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For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov., Smirnovipinidae fam. nov. and Cyclopicinidae fam. nov are proposed as new taxa.

We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae) using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range's geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.

A new copepod species, Speleophriopsis mljetensis , collected from an anchialine cave Bjejajka on Mljet Island (Croatia) is described. The prosome of the new species is 5-segmented; the urosome has five somites in females and six in males; the genital double-somite is symmetrical and is longer than wide; the caudal rami are symmetrical, with seta I well developed; the antennules of both sexes are 27-segmented and symmetrical; the antennal exopod is 7-segmented; the maxillule possesses 15 armature elements on the praecoxal arthrite and the proximal basal endite has three slender setae and one stout claw-like seta, the fifth legs are symmetrical, 4-segmented and uniramous, and the distal segment is elongate and armed with seven and six elements in males and females, respectively. Speleophriopsis mljetensis is comparated with similar species S. balearicus and S. canariensis . The new species is mainly distinguished by the armature of the genital operculum, the fifth legs of both sexes, maxilliped distal segment armature and total length of both sexes. This is the second report of a speleophriid copepod, otherwise thought to be a Tethyan relict, from an Adriatic anchialine cave. In the Bjejajka Cave, the salinity varied between 1.5 at the surface to 39 psu at the bottom, and the temperature ranged between 14.2 and 16.6 °C. It might be assumed that it colonised Bjejajka anchialine cave from its natural deep-sea habitat. However, the distributions of speleophriids in the Mediterranean are difficult to explain; therefore, this finding is of particular importance, contributing to our knowledge of the global biogeography of these Tethyan relicts.

Abstract Phylogenetic relationships between the known genera of the order Misophrioida permit the identification of two lineages: one consisting of the family Misophriidae Brady, 1878 which comprises seven genera, and a new, monotypic family, the Palpophriidae Boxshall & Jaume, 1999; the other consisting of another new family, the Speleophriidae Boxshall & Jaume, 1999, comprising eight genera. Habitat exploitation by these families is discussed: members of the Misophriidae are primarily hyperbenthic, those of the Palpophriidae and Speleophriidae are primarily cavernicolous in anchialine habitats. The occurrence of misophriids in littoral and submarine caves is interpreted as evidence of a relatively recent landward extension of the habitat range in this family, from a shallow-water hyperbenthic ancestor. The distribution of speleophriids in anchialine caves is interpreted as resulting from a colonization episode prior to the closure of the Tethys Sea. The analysis also indicates that deep-water forms may represent a secondary colonization rather than an indication of deep-water ancestry for the entire order. El estudio de las relaciones filogeneticas entre los distintos generos pertenecientes al orden Misophrioida ha permitido la identificacion de dos linajes principales: uno compuesto por la familia Misophriidae Brady, 1878, integrada por siete generos, y una familia nueva, Palpophriidae Boxshall & Jaume, 1999; el otro, integrado por otra nueva familia, Speleophriidae Boxshall & Jaume, 1999, compuesta por ocho generos. Se discute la explotacion que del habitat hacen estas familias: los Misophriidae son primariamente hiperbenticos, mientras que Palpophriidae y Speleophriidae son cavernicolas en medio anquialino. La presencia de misofriidos en cuevas litorales y submarinas es interpretado como evidencia de una relativamente reciente extension tierra adentro del habitat ordinario de esta familia, a partir de un ancestro hiperbentico propio de aguas someras. La distribucion de los espeleofriidos en cuevas anquialinas es interpretada como resultado de un episodio de colonizacion anterior a la oclusion del mar de Tetis. El analisis indica tambien que las formas de aguas profundas representan una colonizacion secundaria mas que indicacion de un ancestro de aguas profundas para el orden entero.