Phylogeny of the leech family Glossiphoniidae based on mitochondrial gene sequences and morphological data

The phylogenetic relationships of the Glossiphoniidae (Rhynchobdellida) were investigated using morphological characters and the mitochondrial genes cytochrome c oxidase subunit I and nicotinamide adenine dinucleotide dehydrogenase subunit 1. Thirty-five taxa representing 10 of the 23 currently recognized glossiphoniid genera were sampled, including more than 70% of known North American species, as well as others from Europe, South America, Africa, and a species endemic to Lake Baikal. Outgroup taxa included species from the Piscicolidae and Ozobranchidae. Cladistic analysis resulted in 1 most-parsimonious tree. Subfamily distinctions, i.e., Haementeriinae, Theromyzinae, and Glossiphoniinae, that have been based on eye morphology and reproductive biology are not corroborated. Results also provide insights into several problematic genus-level classifications. For example, relationships of Placobdella and Haementeria are clarified and elimination of Desserobdella may be necessary. Bloodfeeding from vertebrates is seen to be a primitive characteristic that has been lost twice within the clade. The hypothesis that the biannulate leech, Oligobdella biannulata, represents an important transitional form is re-evaluated in a phylogenetic context.     

Re-evaluation of the phylogenetic relationship among species of the genus Tricholoma

The internal transcribed spacer sequences spanning the regions between the 17S and 25S rRNAs (ITS1 and ITS2) and including the complete sequence of the 5.8S rRNA were used for phylogenetic analyses. This approach to define phylogenetic relationships within the genus Tricholoma was tested using different isolates of T. terreum. Fruitbodies identified in nature were analysed in order to allow use of morphology for taxonomy. The isolates from different locations were closely related as could be expected for one species. Thus, the method could be applied to different Tricholoma species. Three clusters within the genus Tricholoma can be distinguished with four additional species not included in any of these clusters. Molecular analyses of two Cortinarius species confirm a phylogenetically distinct genus.     

Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

Phylogenetic relationships of the genus Dugesia (Platyhelminthes, Tricladida, Paludicola)

A phylogenetic analysis was performed on the genera and subgenera within the freshwater triclad family Dugesiidae, based on 19 terminal taxa and 17 morphological characters. The phylogenetic tree proposed has length of 27 steps and consistency index of 0.66. This phylogenetic hypothesis implies that the current genus Dugesia is paraphyletic and that its subgenera Girardia, Schmidiea and Dugesia S.S. should be elevated to the rank of genus. The genera Cura, Spathula and Neppia are presumed monophyletic by default because the database was unable to provide autapomorphies for any of these genera. The genera Dugesia S.S. and Neppia share sistergroup relationship. Several characters are discussed which were previously considered to be of phylogenetic importance but were not included in the present analysis. It is emphasized that sensory organs form potentially useful set of phylogenetic characters for the Dugesiidae.     

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis

Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.     

Phylogeny of the mud worm genus Marenzelleria (Polychaeta, Spionidae) inferred from mitochondrial DNA sequences

The taxonomy of the cryptic morphospecies of the mud worm genus Marenzelleria is particularly difficult and the phylogenetic relationship within the genus is unknown. Herein we reconstructed the phylogeny of all five species of this genus using sequence data of three mitochondrial genes (16SrDNA, cytochrome b, cytochrome oxidase subunit I) from 104 specimens out of 26 populations. For the three invasive species of the genus, Marenzelleria neglecta, M. viridis and M. arctia , individuals from native populations as well as from recently invaded populations were included. Nuclear 18S rDNA sequences were used to evaluate the appropriate outgroup taxon among several spionid polychaete species. The results supported the monophyly of Marenzelleria , and Malacoceros fuliginosus was found to be a suitable outgroup for the analysis of the mitochondrial gene segments. All phylogenetic reconstructions revealed a basal position of M. arctia and M. wireni , which have primarily Arctic distribution, with M. arctia obtaining the most basal position. Together with the present-day distribution of the species, this indicates an origin of the genus in the Arctic region. The relationship of the species M. neglecta , M. viridis and M. bastropi could not be resolved sufficiently due to genealogical discordance that might reflect relatively young cladogenetic events.     

