexico	4	H12
Z. variegata	1	1. Chiapas, Mexico	9	H1
Z. standleyi	1	1. Honduras	4	H1
Z. tuerckheimii	1	1. Guatemala	5	H1
Z. prasina	1	1. Belize	5	H14: HQ454133
Z. cunaria	1	Panama	1	H1
Z. manicata	1	Colombia	1	H15: HQ454134
Z. pygmea	1	Cuba	1	H6: HQ454125
Z. integrifolia	1	USA	1	H7: HQ454126

Table III.  Comparison of DNA diagnostic sites between the single-individual and the population-level psbK-psbI data sets for Zamia species from Megamexico.

	Diagnostic sites for psbI-psbK (single-individual/population level)
Zamia species	–/1	1/31	–/51	47/74	58/83	143/153	–/202	–/220	251/253	–/319	386/361	439/411	618/–	666/622	709/664
Z. cremnophila	G	A	T	T	T	A	C	C	A	–	–	–	–	C	C
Z. fischeri	T/A*	A	C	T	T	A	C	A/C*	A	C	T	T	T	C	C
Z. furfuracea	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. herrerae	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. inermis	G	A	T	T	T	A	C	C	A	C	T	T	T	T	C
Z. katzeriana	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. lacandona	G	A	T	T	T	A	C	C	A	C	T	T	C	C	C
Z. loddigesii	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. paucijuga	G	A	T	T	T	A	C1–9,13/A10–12	C	A	C	T	T	T	C	C
Z. polymorpha	G	A	T	C	T	G/A*	C	C	A	C	C	T	T	C	C
Z. prasina	G	A	T	T	C	A	C	C	A	C	T	T	T	C	C
Z. purpurea	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. soconuscensis	G	G	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. spartea	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. standleyi	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. tuerckheimii	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. variegata	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. vazquezii^†	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. cunaria^†	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C
Z. integrifolia^†	G	A	T	T	T	A	C	C	A	T	T	T	T	C	C
Z. manicata^†	G	A	T	T	T	A	C	C	C	C	T	C	T	C	G
Z. pygmea^†	G	A	T	T	T	A	C	C	A	C	T	T	T	C	C

Diagnostic sites in common for the two matrices/alignments are indicated with shading. Notice the polymorphisms in Z. fischeri, Z. polymorpha, and particularly in Z. paucijuga.

* Only a few individuals displayed the nucleotidic variant

^† Only one individual was studied in these species.

Nicolalde-Morejón F, Vergara-Silva F, González-Astorga J, Stevenson DW, Vovides AP, Sosa V. 2010. A character-based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding Cladistics, in press. doi:10.1111/j.1096-0031.2010.00321.x.

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