Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

Accurate delimitation of species is a critical first step in protecting biodiversity. Detection of distinct species is especially important for groups of organisms that inhabit sensitive environments subject to recent degradation, such as creeks, springs, and rivers in arid or semi-desert regions. The genus Dionda currently includes six recognized and described species of minnows that live in clear springs and spring-fed creeks of Texas, New Mexico (USA), and northern Mexico, but the boundaries, delimitation, and characterization of species in this genus have not been examined rigorously. The habitats of some of the species in this genus are rapidly deteriorating, and many local populations of Dionda have been extirpated. Considering the increasing concerns over degradation of their habitat, and pending a more detailed morphological revision of the genus, we undertook a molecular survey based on four DNA regions to examine variation over the range of the genus, test species boundaries, and infer phylogenetic relationships within Dionda. Based on analyses of two mitochondrial (cytb and D-loop) and two nuclear (Rag1 and S7) DNA regions from specimens collected throughout the range of Dionda, we identified 12 distinct species in the genus. Formerly synonymized names are available for two of these species, and four other species remain undescribed. We also redefine the known range of six species. The limited distribution of several of the species, coupled with widespread habitat degradation, suggests that many of the species in this genus should be targets for conservation and recovery efforts.     

Morphology and molecular phylogeny of the benthic dinoflagellates (Dinophyceae,Peridiniales) Amphidiniopsis crumena n. sp. and Amphidiniopsis nileribanjensis n. sp.

Amphidiniopsis is a benthic, heterotrophic and thecate dinoflagellate genus that has a smaller epitheca and larger hypotheca. The genus contains 24 described species, but is considered to be polyphyletic based on morphological characters and molecular phylogenetics. In this study, two new species were discovered from two distant sampling localities, Amphidiniopsis crumena sp. nov. from Japan, and Amphidiniopsis nileribanjensis sp. nov., from Australia. These species have a uniquely shaped, additional second postcingular plate. Both species are dorsoventrally flattened, an apical hook is present, and have six postcingular plates. The plate formula is: APC 4′ 3a 7″ ?C 4?S 6″′ 2″″. The cells of these species were examined with LM and SEM, and molecular phylogenic analyses were performed using 18S and 28S rDNA. These species are distinguished by the presence of spines on the hypotheca and touching of the sixth postcingular plate and the anterior sulcal plate. Their shape and disposition of several thecal plates also differ. Molecular phylogenetic analyses showed that the two new species formed a monophyletic clade and did not belong to any morphogroup proposed by previous studies. Considering the morphological features and the molecular phylogenetic results, a new morphogroup is proposed, Amphidiniopsis morphogroup VI (‘crumena group’).     

Phylogeny of Acronychia (Rutaceae) and First Insights into Its Historical Biogeography and the Evolution of Fruit Characters

Background

The genus Acronychia (Citrus family, Rutaceae) contains 49 species of trees and shrubs that are found mainly in rain forest. The genus has a large distributional range from mainland southern Asia to Australia and New Caledonia, but most species are endemic to either New Guinea or Australia. This study aimed to provide the first detailed molecular phylogeny of Acronychia and use it to test the taxonomic value of fruit morphological characters, and infer the historical biogeography of the genus.

Methodology

Phylogenetic analyses (Bayesian Inference, Maximum Likelihood) were undertaken on nucleotide sequence data from two plastid (psbA-trnH, trnL-trnF) and three nuclear markers (ETS, ITS, NIAi3) from 29 Acronychia species (59% of the genus) and representatives of related genera.

Results and Conclusions

The results indicate that the South-East Asian genus Maclurodendron is nested phylogenetically within Acronychia and must be synonymized to render Acronychia monophyletic. Fruit morphological characters have been used previously to infer relationships within Acronychia and our analyses show that these characters are informative for some subclades but are homoplasious for the group as a whole. Apocarpous fruits are the ancestral state in Acronychia and subapocarpous and fully syncarpous fruits are derived. The unisexual flowers of Maclurodendron are derived from bisexual flowers, which are found in all species of Acronychia as well as its relatives. Acronychia probably first evolved on Australia with range expansion to New Guinea via stepping-stone dispersal or direct land connections within the Sahul Shelf, followed by two independent dispersals to areas west of New Guinea. Most species of Acronychia occur in either Australia or New Guinea, but no species occurs in both regions. This is surprising given the close proximity of the landmasses, but might be explained by ecological factors.     

