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.     

New species of the myrmecophile Polyplocotes Westwood (Coleoptera: Ptinidae) from South Australia

Six new species of the Australian myrmecophilous ptinid genus Polyplocotes are described from South Australia. Three are from the deserts of central Australia, one from the Franklin Islands in the Great Australian Bight, one from Eyre Peninsula and one from the Riverland region. Morphologically, the majority of these new species are conventional Polyplocotes , but two are less typical. The characters uniting the genus are explored in the discussion, and comparisons are made to related genera. Although the six new species described here have not been observed in the field, the species of this genus are known to be myrmecophilous, and ant – beetle interactions similar to those seen in other spider beetles might occur between these new species and their host ants.     

Four new species of the myrmecophile Diplocotes Westwood (Coleoptera: Ptinidae) from Queensland and South Australia

Abstract  Four new species of the Australian ptinid genus Diplocotes are described. Two of these species are from the dry tropical and subtropical areas of northern and central Queensland, while the other two are from the arid areas of South Australia. While the four new species described here have not been observed with ants in the field, the species of this genus are known to be myrmecophilous, and similar interactions may occur between the new species and their host ants. Additionally, many characters are shared with other unrelated myrmecophilous species, and may be convergent adaptations to the ant-associated lifestyle.     

Molecular phylogenetics of Triculine snails (Gastropoda: Pomatiopsidae) from southern China

Triculine (Gastropoda: Rissooidea: Pomatiopsidae) snails are involved in the transmission of schistosomiasis and paragonimiasis; their distributions are mainly across southeastern Asia and southern China. In the present investigation, partial sequences of COI, 16S, and 28S were examined to infer the phylogenetic relationships among the species rich and poorly understood gastropod. Samples were collected from 12 geographic locations in six provinces of southern China. Several methods such as maximum parsimony, maximum likelihood and distance analysis were used in phylogenetic analyses among these taxa. The resultant phylogenetic trees showed a similar topology irrespective of the phylogenetic methods used. The taxa fell into two clades, with those from Fujian, Guangxi, and Zhejiang Provinces in one clade and those from Hunan, Sichuan and Hubei in the other. Among the taxa in Hubei Province, five formed a monophyletic clade, but Tricula sp. H-SHY fell into a sister clade of Tricula hortensis of Sichuan, whilst Tricula hongshanensis formed a single clade. Sister taxa Tricula pingi and Tricula hsiangi formed well-supported clade within almost all the trees. These results, while preliminary, represent the first attempt to reconstruct a phylogeny for Triculinae across China.     

Evolutionary relationships among the Scarabaeini (Coleoptera: Scarabaeidae) based on combined molecular and morphological data

The Scarabaeini is an old world tribe of ball-rolling dung beetles that have origins dating back to at least the mid-upper Miocene (19-8 million years ago). The tribe has received little to no attention in morphological or molecular phylogenetics. We obtained sequence data from the mitochondrial cytochrome oxidase subunit I (1,197 bp) and 16S ribosomal RNA (461 bp) genes for 25 species of the Scarabaeini in an attempt to further resolve broad phylogenetic relationships within this tribe. Sequence data from both markers along with 216 morphological and 3 biological characters were analysed separately and combined. Independent analyses showed poorly resolved trees with many of the intermediate and basal nodes collapsed by low bootstrap values. Many sites in both genes exhibited strong A+T nucleotide bias and high interlineage divergences. The combined analysis revealed a number of well supported relationships such as the monophyly of the nocturnal species Scarabaeus satyrus, S. [Neateuchus] proboscideus, and S. zambesianus. Furthermore, the total evidence tree suggested to elevate S. (Pachysoma) to the status of an independent genus, Pachysoma, as a sister taxon to a clade containing Pachylomerus femoralis and Scarabaeus sensu lato. Within the latter, the following subgenera were maintained by the combination of data sets: S. (Scarabaeolus), S. (Sceliages), and S. (Kheper). Both, feeding specialisation and food relocation behaviour, were inferred to be polyphyletic in the Scarabaeini. Total evidence analysis found no support for common ancestry of Scarabaeini and Eucraniini.     

Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora)

In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditional classifications. Based on these results, we propose the following system. The Western Palaearctic Helicidae s.l. consist of two families, Helicidae and Hygromiidae. Within the Helicidae, three well supported subfamilies can be recognised: the Helicinae, Ariantinae, and Helicodontinae. The Hygromiidae consist of three clades: the Hygromiinae, the Helicellinae, and a yet unnamed clade comprising the genera Sphincterochila and Cochlicella. We then used the phylogeny to study the evolution of anatomical, and ecological characters traditionally used for systematic classification. In the Helicidae s.l., two independent evolutionary transitions to life in xeric environments occurred, which allowed the occupation of new niches with a subsequent radiation of the Helicellinae-Cochlicella/Sphincterochila clade and the Helicinae. Whereas, the multiplication of the Glandulae mucosae is a synapomorphy of the Hygromiidae, the lovedart sac apparatus is present in all groups and thus, the trait cannot provide a synapomorphy for either families or subfamilies. Additionally, we evaluated the use of structural molecular genetic characters for taxonomic assessment. The presence of an unique loop region of the 16S rDNA gene and a short tandem repeat in the ITS-1 region provide independent evidence for the monophyly of these major two groups, and can be used for preliminary classification.     

Diversification process of stag beetles belonging to the genus Platycerus Geoffroy (Coleoptera: Lucanidae) in Japan based on nuclear and mitochondrial genes

Molecular phylogenies of the genus Platycerus in Japan were characterized based on the nuclear 28S ribosomal RNA and mitochondrial cytochrome oxidase subunit I (COI) genes. These analyses, combined with our previous morphological information, revealed a detailed diversification process of Platycerus in Japan, as well as estimates of their divergence times. Japanese species were monophyletic and were inferred to have diverged to the acuticollis species group and all other species ca 1.69 Mya. The acuticollis species group then appeared to split into P. viridicuprus and a group including P. takakuwai, P. albisomni and P. acuticollis ca 1.26 Mya. Other specific divergences have occurred primarily since ca 0.33 Mya. Comparing the molecular trees and the morphological tree, we also found introgression of the COI gene in some species. Genetic divergence of Platycerus has occurred intensely in southwestern Japan.     

基于部分18S rDNA, 28S rDNA和COI基因序列的索科线虫亲缘关系

通过PCR扩增获得我国常见昆虫病原索科线虫6属10种18S rDNA、28S rDNA(D3区)和COI基因序列,结合来自GenBank中6属10种索科线虫的18S rDNA同源序列,用邻接法和最大简约法构建系统进化树。结果显示:12属索科线虫分为三大类群,第一大类群是三种罗索属线虫(Romanomermis)先聚在一起,再与两索属(Amphimermis)和蛛索属(Aranimermis)线虫聚为一支;在第二大类群中,六索属(Hexamermis)、卵索属线虫(Ovomermis)和多索属(Agamermis)亲缘关系最近,先聚在一起,再与八腱索属(Octomyomermis)和Thaumamermis线虫聚为一支。第三大类群由索属(Mermis)和异索属(Allomermis)线虫以显著水平的置信度先聚在一起,再与蠓索属(Heleidomermis)和施特克尔霍夫索属(Strelkovimermis)线虫聚为一支。从遗传距离看,基于3个基因的数据集均显示索科线虫属内种间差异明显小于属间差异,武昌罗索线虫(R.wuchangensis)和食蚊罗索线虫(R.culicivorax)同属蚊幼寄生罗索属线虫,其种间的遗传距离最小。     

Physical gills in Elmidae (Coleoptera: Byrrhoidea): Structure and evolutionary pattern of plastron in Stenelmis and related genera

Many species within Elmidae (Coleoptera: Byrrhoidea) have plastrons composed of flattened setae. However, some genera display fine plastrons on the epicuticle, called plastron hairs. In Japanese elmids, members of the genera Stenelmis, Ordobrevia, Nomuraelmis and Leptelmis bear ventral plastron hairs. Based on a maximum likelihood tree including most Japanese genera within Elmidae, we found that these genera are monophyletic and that plastron hairs are a derived character in Elmidae. We also found that the genus Graphelmis bears jigsaw puzzle‐like plastron scales with plastron hair‐like projections, and is sister to the group with plastron hairs.     