Molecular evidence suggests an ancient radiation for the fairy shrimp genus Streptocephalus (Branchiopoda: Anostraca)

Phylogenetic relationships among assumed Gondwanan aquatic inland invertebrate fauna are generally largely neglected, and biogeographical hypotheses for these organisms are generally inferred from historic (palaeogeographical) and contemporary distribution patterns. The distribution of the monogeneric thermophilic freshwater fairy shrimp family Streptocephalidae ( Streptocephalus ) provides a particularly useful framework to test the three contrasting biogeographical scenarios proposed for the evolution of this group: (1) the genus evolved in Laurasia and subsequently dispersed into Africa and North America; (2) the genus evolved and dispersed out of Africa and (3) the current distribution of the genus is the result of vicariance following the fragmentation of Gondwana. In the present study, the phylogenetic relationships of species in this genus are examined with the use of two mitochondrial genes (12S rRNA and COI mtDNA), while the phylogenetic relationships among the North American species and selected African taxa was investigated using the nuclear fragment (5.8S-ITS-1-18S). Phylogenetic results indicate that Streptocephalus probably evolved in Gondwana and that the current distribution patterns are a consequence of a combination of vicariance and limited dispersal. The implications for the evolution of continental freshwater crustaceans are discussed.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 313–327.     

Phylogeny and revision of the leech genus Helobdella (Glossiphoniidae) based on mitochondrial gene sequences and morphological data and a special consideration of the triserialis complex

The relationships, as well as identification of species, within Helobdella (Glossiphoniidae) were explored through phylogenetic analysis and through an overview of the historical systematics of the genus. The phylogeny was determined using morphological data and the mitochondrial gene sequences of cytochrome c oxidase subunit I and nicotinamide adenine dinucleotide dehydrogenase subunit I. A broad representation of 15 ingroup species was sampled, including 10 individuals from South America. Outgroup taxa included five species of Haementeria . Cladistic analysis of all available data resulted in one most parsimonious tree. Results shed light on genetic divergence of members classified as the same species, including those that are not monophyletic. Historically, external morphological characters have played a significant role in contributing to the confusion in the classification of H. triserialis, H. papillata, H. lineata and H. fusca in North America. Re-evaluation of Verril's Clepsine papillifera var. b and var. d in a phylogenetic context provides a solution. Additionally, the genera Adaetobdella, Acritobdella, Dacnobdella and Gloiobdella created by Ringuelet are returned to Helobdella based on overlapping morphological characters.     

Phylogenetic analyses of the rhipicephaline ticks indicate that the genus Rhipicephalus is paraphyletic

We inferred the phylogeny of 21 species and subspecies of ticks from the subfamilies Rhipicephalinae and Hyalomminae using cytochrome c oxidase subunit I (COI) and 12S rRNA mitochondrial gene sequences. Two members of the subfamily Haemaphysalinae were used for outgroup reference. The largest rhipicephaline genus, Rhipicephalus, was represented by ticks from six of the species groups, the second largest genus, Dermacentor, by species from two of three of its subgenera, and the genus Boophilus by 3 of its 5 species. We analyzed the 12S and COI sequences separately and together; statistically significant incongruence between the 12S rDNA and the COI sequences was not detected in the combined dataset using the incongruence length difference test. The combined dataset provided greater phylogenetic resolution than the individual datasets, and although the 12S rDNA data had only 25% of the parsimony-informative characters, it provided half of the total partitioned Bremer support for the combined dataset. We present the first hypothesis of phylogenetic relationships among some species groups of Rhipicephalus but our most controversial result was that the genus Rhipicephalus is apparently paraphyletic, unless species of Boophilus are included in it. The species of Rhipicephalus most closely related to Boophilus spp. were from the R. pravus and R. evertsi species groups, which may implicate an African origin for this important group of ticks.     