Molecular systematics and evolutionary origins of the genus Petaurus (Marsupialia: Petauridae) in Australia and New Guinea

The glider genus Petaurus comprises a group of arboreal and nocturnal marsupial species from New Guinea and Australia. Molecular data were generated in order to examine phylogenetic relationships among species within the genus and explore the time-scale of diversification and biogeographic history of the genus in Australia and New Guinea. All known species and subspecies of Petaurus (with the exception of P. biacensis) were sequenced for two mitochondrial genes (ND2 and ND4) and one nuclear marker (omega-globin gene). Phylogenetic analyses confirmed the monophyly of the genus relative to other petaurids and showed a sister relationship of P. australis to the rest of Petaurus. The analyses revealed that currently recognised species of Petaurus formed distinct mitochondrial DNA (mtDNA) clades. Considerable mtDNA diversity and seven distinct clades were identified within the species P. breviceps, with the distribution of each clade showing no correspondence with the distributional limits of known subspecies. Molecular dating analyses using BEAST suggested an early to mid-Miocene origin (18–24 mya) for the genus. Ancestral area reconstructions, using BayesTraits, did not resolve the location for the centre of origin of Petaurus, but provided evidence for at least one dispersal event from New Guinea to Australia that led to the evolution of extant Australian populations of P. breviceps, P. norfolcensis and P. gracilis. The timing of this dispersal event appears to pre-date the Pleistocene, adding to the growing number of studies that suggest faunal connections occurred between Australia and New Guinea in the Late Miocene to Pliocene period.     

Review of haploporid (Trematoda) genera with ornate muscularisation in the region of the oral sucker, including four new species and a new genus

Species of the Haploporidae Nicoll, 1914 with elaborate muscularisation of the oral sucker belong in three trematode genera, including three new species and a new genus from the intestine of fishes in Australian waters. Spiritestis Nagaty, 1948 is resurrected and S. herveyensis n. sp. is described from the mullet Moolgarda seheli (Forsskål) collected in Hervey Bay, Queensland, Australia; the latter differs from S. arabii Nagaty, 1948 in that the position of the genital pore is pharyngeal rather than post-pharyngeal and the geographical range is off Australia rather than the Red Sea. A new genus is proposed for two new species, with a uniquely ornamented oral sucker, which infect Australian scatophagids. Members of Capitimitta n. g. are distinguished from Waretrema Srivastava, 1937, species of which have a simple oral sucker with six radially arranged anterior muscular lobes, in that their oral sucker is V-shaped with six embedded muscular finger-like structures in the anteroventral portion. The relatively small C. darwinensis n. sp., collected from Selenotoca multifasciata (Richardson) at Darwin, Northern Territory, Australia, is distinguished from C. costata n. sp., collected from Scatophagus argus (Linnaeus) in the same locality and S. multifasciata off Brisbane, Australia, and by having smaller eggs, a vitellarium commencing at a level close to the ventral sucker rather than at greater than one ovarian length posterior to the ventral sucker, and shorter tegumental body spines. Sequence data of a c.2,500 bp region of the 3′ end of 18S, the entire ITS region and the 5′ end of the 28S revealed that Spiritestis and Capitimitta are not as closely related as some morphological features would suggest and are probably not the closest relative of each other. What has been reported as Waretrema piscicolum Srivastava, 1937 probably consists of several species, some in different genera, and one, based on material collected by Dr Masaaki Machida, is proposed as Spiritestis machidai n. sp. from Crenimugil crenilabis (Forsskål) off Japan. Phylogenetic hypotheses, based on analysis of an alignment of partial 28S sequences with other haploporids, provide a framework for the evaluation of interrelationships within the Haploporidae. These analyses show that: (1) Spiritestis and Capitimitta are supported within the Haploporidae; (2) branches to Forticulcita Overstreet, 1982, Saccocoelioides Szidat, 1954, Spiritestis and Capitimitta create a clade that is sister to haploporines from the Mediterranean Sea; (3) the branch to Saccocoelioides, Spiritestis and Capitimitta create a polytomy; and (4) the two new species of Capitimitta, plus an immature specimen of an unnamed species, form a monophyletic clade.     