Molecular phylogeny in endemic weevils: revision of the genera of Macaronesian Cryptorhynchinae (Coleoptera: Curculionidae)

A molecular phylogeny and lineage age estimates are presented for the Macaronesian representatives of the weevil subfamily Cryptorhynchinae, using two mitochondrial genes (cytochrome c oxidase subunit 1 and 16S). The Bayesian reconstruction is supplemented by observations on morphology, ecology, and reproductive biology. The present study often corroborates the groups previously outlined in higher‐level informal taxonomies. These and further groups are now assigned new taxonomic status. The following genera and subgenera are described (formerly Acalles): Aeoniacalles gen. nov. , Canariacalles gen. nov. , Ficusacalles gen. nov. , Madeiracalles gen. nov. , Silvacalles gen. nov. (with Tolpiacalles subgen. nov. , Tagasastacalles subgen. nov. ), Sonchiacalles gen. nov. , Echiumacalles gen. nov. (monotypic), Lauriacalles gen. nov. (monotypic), and Pseudodichromacalles gen. nov. (monotypic; formerly Dichromacalles). For the western Palaearctic genus Acalles Schoenherr, 1825 the first subgenus Origoacalles subgen. nov. is described and for the genus Onyxacalles Stüben, 1999 the first subgenus Araneacalles subgen. nov. ; Paratorneuma Roudier 1956 resyn. Except for one species of Acalles (Origoacalles), all of these new higher taxa are endemic to the Macaronesian Islands. All new taxa are presented, together with their host plants and further data, in a synoptic tabular overview. Based on the results of our phylogenetic analysis, we advocate the hypothesis that the evolution of the species in the new genera (of which most group into a ‘Macaronesian clade’) began in the comparatively arid succulent bush zone and that the shady and humid laurel forest of the thermo‐Canarian and thermo‐Madeiran zone was entered much later. Our reconstruction implies that the Canarian and Madeiran archipelagos were colonized by Cryptorhynchinae at least seven times from the continent but saw only one considerable adaptive radiation. It also becomes apparent that it is the ancestor species of the genus Canariacalles– and not Pseudodichromacalles– that features a close connection to the south‐western European and north‐western African species of Dichromacalles s.s. Finally, a key is presented for all genera and subgenera of the Macaronesian Cryptorhynchinae. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 40–87.     

Molecular systematics of sponges (Porifera)

The first application of molecular systematics to sponges was in the 1980s, using allozyme divergence to dis-criminate between conspecific and congeneric sponge populations. Since this time, a fairly large database has been accumulated and, although the first findings seemed to indicate that sponge species were genetically more divergent than those of other marine invertebrates, a recent review of the available dataset indicates that levels of interspecific gene identities in most sponges fall within the normal range found between species of other invertebrates. Nevertheless, some sponge genera have species that are extremely divergent from each other, suggesting a possible polyphyly of these genera. In the 1990s, molecular studies comparing sequences of ribosomal RNA have been used to reappraise the phylogenetic relationships among sponge genera, families, orders and classes. Both the 18S small subunit and the 28S large subunit rRNA genes have been sequenced (41 complete or partial and 75 partial sequences, respectively). Sequences of 18S rRNA show good support for Porifera being true Metazoa, but they are not informative for resolving relationships among genera, families or orders. 28S rRNA domains D1 and D2 appear to be more informative for the terminal nodes and provide resolution for internal topologies in sufficiently closely related species, but the deep nodes between orders or classes cannot be resolved using this molecule. Recently, a more conserved gene, Hsp70, has been used to try to resolve the relationships in the deep nodes. Metazoan monophyly is very well supported. Nevertheless, the divergence between the three classes of Porifera, as well as the divergence between Porifera, Cnidaria and Ctenophora, is not resolved. Research is in progress using other genes such as those of the homeodomain, the tyrosine kinase domain, and those coding for the aggregation factor. For the moment the dataset for these genes is too restricted to resolve the phylogenetic relationships of these phyla. However, whichever the genes, the phylogenies obtained suggest that Porifera could be paraphyletic and that the phylogenetic relationships of most of the families and orders of the Demospongiae have to be reassessed. The Calcarea and Hexactinellida are still to be studied at the molecular level.     

