Two new decapod (Crustacea,Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Recent advances in molecular phylogenetics are continuously changing our perception of decapod phylogeny. Although the two suborders Dendrobranchiata and Pleocyemata within the Decapoda are widely accepted, this taxonomic view is now challenged when using mitochondrial protein‐coding genes to investigate the decapod phylogeny, especially for the basal pleocyematan groups. Here, we enhanced taxonomic coverage by sequencing the genomes of two basal decapod taxa Alpheus distinguendus and Panulirus ornatus, representing two infraorders, Caridea and Achelata, respectively. Based on these two and other available mitochondrial genomes, we evaluated the usefulness of protein‐coding genes in resolving deep phylogenetic relationships of the Decapoda using maximum likelihood and Bayesian analyses. The mt genomic results revealed a novel gene order because of the reverse transposition of trnE (transfer, trn for Glutamate) and a pseudogene‐like trnS (AGN) [trn for Serine (S₁, AGN)] in the mitochondrial genome of A. distinguendus, and a duplicate of 89 bp sequences in the putative noncoding region of P. ornatus. Our phylogenetic inferences suggest monophyly of the Decapoda and its two suborders, and that several lineages within the Reptantia are consistently recovered with high nodal supports. Our findings suggest that the best mitochondrial genome phylogeny can be found on the premise that systematic errors should be minimized as much as possible. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 471–481.     

On the phylogenetic position of the scrub-birds (Passeriformes: Menurae: Atrichornithidae) of Australia

Evolutionary relationships of the scrub-birds Atrichornis were investigated using complete sequences of the recombination-activating gene RAG-1 and the proto-oncogene c-mos for two individuals of the noisy scrub-bird Atrichornis clamosus. Phylogenetic analysis revealed that Atrichornis was sister to the genus Menura (the lyrebirds) and that these two genera (the Menurae) were sister to the rest of the oscine passerines. A sister relationship between Atrichornis and Menura supports the traditional view, based on morphology and DNA hybridization, that these taxa are closely related. Similarly, a sister relationship with the remaining oscine passerines agrees with the morphological distinctiveness of Atrichornis and Menura, although this result contradicts conclusions based on DNA hybridization studies. Although Atrichornis is very well known morphologically, previous conclusions regarding its relationships were hampered by a lack of comparative knowledge of other passerines, making concurrence of the sequence data of particular significance.     

Novelty and phylogenetic affinities of a new family of tapeworms (Cestoda: Rhinebothriidea) from endangered sawfish and guitarfish

The parasites of hosts of conservation concern are often poorly known. This is the case with the iconic group of elasmobranchs known as the sawfish of the genus Pristis, all four species of which are considered as Endangered or Critically Endangered by the International Union for Conservation of Nature (IUCN, Switzerland). Examination of cestodes from three species of sawfish (Pristis pristis, Pristis clavata, and Pristis zijsron) in Australia and one of their close relatives, the also critically endangered widenose guitarfish, Glaucostegus obtusus, in India, collected over the past 25 years, yielded four new species of tapeworms which are described herein. All four belong to the previously monotypic Mixobothrium; the diagnosis of the genus is revised to accommodate the new species. Among the new taxa is a species that had been included in previous molecular phylogenies but whose identity and affinities within the order Rhinebothriidea, and thus also its familial placement, were unclear. This species exhibits the morphological features of Mixobothrium and thus its identity is, at long last, revealed. Sequence data generated for the 28S rDNA gene for three of the new species, as well as an additional new but yet undescribed species from Pristis pectinata from Florida (USA), confirms the uniqueness of this group among the rhinebothriideans. The new family Mixobothriidae is established to house these taxa. The members of this family differ from all but one of the five other families of rhinebothriideans in lacking apical suckers on their bothridia. They are also distinctive in that their bothridia are divided into three regions. The anterior and posterior regions have similar locular configurations to one another and differ from the locular configuration of the middle region. As a consequence, the bothridia are symmetrical along both their vertical and horizontal axes. We predict that a focus on species of guitarfish in the genus Glaucostegus will be the most productive approach for discovering additional diversity in this family of cestodes.     

