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1.
Phylogenetic relationships of the genera Russula and Lactarius were investigated using sequence data from the nuclear-encoded large subunit ribosomal DNA (LSU rDNA). Ninety-five sequences belonging to the genera Russula and Lactarius, including 31 sequences from the databases, were used in this study. Analysis of the LSU rDNA region indicated that Russulaceae was divided into six groups (group A–F) in the neighbor-joining (NJ) tree. Lactarius consisted of one large clade (group A). Therefore, this genus was found to be monophyletic. However, the monophyly of genus Russula remained unclear. The genus Russula consisted of five groups in the NJ tree. Group B includes sects. Plorantes and Archaeinae (Heim), and group C includes sects. Delicoarchaeae and Russula in the NJ tree. Neither of the two groups formed a single clade in the most parsimonius (MP) tree. Group D includes many taxa having colored spore prints and amyloid in suprahilar plage of spores in sect. Russula and sect. Rigidae. Group E consists of only sect. Compactae and is further divided into three subclades, represented by R. densifolia, R. nigricans, and R. subnigricans, respectively. Group F contains sects. Rigidae, Ingratae, and Pelliculariae. Sect. Compactae and sect. Plorantes should not be as closely related as previously supposed. Russula earlei may be placed in sect. Archaeinae Heim. Russula flavida (subsect. Amoeninae) is placed in sect. Russula with R. aurea with a high bootstrap value (99%). The nuclear LSU rDNA region is a useful tool in recognization of species of Russulaceae and may provide information concerning phylogenetic relationships between the genera Russula and Lactarius. 相似文献
2.
Billy Sinclair Leica Briskey William Aspden Graham Pegg 《Reviews in Fish Biology and Fisheries》2007,17(2-3):223-235
Nautilus species are the only remaining cephalopods with an external shell. Targeted heavily by the shell trade across their distribution
area, these species have a poorly known population structure and genetics. Molecular techniques have been used to assess levels
of inter- and intra-population genetic diversity in isolated populations of Nautilus in the northern sections of the Great Barrier Reef (GBR), Australia and in the Coral Sea. Distinct populations, physically
separated by depths in excess of 1,000 m were examined. RAPD analysis of genetic differences showed limited differentiation
of the “Northern GBR” populations and the “Coral Sea” populations. Discrimination between the two geographic groups was observed
from these data. In addition, partial sequencing of the CoxI gene region, yielded 575 bp of sequence, which was aligned for 43 samples and phylogenetic trees constructed to examine genetic
relationships. Two distinct clades were resolved in the resulting trees, representing the “Northern GBR” and “Coral Sea” population
groups. Inter- and intra-population relationships are presented and discussed. The differentiation of the Nautilus populations from the Northern section of the Great Barrier Reef and those from the Coral Sea were supported by two distinctly
different methodologies and the significance of this separation and the potential evolutionary divergence of these two population
groups is discussed. 相似文献
3.
Valérie Stiger † Takeo Horiguchi Tadao Yoshida Annette W. Coleman Michio Masuda 《Phycological Research》2003,51(1):1-10
Sequences from the ribosomal DNA internal transcribed spacer‐2 (ITS‐2) were compared among species of Sargassaceae including the genera Sargassum and Hizikia. Species of different subgenera and sections of Sargassum were used to assess the taxonomic relationships within the genus, especially the subdivisions of the subgenus Bactrophycus. Sequences were aligned in accordance with their common secondary structure. Phylogenetic trees were constructed using neighbor‐joining, maximum likelihood and maximum parsimony methods with three species of Turbinaria as outgroups. The resulting phylogenetic trees showed that the genus Sargassum is divided into three clades corresponding to the subgenera Phyllotrichia, Sargassum and Bactrophycus. This last subgenus is further divided into four distinct groups: a Spongocarpus clade, a Teretia clade, a Hizikia clade, and a Halochloa/ Repentia clade. The position of the section Phyllo‐cystae, excluded from the subgenus Bactrophycus and included within the subgenus Sargassum is once again confirmed by the present study. Current results strongly support the assignation of Hizikia fusiformis to the genus Sargassum. Based on morphological differences and a distinct position in the molecular trees, Hizikia should be recognized as a section in the subgenus Bactrophycus so that Hizikia (Okamura) Yoshida, stat. nov. is proposed. A remarkably low divergence of ITS‐2 sequences was observed for the species in the sections Repentia and Halochloa, suggesting very recent radiation of these species. The subgenus Sargassum is divided into three clades corresponding to the three known sections: Acanthocarpicae, Malacocarpicae and Zygocarpicae, previously recognized by the morphology of receptacles. The position of Sargassum duplicatum, S. carpophyllum, S.yendoi, S. piluliferum and S. patens within the subgenus Sargassum is discussed. 相似文献
4.
