Search

Since the 19th century, oceanic explorations have confirmed that the hadal zone (water depth > 6000 m) is not lifeless, but contains many fascinating organisms. Amongst them are the Mysida, which is a group of crustaceans found in many deep-sea trenches. Based on morphological observations and molecular phylogenetic analyses of an undescribed taxon within the subfamily Erythropinae, a new genus of deep-sea mysids, Xenomysis gen. n., is described from the Challenger Deep in the Mariana Trench. The new genus is not assigned to any of the tribes within the Erythropinae, as our analyses do not support the current classification scheme of Erythropinae. The result of a molecular-clock analysis with fossil calibration reveals that several groups of Mysida have independently colonized deep water habitats in different geological periods, from Triassic to Cretaceous. In addition, ancestral state reconstruction analyses indicate the degenerate eyes in both Mysidae and Petalophthalmidae is a result of parallel evolution, and the reduction of compound eyes to both "single fused eyeplate" and "two separate eyeplates" occurred multiple times independently in the evolution of Erythropinae., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Like other crustacean families, the Parabathynellidae is a poorly studied subterranean and aquatic (stygobiontic) group in Australia, with many regions of available habitat having not yet been surveyed. Here we used a combined approach of molecular species delimitation methods, applied to mitochondrial and nuclear genetic data, to identify putative new species from material obtained from remote subterranean habitats in the Pilbara region of Western Australia. Based on collections from these new localities, we delineated a minimum of eight and up to 24 putative new species using a consensus from a range of molecular delineation methods and additional evidence. When we placed our new putative species into the broader phylogenetic framework of Australian Parabathynellidae, they grouped with two known genera and also within one new and distinct Pilbara-only clade. These new species significantly expand the known diversity of Parabathynellidae in that they represent a 22% increase to the 109 currently recognised species globally. Our investigations showed that sampling at new localities can yield extraordinary levels of new species diversity, with the majority of species showing likely restricted endemic geographical ranges. These findings represent only a small sample from a region comprising less than 2.5% of the Australian continent., (Crown Copyright © 2019. Published by Elsevier Inc. All rights reserved.)

Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Rickettsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%., (Copyright © 2018 Elsevier Inc. All rights reserved.)