Laurentaeglyphea, a new genus for the second recent species of Glypheid recently discovered. (Crustacea Decapoda Glypheidae)

In 1975, a recent member of a large group of Crustacea Decapoda was described as Neoglyphea inopinata Forest & de Saint Laurent, until now only known as fossils and presumed extinct since the Eocene. The only known specimen had been collected in the Philippine waters, in 1908, at a depth of 200 m. During the next years, three oceanographical expeditions gave more adult specimens, allowing complete study of the species. From its morphology, it appeared that the status attributed to glypheids in the past in the classification of Decapoda Crustacea was quite erroneous. This group, until then considered as related to Palinurids (rock lobsters) was in fact much closer to Astacids (lobster, crayfish, etc.). In 1982, N. inopinata was recorded from the other side of Equator, from the Timor Sea. In October 2005, a second living species of glypheid was discovered southwest of New Caledonia. It was named Neoglyphea neocaledonica B. Richer de Forges, 2006. However, important and significant differences set apart the two species, especially the ornamentation of the cephalothorax, the conformation of the cephalic part and the proportions of epistom and thoracic appendages, being much more robust. It seems justified to establish, for the more recently described species, a new genus, Laurentaeglyphea, much closer to fossil forms.     

Bifidobacterium xylocopae sp. nov. and Bifidobacterium aemilianum sp. nov., from the carpenter bee (Xylocopa violacea) digestive tract

Social bees harbor a community of gut mutualistic bacteria, among which bifidobacteria occupy an important niche. Recently, four novel species have been isolated from guts of different bumblebees, thus allowing to suppose that a core bifidobacterial population may be present in wild solitary bees. To date there is sparse information about bifidobacteria in solitary bees such as Xylocopa and Osmia spp., this study is therefore focused on the isolation and characterization of bifidobacterial strains from solitary bees, in particular carpenter bee (Xylocopa violacea), builder bee (Osmia cornuta), and red mason bee (Osmia rufa). Among the isolates from Osmia spp. no new species have been detected whereas among Xylocopa isolates four strains (XV2, XV4, XV10, XV16) belonging to putative new species were found. Isolated strains are Gram-positive, lactate- and acetate-producing and possess the fructose-6-phosphate phosphoketolase enzyme. Full genome sequencing and genome annotation were performed for XV2 and XV10. Phylogenetic relationships were determined using partial and complete 16S rRNA sequences and hsp60 restriction analysis that confirmed the belonging of the new strains to Bifidobacterium genus and the relatedness of the strains XV2 and XV10 with XV16 and XV4, respectively. Phenotypic tests were performed for the proposed type strains, reference strains and their closest neighbor in the phylogenetic tree. The results support the proposal of two novel species Bifidobacterium xylocopae sp. nov. whose type strain is XV2 (=DSM 104955^T = LMG 30142^T), reference strain XV16 and Bifidobacterium aemilianum sp. nov. whose type strain is XV10 (=DSM 104956^T = LMG 30143^T), reference strain XV4.     

Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)

We propose a method using next generation sequencing technology for phylogenetics. The method is PCR based, requires little training beyond basic lab skills and is both cost and time effective. With this method we generated data for and produced a phylogeny of Decapoda that demonstrates this method's potential, the quality of the data, and the ability for the method to fit or even replace current Sanger based methods of generating DNA data for phylogenetic reconstruction. Finally, we discuss advantages and current challenges of the directed next generation sequencing approach.     

Molecular data confirm family status for the Tryonicus-Lauraesilpha group (Insecta: Blattodea: Tryonicidae)

Family status was recently proposed for the Tryonicus-Lauraesilpha group (Insecta: Blattodea: Tryonicidae), which had been assigned to Blattidae before. In order to test this hypothesis, a molecular phylogenetic analysis of Blattodea was conducted using the 12S and H3 genes. The results show that Tryonicidae indeed form a lineage distinct from Blattidae. The results are compared to the previous classifications and phylogenetic hypotheses (morphology- and molecular-based). It is suggested that the Polyzosteriinae tribe Methanini should remain in Polyzosteriinae (Blattodea: Blattidae).     

