scholarly journals Phylogenetic Analysis of Wing Feather Taxis in Birds: Macroevolutionary Patterns of Genetic Drift?

The Auk ◽  
2002 ◽  
Vol 119 (4) ◽  
pp. 943-954 ◽  
Author(s):  
Kimberly S. Bostwick ◽  
Matthew J. Brady
Keyword(s):  
Genetic Drift ◽  
Dna Hybridization ◽  
Character Evolution ◽  
Adaptive Function ◽  
Ecological Traits ◽  
Wing Feather ◽  
The Family ◽  
Tree Length ◽  
Preliminary Consideration ◽  
Selective Regime

Abstract Most recent research on character evolution attempts to identify either (1) homology or homoplasy (systematic use of the term character), or (2) the adaptive function or selective regime underlying the origin of a character (“adaptationist” use of the term character). There have been relatively few serious considerations or examples of neutral character evolution above the molecular level. Wing feather taxis in birds, the presence or absence of the fifth secondary feather, provides an intriguing possible example of nonadaptive character evolution. We examine the phylogenetic pattern of wing feather taxis among birds to (1) determine its polarity in modern birds (Neornithes), (2) hypothesize the frequency and taxonomic locations of changes in the taxic state, (3) test whether taxis is relatively labile or inert phylogenetically, and (4) allow preliminary consideration of whether adaptive or selectively neutral processes have produced those patterns. Minimum tree length necessary to explain the distribution of wing feather taxis was calculated at the family level using Sibley and Ahlquist's DNA–DNA hybridization tree (1990). Parsimony analysis indicates that the eutaxic condition (fifth secondary present) is ancestral in modern birds, and that diastataxy (fifth secondary absent) has originated independently at least 7 times and reversed to the eutaxic condition on at least 13 occasions within modern birds. Despite multiple independent origins and reversals, wing feather taxis is extremely conserved throughout the tree, such that one or the other state completely characterizes many large multiordinal or multifamilial clades. Lack of obvious correlations with morphological and ecological traits suggest that no single adaptive scenario will explain the evolution of wing feather taxis. Instead, the biological details and phylogenetic patterns make nonadaptive, or selectively neutral evolutionary processes, such as genetic drift, an equally if not more plausible explanation for the distribution of wing feather taxis.

Phylogeny of the family Pasteurellaceae based on rpoB sequences

2004 ◽  
Vol 54 (4) ◽  
pp. 1393-1399 ◽  
Author(s):  
Bożena Korczak ◽  
Henrik Christensen ◽  
Stefan Emler ◽  
Joachim Frey ◽  
Peter Kuhnert
Keyword(s):  
16S Rdna ◽  
Dna Hybridization ◽  
Gene Encoding ◽  
Phylogenetic Studies ◽  
Study Selection ◽  
Gene Sequence Analysis ◽  
Rdna Sequencing ◽  
The Family ◽  
Type Strains ◽  
Selection Of

Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.

Phylogenetic relationships of the subfamily Pyrgulinae (Gastropoda: Caenogastropoda: Hydrobiidae) with emphasis on the genus Dianella Gude, 1913

Zootaxa ◽  
2005 ◽  
Vol 891 (1) ◽  
pp. 1 ◽  
Author(s):  
Magdalena Szarowska ◽  
Andrzej Falniowski ◽  
FRANK Riedel ◽  
Thomas Wilke
Keyword(s):  
Type Species ◽  
Sister Group ◽  
Molecular Data ◽  
Character Evolution ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Data Sets ◽  
Sequencing Data ◽  
The Family ◽  
Anatomical Characters