Isolates from the marine actinobacterial genus Salinispora were cultured from marine sponges collected from along the length of the Great Barrier Reef (GBR), Queensland, Australia.
Strains of two species of Salinispora, Salinispora arenicola and “Salinispora pacifica”, were isolated from GBR sponges Dercitus
xanthus, Cinachyrella australiensis and Hyattella intestinalis. Phylogenetic analysis of the 16S rRNA gene sequences of representative strains, selected via BOX-PCR screening, identified
previously unreported phylotypes of the species “S. pacifica”. The classification of these microdiverse 16S rRNA groups was further confirmed by analysis of the ribonuclease P RNA (RNase
P RNA) gene through both phylogenetic and secondary structure analysis. The use of RNase P RNA sequences combined with 16S
rRNA sequences allowed distinction of six new intraspecies phylotypes of “S. pacifica” within the geographical area of the GBR alone. One of these new phylotypes possessed a localised regional distribution within
the GBR. 相似文献
5.
S. Moja Y. Guitton F. Nicolè L. Legendre B. Pasquier T. Upson 《Plant biosystems》2016,150(6):1216-1224
The genus Lavandula L. consists of 39 species distributed from the North Atlantic Islands, across the Mediterranean Basin to India. We analysed 36 taxa of the genus Lavandula representing two of the three subgenera and six of the eight sections according to the most recent classification (Upson & Andrews 2004). We achieved a phylogenetic reconstruction from partial sequences from plastid trnK and matK genes; the genome size was estimated by flow cytometer measurements. The primary aim was to track phylogenetic patterns through the maternal inherited marker at the sectional level and identify possible genome duplications. The cpDNA tree shows the phylogenetic relationships between subgenus, sections and also elucidates for the first time the relationships between the endemic species of Macaronesia, Morocco and Arabia. The ancestral split between the two subgenera could be explained by dispersal followed by an early vicariance event. The C-value shows genome up-sizing within several phylogenetic clades and geographical areas. An ancestral genome-up sizing is characterized at the node of section Dentatae and Lavandula. The cpDNA tree suggests that the taxa L. angustifolia subsp. pyrenaica (DC.) Guinea and L. stoechas subsp. luiseiri are best treated as a distinct species. 相似文献
6.
Tsuyoshi Hosoya Rei Sasagawa Kentaro Hosaka Sung Gi-Ho Yumiko Hirayama Kaoru Yamaguchi Kyoko Toyama Makoto Kakishima 《Mycoscience》2010,51(3):170-181
Molecular phylogenetic studies were carried out based on ITS-5.8S rDNA, the D1–D2 region of the large subunit rRNA gene, RPB2,
and combined data of D1–D2 and RPB2 as well as these three genes on 36 species among 7 genera for Lachnum and allied genera in the family Hyaloscyphaceae. In the combined data of all three regions, seven strongly supported clades
were obtained. The same clades were also recognized in most of the trees based on each gene, and the combined data of D1–D2
and RPB2, although some of them were not strongly supported. Four clades represented Albotricha, Brunnipila, Incrucipulum, and Lachnellula, respectively, whereas Lachnum was distributed to the remaining three clades. The molecular phylogenies strongly supported a group of species with granulate
hairs, and we suggest the concept of Lachnaceae should be restricted to these species. Based on the molecular phylogenetic
analysis, three new combinations—Incrucipulum longispineum, I. radiatum, and Lachnellula pulverulentum from Lachnum—are proposed. 相似文献
7.