We used a combined analysis of one nuclear (28S rDNA) and three mitochondrial markers (COI, 12S rDNA, 16S rDNA) to infer the molecular phylogeny of the Notostraca, represented by samples from the six continents that are inhabited by this group of branchiopod crustaceans. Our results confirm the monophyly of both extant notostracan genera Triops and Lepidurus with good support in model based and maximum parsimony analyses. We used branchiopod fossils as a calibration to infer divergence times among notostracan lineages and accounted for rate heterogeneity among lineages by applying relaxed-clock models. Our divergence date estimates indicate an initial diversification into the genera Triops and Lepidurus in the Mesozoic, most likely at a minimum age of 152.3-233.5 Ma, i.e., in the Triassic or Jurassic. Implications for the interpretation of fossils and the evolution of notostracan morphology are discussed. We further use the divergence date estimates to formulate a biogeographic hypothesis that explains distributions of extant lineages predominantly by overland dispersal routes. We identified an additional hitherto unrecognised highly diverged lineage within Lepidurus apus lubbocki and three additional previously unknown major lineages within Triops. Within T. granarius we found deep differentiation, with representatives distributed among three major phylogenetic lineages. One of these major lineages comprises T. cancriformis, the T. mauritanicus species group and two hitherto unrecognised T. granarius lineages. Samples that were morphologically identified as T. granarius diverged from the most basal nodes within this major lineage, and divergence dates suggested an approximate age of 23.7-49.6 Ma for T. cancriformis, indicating the need for a taxonomic revision of Triassic and Permian fossils that are currently attributed to the extant T. cancriformis. We thus elevate T. cancriformis minor to full species status as Triops minorTrusheim, 1938 and include in this species the additional Upper Triassic samples that were attributed to T. cancriformis. We further elevate T. cancriformis permiensis to full species status as Triops permiensisGand et al., 1997., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Cyclestheria hislopi is thought to be the only extant species of Cyclestherida. It is the sister taxon of all Cladocera and displays morphological characteristics intermediate of Spinicaudata and Cladocera. Using one mitochondrial (COI) and two nuclear (EF1α and 28S rRNA) markers, we tested the hypothesis that C. hislopi represents a single circumtropic species. South American (French Guiana), Asian (India, Indonesia, Singapore) and several Australian populations were included in our investigation. Phylogenetic and genetic distance analyses revealed remarkable intercontinental genetic differentiation (uncorrected p-distances COI>13%, EF1α>3% and 28S>4%). Each continent was found to have at least one distinct Cyclestheria species, with Australia boasting four distinct main lineages which may be attributed to two to three species. The divergence of these species (constituting crown group Cyclestherida) was, on the basis of phylogenetic analyses of COI and EF1α combined with molecular clock estimates using several fossil branchiopod calibration points or a COI substitution rate of 1.4% per million years, dated to the Cretaceous. This was when the South American lineage split from the Asian-Australian lineage, with the latter diverging further in the Paleogene. Today's circumtropic distribution of Cyclestheria may be best explained by a combination of Gondwana vicariance and later dispersal across Asia and Australia when the tectonic plates of the two continents drew closer in the early Miocene. The lack of morphological differentiation that has taken place in this taxon over such a long evolutionary period contrasts with the high level of differentiation and diversification observed in its sister taxon the Cladocera. Further insights into the evolution of Cyclestheria may help us to understand the evolutionary success of the Cladocera., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The crustacean family Parabathynellidae is an ancient and significant faunal component of subterranean ecosystems. Molecular data were generated in order to examine phylogenetic relationships amongst Australian genera and assess the species diversity of this group within Australia. We also used the resultant phylogenetic framework, in combination with an ancestral state reconstruction (ASR) analysis, to explore the evolution of two key morphological characters (number of segments of the first and second antennae), previously used to define genera, and assess the oligomerization principle (i.e. serial appendage reduction over time), which is commonly invoked in crustacean systematics. The ASR approach also allowed an assessment of whether there has been convergent evolution of appendage numbers during the evolution of Australian parabathynellids. Sequence data from the mtDNA COI and nDNA 18S rRNA genes were obtained from 32 parabathynellid species (100% of described genera and ~25% of described species) from key groundwater regions across Australia. Phylogenetic analyses revealed that species of each known genus, defined by traditional morphological methods, were monophyletic, suggesting that the commonly used generic characters are robust for defining distinct evolutionary lineages. Additionally, ancestral state reconstruction analysis provided evidence for multiple cases of convergent evolution for the two morphological characters evaluated, suggesting that caution needs to be shown when using these characters for elucidating phylogenetic relationships, particularly when there are few morphological characters available for reconstructing relationships. The ancestral state analysis contradicted the conventional view of parabathynellid evolution, which assumes that more simplified taxa (i.e. those with fewer-segmented appendages and setae) are derived and more complex taxa are primitive., (Copyright © 2012 Elsevier Inc. All rights reserved.)

The ostracod genus Macroscapha is used as a model to test theories predicting circumantarctic distribution of benthic species from the Southern Ocean. Earlier works on Antarctic Ostracoda reported five circumantarctic and/or eurybathic Macroscapha species. However, a recent taxonomic revision used a narrow morphological species definition and subdivided these five species into 20 morphospecies. Most of these narrowly defined species showed restricted depth and geographical distribution. Here, genetic markers are used to investigate the geographic and bathymetric distribution of seven species of the genus Macroscapha. The genetic results (especially COI, but partially also ITS) support more restricted geographical ranges and indicate more restricted depth distributions. Our results therefore corroborate the usefulness of a narrow morphological species definition. Our dataset also indicates that the 'genetic entities' of one species group (i.e. 'Mh. tensa-opaca') are not only geographically but also bathymetrically segregated. For that reason, a re-evaluation of the prevailing theories on the circumantarctic and eurybathic distribution of Southern Ocean benthic species is suggested., (2010 Elsevier Inc. All rights reserved.)

The persistence of asexual reproduction in many taxa depends on a balance between the origin of new asexual lineages and the extinction of old ones. This turnover determines the diversity of extant asexual populations and so influences the interaction between sexual and asexual modes of reproduction. Species with mixed reproduction, like the freshwater ostracod (Crustacea) morphospecies Eucypris virens, are a good model to examine these dynamics. This species is also a geographic parthenogen, in which sexual females and males co-exist with asexual females in the circum-Mediterranean area only, whereas asexual females occur all over Europe. A molecular phylogeny of E. virens based on the mitochondrial COI and 16S fragments is presented. It is characterised by many distinct clusters of haplotypes which are either exclusively sexual or asexual, with only one exception, and are often separated by deep branches. Analysis of the phylogeny reveals an astonishing cryptic diversity, which indicates the existence of a species complex with more than 40 cryptic taxa. We therefore suggest a revision of the single species status of E. virens. The phylogeny indicates multiple transitions from diverse sexual ancestor populations to asexuality. Although many transitions appear to be ancient, we argue that this may be an artefact of the existence of unsampled or extinct sexual lineages., (Copyright (c) 2009 Elsevier Inc. All rights reserved.)