Integrative taxonomy of New Caledonian beetles: species delimitation and definition of the Uloma isoceroides species group (Coleoptera,Tenebrionidae, Ulomini), with the description of four new species

New Caledonia is an important biodiversity hotspot with much undocumented biodiversity, especially in many insect groups. Here we used an integrative approach to explore species diversity in the tenebrionid genus Uloma (Coleoptera, Tenebrionidae, Ulomini), which encompasses about 150 species, of which 22 are known from New Caledonia. To do so, we focused on a morphologically homogeneous group by comparing museum specimens with material collected during several recent field trips. We also conducted molecular phylogenetic analyses based on a concatenated matrix of four mitochondrial and three nuclear genes for 46 specimens. The morphological study allowed us to discover and describe four new species that belong to the group of interest, the Uloma isoceroides group. Molecular analyses confirmed the species boundaries of several of the previously described species and established the validity of the four new species. The phylogenetic analyses also provided additional information on the evolutionary history of the group, highlighting that a species that was thought to be unrelated to the group was in fact a member of the same evolutionary lineage. Molecular species delimitation confirmed the status of the sampled species of the group and also suggested some hidden (cryptic) biodiversity for at least two species of the group. Altogether this integrative taxonomic approach has allowed us to better define the boundaries of the Uloma isoceroides species group, which comprises at least 10 species: Uloma isoceroides (Fauvel, 1904), Uloma opacipennis (Fauvel, 1904), Uloma caledonica Kaszab, 1982, Uloma paniei Kaszab, 1982, Uloma monteithi Kaszab, 1986, Uloma robusta Kaszab, 1986, Uloma clamensae sp. n., Uloma condaminei sp. n., Uloma jourdani sp. n., and Uloma kergoati sp. n. We advocate more studies on other New Caledonian groups, as we expect that much undocumented biodiversity can be unveiled through the use of similar approaches.     

Molecular systematics of the Kakaducarididae (Crustacea: Decapoda: Caridea)

The systematic relationships of the freshwater shrimp family, Kakaducarididae, were examined using mitochondrial and nuclear DNA sequences. Combined nuclear (18S rDNA, 28S rDNA, Histone) and mitochondrial (16S rDNA) analyses placed the kakaducaridid genera, Kakaducaris and Leptopalaemon, as a strongly supported clade within the Palaemonidae, in a close relationship with the genus Macrobrachium. Monophyly of the Australian Kakaducarididae was strongly supported by the molecular data. Estimated net divergence times between Kakaducaris and Leptopalaemon using mitochondrial 16S rDNA equate to a late Miocene/Pliocene split. Within Leptopalaemon, each locality was distinct for mitochondrial COI haplotypes, suggesting long-term isolation or recent genetic bottlenecks, a lack of contemporary gene flow amongst sites and a small Ne. Mitochondrial groupings within Leptopalaemon were largely congruent with several previously recognised morphotypes. Estimated net divergence times between L. gagadjui and the new Leptopalaemon morphotypes equate to a split in the late Pliocene/early Pleistocene. The hypothesis that the Kakaducarididae is comprised of relict species in specialised ecological niches is not supported by the molecular data, which instead suggest a relatively recent origin for the group in northern Australia, sometime in the late Miocene or Pliocene.     

Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea)

Aim A New Caledonian insect group was studied in a world‐wide phylogenetic context to test: (1) whether local or regional island clades are older than 37 Ma, the postulated re‐emergence time of New Caledonia; (2) whether these clades show evidence for local radiations or multiple colonizations; and (3) whether there is evidence for relict taxa with long branches in phylogenetic trees that relate New Caledonian species to geographically distant taxa. Location New Caledonia, south‐west Pacific. Methods We sampled 43 cricket species representing all tribes of the subfamily Eneopterinae and 15 of the 17 described genera, focusing on taxa distributed in the South Pacific and around New Caledonia. One nuclear and three mitochondrial genes were analysed using Bayesian and parsimony methods. Phylogenetic divergence times were estimated using a relaxed clock method and several calibration criteria. Results The analyses indicate that, under the most conservative dating scenario, New Caledonian eneopterines are 5–16 million years old. The largest group in the Pacific region dates to 18–29 Ma. New Caledonia has been colonized in two phases: the first around 10.6 Ma, with the subsequent diversification of the endemic genus Agnotecous, and the second with more recent events around 1–4 Ma. The distribution of the sister group of Agnotecous and the lack of phylogenetic long branches in the genus refute an assumption of major extinction events in this clade and the hypothesis of local relicts. Main conclusions Our phylogenetic studies invalidate a simple scenario of local persistence of this group in New Caledonia since 80 Ma, either by survival on the New Caledonian island since its rift from Australia, or, if one accepts the submergence of New Caledonia, by local island‐hopping among other subaerial islands, now drowned, in the region during periods of New Caledonian submergence.     

