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Approximately 120 (sub)species of Cyclopidae have been reported from South and Southeast (SE) Asia, where the Philippine archipelago – with 16 (including two endemic) taxa – is one of the least explored parts of the region. Our study, part of current efforts to assess freshwater biodiversity, was undertaken to update the diversity and geographic distribution of the cyclopid copepods living in the limnetic zone of the freshwater lakes in the Philippines. Examination of the samples from 22 lakes in five islands (Luzon, Mindoro, Cebu, Leyte and Mindanao) revealed a novel species from lake Siloton (Mindanao), Mesocyclops augusti n. sp. The new species can be distinguished from the congeners by the surface ornamentation of the hindgut, among others. The same character state was found in a Mesocyclops from North Vietnam, which is provisionally identified as M. augusti n. sp., though the Vietnam and Mindanao specimens differ in a few (yet polymorphic in the close relatives) characters. Mesocyclops microlasius Kiefer, 1981 endemic to the Philippines is redescribed, based on females and males from lake Paoay (North Luzon). Sister relationships of M. augusti n. sp. and M. microlasius were tested in a phylogenetic analysis that included the closely related Old World representatives of the genus. The max. parsimony trees show M. dissimilis Defaye et Kawabata, 1993 (East Asia) as the closest relative of M. augusti n. sp. (Mindanao, Vietnam), and support sister relationship between M. geminus Holynska, 2000 (East Borneo) and M. microlasius (Luzon, Mindanao). A mainland clade (M. francisci, M. parentium, M. woutersi, M. dissimilis, M. augusti) appears in most reconstructions; all members of the clade occur in continental Asia though some species also live in islands that have never been connected to the SE Asian shelf. In most trees with the mainland clade the insular taxa (M. microlasius, M. geminus, M. friendorum) form either a paraphyletic (basal to mainland) or monophyletic sister group of the mainland clade. We also established the first records of Thermocyclops taihokuensis (Harada, 1931) in the Philippines (Luzon), so far known from East and Central Asia. In all, 11 taxa [Mesocyclops (4), Thermocyclops (4), Microcyclops (1), Tropocyclops (1) and Paracyclops (1)] including only one endemic species (M. microlasius) have so far been found in the limnetic waters. We expect significantly higher diversity and higher rate of endemism of the freshwater cyclopids in the littoral (paludal) and subterranean habitats in the Philippines.
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