Helleria brevicornis has a disjunct, peri-Tyrrhenian distribution that mirrors that of several organisms, for which geographic vicariance is invoked, due to the geological events started with the Oligocene split of the Sardo-Corsican microplate from the Pyrenees, and successive separation between Sardinia and Corsica. Molecular phylogenetic analyses demonstrated that such a biogeographic model does not apply to Helleria. The original split of the Sardinian and Corsican lineages originated in the Early Pliocene. Further diversification occurred later. The colonization of the Tuscan archipelago, French, and Italian mainland occurred most recently, but a possible time dependency bias suggests that such colonization was driven by human-transport., (Copyright (c) 2009 Elsevier Inc. All rights reserved.)

Taxonomy and phylogeny within the branchiopod taxon Spinicaudata are still controversial. We analyzed sequences of three gene fragments (28S rRNA, 16S rRNA and COI) from up to 41 species of the Cyzicidae, Limnadiidae and Leptestheriidae to infer their phylogenetic relationships, focusing in particular on species from Australia and their phylogenetic position within Spinicaudata. Four major monophyletic lineages could be distinguished: Limnadiidae, Leptestheriidae, Eocyzicus and all Cyzicidae except Eocyzicus. A clear genetic distinction between Australian and non-Australian Cyzicidae is well supported (i.e. Caenestheria and Caenestheriella species from Australia and Caenestheriella and Cyzicus species from Europe, Asia and North America). In the genera Eocyzicus and Eulimnadia the Australian species were closely related to those from other continents. The species of the Australian endemic genus Limnadopsis and Australian Limnadia species form a monophylum. This suggests that the origin of Limnadopsis lies in Australia and that Limnadia is not monophyletic.

Dating evolutionary origins of taxa is essential for understanding rates and timing of evolutionary events, often inciting intense debate when molecular estimates differ from first fossil appearances. For numerous reasons, ostracods present a challenging case study of rates of evolution and congruence of fossil and molecular divergence time estimates. On the one hand, ostracods have one of the densest fossil records of any metazoan group. However, taxonomy of fossil ostracods is controversial, owing at least in part to homoplasy of carapaces, the most commonly fossilized part. In addition, rates of evolution are variable in ostracods. Here, we report evidence of extreme variation in the rate of molecular evolution in different ostracod groups. This rate is significantly elevated in Halocyprid ostracods, a widespread planktonic group, consistent with previous observations that planktonic groups show elevated rates of molecular evolution. At the same time, the rate of molecular evolution is slow in the lineage leading to Manawa staceyi, a relict species that we estimate diverged approximately 500 million years ago from its closest known living relative. We also report multiple cases of significant incongruence between fossil and molecular estimates of divergence times in Ostracoda. Although relaxed clock methods improve the congruence of fossil and molecular divergence estimates over strict clock models, incongruence is present regardless of method. We hypothesize that this observed incongruence is driven largely by problems with taxonomy of fossil Ostracoda. Our results illustrate the difficulty in consistently estimating lineage divergence times, even in the presence of a voluminous fossil record.

The Ponto-Caspian (Black and Caspian seas) brackish-water fauna represents a special case of the endemic diversification in world's ancient lakes; it also involves a hotspot of continental diversity in the predominantly marine mysid crustaceans. We explored the origins and history of the mysid diversification in a phylogenetic analysis of some 20 endemic Ponto-Caspian species mainly of the genus Paramysis and their marine congeners, using sequences of two nuclear protein-coding genes, two nuclear rRNA genes, the mitochondrial COI gene and morphological data. A nearly completely resolved phylogeny was recovered, with no indication of rapid diversification bursts. Deep divergences were found among the main endemic clades, attesting to a long independent faunal history in the continental Paratethys waters. The current marine Paramysis species make a monophyletic cluster secondarily derived from the continental Paratethyan (Ponto-Caspian) Paramysis ancestors. The good phylogenetic resolution was mainly due to the two nuclear protein-coding genes, opsin and EPRS, here for the first time applied to peracarid systematics. In contrast, 'conventional' mtDNA and nuclear rRNA genes provided poor topological resolution and weak congruence of divergence rates. The two nuclear protein-coding genes had more congruent rates of evolution, and were about 10-15 times slower than the mitochondrial COI gene.