The phylogenetic position of the subfamily Pyrgulinae within the superfamily Rissooidea has been discussed very controversially. Different data sets not only led to different evolutionary scenarios but also to different systematic classifications of the taxon. The present study uses detailed anatomical data for two pyrgulinid taxa, the type species of the subfamily, Pyrgula annulata (Linnaeus, 1767), and the type species of the little known genus Dianella, D. thiesseana (Kobelt, 1878), as well as DNA sequencing data of three gene fragments from representatives of eight rissooidean families to A) infer the phylogenetic position of Pyrgulinae with emphasis on its relationships within the family Hydrobiidae, B) to study the degree of concordance between anatomyand DNAbased phylogenies and C) to trace the evolution of anatomical characters along a multi-gene molecular phylogeny to find the anatomical characters that might be informative for future cladistic analyses. Both anatomical and molecular data sets indicate either a very close or even sister-group relationship of Pyrgulinae and Hydrobiinae. However, there are major conflicts between the two data sets on and above the family level. Notably, Hydrobiidae is not monophyletic in the anatomical analysis. The reconstruction of anatomical character evolution indicates that many of the characters on which the European hydrobioid taxonomy is primarily based upon are problematic. The inability to clearly separate some hydrobiids from other distinct families based on those characters might explain why until only a few years ago, "Hydrobiidae" was a collecting box for numerous rissooidean taxa (mostly species with shells small and lacking any characteristic features). The present study not only stresses the need for comprehensive molecular studies of rissooidean taxa, it also demonstrates that much of the problems surrounding anatomical analyses in rissooidean taxa are due to the lack of comprehensive data for many representatives. In order to aid future comparativeanatomical studies and a better understanding of character evolution in the species-rich family Hydrobiidae, detailed anatomical descriptions for P. annulata and D. thiesseana are provided.Key words: Pyrgulinae, Pyrgula, Dianella, Hydrobiidae, phylogeny, DNA, anatomy, Greece

scholarly journals Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family ‘Thermoactinomycetaceae’ isolated from compost

2005 ◽  
Vol 55 (5) ◽  
pp. 2101-2104 ◽  
Author(s):  
Kouta Hatayama ◽  
Hirofumi Shoun ◽  
Yasuichi Ueda ◽  
Akira Nakamura
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Type Strains

Four thermophilic, Gram-positive strains, designated H0165T, 500275T, C0170 and 700375, were isolated from a composting process in Japan. The isolates grew aerobically at about 65 °C on a solid medium with formation of substrate mycelia; spores were produced singly along the mycelia. These morphological characters resembled those of some type strains of species belonging to the family ‘Thermoactinomycetaceae’, except that aerial mycelia were not formed. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest related species to the isolates were members of the family ‘Thermoactinomycetaceae’, but that the isolates formed an independent phylogenetic lineage. Some chemotaxonomic characters of the isolates, such as DNA G+C contents of 58·7–60·3 mol%, MK-7 as the major menaquinone and cellular fatty acid profiles, differed from those of members of the family ‘Thermoactinomycetaceae’. DNA–DNA hybridization showed that the isolates could be divided into two genomic groups, strain H0165T and the other three strains. These results indicated that the four isolates should be classified into two species of a novel genus in the family ‘Thermoactinomycetaceae’, for which the names Planifilum fimeticola gen. nov., sp. nov. (type strain H0165T=ATCC BAA-969T=JCM 12507T) and Planifilum fulgidum sp. nov. (type strain 500275T=ATCC BAA-970T=JCM 12508T) are proposed.

scholarly journals Prediction of whole-genome DNA–DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Microbiology ◽  
2006 ◽  
Vol 152 (9) ◽  
pp. 2537-2548 ◽  
Author(s):  
Peter Kuhnert ◽  
Bożena M. Korczak
Keyword(s):  
Dna Hybridization ◽  
Gold Standard ◽  
Classical Method ◽  
Gene Sequencing ◽  
Dna Relatedness ◽  
Experimental Variation ◽  
The Family ◽  
Taxonomic Studies ◽  
Species Descriptions

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA–DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA–DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA–DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA–DNA hybridization.

scholarly journals Actinopolymorpha pittospori sp. nov., an endophyte isolated from surface-sterilized leaves of an apricot tree (Pittosporum phylliraeoides)

2011 ◽  
Vol 61 (11) ◽  
pp. 2616-2620 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher M. M. Franco
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Biochemical Studies ◽  
Apricot Tree ◽  
Physiological And Biochemical ◽  
Wall Components

