Diversity 2013, 5, 796-810; doi:10.3390/d5040796 OPEN ACCESS diversity ISSN 1424-2818 www.mdpi.com/journal/diversity Article Genetic Diversity and Population Structure of Two Freshwater Copepods (Copepoda: Diaptomidae), Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan Shuh-Sen Young 1,*, Shu-Chuan Lin 1,2 and Min-Yun Liu 3 1 Department of Applied Science, National Hsinchu University of Education, Hsinchu 300, Taiwan 2 Hsinchu Municipal Hsinchu Elementary School, 106, Shingshiue Street, Hsinchu 300, Taiwan; E-Mail:
[email protected] 3 National Applied Research Laboratories, Taiwan Ocean Research Institute, 3F, 106, Hoping Road, Section 2, Taipei 106, Taiwan; E-Mail:
[email protected] * Author to whom correspondence should be addressed; E-Mail:
[email protected]; Tel.: +886-521-3132-2712; Fax: +886-525-7178. Received: 22 September 2013; in revised form: 15 November 2013 / Accepted: 18 November 2013 / Published: 22 November 2013 Abstract: We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four populations with 51 individuals of N. schmackeri and five populations with 65 individuals of M. birulai were included. We compared the nucleotide sequences of a 635-bp fragment of the COI gene of N. schmackeri and a 655-bp fragment of the COI gene of M. birulai, and eight and 14 unique haplotypes were recorded, respectively. Tseng-Wen reservoir and Wu-San-Tao reservoir are linked by a channel, and the gene flow between them was unrestricted (Fst = 0.058; Nm = 4.04; Fst, population differentiation parameter; Nm, the number of succesfull migrants per generation); the gene flow between all other populations of both species was restricted (Fst = 0.4–0.99; Nm = 0–0.37).