Inferring the Evolutionary History of Mo-Dependent Nitrogen Fixation from Phylogenetic Studies of nifK and nifDK

2010 ◽  
Vol 71 (1) ◽  
pp. 70-85 ◽  
Author(s):  
Linda S. Hartmann ◽  
Susan R. Barnum
Keyword(s):  
Nitrogen Fixation ◽  
Evolutionary History ◽  
Phylogenetic Studies ◽  
History Of

scholarly journals Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

Diversity ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 70 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Emily Moriarty Lemmon ◽  
Alan R. Lemmon ◽  
Nigel French
Keyword(s):  
Evolutionary History ◽  
State Of The Art ◽  
Molecular Techniques ◽  
Evolutionary Significance ◽  
Phylogenetic Structure ◽  
Bayesian Approaches ◽  
Phylogenetic Studies ◽  
Anchored Phylogenomics ◽  
History Of ◽  
Phylogenomic Analyses

The integration of state-of-the-art molecular techniques and analyses, together with a broad taxonomic sampling, can provide new insights into bird interrelationships and divergence. Despite their evolutionary significance, the relationships among several rail lineages remain unresolved as does the general timescale of rail evolution. Here, we disentangle the deep phylogenetic structure of rails using anchored phylogenomics. We analysed a set of 393 loci from 63 species, representing approximately 40% of the extant familial diversity. Our phylogenomic analyses reconstruct the phylogeny of rails and robustly infer several previously contentious relationships. Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support. The results are concordant with previous phylogenetic studies using small DNA datasets, but they also supply an additional resolution. Our dating analysis provides contrasting divergence times using fossils and Bayesian and non-Bayesian approaches. Our study refines the evolutionary history of rails, offering a foundation for future evolutionary studies of birds.

Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colón Province, Panama

2018 ◽  
Vol 92 (5) ◽  
pp. 804-837 ◽  
Author(s):  
Jonathan R. Hendricks
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Feeding Habits ◽  
Shell Morphology ◽  
Snail Species ◽  
Cone Snail ◽  
Phylogenetic Studies ◽  
Biogeographic History ◽  
History Of ◽  
Coloration Patterns

AbstractExtant members of the neogastropod family Conidae (cone snails) are renowned for their often dazzling shell coloration patterns and venomous feeding habits. Many cone snail species have also been described from the fossil record, but to date have been little used to understand the evolutionary history of extant clades. The cone snail fauna of the Miocene Gatun Formation of Colón Province, Panama is especially important for understanding the temporal and biogeographic history of tropical American Conidae. Intensive, focused collecting from an exposure of the lower Gatun Formation (deposited ca. 11–10 Ma) resulted in the discovery of nearly 900 specimens of Conidae. Remarkably, many of these well-preserved specimens exhibit revealed coloration patterns when exposed to ultraviolet light. The fluorescing coloration patterns were used in conjunction with other features of shell morphology to differentiate species and, in most cases, evaluate their potential relationships to members of the extant tropical American fauna. Nine species are fully described from this locality, one of which is recognized as new:Conus(Stephanoconus)woodringin. sp. At least one, and perhaps more, additional Conidae species are also present at the study locality. The diversity of this Conidae fauna is considered moderate relative to other recently analyzed tropical American fossil assemblages. The phylogenetic diversity of the assemblage, however, is noteworthy: six of the ten species can be confidently assigned to six different clades of extant Conidae, providing potentially useful calibration points for future phylogenetic studies.http://zoobank.org/8fe00c31-8f3f-4514-85af-29068e468cd3

scholarly journals A theory about the evolutionary history of Lachnidae and comments on the results of some molecular phylogenetic studies of aphids (Hemiptera: Aphidoidea)

2015 ◽  
Vol 84 (4) ◽  
pp. 275-287 ◽  
Author(s):  
Ole E. Heie
Keyword(s):  
Evolutionary History ◽  
Sister Group ◽  
Compound Eyes ◽  
Host Alternation ◽  
Phylogenetic Studies ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of

Abstract Several characters of the Lachnidae are discussed, and it is explained why some of them are not plesiomorphies as previously believed, but apomorphies. This applies e.g. to the absence of host alternation in the extant genera, to the short cauda and to the presence of compound eyes in the nymphs and the apterous adults. Some characters are adaptations to attention by ants or ways of feeding. It is concluded that many characters show that the family is relatively young and probably originally had host alternation of the same kind as Aphididae, which is regarded as the sister group. The results of some molecular phylogenetic studies are discussed.

scholarly journals The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1032 ◽  
Author(s):  
Yulia Vakulenko ◽  
Andrei Deviatkin ◽  
Alexander Lukashev
Keyword(s):  
Evolutionary History ◽  
Large Datasets ◽  
Sequencing Errors ◽  
Sample Bias ◽  
Phylogenetic Studies ◽  
Phylogenetic Methods ◽  
History Of ◽  
Sequence Position ◽  
Annotation Errors ◽  
Selection Of

Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.