Bacterial species of the genusPrevotella represent a numerically dominant microbial population in the rumen of cattle. They belong to the phylogenetic divisionCytophaga-Flexibacter-Bacteroides (CFB) which is a large group of ecologically diverse bacteria with only a few shared traits. The phylogenetic descent from
a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal RNA analysis. Only 4 ruminalPrevotella species have been described to date, even though the sequence analysis of directly retrieved 16S rRNA genes indicates a large
genetic diversity within this group of rumen bacteria. The closest relatives of ruminalPrevotella spp. are not surprisingly other species of the genusPrevotella, typically inhabiting the gastrointestinal tract, oral cavity and genital areas of other animals and man. The previous phylogenetic
analysis showed that species of the genusPrevotella can be split into two groups or superclusters, the “ruminal” and the “non-ruminal prevotellas”. One of 4 currently described
ruminalPrevotella spp.,i.e. P. albensis, has been placed outside the supercluster containing ruminalPrevotella spp. and within the supercluster containing the non-ruminalPrevotella spp. However, the number of available small subunit rRNA sequences from this species represents only a fraction of all known
ruminalPrevotella sequences. 相似文献
8.
Nicolas Puillandre Maren Watkins Baldomero M. Olivera 《Journal of molecular evolution》2010,70(2):190-202
A remarkable diversity of venom peptides is expressed in the genus Conus (known as “conotoxins” or “conopeptides”). Between 50 and 200 different venom peptides can be found in a single Conus species, each having its own complement of peptides. Conopeptides are encoded by a few gene superfamilies; here we analyze
the evolution of the A-superfamily in a fish-hunting species clade, Pionoconus. More than 90 conopeptide sequences from 11 different Conus species were used to build a phylogenetic tree. Comparison with a species tree based on standard genes reveals multiple gene
duplication events, some of which took place before the Pionoconus radiation. By analysing several A-conopeptides from other Conus species recorded in GenBank, we date the major duplication events after the divergence between fish-hunting and non-fish-hunting
species. Furthermore, likelihood approaches revealed strong positive selection; the magnitude depends on which A-conopeptide
lineage and amino-acid locus is analyzed. The four major A-conopeptide clades defined are consistent with the current division
of the superfamily into families and subfamilies based on the Cys pattern. The function of three of these clades (the κA-family,
the α4/7-subfamily, and α3/5-subfamily) has previously been characterized. The function of the remaining clade, corresponding
to the α4/4-subfamily, has not been elucidated. This subfamily is also found in several other fish-hunting species clades
within Conus. The analysis revealed a surprisingly diverse origin of α4/4 conopeptides from a single species, Conus bullatus. This phylogenetic approach that defines different genetic lineages of Conus venom peptides provides a guidepost for identifying conopeptides with potentially novel functions. 相似文献
9.
Seiji Matsumoto Takeshi Kon Motoomi Yamaguchi Hirohiko Takeshima Yuji Yamazaki Takahiko Mukai Kaoru Kuriiwa Masanori Kohda Mutsumi Nishida 《Ichthyological Research》2010,57(1):71-77
The swamp eel Monopterus albus is widely distributed in tropical and subtropical freshwaters ranging from Southeast Asia to East Asia, and is unique in
its ability to breathe air through the buccal mucosa. To examine the genetic structure of this widespread species, molecular
phylogenetic analyses of mitochondrial 16S rRNA sequence (514 bp) were conducted for 84 specimens from 13 localities in Southeast
and East Asia. The analyses showed clearly that this species can be genetically delineated into three clades based on geographical
populations [China–Japan (Honshu + Kyushu), Ryukyu Islands, and Southeast Asia clades], with each clade exhibiting its own
reproductive behavior. Therefore, “M. albus” is believed to be composed of at least three species. The Southeast Asia clade with the highest genetic diversity may include
more species. The Ryukyu clade was estimated to have diverged more than 5.7 million years ago, suggesting that the Ryukyuan
“M. albus” is native. In contrast, in the China–Japan clade, all haplotypes from Japan were closely related to those from China, suggesting
artificial introduction(s). 相似文献
10.