Siptionella,a new bivalve genus of Parallelodontidae from the Upper Eocene of Ukraine

A new genus of the family Parallelodontidae (Bivalvia: Arcoidea), Siptionella gen. nov., with four species from the Upper Eocene of Ukraine and Germany and the Maestrichtian of Denmark is described. From the Upper Eocene of Ukraine, two species, the type species of the genus S. prompta (Berezovsky, 2002), previously described by the author within the genus Porterius, and the new species S. demissa sp. nov. are described and figured.     

Integrative revision of the giant pill-millipede genus Sphaeromimus from Madagascar,with the description of seven new species (Diplopoda,Sphaerotheriida, Arthrosphaeridae)

The Malagasy giant pill-millipede genus Sphaeromimus de Saussure & Zehntner, 1902 is revised. Seven new species, S. titanus sp. n., S. vatovavy sp. n., S. lavasoa sp. n., S. andohahela sp. n., S. ivohibe sp. n., S. saintelucei sp. n., and S. andrahomana sp. n. were discovered, in one case with the help of sequence data, in the rainforests of southeastern Madagascar. The species are described using light- and scanning electron microscopy. A key to all 10 species of the genus is presented. All but one (S. andohahela) of the newly discovered species are microendemics each occurring in isolated forest fragments. The mitochondrial COI barcoding gene was amplified and sequenced for 18 Sphaeromimus specimens, and a dataset containing COI sequences of 28 specimens representing all Sphaeromimus species (except S. vatovavy) was analyzed. All species are genetically monophyletic. Interspecific uncorrected genetic distances were moderate (4–10%) to high (18–25%), whereas intraspecific variation is low (0–3.5%). Sequence data allowed the correct identification of three colour morphs of S. musicus, as well as the identity of a cave specimen, which although aberrant in its morphology and colouration, was genetically identical to the holotype of S. andrahoma.     

The More We Search,the More We Find: Discovery of a New Lineage and a New Species Complex in the Genus Asparagopsis

In the past few decades, in the marine realm in particular, the use of molecular tools has led to the discovery of hidden taxonomic diversity, revealing complexes of sister species. A good example is the red algal genus Asparagopsis. The two species (A. armata and A. taxiformis) recognized in this genus have been introduced in many places around the world. Within the nominal species A. taxiformis, previous molecular analyses have uncovered several lineages, suggesting the existence of sister species or subspecies. Although the genus has been well studied in some regions (e.g., the Mediterranean Sea and Hawaii), it remains poorly investigated in others (e.g., South Pacific). Our study mainly focused on these latter areas to clarify lineages and better determine lineage status (i.e., native vs. introduced). A total of 188 specimens were collected from 61 sites, 58 of which had never been sampled before. We sequenced the DNA from samples for three markers and obtained 112 sequences for the chloroplastic RuBisCo spacer, 118 sequences for the nuclear LSU rRNA gene, and 174 for the mitochondrial spacer cox2-3. Phylogenetic analyses using all three markers suggested the existence of two cryptic sister species with the discovery of a new clade within A. armata. This clade was found only in Western Australia, Tasmania and New Zealand, and is thus restricted to a subregional biogeographic unit. We also discovered a new, fifth lineage for A. taxiformis restricted to the South Pacific and Western Australia. Except for this newly described lineage, all other lineages showed a global distribution influenced by introduction events. These results illustrate the difficulty in accurately defining cosmopolitan species. Our findings also highlight the need for targeted (i.e., in poorly studied areas) and geographically extensive sampling efforts when studying taxa that have been introduced globally and that are likely to hide species complexes.     

New lucinid bivalves from shallow and deeper water of the Indian and West Pacific Oceans (Mollusca,Bivalvia, Lucinidae)

Four new species and a new genus of lucinid bivalves are described from shallow and deeper waters in the Indian and West Pacific Oceans. The new genus Scabrilucina (subfamily Lucininae) includes the little-known Scabrilucina victorialis (Melvill, 1899) from the Arabian Sea and Scabrilucina vitrea (Deshayes, 1844) from the Andaman Sea as well as a new species Scabrilucina melvilli from the Torres Strait off northeastern Australia. Ferrocina brunei new species (Lucininae) was recovered from 60 m near oil drilling activities off Borneo; its anatomy confirmed the presence of symbiotic bacteria. Two unusual deeper water species of Leucosphaerinae are described, both species included in on-going molecular analyses; Gonimyrtea ferruginea from 400–650 m in the southwest Pacific and Myrtina reflexa from 200–825 m off Zanzibar and Madagascar.     