New studies on malacostracan relationships have drawn attention to issues concerning monophyly of the order Mysidacea, manifested in recent crustacean classifications that treat the taxon as two separate orders, Lophogastrida and Mysida. We present molecular phylogenies of these orders based on complete sequences of nuclear small-subunit ribosomal DNA (18S rRNA), and morphological evidence is used to revise the classification of the order Mysida to better reflect evolutionary history. A secondary structure model for 18S rRNA was constructed and used to assign putative stem and loop regions to two groups of partitions for phylogenetic analyses. Phylogenies were estimated by maximum-likelihood, Bayesian inference, and maximum-parsimony. The analyses gave strong support for three independently derived lineages, represented by three monophyletic groups, Lophogastrida, Stygiomysida, and Mysida. The family Petalophthalmidae is considered as sister group to the family Mysidae, and Boreomysinae and Rhopalophthalminae are the most early derived of the Mysidae. The tribes contained in the current classification of the subfamily Mysinae are not well-supported by either molecular data or morphology.

Coexisting bisexual and unisexual populations of individuals belonging to the genus Heterocypris are found in ephemeral freshwater ponds on the island of Lampedusa (Pelagie Islands, Italy). Different reproductive modes were associated with a peculiar morphological trait: a lamella hyalina on the posterior margin of the left valve was observed in amphimictic females, a feature missing in apomictic females. In order to clarify the phylogenetic relationships among taxa with different morphological traits and reproductive modes, we used four polymorphic enzyme loci (GPI, ICD2, MPI and PGM) and mitochondrial DNA 16S ribosomal sequences. We identified three main evolutionary units that showed a combination of morphological and reproductive characteristics: (1) amphimictic females of H. barbara with a lamella hyalina, according to the typical feature of the species, and apomictic females of H. barbara without lamella that are sympatric in one temporary pond; (2) apomictic females of H. incongruens without a lamella, as typical of the species; (3) apomictic females without a lamella, living in sympatry with H. barbara, but characterised by a high genetic diversity from both H. incongruens and H. barbara. We discuss the possible origin of apomictic lineages as a result of independent transition episodes to apomixis from different sexual ancestors. Time of divergence reflected the genetic differentiation within and among multiple ancestors and different possible routes to parthenogenesis.

The evolutionary history of Branchiopoda (Crustacea) traditionally has attracted considerable interest due to the diversity of the group. Recently molecular methods have been applied to the study of branchiopod systematics with some success, but central questions, such as the phylogenetic position of Laevicaudata and Notostraca, and the intrinsic cladoceran phylogeny, remain unanswered. We examined the phylogeny of Branchiopoda by using two genes, mitochondrial 16S rRNA and nuclear 28S rRNA, which previously have seen little use for inferring branchiopod phylogeny. The number of ingroup taxa included was 42, representing all eight extant branchiopod orders. The data were analyzed using parsimony, maximum likelihood, and Bayesian Inference of phylogeny. Some higher-level taxa were supported in all analyses of the combined data: Phyllopoda, Cladoceromorpha, Cladocera, and Gymnomera. Other higher-level taxa were not supported in any trees: Diplostraca and Conchostraca. A case is made for a possible diplostracan ingroup position of Notostraca based on our data and on previously published molecular and morphological evidence. The recent discovery of a Devonian branchiopod, which is morphologically an intermediate between a notostracan and a 'conchostracan', is congruent with a diplostracan ancestry of Notostraca.

With today's technology for production of molecular sequences, DNA taxonomy and barcoding arose as a new tool for evolutionary biology and ecology. However, their validities still need to be empirically evaluated. Of most importance is the strength of the correlation between morphological taxonomy and molecular divergence and the possibility to define some molecular thresholds. Here, we report measurements of this correlation for two mitochondrial genes (COI and 16S rRNA) within the sub-phylum Crustacea. Perl scripts were developed to ensure objectivity, reproducibility, and exhaustiveness of our tests. Our analysis reveals a general correlation between molecular divergence and taxonomy. This correlation is particularly high for shallow taxonomic levels allowing us to propose a COI universal crustacean threshold to help species delimitation. At higher taxonomic levels this correlation decreases, particularly when comparing different families. Those results plead for DNA use in taxonomy and suggest an operational method to help crustacean species delimitation that is linked to the phylogenetic species definition. This pragmatic tool is expected to fine tune the present classification, and not, as some would have believed, to tear it apart.