Molecular phylogeny and DNA barcoding confirm cryptic species in the African freshwater oyster Etheria elliptica Lamarck, 1807 (Bivalvia: Etheriidae)

Recent molecular approaches to taxonomy have led to a steady increase in the identification of cryptic species. Within the Etheriidae, the species Etheria elliptica (freshwater oyster) is widespread and common and exists in most of the major African drainages. Within the African freshwater ecosystems, there are major threats to biodiversity and cryptic species complicate conservation strategies; unknown species exist and no conservation status has been assigned. Our objective here was to determine if E. elliptica from several locations in the Congo drainage are correctly classified as representing a single species. We analysed the genetic diversity at two mitochondrial loci (COI and 16S) and two nuclear loci (H3 and 28S), and estimated evolutionary relationships using phylogenetic and DNA barcoding techniques. Bayesian inference yielded three cryptic species of Etheria, and mismatch analysis revealed discrete differences between the cryptic species. We identified three cryptic species within these collections, and evidence indicates that the third species may resolve further with more sampling. In conclusion, the taxonomic history of E. elliptica makes finding cryptic species unsurprising. However, molecular studies such as this may finally help to resolve the number of species within this genus.     

Molecular systematics of the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera')

Phylogenetic relationships among extant families in the suborder Trogiomorpha (Insecta: Psocodea: 'Psocoptera') were inferred from partial sequences of the nuclear 18S rDNA and Histone 3 and mitochondrial 16S rDNA genes. Analyses of these data produced trees that largely supported the traditional classification; however, monophyly of the infraorder Psocathropetae (= Psyllipsocidae + Prionoglarididae) was not recovered. Instead, the family Psyllipsocidae was recovered as the sister taxon to the infraorder Atropetae (= Lepidopsocidae + Trogiidae + Psoquillidae), and the Prionoglarididae was recovered as sister to all other families in the suborder. Character states previously used to diagnose Psocathropetae are shown to be plesiomorphic. The sister group relationship between Psyllipsocidae and Atropetae was supported by two morphological apomorphies: the presence of a paraproctal anal spine and an anteriorly opened phallosome. Based on these sequence data and morphological observations, we propose a new classification scheme for the Trogiomorpha as follows: infraorder Prionoglaridetae (Prionoglarididae), infraorder Psyllipsocetae (Psyllipsocidae), infraorder Atropetae (Lepidopsocidae, Trogiidae, Psoquillidae).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 287–299.     

Discovery of swimming larvae in Elmidae (Coleoptera: Byrrhoidea)

The aquatic larvae of the family Elmidae (Coleoptera) have been considered unable to swim because they lack swimming setae on their body and legs. We discovered that riffle beetle larvae (Leptelmis gracilis Sharp) are in fact able to swim. After opening the tuft‐like gills on the last abdominal segment they swim by repeatedly bending the abdomen into a U‐shape very quickly and in a wavy manner, while their head and thorax move anteriorly, resulting in a sigmoidal body shape. The flat bodies of L. gracilis larvae could be advantageous for swimming compared to the cylindrical or semicylindrical bodies of larvae in related genera.     

Molecular phylogeny, taxonomy and evolution of the land snail genus Iberus (Pulmonata: Helicidae)

Partial DNA sequences of two mitochondrial genes [cytochrome oxidase subunit I (COI) and 16S rRNA] from 59 specimens of Iberus were used to test the validity of the described morphospecies of this genus, and examine genetic divergences within and between main phylogenetic groups. Both gene fragments showed phylogenetic concordance. The COI gene was found to be faster evolving than the 16S gene and was fully protein-coding with no insertions or deletions. 16S rRNA was more informative than COI for resolving basal nodes. Both individual and combined analyses of the two gene fragments revealed five main phylogroups. These five groups are genetically unique lineages that are allopatrically distributed and considered to have full species status. Further subdivisions were also considered. Shell morphology was suitable for delimiting species boundaries, but several incongruences between morphology and mtDNA phylogeny were observed. These incongruences were considered consequence of hybridization between Iberus cobosi and Iberus marmoratus , and the result of shell shape polymorphism in Iberus rositai . According to spatial patterns of sequence divergence, life habits and shell morphology may be concluded that the keeled-flat shelled snails independently originated several times within Iberus and they could represent cases of similar shell adaptation to a karstic arid environment.     