Molecular Phylogeny of Weakfish Species of the Stellifer Group (Sciaenidae,Perciformes) of the Western South Atlantic Based on Mitochondrial and Nuclear Data

The phylogenetic relationships within the Stellifer group of weakfishes (Stellifer, Odontoscion, Ophioscion, and Bairdiella) were evaluated using 2723 base pairs comprising sequences of nuclear (rhodopsin, TMO-4C4, RAG-1) and mitochondrial (16S rRNA and COI) markers obtained from specimens of nine species. Our results indicate a close relationship between Bairdiella and Odontoscion, and also that the genus Stellifer is not monophyletic, but rather that it consists of two distinct lineages, one clade containing S. microps/S. naso/S. brasiliensis and the other, S. rastrifer/S. stellifer/Stellifer sp. B, which is closer to Ophioscion than the former clade. The O. punctatissimus populations from the northern and southern Brazilian coast were also highly divergent in both nuclear (0.8% for rhodopsin and 0.9% for RAG-1) and mitochondrial sequences (2.2% for 16S rRNA and 7.3% for COI), which we conclude is consistent with the presence of two distinct species. The morphological similarities of the members of the Stellifer group is reinforced by the molecular data from both the present study and previous analyses, which have questioned the taxonomic status of the Stellifer group. If, on the one hand, the group is in fact composed of four genera (Stellifer, Ophioscion, Odontoscion, and Bairdiella), one of the two Stellifer clades should be reclassified as a new genus. However, if the close relationship and the reduced genetic divergence found within the group is confirmed in a more extensive study, including representatives of additional taxa, this, together with the morphological evidence, would support downgrading the whole group to a single genus. Obviously, these contradictory findings reinforce the need for a more systematic taxonomic revision of the Stellifer group as a whole.     

Taxonomic revision of the East Asian genus Scleropteroides Colonnelli, 1979 (Coleoptera,Curculionidae, Ceutorhynchinae)

The genus Scleropteroides Colonnelli, 1979 (Ceutorhynchinae: Scleropterini) was revised on the basis of detailed morphological observations. The genus was redefined to include three species from East Asia: S. hypocrita (Hustache, 1916) is redescribed and recorded from northeastern China and northern Korea for the first time; S. horridulus (Voss, 1958) is redescribed with new records from southern Korea; S. insularis Voss, 1971 was moved from synonymy with S. hypocrita to that with S. horridulus (syn. n.), and S. longiprocessus Huang & Yoshitake, sp. n. is described as new, sympatric with S. hypocrita in Japan. All the species are associated with woody Rubus species (Rosaceae). A key to species, habitus photographs, illustrations of important characters, and distribution maps are provided for each species.     

Polymorphism of the KPI-A gene sequence in the potato subgenera Potatoe (Sect. Petota, Esolonifera, and Lycopersicum) and Solanum

Group A Kunitz-type protease inhibitors (KPI-A) are involved in protecting potato plants from microorganisms and pests. While the nucleotide sequence is known for many KPI-A genes of various potato cultivars (Solanum tuberosum subsp. tuberosum) and a few genes of tomato (Solanum lycopersicum), there are no data on their allelic diversity in other species of the genus Solanum. KPI-A fragments were cloned, amplified, sequenced, and analyzed from plants of the subgenera Potatoe sect. Petota (five genes from S. tuberosum ssp. andigenum and two genes from S. stoloniferum) and Solanum (five genes from S. nugrum), and their consensus sequences were established. An identity of 97–100% was observed among these sequences and the KPI-A sequences of the sections Petota (cultivated potato Solanum tuberosum ssp. tuberosum) and Etuberosum (S. palustre) The interspecific variation of KPI-A did not exceed its intraspecific variation for all but one species (S. lycopersicum). The distribution of highly variable and conserved sequences in the mature protein-coding region was the same in all of the above species. The same primers failed to amplify the homologous genes from Solanum dulcamara, S. lycopersicum, and Mandragora officinarum. Phylogenetic analysis of the KPI-A sequences showed that S. lycopersicum clustered separately from all of the other species examined, that S. nigrum clustered together with species of the sections Etuberosum and Petota, and that these species produced no species-specific clusters. Although S. nigrum is resistant to all known races of the oomycete Phytophthora infestans, which causes one of the most economically important diseases of Solanaceae, the amino acid sequences encoded by S. nigrum KPI-A differed slightly, if at all, from their counterparts of cultivated potato, which is susceptible to P. infestans infection.     