Mariner-like elements (MLEs) have been widely detected in terrestrial species. The first complete MLE isolated from a marine invertebrate was detected in the genome of the hydrothermal crab Bythograea thermydron by Halaimia-Toumi et al. [Halaimia-Toumi, N., Casse, N., Demattei, M.V., Renault, S., Pradier, E., Bigot, Y., Laulier, M., 2004. The GC-rich transposon Bytmar1 from the deep-sea hydrothermal crab, Bythograea thermydron, may encode three transposase isoforms from a single ORF. J. Mol. Evol. 59, 747-760] and called Bytmar1. Here, we report the isolation of three new Bytmar1 relatives from the genomes of one hydrothermal amphipod Ventiella sulfuris (Vensmar1) and two coastal crustacea, Maia brachydactila (Maibmar1) and Cancer pagurus (Canpmar1). Like Bytmar1, these MLEs have an unusually high GC content, a high CpG ratio, and a low TpA ratio. Their consensus sequence encodes a transposase that is preceded by an N-flag, as in Bytmar1, which could be a marine feature. Only one of the 19 clones obtained, Vensmar1.3, encoded for a full-length transposase. The phylogenetic analyses revealed that all these Bytmar1-related elements can be differentiated into two clusters, corresponding to the coastal or hydrothermal origin of their hosts. They also confirmed that the irritans sub-family comprises at least four lineages that seem to depend on the taxonomical position and habitat of their hosts. Finally, we observed that elements coding for two potentially complete transposases exhibiting 99.5% similarity, Bytmar1.11 and Vensmar1.3, were present in the genome of two distantly related hydrothermal crustacea, one Amphipod and one Decapod. The hypothesis of horizontal transfers is discussed in the light of the sequence similarities observed.

The Branchiopoda display extraordinary variation in body form, even within the morphologically diverse crustaceans. To fully understand the origin and evolution of these morphological reconfigurations, a robust phylogeny of the group is essential. To infer the affinities among branchiopods, we employed two approaches to taxon and gene sampling, presented new sequence data from three genes, incorporated previously published sequence data from three additional genes, and utilized comprehensive techniques of phylogeny reconstruction. The results provided support for a number of longstanding hypotheses concerning the relationships among the orders. For example, we obtained support for the Cladoceromorpha and Gymnomera, and favoured a unique arrangement of the cladoceran orders. A few affinities remain to be resolved, particularly at the base of the Phyllopoda and within the Anomopoda. However, the results suggest that increased gene sampling is recommended for future investigations of branchiopod systematics.

The complete mitochondrial DNA sequence was determined for the mantid shrimp Harpiosquilla harpax. These data demonstrate that the H. harpax mitochondrial genome is a 15,714 bp circular molecule and encodes the typical 37 metazoan mitochondrial genes (13 protein-coding, 22 tRNA, and two rRNA genes). The gene arrangement of H. harpax is consistent with that of the putative arthropod ancestral gene order as depicted by Limulus polyphemus. H. harpax was employed as an outgroup taxon for a phylogenetic investigation of the Decapoda using sequences from complete mitochondrial genomes. Whilst our results are largely in agreement with current taxonomic treatments, the relationships indicated among the reptantian decapods are novel. Our results provide strong statistical support for a sister-group relationship between the Achelata and the Astacida. These findings not only refute previous phylogenetic hypotheses, but also have serious implications for the interpretation of morphological and developmental evolution in the Decapoda. In addition we also investigated the effects of outgroup selection on the resolution of ingroup relationships. We found outgroup choice to significantly influence tree topology thus reinforcing the importance of appropriate outgroup selection in phylogenetic studies.

Lake Baikal, in Siberia, Russia, contains the highest biodiversity of any extant lake, including an impressive radiation of gammaroidean amphipods that are often cited as a classic case of adaptive radiation. However, relationships among Baikal's amphipods remain poorly understood. The phylogenetic history of 32 Lake Baikal amphipod species, representing most major lineages of the endemic fauna, was examined using three genes (COI, 16S rRNA, and 18S rRNA), and 152 morphological characters. Results support monophyly of the largest and most diverse of the Baikalian families, the Acanthogammaridae. Analyses suggest that a second Baikalian family, the fossorial Micruropodidae, is paraphyletic and composed of two divergent clades, one of which includes Macrohectopus branickii, a morphologically specialized pelagic planktivore traditionally assigned its own family. The extreme morphological and ecological divergence of Macrohectopus from its close genetic relatives, and conversely, the large genetic distances among other morphologically similar micruropodids, suggest that morphological and molecular evolution have often been uncoupled during the radiation of Baikal's amphipods. This study suggests that the amphipod fauna of Lake Baikal is polyphyletic; originating from two independent invasions of the lake.