Molecular phylogeny of the green lacewings (Neuroptera: Chrysopidae)

Abstract  The first quantitative analysis of phylogenetic relationships of green lacewings (Chrysopidae) is presented based on DNA sequence data. A single nuclear and two mitochondrial genes are used in the analysis: carbomoylphosphate synthase (CPS) domain of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase (CAD) (i.e. rudimentary locus), large subunit ribosomal gene (16S) and cytochrome oxidase I (COI). This study represents the first use of the CAD gene to investigate phylogenetic relationships of the lacewings. DNA sequences for 33 chrysopid species from 18 genera, representing all subfamilies and tribes, were compared with outgroups sampled from families Hemerobiidae, Osmylidae and Polystoechotidae. Parsimony analyses of the combined data set recovered all of the previously established subfamilial and tribal groups as monophyletic clades (although relatively weakly supported) except Apochrysinae sensu lato . The enigmatic Nothancyla verreauxi Navás has historically been difficult to place in a subfamily group based on morphological characteristics; molecular data presented herein do not adequately resolve this problem.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae

In previous molecular phylogenetic analyses of the freshwater mussel family Unionidae (Bivalvia: Unionoida), the Afrotropical genus Coelatura had been recovered in various positions, generally indicating a paraphyletic Unionidae. However that result was typically poorly supported and in conflict with morphology-based analyses. We set out to test the phylogenetic position of Coelatura by sampling tropical lineages omitted from previous studies. Forty-one partial 28S nuclear rDNA and partial COI mtDNA sequences (1130 total aligned nucleotides) were analyzed separately and in combination under both maximum parsimony and likelihood, as well as Bayesian inference. There was significant phylogenetic incongruence between the character sets (partition homogeneity test, p < 0.01), but a novel heuristic for comparing bootstrap values among character sets analyzed separately and in combination illustrated that the observed conflict was due to homoplasy rather than separate gene histories. Phylogenetic analyses robustly supported a monophyletic Unionidae, with Coelatura recovered as part of a well-supported Africa–India clade (= Parreysiinae). The implications of this result are discussed in the context of Afrotropical freshwater mussel evolution and the classification of the family Unionidae.     

DNA条形码试剂盒检测技术在大小蠹属种类鉴定中的应用

[目的]DNA条形码技术已成为生物分类鉴定的有力工具.DNA条形码技术的相关问题,如物种种内和种间的遗传距离出现重叠区域,将直接影响到物种鉴定的准确性.我们应用DNA条形码试剂盒检测技术来快速、准确地鉴定口岸截获的检疫性大小蠹属种类.[方法]针对大小蠹昆虫设计引物以提高PCR扩增效率.运用自主研发的基因条码分析软件找出基因片段上区分每个物种的多态位点规律,作为该物种的鉴定特征并建立数据库,应用于物种鉴定.[结果]使用针对大小蠹属昆虫设计的引物成功扩增出325 bp的COI基因片段.将大小蠹属12种昆虫的COI基因片段上的核苷酸诊断位点的组合作为物种的鉴定特征,可以准确地区分近似种.通过比对植物检疫鉴定系统数据库里的鉴定特征,将6个大小蠹属的未知样品成功鉴定到种(核苷酸序列一致性为100％),与形态鉴定结果一致.[结论]结果表明DNA条形码试剂盒检测技术可以准确鉴定大小蠹属的种类.该检测技术可以应用于其他经济重要性有害生物的检测鉴定.     

Molecular systematics and patterns of morphological evolution in the Centropagidae (Copepoda: Calanoida) of Argentina

Recent studies have shown the value of complementing standard taxonomy with genetic analyses to reveal cryptic diversity and to aid in the understanding of patterns of evolution. We surveyed variation in the COI mitochondrial gene in members of the three genera of centropagid copepods from the inland waters in Argentina. In general, we found a close association between molecular and morphological systematics in this group. Similar to findings for marine calanoids, genetic distances within Boeckella species were modest (< 4%), while distances among morphospecies were much larger (> 11%). Parabroteas is currently monotypic, although we detected cryptic genetic diversity, with two lineages showing 5.5% divergence. In contrast, Karukinka was not a valid genus, apparently representing an interesting and atavistic offshoot of B. poppei , a result reinforcing the value of considering both morphological and molecular evidence. Moreover, we used combined genetic and morphological information, analysed with maximum likelihood methods, to evaluate the common assumption that evolution tends to proceed via the loss of structures in crustaceans. Although analysis of other taxa and character types is required to evaluate fully the reduction hypothesis, our results suggest that structures may be gained readily as well as lost.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 279–292.