B. L. Rodrigues L. A. Baton P. H. F. Shimabukuro 《Medical and veterinary entomology》2020,34(4):420-431
Sandfly specimens from the subgenus Evandromyia (Aldamyia) Galati, 2003 (Diptera: Psychodidae: Phlebotominae) were collected between 2012 and 2019 from nine localities in seven Brazilian states, morphologically-identified, and then DNA barcoded by sequencing the mitochondrial cytochrome c oxidase subunit I (coi) gene. Forty-four new barcode sequences generated from 10 morphospecies were combined with 49 previously published sequences from the same subgenus and analysed using sequence-similarity methods (best-match criteria) to assess their ability at specimen identification, while four different species delimitation methods (ABGD, GMYC, PTP and TCS) were used to infer molecular operational taxonomic units (MOTUs). Overall, seven of the 11 morphospecies analysed were congruent with both the well-supported clades identified by phylogenetic analysis and the MOTUs inferred by species delimitation, while the remaining four morphospecies – E. carmelinoi, E. evandroi, E. lenti and E. piperiformis – were merged into a single well-supported clade/MOTU. Although E. carmelinoi, E. evandroi and E. lenti were indistinguishable using coi DNA barcodes, E. piperiformis did form a distinct phylogenetic cluster and could be correctly identified using best-match criteria. Despite their apparent morphological differences, we propose on the basis of the molecular similarity of their DNA barcodes that these latter four morphospecies should be considered members of a recently-diverged species complex. 相似文献
11.
Natalia Tkach Martin Rser Matthias H. Hoffmann 《Botanical journal of the Linnean Society. Linnean Society of London》2015,178(1):47-66
With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66. 相似文献
12.
B. M. Kataev 《Entomological Review》2011,91(1):90-95
Harpalus apache sp. n. is described from the eastern part of New Mexico, USA (type locality: Hwy I 40, near Santa Rosa, Guadalupe Co). The
new species is very similar in appearance to H. cordatus (Le-Conte, 1853) but readily distinguished from it by the male genitalia structure. These two species constitute a natural
taxon which is included as the “cordatus” group (= Opadius Casey, 1914) in the subgenus Glanodes Casey, 1914. Distinctive characters, distribution and composition of the subgenus Glanodes and two its species groups (“obliquus” and “cordatus”) are provided. Two names, H. cordatus (LeConte, 1853) (= H. tadorcus Ball, 1972) and H. puncticeps (Casey, 1914) (= H. cunctipeps Ball, 1973), rejected because of the secondary homonymy, are reinstated as valid since they are not homonyms of Ophonus cordatus (Duftschmid, 1812) and Ophonus puncticeps Stephens, 1828, respectively. 相似文献
13.
Melisa Olave Luciano J. Avila Jack W. Sites Jr. Mariana Morando 《Zoologica scripta》2014,43(4):323-337
The lizard genus Liolaemus and different clades within it have been the focus of several recent phylogenetic studies mainly based on morphology and mtDNA. Although there is general consensus for recognizing two clades (subgenera) within the genus, [Liolaemus (sensu stricto) and Eulaemus], phylogenetic relationships within each subgenus remain difficult to elucidate, given incomplete taxonomic sampling and large discordance between published studies. Here, new phylogenetic relationships for the Eulaemus subgenus are proposed based on the largest molecular data set ever used for this clade, which includes 188 individuals and 14 loci representing different parts of the genome (mtDNA, anonymous nuclear loci and nuclear protein‐coding loci). This data set was analysed using two species tree approaches (*beast and MDC). Levels of discordance among methods were found, and with previously published studies, but results are robust enough to propose new phylogenetic hypotheses for the Eulaemus clade. Specifically well‐resolved and well‐supported novel hypotheses are provided within the lineomaculatus section, and we formally recognize the zullyae clade, the sarmientoi clade and the hatcheri group. We also resolve species relationships within the montanus section, and particularly within the melanops series. We found discordance between mitochondrial and nuclear trees and discussed alternative hypotheses for the lineomaculatus and montanus sections, as well as the challenge in resolving phylogenetic relationships for large clades in general. 相似文献
14.
The phylogenetic relationships of Lactarius
volemus and its relatives were investigated using the nucleotide sequences of the nuclear-encoded large subunit ribosomal DNA (LSU
rDNA). Thirty-six sequences from L. volemus, L. corrugis, and L. hygrophoroides, including three sequences obtained from the GenBank database, were used in this study. Samples studied were divided into
four major subclades (A–D) in both neighbor-joining (NJ) and maximum-parsimony (MP) trees. Lactarius volemus and L. corrugis formed one large clade in both NJ and MP trees (bootstrap value, 100%), which was divided into three subclades (A–C). Subclade
A included three clusters of L. volemus strains, i.e., velvet, red, and Chinese types. Subclade B included the common and red types of L. corrugis. Subclade C included the common and yellow types of L. volemus. Subclade D included only one type of L. hygrophoroides. An analysis of the fatty acid composition supported the divisions found in the molecular analysis. Analyses of nucleotide
sequence, fatty acid composition, morphological characteristics, and the taste of the fruiting bodies all led us to conclude
that the common, velvet, red, and Chinese types of L. volemus, and the common and red types of L. corrugis, may each belong to different species, subspecies, or varieties. Further studies with more material from a wide range of
regions are required to conduct taxonomic revision of these types. The LSU rDNA region may be a useful tool to investigate
phylogenetic relationships within the section Dulces of the genus Lactarius. 相似文献
15.