The phylogenetic position of Aulotandra (Zingiberaceae)

The phylogenetic position ofAulotandra (Zingiberaceae).—Nord. J. Bot. 23 : 725–734. Copenhagen. ISSN 0107–055X.
Molecular data for 41 representatives of Zingiberaceae are analysed focusing on the phylogenetic position of Aulotandra and its relationship to Siphonochilus. Sequence divergences indicate that accessions of Aulotandra from Madagascar are closest to those of African Siphonochilus in both ITS and trnL-F data sets, indicating a close relationship. Together these genera form a highly supported monophyletic clade. This African-Madagascan lineage is sister to the rest of the family with African, Asian and South American members, showing that Aulotandra does not belong in the tribe Alpinieae, where it has been traditionally placed, but in the subfamily Siphonochiloideae with the genus Siphonochilus.     

Old and new DNA unweave the phylogenetic position of the eastern Atlantic gall crab Detocarcinus balssi (Monod, 1956) (Decapoda: Cryptochiridae)

Phylogeny reconstructions based on mtDNA and nDNA have become the standard in studies on relationships between taxa. Difficulties in obtaining material, for example because of small endemic distributions, often lead to gaps in datasets. Collections in natural history museums can provide us with material to fill these gaps, but extracting DNA from historical specimens can be challenging. We used a PCR protocol for small amounts of sample material and high PCR yield on eggs of specimens of the coral‐dwelling gall crab family Cryptochiridae collected in 1984, including material from the eastern Atlantic species Detocarcinus balssi. We obtained DNA sequences from seven older museum specimens using newly developed primers, which we combined with COI sequences from recently collected material. Results show that D. balssi is closest to the Indo‐Pacific species Utinomiella dimorpha and not closely related to one of the other three Atlantic Cryptochiridae species. The remaining newly acquired DNA sequences from museum material cluster with the respective sequences from recently collected specimens.     

The effect of temperature on the egg incubation period and nymphal growth of two Nemoura species (Plecoptera) from subarctic fennoscandia

Field studies of Nemoura arctica and N. viki showed that the two species preferred different biotopes and indicated differences in their life‐cycles. N. arctica seemed to have a semivoltine life‐cycle, at least in some years, this was not the case for N. viki.

Laboratory studies showed that the temperature tolerance of the eggs of N. arctica was wider than for those of N. viki. The length of the egg incubation period of both species was influenced by the ambient temperature, but no significant interspecific difference existed between the regression lines of the relationship between the temperature (T°C) and egg incubation period (Y days), as given by the regression equation Y = aT^?b for the log values. Reared at constant food supply, nymphal growth occurred in two periods. Firstly a rapid growth to about 4 mm, followed by a period of slow growth until emergence. During the first period growth (G)at (D) days was linear, according to the simple linear regression equation G = a+bD . The temperature tolerance of the nymphs of N. arctica was wider than for those of N. viki and significant interspecific differences between the species in growth were recorded at relatively high rearing temperatures, such as 12° and 16°C, but not at low temperatures. At constant food supply, nymphal growth was greatly influenced by the rearing temperature. At a mean temperature of 16°C N. arctica nymphs grew rapidly and emerged after 120 days; whereas at a mean temperature of 4°C growt h was slow and the nymphs did not even manage to reach the emergence stage after 700 days.     