Phylogeny of the three brown banded land snail genus Humboldtiana (Pulmonata: Humboldtianidae)

The three brown banded land snail genus Humboldtiana (Pulmonata: Humboldtianidae) comprises 50 species of insular distribution from southern Texas to central México; its low vagility and dispersal potential are reflected in high levels of endemism and highly restricted distributions. A current scheme of classification recognizes six subgenera: Polyomphala, Oreades, Gymnopallax, Clydonacme, Aglotrochus, and Humboldtiana (the latter containing three species groups). In the present work, mitochondrial 16S rDNA and partial ITS region and ribosomal large subunit (5.8S+ITS-2+28S) sequences from 26 recognized species and 2 populations of unknown identity were studied to assess phylogenetic relationships of Humboldtiana species using parsimony and Bayesian analysis, and AU test was used to compare the different phylogenetic hypotheses. The same four major clades were recovered by both methods (buffoniana, queretaroana, montezumae and fortis), although none of them support the current scheme of classification, with the only exception being the subgenus Gymnopallax included in the clade buffoniana. The results suggest that speciation patterns observed in the genus Humboldtiana could be explained as a morphostatic radiation.     

中国沙塘鳢属鱼类线粒体12S rRNA基因序列分析

沙塘鳢属鱼类为东亚特有的小型淡水经济鱼类,中国产沙塘鳢属鱼类分类问题长期存在争议。本文测定了中国产沙塘鳢属鱼类全部种类的线粒体12S rRNA基因部分序列,结合GenBank中下载的2种日本沙塘鳢属鱼类和塘鳢科鱼类同源序列,探讨中国产4种沙塘鳢属鱼类的物种有效性,分析沙塘鳢属鱼类的系统发育关系。作者所使用的同源序列长度为690bp,其中变异位点258个,简约信息位点201个,包括插入/缺失位点34个,转换/颠换平均值为3.0,表明12S rRNA基因是研究沙塘鳢属鱼类系统发育关系的合适分子标记。基于p-distance模型的6种沙塘鳢属鱼类种内遗传距离为0.000—0.024,种间遗传距离为0.058—0.064,支持暗色沙塘鳢和中华沙塘鳢为不同种,中国产沙塘鳢属鱼类包括中华沙塘鳢、河川沙塘鳢、海丰沙塘鳢、鸭绿江沙塘鳢4个种的观点;至于中国还有没有新的沙塘鳢属鱼类,尚有待进一步研究。系统发育分析表明海丰海塘鳢是河川沙塘鳢的姐妹群,暗色沙塘鳢与O.hikimius的亲缘关系最为密切,而同属其余类群之间的系统发育关系则由于自展数据支持率较低而尚不明确。中国产沙塘鳢和日本产沙塘鳢并未单独分群,推测沙塘鳢属鱼类的共同原始祖先可能广泛分布于中国、朝鲜和日本等东亚地区,约在4.9—6.5百万年前的上新世开始分化,系统发育过程比较适合离散假说。     

Phylogenetic basis for a taxonomic dissection of the genus Clostridium

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.     

Phylogeny of the genus Merluccius based on mitochondrial and nuclear genes

Genus Merluccius is considered one of the most important groups within the Teleostei, and comprises 12 extant species distributed along the coasts of America, Europe and Africa, being its fisheries very important in these continents. Despite their noticeable economical importance for humans, to date the phylogeny of hakes has not been clearly established. In this study we used mitochondrial sequences (the ribosomal genes 12S rDNA and 16S rDNA, the coding gene cytochrome b and the control region) and the nuclear 5S rDNA conserved region in order to determine the phylogenetic and biogeographical relationships within the genus Merluccius. This is the first time that all the species of this genus recognized by the FAO are included in a phylogeny. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the mitochondrial sequences suggest that the geographical origin of the genus was the North Atlantic Ocean, and indicate that two main clades, early separated in the evolution, exist within the genus: one American (7 species) and one Euro-African (5 species). Among the American species, M. bilinearis seems to be the most ancient one, and the rise of the Panama Isthmus could act as a physical barrier leading to further processes of speciation. Within the Euro-African clade, successive events of geographical differentiation could explain the observed pattern of species distribution. Therefore, we propose both vicariant speciation and geographical dispersion as main mechanisms to explain the evolutionary history of the genus Merluccius.     