The Evolutionary History of Nitrogen Fixation, as Assessed by Nif D

2004 ◽  
Vol 58 (4) ◽  
pp. 390-399 ◽  
Author(s):  
Susan R. Barnum ◽  
Brian J. Henson ◽  
Linda E. Watson
Keyword(s):  
Nitrogen Fixation ◽  
Evolutionary History ◽  
History Of

scholarly journals Distribution and functional potential of photoautotrophic bacteria in alkaline hot springs

2020 ◽  
Author(s):  
Annastacia C. Bennett ◽  
Senthil K. Murugapiran ◽  
Eric D. Kees ◽  
Trinity L. Hamilton
Keyword(s):  
Nitrogen Fixation ◽  
Yellowstone National Park ◽  
National Park ◽  
Evolutionary History ◽  
Photosynthetic Bacteria ◽  
Hot Springs ◽  
The Body ◽  
Anoxygenic Phototrophs ◽  
Carbon And Nitrogen ◽  
History Of

ABSTRACTAlkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on cyanobacteria (oxygenic phototrophs), but anoxygenic phototrophs are critical parts of the evolutionary history of life on Earth and and are abundant across temperature gradients in alkaline hot springs. However, many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. Here, we examined the distribution of genes involved in phototrophy and carbon and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites approaching the upper temperature limit of photosynthesis (~72°C) in YNP using metagenome sequencing. Genes associated with cyanobacteria are abundant throughout our data and more diverse at temperatures > 63°C, genes for autotrophic Chloroflexi are more abundant in sites > 63°C and genes associated with phototrophic Chloroflexi are abundant throughout. Additionally, we recovered deep branching nitrogen fixation genes from our metagenomes, which could inform the evolutionary history of nitrogen fixation. Lastly, we recovered 25 metagenome assembled genomes of Chloroflexi. We found distinct differences in carbon fixation genes in Roseiflexus and Chloroflexus bins, in addition to several novel Chloroflexi bins. Our results highlight the physiological diversity and evolutionary history of the understudied, anoxygenic autotrophic Chloroflex. Furthermore, we provide evidence that genes involved in nitrogen fixation in Chloroflexi is more widespread than previously assumed.IMPORTANCEPhotosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology because they are responsible for the rise of oxygen and are critical to nutrient cycling. While a large body of work has focused on the oxygenic photosynthesis in cyanobacteria, many questions remain regarding the metabolic potential of anoxygenic phototrophs but are further compounded by their metabolic and taxonomic diversity. Here, we have recovered several novel metagenome bins and quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Together, our results add to the body of work focusing on photosynthetic bacteria in hot springs in Yellowstone National Park.

scholarly journals Genomic Insights into the Evolutionary Origin of Xanthomonas axonopodis pv. citri and Its Ecological Relatives

2014 ◽  
Vol 80 (20) ◽  
pp. 6266-6279 ◽  
Author(s):  
Samriti Midha ◽  
Prabhu B. Patil
Keyword(s):  
Evolutionary History ◽  
Single Species ◽  
Content Type ◽  
Xanthomonas Axonopodis ◽  
Phylogenetic Studies ◽  
Sequencing Studies ◽  
Long Time ◽  
History Of ◽  
Citrus Bacterial Canker ◽  
Time Form

ABSTRACTXanthomonas axonopodispv. citri (Xac) is the causal agent of citrus bacterial canker (CBC) and is a serious problem worldwide. Like CBC, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused byXanthomonaspathovars that display remarkable specificity toward their hosts. While citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. Interestingly, diseases caused by all these pathovars were noted first in India. Our genome-based phylogenetic studies suggest that these diverse pathogens belong to a single species and these pathovars may be just a group of rapidly evolving strains. Furthermore, the recently reported pathovars, such as those infecting grape and pomegranate, form independent clonal lineages, while the citrus and mango pathovars that have been known for a long time form one clonal lineage. Such an understanding of their phylogenomic relationship has further allowed us to understand major and unique variations in the lineages that give rise to these pathovars. Whole-genome sequencing studies including ecological relatives from their putative country of origin has allowed us to understand the evolutionary history of Xac and other pathovars that infect fruits.

Systematics of the Gracilariales (Rhodophyta) including new subfamilies, tribes, subgenera, and two new genera, Agarophyton gen. nov. and Crassa gen. nov.

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 1 ◽  
Author(s):  
CARLOS FREDERICO D. GURGEL ◽  
JAMES N. NORRIS ◽  
WILLIAM E. SCHMIDT ◽  
HAU NHU LE ◽  
SUZANNE FREDERICQ
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
New Genera ◽  
New Classification ◽  
Free Living ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Evolutionary Lineages ◽  
Stable Classification

The Gracilariales is a red macroalgal order and the main global source of the economically important agar, a marine phycocolloid. Independent comparative morphological and molecular phylogenetic studies over the last 20 years have revealed the existence of seven major clades recognizable as distinct genera. Of these major clades only four free-living genera have been widely accepted taxonomically: Curdiea, Melanthalia, Gracilariopsis, and Gracilaria. Three other clades comprise the reinstatement of the genus Hydropuntia and the proposal of two new genera, Agarophyton and Crassa, described herein. Based on new rbcL DNA sequences, and along with a reassessment of published comparative morphological and molecular phylogenetic studies, we argue that the latter three genera represent distinct evolutionary lineages in the Gracilariaceae, and propose a new classification for the order Gracilariales. Our new proposal incorporates the most current understanding of the evolutionary history of the order, establishes a natural and stable classification system, and provides the basis for the recognization of intra-family ranks. Our classification scheme reconciles all molecular phylogenetic studies published to date.

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