Species of the order Mysida (Crustacea, Peracarida) are shrimp-like animals that occur in vast numbers in coastal regions of the world. The order Mysida comprises 1,053 species and 165 genera. The present study covers 25 species of the well-defined Mysidae, the most speciose family within the order Mysida. 18S rRNA sequence analysis confirms that the subfamily Siriellinae is monophyletic. On the other hand the subfamily Gastrosaccinae is paraphyletic and the subfamily Mysinae, represented in this study by the tribes Mysini and Leptomysini, consistently resolves into three independent clades, and hence is clearly not monophyletic. The tribe Mysini is not monophyletic either, and forms two clades of which one appears to be closely related to the Leptomysini. Our results are concordant with a number of morphological differences urging a taxonomic revision of the Mysidae.

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.

To help resolve phylogenetic relationships among the mitten crabs, complete sequences of the nuclear DNA internal transcribed spacer (ITS) and portions of the mitochondrial genome corresponding to the cytochrome oxidase I (COI), were sequenced for all Asian mitten crabs of the genus Eriocheir and seven species of the Grapsoidea. The resulting phylogeny supports the establishment of a separate genus Neoeriocheir, but does not provide justification for the recognition of Platyeriocheir. A female mitten crab specimen from the Zhujiang River, China, was considered to be Eriocheir recta (), a species previously synonymized with Eriocheir japonica (de Haan, 1835). In the ITS analysis, a sequence from Eriocheir formosa (from Taiwan) falls within a well-supported E. recta group, which indicates that E. formosa may have to be synonymized with E. recta. Three previously recognized members of the genus, E. japonica, Eriocheir sinensis, and Eriocheir hepuensis constitute a monophyletic sister group to E. recta in all phylogenetic trees. We provide evidence for the conspecific status of these taxa. Phylogenetic trees based on COI and combined COI and ITS sequences indicate that E. japonica consists of three subgroups. Since the name E. japonica (de Haan, 1835) takes precedence over E. sinensis (H. Milne Edwards, 1853) and E. hepuensis, we suggest that these three subgroups correspond to three subspecies of E. japonica: E. j. japonica, E. j. sinensis, and E. j. hepuensis.

For several decades the relationships within the Branchiopoda (Anostraca + Phyllopoda) have been a matter of controversy. Interpretations of plesiomorphic or apomorphic character states are a difficult venture, in particular in the Phyllopoda. We explore the relationships within the Phyllopoda at the level of nucleotid comparisons of the two genes 12S rDNA (mitochondrial) and EF1alpha (nuclear), and at a higher molecular level based on introns found in the gene EF1alpha. Within the Phyllopoda our explorations show further evidence for a non-monophyletic Conchostraca (Spinicaudata + Cyclestherida + Laevicaudata). The monotypic Cyclestherida is more closely related to the Cladocera, both together forming the Cladoceromorpha. The Spinicaudata (Leptestheriidae, Limnadiidae, and Cyzicidae) is well supported. Spinicaudata and Cladoceromorpha form a monophylum. The position of the Laevicaudata remains unclear but we find neither support for a sister group relationship to the Spinicaudata nor for a close relationship of Laevicaudata and Cladocera. Within the Cladocera, we favour the Gymnomera concept with the monotypic Haplopoda being the sister group to the monophyletic Onychopoda. The Ctenopoda seems to be the sister group to the Gymnomera, which contradicts the common view of a more basal position of the Ctenopoda., (Copyright 2002 Elsevier Science (USA))

We assessed evolutionary relationships among Hawaiian cave-adapted isopods using a maximum-likelihood criterion to analyze cytochrome oxidase I nucleotide sequences. Results support morphological data that two genera of philosciid isopods have invaded caves independently in the islands. In the genus Littorophiloscia, a sister relationship between a surface-dwelling species, L. hawaiiensis, and an undescribed cave species was corroborated. This evidence, along with the known parapatric distributions between species, supports a speciation event by an adaptive shift on the island of Hawaii from a marine littoral to a terrestrial subterranean habitat. The monophyletic genus Hawaiioscia contains four known obligate cave-dwelling species, each of which occurs on a separate island. However, despite present-day allopatric distributions between Hawaiioscia species, the geographic and phylogenetic patterns are not sufficient to support a vicariant mode of speciation. Instead, we believe that the known species of Hawaiioscia evolved from a widespread ancestral surface species or a group of closely related species through multiple, independent adaptive shifts on each of the islands of Kauai, Oahu, Molokai, and Maui. This is the first molecular investigation of evolutionary relationships between surface-dwelling and cavernicolous arthropods in Hawaii and it suggests that simple vicariance is insufficient to explain the evolution of troglobites in tropical zones.