Conservation of 16 nuclear microsatellite loci, originally developed for Quercus macrocarpa (section Albae), Q. petraea, Q. robur (section Robur), and Q. myrsinifolia, (subgenus Cyclobalanopsis) was tested in a Q. infectoria ssp. veneris population from Cyprus. All loci could be amplified successfully and displayed allele size and diversity patterns that match
those of oak species belonging to the section Robur. At least in one case, limited amplification and high levels of homozygosity support the occurrence of “null alleles” caused
by a possible mutation in the highly conserved primer areas, thus hindering PCR. The sampled population exhibited high levels
of diversity despite the very limited distribution of this species in Cyprus and extended population fragmentation. Allele
sizes of Q. infectoria at locus QpZAG9 partially match those of Q. alnifolia and Q. coccifera from neighboring populations. However, sequencing showed homoplasy, excluding a case of interspecific introgression with
the latter, phylogenetically remote species. Q. infectoria ssp. veneris sequences at this locus were concordant to those of other species of section Robur, while sequences of Quercus alnifolia and Quercus coccifera were almost identical to Q. cerris. 相似文献
16.
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18.
Exceptional chromosomal variability makesCtenomys an excellent model for evolutionary cytogenetic analysis. Six species belonging to three evolutionary lineages were studied
by means of restriction endonuclease and C-chromosome banding. The resulting banding patterns were used for comparative analysis
of heterochromatin distribution on chromosomes. This combined analysis allowed intra- and inter-specific heterochromatin variability
to be detected, groups of species belonging to different lineages to be characterized, and phylogenetic relationships hypothesized
from other data to be supported. The “ancestral group”,Ctenomys pundti andC. talarum, share three types of heterochromatin, the most abundant of which was also found in C. aff.C. opimus, suggesting that the latter species also belongs to the “ancestral group”. Additionally, within the subspeciesC. t. talarum, putative chromosomal rearrangements distinguishing two of the three chromosomal races were identified. Two species belong
to an “eastern lineage”,C. osvaldoreigi andC. rosendopascuali, and share only one type of heterochromatin homogeneously distributed across their karyotypes.C. latro, the only analyzed species from the “chacoan” lineage, showed three types of heterochromatin, one of them being that which
characterizes the “eastern lineage”.C. aff.C. opimus, because of its low heterochromatin content, is the most primitive karyotype of the genus yet described. The heterochromatin
variability showed by these species, reflecting the evolutionary divergence toward different heterochromatin types, may have
diverged since the origin of the genus. Heterochromatin amplification is proposed as a trend withinCtenomys, occurring independently of chromosomal change in diploid numbers. 相似文献
19.
M. Hendrichs F. Oberwinkler D. Begerow R. Bauer 《Plant Systematics and Evolution》2004,246(1-2):89-107
To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed. 相似文献
20.
Mingli Zhang Peter W. Fritsch Boni C. Cruz 《Molecular phylogenetics and evolution》2009,50(3):547-559
Phylogenetic relationships of 48 species of Caragana (Fabaceae: tribe Hedysareae) and one representative each of Astragalus, Calophaca, Halimodendron, and Hedysarum are estimated from DNA sequences of the rbcL gene, trnS–trnG intron and spacer, and ITS region. At least one representative of all five sections and 12 series within Caragana are included. Analyses yielded strongly supported clades corresponding to sections Caragana, Bracteolatae, and Frutescentes. The species of section Jubatae are distributed among three strongly supported clades, i.e., one with the species of section Bracteolatae, another with two species of section Spinosae, and a third as sister to section Frutescentes. All but the last of these six clades are corroborated by at least one unambiguously traced morphological character. The placement of the other four species of section Spinosae are not well supported and lack unambiguous morphological synapomorphies, and the samples of Calophaca and Halimodendron nest within Caragana with weak support. 相似文献