Multilocus sequence analysis of the actinobacterial genus Kribbella

Multilocus sequence analysis (MLSA) was used to refine the phylogenetic analysis of the genus Kribbella, which currently contains 17 species with validly-published names. Sequences were obtained for the 16S rRNA, gyrB, rpoB, recA, relA and atpD genes for 16 of the 17 type strains of the genus plus seven non-type strains. A five-gene concatenated sequence of 4099 nt was used to examine the phylogenetic relationships between the species of the genus Kribbella. Using the concatenated sequence of the gyrB-rpoB-recA-relA and atpD genes, most Kribbella type strains can be distinguished by a genetic distance of >0.04. Each single-gene tree had an overall topology similar to that of the concatenated sequence tree. The single-gene relA tree, used here for the first time in MLSA of actinobacteria, had good bootstrap support, comparable to the rpoB and atpD gene trees, which had topologies closest to that of the concatenated sequence tree. This illustrates that relA is a useful addition in MLSA studies of the genus Kribbella. We propose that concatenated gyrB-rpoB-recA-relA-atpD gene sequences be used for examining the phylogenetic relationships within the genus Kribbella and for determining the closest phylogenetic relatives to be used for taxonomic comparisons.     

The Baikalian genus Rhyacodriloides in Europe: phylogenetic assessment of Rhyacodriloidinae subfam. n. within the Naididae (Annelida)

Martin, P., Martínez‐Ansemil, E. & Sambugar, B. (2010). The Baikalian genus Rhyacodriloides in Europe: phylogenetic assessment of Rhyacodriloidinae subfam. n. within the Naididae (Annelida). —Zoologica Scripta, 39, 462–482. Two new species of the oligochaete genus Rhyacodriloides Chekanovskaya, Rhyacodriloides aeternorum sp. n. and Rhyacodriloides latinus sp. n., are described from subterranean water bodies of Italy and Slovenia. A comparison with the known species of this genus, Rhyacodriloides abyssalis Chekanovskaya, 1975 and Rhyacodriloides gladiiseta Martin & Brinkhurst, 1998, both from Lake Baikal, shows that the enigmatic ‘cellular masses’ of the latter two species must be interpreted as different, not homologous structures. As a result, R. gladiiseta is to be ascribed to the Phallodrilinae, a primarily marine naidid subfamily, mentioned for the first time in Lake Baikal, and placed in its own genus, Phallobaikalus gen. n. The two new species are morphologically very similar, but their penial setae differ slightly. The phylogenetic relationships of R. latinus sp. n. and R. abyssalis within the Naididae (formerly the Tubificidae) were investigated using a combination of three genes, one nuclear (18S rDNA) and two mitochondrial (12S rDNA and 16S rDNA). A fragment of the mitochondrial COI gene, used as a barcode, also genetically characterized all Rhyacodriloides species. Sequences of 34 Naididae were obtained from EMBL, representative of five naidid subfamilies, and including five oligochaete outgroups. The data were analysed by parsimony, maximum likelihood and Bayesian inference. Taken in combination, the three genes investigated confirm that the two Rhyacodriloides species analysed are closer to each other than to any other naidid species. However, they are separated by 16S and COI distances that amount to 18.5% and 27.2%, respectively, suggesting an ancient separation between species, in good accordance with their present biogeographic distribution. Rhyacodriloides cannot be considered as a rhyacodriline, as assumed so far, as they never appeared related to this subfamily in any analysis considered. In contrast, they appear at the base of a naidid group, including the Tubificinae, the Phallodrilinae, the Limnodrilinae, as well as Branchiura sowerbyi, a species whose phylogenetic association with the rhyacodrilines has been questioned for a long time. Despite a lack of phylogenetic support, this position is congruent with a morphological reassessment of the Rhyacodrilinae, and strongly supports the erection of a new naidid subfamily to accommodate Rhyacodriloides.     