The small subunit ribosomal DNA (ssu rDNA) of 13 isopods was sequenced. The entire length of the ribosomal gene is unusually long, resulting from the presence of five expansion elements accounting for more than 40% of the gene. We found that in terrestrial isopods the length of the ssu rDNA ranges from 2414 bp (Ligidium hypnorum) to 3537 bp (Cubaris murina). This is the longest metazoan ssu rDNA reported to date. The conserved regions are highly informative for analysis of the early nodes of the tree, whereas the variable expansion elements are better suited to reconstruction of the branching pattern between closely related taxa. The suggested relationship among Synochaeta, Crinochaeta, and Diplochaeta based on the conserved regions confirms that based on previous morphological analyses. In contrast, the phylogeny within the Crinochaeta based on the entire ssu rDNA including the variable domains is in conflict with that based on most of the morphological analyses. The phylogenetic analyses of the ssu rDNA support a repeated independent evolution of the three different types of pleopodal lungs in the Crinochaeta., (Copyright 2001 Academic Press.)

The Malacostraca are an ancient and morphologically diverse class of Crustacea. The phylogenetic position of one order within this class, the Euphausiacea ("krill," subclass Eumalacostraca) was investigated using 28S rDNA sequences from representatives of several malacostracan orders. Phylogenies for these sequences were estimated by maximum-likelihood and maximum-parsimony analysis. The results of these analyses produced a new scheme for evolution within the Eumalacostraca. The new phylogenies suggested that Euphausiacea are most closely related to the Mysida and not the Decapoda, as is generally thought. Furthermore, the Mysida were found not to be closely related to the Lophogastrida, which are often considered their sister taxon. These hypotheses were tested against the hypotheses of monophyly for the Eucarida, Mysidacea, and Peracarida and found to be significantly better on the basis of the 28S rDNA data., (Copyright 2000 Academic Press.)

To gain insights into the relationships among anostracan families, molecular phylogenetic analyses were performed on nuclear (28S D1-D3 ribosomal DNA) and mitochondrial (16S rDNA, COI) gene regions for representatives of seven families and an outgroup. Data matrices used in the analyses included 951 base pairs (bp) of aligned sequences for 28S, 465 bp for 16S, and 658 bp (219 amino acids) for COI. Maximum-parsimony and maximum-likelihood methods were used to construct phylogenetic trees, enabling the evaluation of both previous hypotheses of taxonomic relationships among families based on morphology, and of the relative merits of independent versus simultaneous analyses of multiple data sets for phylogeny construction. Data from various combinations of the gene regions produced relatively congruent patterns of phylogenetic affinity. In most analyses, two monophyletic groups were resolved: one cluster included the families Polyartemiidae, Chirocephalidae, Branchinectidae, Streptocephalidae, and Thamnocephalidae, while the other contained the Artemiidae and Branchipodidae. Comparative analyses showed that combining gene regions in a single matrix generally resulted in increased resolution and support for each cluster relative to those obtained from single-gene analyses. Statistical tests demonstrated that morphology-based hypotheses of relationships among families had poorer support than those determined from molecular data, reflecting the homoplasy in characters used to differentiate families., (Copyright 2000 Academic Press.)

In this study, a molecular phylogenetic hypothesis for 16 species of serolid isopods (Crustacea, Isopoda, Serolidae) from Antarctic waters, the deep sea, South America, and Australia is presented. The genes used are a 500-bp fragment of the mitochondrial LSU rRNA gene and a 700-bp fragment located in the variable region V4 of the nuclear SSU rRNA gene. The species composition and monophyly of morphologically defined genera of which several members were available are confirmed by the molecular data (Ceratoserolis, Spinoserolis, and Cuspidoserolis). The molecular data also support the redefinition of Frontoserolis s.l. and Serolella and the erection of the new genera Septemserolis and Paraserolis, as proposed by W]agele. The relationship among several genera is resolved differently in the molecular hypothesis than in the two existing morphological hypotheses, however. The molecular phylogeny may have important consequences for understanding the biogeography of the Serolidae, indicating that all Antarctic species in this study form a monophyletic group which has probably derived from species with closest extant relatives in South America. All 3 species included in this study living today in deep waters (>2000 m) of the Southern Ocean are most closely related to species living on the Antarctic shelf, so that parallel colonization of the deep sea by way of polar submergence can be reconstructed. In this study, a V4 expansion segment is reported which exceeds the longest crustacean sequences known until now by more than 270 bp. Although the V4 expansion segment has proven useful for phylogenetic purposes in this study, there is circumstantial evidence that its mechanism of evolution may depend not only on inheritance of single-site substitutions, making its routine use in phylogenetic studies potentially dangerous., (Copyright 2000 Academic Press.)

