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ABSTRACT Nucleotide sequences from mitochondrial 12S ribosomal DNA are determined for 7 species of branchiopod crustaceans: 2 from the order Anostraca (Streptocephalus texanus and Linderiella santarosae), 2 from the order Conchostraca (Cyzicus mexicanus and Eulimnadia texana), 2 from the order Notostraca (Triops longicaudatus and Lepidurus bilobatus), and one from the order Cladocera (Moina brachycephala). They are compared to other branchiopod (Anostraca: Artemia franciscana, Cladocera: Daphnia pulex), and maxillopod (Branchiura: Savignium crenatum)sequences from the literature. The total set of nucleotides analyzed consists of sequences ranging in length from 250-267 bases. Multiple sequence alignments are generated and compared to assess the effects of alignment ambiguity on phylogenetic inference. Comparison of sequences among taxa revealed that (1) there is sufficient variation for phylogenetic analysis, (2) the variation is phylogenetically informative within and between some branchiopod orders, and (3) deep-branch phylogenetic resolution is limited by saturation effects. Phylogenetic relationships are inferred by parsimony analysis treating gaps as characters, confidence limits are estimated by both bootstrapping and the decay index. With a maxillopod sequence (Savignium crenatum) designated as an outgroup, the following results are obtained: branchiopod orders are monophyletic as sampled in this survey, with the orders Conchostraca and Notostraca clustering as sister taxa. Evidence for lineage specific rate heterogeneity of molecular evolution is discussed.


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