Distribution of sarcophytol A in soft coral of the Sarcophyton genus

The distribution of sarcophytol-A in the Sarcophyton genus was investigated in seven samples belonging to S. glaucum (3 samples), S. infundibulifurme (2 samples), S. crassocaule (1 sample) and S. trocheliophorum (1 sample) that were collected on Ishigaki Island in Okinawa Prefecture. Sarcophytol-A was present in one sample each of S. glaucum and S. infundibulifurme. This study indicates that the composition of cembranoids in the Sarcophyton genus is not related with the respective species, but with the individual samples collected.     

Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales)

Durvillaea (southern bull-kelp) is an economically and ecologically important brown algal genus that dominates many exposed, rocky coasts in the cold-temperate Southern Hemisphere. Of its five currently-recognized species, four are non-buoyant and restricted to the south-western Pacific, whereas one is both buoyant and widely distributed. Durvillaea has had an unsettled taxonomic history. Although its position within the brown algae (Phaeophyceae) has now been largely resolved through the use of molecular techniques, the taxonomic status of several Durvillaea species/morphotypes remains unresolved. Previous molecular phylogenetic studies of phaeophycean taxa have included few Durvillaea samples, and have consequently paid little or no attention to variation within this genus. The current study presents phylogenetic analyses of four genetic markers (mitchondrial: COI; chloroplast: rbcL; and nuclear: 18S and 28S) to resolve phylogenetic relationships within Durvillaea. Results support the monophyly of solid-bladed taxa D. willana, D. potatorum, and D. sp. A (an undescribed species from the Antipodes Islands), whereas the widespread, buoyant D. antarctica is paraphyletic, with solid-bladed D.chathamensis placed sister to a D. antarctica clade from northern NZ but within D. antarctica sensu lato. The phylogenetic and ecological diversity detected within D. antarctica indicate that it is a species complex of five deeply divergent clades. Under a phylogenetic species concept, Durvillaea can be interpreted as a complex of nine distinct evolutionary lineages, only one of which has an intercontinental distribution ('subantarctic'D. antarctica).     

Multilocus phylogenetic analysis of the genus Atherina (Pisces: Atherinidae)

Sand-smelts are small fishes inhabiting inshore, brackish and freshwater environments and with a distribution in the eastern Atlantic and Mediterranean Sea, extending south into the Indian Ocean. Here, we present a broad phylogenetic analysis of the genus Atherina using three mitochondrial (control region, 12S and 16S) and two nuclear markers (rhodopsin and 2nd intron of S7). Phylogenetic analyses fully support the monophyly of the genus. Two anti-tropical clades were identified, separating the South African Atherina breviceps from the north-eastern Atlantic and Mediterranean Atherina' species. In European waters, two groups were found. The first clade formed by a well supported species-pair: Atherina presbyter (eastern Atlantic) and Atherina hepsetus (Mediterranean), both living in marine waters; a second clade included Atherina boyeri (brackish and freshwater environments) and two independent lineages of marine punctated and non-punctated fishes, recently proposed as separate species. Sequence divergence values strongly suggest multiple species within the A. boyeri complex.     

Phylogeny of the staphylococcal major autolysin and its use in genus and species typing

The major staphylococcal autolysin Atl is an important player in cell separation and daughter cell formation. In this study, we investigated the amino acid sequences of Atl proteins derived from 15 staphylococcal and 1 macrococcal species representatives. The overall organization of the bifunctional precursor protein consisting of the signal peptide, a propeptide (PP), the amidase (AM), six repeat sequences (R(1) to R(6)), and the glucosaminidase (GL) was highly conserved in all of the species. The most-conserved domains were the enzyme domains AM and GL; the least-conserved regions were the PP and R regions. An Atl-based phylogenetic tree for the various species representatives correlated well with the corresponding 16S rRNA-based tree and also perfectly matched the phylogenetic trees based on core genome analysis. The phylogenetic distance analysis of 18 AtlA proteins of various Staphylococcus aureus strains and 15 AtlE proteins of S. epidermidis revealed that both species representatives formed a relatively homogeneous cluster. Two S. epidermidis strains, M23864:W1 and VCU116, were identified by Atl typing that clustered far more distantly and belonged to either S. caprae and S. capitis or a new subspecies. Here we show that Atl typing is a useful tool for staphylococcal genus and species typing by using either the highly conserved AM domain or the less-conserved PP domain.