The evolutionary history of the cryptic Gammarus fossarum species complex (Crustacea, Amphipoda) in Central Europe was approached by investigating the genetic variation in populations of a natural contact zone. Nucleotide sequence variation of a 395-bp segment of the mitochondrial 16S rRNA gene was compared to that of six nuclear allozyme loci. Three major mtDNA lineages were found, the eastern clade being consistent with the former allozyme type A. The two western clades (types B and C) were not distinguished previously. Strong sequence divergence and correlation with nuclear genetic isolation in syntopic populations, however, justifies the specific status of the three G. fossarum types. The common speciation event is believed to be very old (Miocene). The within-type mtDNA variation is probably molded by the ice ages, with type B populations being most affected. Moreover, the patch-like distribution of mtDNA type B lineages in an area near the contact zone corroborates the hypothesis of a recent colonization., (Copyright 2000 Academic Press.)

The Baikalian gammarids (Crustacea, Amphipoda) are the most widely known and most spectacular example of an adaptive radiation among contemporary freshwater invertebrates. To study the phylogeny of the Baikalian gammarids we sequenced a 622-bp-long fragment of the nuclear gene coding for 18S rRNA from species of 18 endemic Baikalian genera and Gammarus pulex-a non-Baikalian taxon. Some important morphological characters appear independently in both lineages and suggest parallelism in the development of gigantism and body armament. The first lineage comprises benthic, mostly unarmed taxa. The second lineage contains predominantly armed taxa, most of which are detrivorous or carnivorous., (Copyright 1998 Academic Press.)

Among arthropods, Cirripedia (barnacles) are remarkable in that they completely lack abdominal segments. This feature prompted us to study the Hox genes of three cirripede species, representing a wide array of the diversity of these organisms, a segmented sessile barnacle, Elminius modestus (Thoracica), the parasite of a crab, Sacculina carcini (Rhizocephala), and the burrowing barnacle Trypetesa lampas (Acrothoracica). Using PCR amplification of genomic DNA and cDNA and library probing, we have found seven clear cirripedian homologues of the eight homeotic Hox genes known in insects, including labial and proboscipedia homologues, that were not previously reported in crustaceans. In addition we have isolated a divergent Antp-like gene, named Diva, that we homologize to the ftz gene of insects. The homeotic gene abdominalA (abdA) was not retrieved from any of these three cirripede species. By contrast, we have found all eight homeotic homologue genes, including abdA, in Ulophysema oeresundense, a crustacean possessing a well-developed abdomen, belonging to the Ascothoracica, generally thought to be the sister group of Cirripedia. Since we have found in barnacles homeobox-containing genes that are more divergent from the Antennapedia type than the typical abdA, we believe that a bona fide abdA gene would not have escaped our search. Hence, the abdA gene has been lost or is profoundly derived in sequence during the evolution leading to the cirripedian lineage. If confirmed, the lack of abdA would represent the first case in which the loss of a homeotic gene is correlated with a change in body plan during the evolution of metazoans., (Copyright 1998 Academic Press.)

Mitochondrial DNA nucleotide sequence analysis was used to determine the extent of genetic differentiation among six species of the genus Gammarus (Crustacea, Amphipoda) common in France (G. fossarum, G. pulex, G. lacustris, G. wautieri, G. roeseli, G. marinus). From 23 different populations, 104 specimens were compared to examine their taxonomic status and their phylogenetic relationships. Nucleotide sequences for a 376-base segment of the cytochrome c oxidase subunit I (COI) gene were obtained through direct sequencing of amplified DNA. The strong sequence variability found at the interspecific level, generally masked by morphological or ecological similarities, is consistent with that observed for other crustaceans and supports existing species classifications. A high level of genetic variation was observed at the intraspecific level, suggesting that the COI gene will be a powerful marker for amphipod population biology. Based on the mitochondrial population biology. Based on the mitochondrial DNA results, we propose a phylogenetic hypothesis of the relationships among the six studied species, which is discussed in biogeographic and evolutionary terms.