A revision of the genus Alofia Giglioli, 1922 and a description of a new monotypic genus,Selfia: two genera of pentastomid parasites (Porocephalida: Sebekidae) inhabiting the bronchioles of the marine crocodile Crocodylus porosus and other crocodilians

The pentastomid genus Alofia Giglioli, 1922 (Porocephalida: Sebekidae), which is exclusively parasitic in the bronchioles of crocodiles, is reviewed. The type-species of the taxon, A. ginae Giglioli, 1922 from an unknown host allegedly taken in Samoa, had very distinctive, fine hooks with long slender blades bent at right angles. I describe a single female with identical hooks from the Philippines which was almost certainly derived from the marine crocodile Crocodylus porosus. This same host harboured two specimens of another Alofia species, tentatively identified as A. merki Giglioli, 1922, a species originally described with A. ginae (and, in all probability, from the same (unknown) host). Additional male and female specimens of A. merki, from several specimens of Australian C. porosus, re-affirm the characteristics of this species. Another new Alofia species, A. simpsoni, from an unknown host in Ghana, is established from measurements of two slide-mounted specimens (previously labelled Sebekia) from The Natural History Museum. There can be little doubt that its host is also a crocodile. A new monotypic genus Selfia is described, based on a type-series of 14 female and one male pentastomids dissected from the bronchioles of five specimens of C. porosus, all taken in Australia. Of the genera comprising the family Sebekidae (Alofia, Sebekia, Diesingia and Leiperia) Selfia is closest to the first, and its main diagnostic characteristics include a massive Alofia-like body, but with a markedly tapered, bluntly-rounded tail, and small, smooth ‘linear’ hooks with minute blades. The rear part of the anterior hooks are enveloped by a soft, cowl-like extension to the fulcrum, covered by small spines. The oral cadre is not U-shaped as in Alofia, but is more like that of Sebekia, whereas by contrast the male copulatory spicules of Selfia porosus and Alofia spp. are virtually identical, except in size. One previously described Alofia sp. from South American crocodilians is well characterized and valid, but two others are considered species inquirendae.     

Five new species of dicyemid mesozoans (Dicyemida: Dicyemidae) from two Australian cuttlefish species, with comments on dicyemid fauna composition

Five new species of dicyemid mesozoans in two genera are described from two Australian cuttlefish species, Sepia apama Gray (giant Australian cuttlefish) and S. novaehollandiae Hoyle (nova cuttlefish): Dicyema coffinense n. sp. from S. apama collected from Coffin Bay, South Australia (SA), Australia; D. koinonum n. sp. from S. apama and S. novaehollandiae collected from Gulf St Vincent (GSV) and Spencer Gulf (SG), SA, Australia; D. multimegalum n. sp. from S. apama collected from Cronulla and North Bondi, New South Wales, Australia; D. vincentense n. sp. from S. novaehollandiae collected from GSV, SA, Australia; and Dicyemennea spencerense n. sp. from S. novaehollandiae and S. apama collected from SG, SA, Australia. Totals of 51 S. apama and 27 S. novaehollandiae individuals were examined, of which all except for four S. apama were infected by at least one dicyemid species. Dicyemid parasites were also observed in host individuals that were held in tanks for 2–3 months prior to examination, including nematogen-exclusive infections, leading to questions about persistence of dicyemids after host death and the mechanism responsible for the switch between a nematogen phase and a rhombogen phase. Variations in host size, calotte shape and collection locality are explored as predictors of differences in observed composition of the parasite fauna. In particular, dicyemid parasite fauna varied with host collection locality. As these parasites are highly host-species specific, their use as biological tags to assess cephalopod population structure using a combined morphological and molecular approach is discussed. This study increases the number of dicyemid species described from Australian cephalopods from five to ten, and from 117 to 122 species described worldwide.