title: Molecular phylogeny and patterns of diversification in syngnathid fishes.
abstract: The family Syngnathidae is a large and diverse clade of morphologically unique bony fishes, with 57 genera and 300 described species of seahorses, pipefishes, pipehorses, and seadragons. They primarily inhabit shallow coastal waters in temperate and tropical oceans, and are characterized by a fused jaw, male brooding, and extraordinary crypsis. Phylogenetic relationships within the Syngnathidae remain poorly resolved due to lack of generic taxon sampling, few diagnostic morphological characters, and limited molecular data. The phylogenetic placement of the threatened, commercially exploited seahorses remains a topic of intense interest, with conflicting topologies based on morphology and predominantly mitochondrial genetic data. In this study, we integrate eight nuclear and mitochondrial markers and 17 morphological characters to investigate the phylogenetic structure of the family Syngnathidae at the generic level. We include 91 syngnathid species representing 48 of the 57 recognized genera, all major ocean basins, and a broad array of temperate and tropical habitats including rocky and coral reefs, sand and silt, mangroves, seagrass beds, estuaries, and rivers. Maximum likelihood and Bayesian analyses of 5160bp from eight loci produced high congruence among alternate topologies, defining well-supported and sometimes novel clades. We present a hypothesis that confirms a deep phylogenetic split between lineages with trunk- or tail-brood pouch placement, and provides significant new insights into the morphological evolution and biogeography of this highly derived fish clade. Based on the fundamental division between lineages - the tail brooding "Urophori" and the trunk brooding "Gastrophori" - we propose a revision of Syngnathidae classification into only two subfamilies: the Nerophinae and the Syngnathinae. We find support for distinct principal clades within the trunk-brooders and tail-brooders, the latter of which include seahorses, seadragons, independent lineages of pipehorses, and clades that originated in southern Australia and the Western Atlantic. We suggest the seahorse genus Hippocampus is of Indo-Pacific origin and its sister clade is an unexpected grouping of several morphologically disparate Indo-Pacific genera, including the Pacific pygmy pipehorses. Taxonomic revision is required for multiple genera, particularly to reflect deep evolutionary splits in nominal lineages from the Atlantic versus the Indo-Pacific.
authors.affiliation: NatureServe, 4600 N Fairfax Drive, 7th Floor, Arlington, VA 22203, United States; Marine Conservation Institute, 4010 Stone Way N., Suite 210, Seattle, WA 98103, United States. Electronic address: healy_hamilton@natureserve.org.
authors.forename: Healy
authors.initials: H
authors.lastname: Hamilton
authors.affiliation: Yale University, Ecology and Evolutionary Biology Department, New Haven, CT 06520, United States.
authors.forename: Norah
authors.initials: N
authors.lastname: Saarman
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States.
authors.forename: Graham
authors.initials: G
authors.lastname: Short
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States.
authors.forename: Anna B
authors.initials: AB
authors.lastname: Sellas
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States.
authors.forename: Beth
authors.initials: B
authors.lastname: Moore
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States.
authors.forename: Tinya
authors.initials: T
authors.lastname: Hoang
authors.affiliation: Clark University, Department of Biology, 950 Main St., Worcester, MA 01610, United States.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Grace
authors.affiliation: Sciences Department, Museum Victoria GPO Box 666, Melbourne, VIC 3001, Australia.
authors.forename: Martin
authors.initials: M
authors.lastname: Gomon
authors.affiliation: San Francisco State University, Department of Biology, San Francisco, CA 94132, United States.
authors.forename: Karen
authors.initials: K
authors.lastname: Crow
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, United States.
authors.forename: W
authors.initials: W
authors.lastname: Brian Simison
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D019143:Evolution, Molecular; D005399:Fishes / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics*; D014644:Genetic Variation; D008297:Male; D010802:Phylogeny; D058974:Phylogeography
keywords: Australia; DNA; Morphological evolution; Pipefish; Seahorse; Syngnathidae