A member of the genus Actinopolymorpha, designated PIP 143T, was isolated from the leaves of an Australian native apricot tree (Pittosporum phylliraeoides). The isolate was a Gram-reaction-positive, aerobic actinobacterium, with a well-developed substrate mycelium that fragmented into small rods. Phylogenetic evaluation based on 16S rRNA gene sequences placed the isolate in the family Nocardioidaceae. Strain PIP 143T was most closely related to Actinopolymorpha cephalotaxi I06-2230T (98.7 %) and Actinopolymorpha rutila YIM 45725T (98.1 %). Chemotaxonomic data, including cell-wall components, menaquinones and fatty acids, confirmed the affiliation of strain PIP 143T to the genus Actinopolymorpha. Phylogenetic analysis and physiological and biochemical studies, in combination with DNA–DNA hybridization studies, allowed the differentiation of strain PIP 143T from its closest phylogenetic neighbours with validly published names. Therefore, a novel species is proposed, with the name Actinopolymorpha pittospori sp. nov. The type strain is PIP 143T ( = DSM 45354T  = ACM 5288T  = NRRL B-24810T).

scholarly journals Characterization ofHalorubrum sfaxensesp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Hana Trigui ◽  
Salma Masmoudi ◽  
Céline Brochier-Armanet ◽  
Sami Maalej ◽  
Sam Dukan
Keyword(s):  
Dna Hybridization ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Solar Saltern ◽  
Halophilic Archaeon ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
The Family ◽  
Close Relationship ◽  
Extremely Halophilic Archaeon

An extremely halophilic archaeon, strain ETD6, was isolated from a marine solar saltern in Sfax, Tunisia. Analysis of the 16S rRNA gene sequence showed that the isolate was phylogenetically related to species of the genusHalorubrumamong the familyHalobacteriaceae, with a close relationship toHrr. xinjiangense(99.77% of identity). However, value for DNA-DNA hybridization between strain ETD6 andHrr.xinjiangensewere about 24.5%. The G+C content of the genomic DNA was 65.1 mol% (T(m)). Strain ETD6 grew in 15–35% (w/v) NaCl. The temperature and pH ranges for growth were 20–55°C and 6–9, respectively. Optimal growth occurred at 25% NaCl, 37°C, and pH 7.4. The results of the DNA hybridization againstHrr. xinjiangenseand physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain ETD6 from otherHrr.species. Therefore, strain ETD6 represents a novel species of the genusHalorubrum, for which the nameHrr. sfaxensesp. nov. is proposed. The Genbank EMBL-EBI accession number is GU724599.

scholarly journals Not so sluggish: the success of the Felimare picta complex (Gastropoda, Nudibranchia) crossing Atlantic biogeographic barriers

2015 ◽  
Author(s):  
Frederico Almada ◽  
André Levy ◽  
Joana I Robalo
Keyword(s):  
Morphological Characteristics ◽  
Mediterranean Species ◽  
Ecological Traits ◽  
Western Atlantic ◽  
Demersal Eggs ◽  
The Family ◽  
Group A ◽  
Paraphyletic Group ◽  
Planktotrophic Larvae ◽  
Independent Species

The molecular phylogeny of the Atlanto-Mediterranean species of the genus Felimare, particularly those attributed to the species F. picta, was inferred using two mitochondrial markers (16S and COI). A recent revision of the Chromodorididae clarified the taxonomic relationships at the family level reclassifying all eastern Pacific, Atlantic and Mediterranean species of the genus Hypselodoris and two species of the genus Mexichromis, within the genus Felimare. However, conflicting taxonomic classifications have been proposed for a group with overlapping morphological characteristics and geographical distributions designated here as the Felimare picta complex. Three major groups were identified: one Mediterranean and amphi-Atlantic group; a western Atlantic group and a tropical eastern Atlantic group. F. picta forms a paraphyletic group since some subspecies are more closely related with taxa traditionaly classified as independent species (e.g. F. zebra) than with other subspecies with allopatric distributions (e.g. F. picta picta and F. picta tema). Usually, nudibranchs have adhesive demersal eggs, short planktonic larval phases and low mobility as adults unless rafting on floating materials occurs. However, the phylogeny of the F. picta complex suggests they had an unusual success crossing main Atlantic biogeographic barriers including the mid-Atlantic barrier. This ability to cross different biogeographic barriers may be related with F. picta distinct life history and ecological traits. Compared to other Chromodorididae F. picta presents large eggs and planktotrophic larvae which could be related with a longer planktonic phase.

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