Solving alpha‐diversity by morphological markers contributes to arranging the systematic status of a crayfish species complex (Crustacea,Decapoda)

Since innovative molecular approaches in phylogenetics solely based on small gene fragments have often generated widely complicated interpretations of crayfish diversity, we propose a geometric morphometric study integrated with previous molecular data to provide robust estimates of phylogeny and classification of the Austropotamobius pallipes complex, genetically divided into several species and subspecies. We discuss whether cephalothorax shape variation can show phylogenetic signals congruent to those derived from analyses of mitochondrial and nuclear markers. Our results support the hypothesis that carapace form is potentially informative in the reconstruction of crayfish phylogeny. In the phenetic analyses, populations collected within the Italian territory form different unexpected clusters, each involving distant populations of different genetic haplogroups, suggesting a within‐species convergence probably due to a series of local adaptations. The phylogenetic analysis performed using a neighbour‐joining algorithm showed interesting relationships amongst the studied populations. In particular, the geometric morphometric matrices showed a slight congruence with some genetic distances, allowing the discrimination of three major lineages: (1) Istran + Apennine group; (2) Arno group; (3) north‐western group. Finally, our observations support some molecular data with a lighter phylogenetic signal that do not suggest a strong separation of A. pallipes into clades and sub‐clades.     

Asterorhombus annulatus (Weber, 1913), a valid species distinct from Asterorhombus intermedius (Bleeker, 1865) (Pleuronectiformes: Bothidae)

Asterorhombus annulatus was long synonymized with A. intermedius. Twenty-nine specimens from the Coral Sea revealed that the former is clearly separable from the latter in having a short first dorsal fin ray, slender gill rakers with spinules, distinctly shorter blind-side pelvic fin base, an absence of conspicuous black spots on the ocular side of the body, greater eye diameter and greater interorbital width, and somewhat higher ranges of upper jaw lengths. A. annulatus is redescribed as a valid species. Received: March 4, 2000 / Revised: September 13, 2000 / Accepted: January 12, 2001     

Evolution underground: A molecular phylogenetic investigation of Australian burrowing freshwater crayfish (Decapoda: Parastacidae) with particular focus on Engaeus Erichson

Phylogenetic relationships and species boundaries of Australian burrowing freshwater crayfish belonging to the genera Engaeus, Engaewa, Geocharax, Gramastacus and Tenuibranchiurus are investigated using combined mitochondrial and nuclear DNA sequence data and Bayesian and Maximum Parsimony methods. Phylogenies are statistically compared to previously published hypotheses. Engaeus, Engaewa, Geocharax, Gramastacus and Tenuibranchiurus form a strongly supported monophyletic clade. This grouping is independently supported by morphology but unites geographically highly disjunct lineages. Our data show two cryptic species in Geocharax, one cryptic species in Gramastacus and two cryptic species within the highly divergent Engaeus lyelli lineage. Using a Bayesian relaxed molecular clock method, the 16S rDNA data show generic-level diversification coinciding with the transition from a wet to arid palaeoclimate near the mid Miocene.     

A new species of the Melanesian genus Kanaliella (Coleoptera: Cleridae)

Kanaliella balkorum n. sp., a new species of checkered beetles (Cleridae) from New Caledonia is described and figured.urn:lsid:zoobank.org:pub:FA16DD22-2C83-4677-8B1C-E3A317BF150E.     

New species of Pachycotes Sharp and Xylechinus Chapuis (Coleoptera: Curculionidae: Scolytinae,Tomicini) from New Caledonian Araucaria spp. (Coniferales: Araucariaceae)

Abstract

Three new bark beetle species, Pachycotes grandis sp. n., P. engelsi sp. n., and Xylechinus araucariae sp. n. (Curculionidae, Scolytinae, Tomicini), are described and illustrated. Brief notes on their life histories are given. The beetles were collected from dead branches and logs of Araucaria laubenfelsii and A. muelleri trees in New Caledonia. In addition, a key for all nine known Pachycotes species (P. araucariae Schedl, P. australis Schedl, P. clavatus Schedl, P. grandis sp. n., P. engelsi sp. n., P. kuscheli Schedl, P. minor Wood, P. peregrinus (Chapuis), and P. villosus Schedl) is presented.