scholarly journals A new symbiotic lineage related to Neisseria and Snodgrassella arises from the dynamic and diverse microbiomes in sucking lice

2019 ◽  
Author(s):  
Jana Říhová ◽  
Giampiero Batani ◽  
Sonia M. Rodríguez-Ruano ◽  
Jana Martinů ◽  
Eva Nováková ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Symbiotic Bacteria ◽  
Lower Abundance ◽  
Independent Origin ◽  
Obligate Symbiont ◽  
Related Bacterium ◽  
Sucking Lice ◽  
History Of ◽  
Symbiont Acquisition

AbstractPhylogenetic diversity of symbiotic bacteria in sucking lice suggests that lice have experienced a complex history of symbiont acquisition, loss, and replacement during their evolution. By combining metagenomics and amplicon screening across several populations of two louse genera (Polyplax and Hoplopleura) we describe a novel louse symbiont lineage related to Neisseria and Snodgrassella, and show its’ independent origin within dynamic lice microbiomes. While the genomes of these symbionts are highly similar in both lice genera, their respective distributions and status within lice microbiomes indicate that they have different functions and history. In Hoplopleura acanthopus, the Neisseria-related bacterium is a dominant obligate symbiont universally present across several host’s populations, and seems to be replacing a presumably older and more degenerated obligate symbiont. In contrast, the Polyplax microbiomes are dominated by the obligate symbiont Legionella polyplacis, with the Neisseria-related bacterium co-occurring only in some samples and with much lower abundance.

scholarly journals Highly Divergent Genes for Methanopterin-Linked C1 Transfer Reactions in Lake Washington, Assessed via Metagenomic Analysis and mRNA Detection

2005 ◽  
Vol 71 (12) ◽  
pp. 8846-8854 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
Sarah Bowerman ◽  
Olivier Nercessian ◽  
Mary E. Lidstrom ◽  
Ludmila Chistoserdova
Keyword(s):  
Phylogenetic Diversity ◽  
Potential Role ◽  
Phylogenetic Analyses ◽  
Transfer Reactions ◽  
Microb Ecol ◽  
Mrna Detection ◽  
Lake Washington ◽  
History Of ◽  
Metagenomic Approach ◽  
Specific Mrna

ABSTRACT The origins and the evolutionary history of tetrahydromethanopterin-linked C1 transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. In previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated Proteobacteria, Planctomycetes, or Archaea (M. G. Kalyuzhnaya, M. E. Lidstrom, and L. Chistoserdova, Microb. Ecol. 48:463-472, 2004; M. G. Kalyuzhnaya, O. Nercessian, M. E. Lidstrom, and L. Chistoserdova, Environ. Microbiol. 7:1269-1274, 2005). Here we used a metagenomic approach to demonstrate that these divergent genes are present with high abundance in the microbial community inhabiting Lake Washington sediment. We also gained preliminary insights into the genomic composition of the organisms possessing these genes by sequencing genomic fragments from three uncultured microbes possessing the genes of interest. Phylogenetic analyses suggested that, although distantly related to each other, these organisms deeply diverge from known Bacteria and Archaea, with more relation to the former, suggesting their affiliation with a new bacterial phylum. We also demonstrate, via specific mRNA detection, that these divergent genes are expressed in the environment, pointing toward their potential role in local carbon cycling.

scholarly journals Diversity in obscurity: fossil flowers and the early history of angiosperms

2010 ◽  
Vol 365 (1539) ◽  
pp. 369-382 ◽  
Author(s):  
Else Marie Friis ◽  
Kaj Raunsgaard Pedersen ◽  
Peter R. Crane
Keyword(s):  
Early Cretaceous ◽  
Phylogenetic Diversity ◽  
Rapid Development ◽  
Distinct Pattern ◽  
Fossil Plants ◽  
Early Angiosperm ◽  
Early Diversification ◽  
History Of ◽  
Fossil Flowers ◽  
Ecological Dominance

In the second half of the nineteenth century, pioneering discoveries of rich assemblages of fossil plants from the Cretaceous resulted in considerable interest in the first appearance of angiosperms in the geological record. Darwin's famous comment, which labelled the ‘rapid development’ of angiosperms an ‘abominable mystery’, dates from this time. Darwin and his contemporaries were puzzled by the relatively late, seemingly sudden and geographically widespread appearance of modern-looking angiosperms in Late Cretaceous floras. Today, the early diversification of angiosperms seems much less ‘rapid’. Angiosperms were clearly present in the Early Cretaceous, 20–30 Myr before they attained the level of ecological dominance reflected in some mid-Cretaceous floras, and angiosperm leaves and pollen show a distinct pattern of steadily increasing diversity and complexity through this interval. Early angiosperm fossil flowers show a similar orderly diversification and also provide detailed insights into the changing reproductive biology and phylogenetic diversity of angiosperms from the Early Cretaceous. In addition, newly discovered fossil flowers indicate considerable, previously unrecognized, cryptic diversity among the earliest angiosperms known from the fossil record. Lineages that today have an herbaceous or shrubby habit were well represented. Monocotyledons, which have previously been difficult to recognize among assemblages of early fossil angiosperms, were also diverse and prominent in many Early Cretaceous ecosystems.

scholarly journals Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

2011 ◽  
Vol 366 (1576) ◽  
pp. 2414-2425 ◽  
Author(s):  
T. Jonathan Davies ◽  
Lauren B. Buckley
Keyword(s):  
Species Richness ◽  
Phylogenetic Diversity ◽  
Diversity Indices ◽  
Environmental Predictors ◽  
Terrestrial Mammals ◽  
Extinction Rates ◽  
Biogeographic History ◽  
Shared Ancestry ◽  
History Of ◽  
Dispersal Events

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.

scholarly journals How global extinctions impact regional biodiversity in mammals

2011 ◽  
Vol 8 (2) ◽  
pp. 222-225 ◽  
Author(s):  
Shan Huang ◽  
T. Jonathan Davies ◽  
John L. Gittleman
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Spatial Scales ◽  
Spatial Location ◽  
Ecosystem Processes ◽  
Biodiversity Hotspots ◽  
Species Assemblage ◽  
Species Extinction ◽  
History Of ◽  
And Function

Phylogenetic diversity (PD) represents the evolutionary history of a species assemblage and is a valuable measure of biodiversity because it captures not only species richness but potentially also genetic and functional diversity. Preserving PD could be critical for maintaining the functional integrity of the world's ecosystems, and species extinction will have a large impact on ecosystems in areas where the ecosystem cost per species extinction is high. Here, we show that impacts from global extinctions are linked to spatial location. Using a phylogeny of all mammals, we compare regional losses of PD against a model of random extinction. At regional scales, losses differ dramatically: several biodiversity hotspots in southern Asia and Amazonia will lose an unexpectedly large proportion of PD. Global analyses may therefore underestimate the impacts of extinction on ecosystem processes and function because they occur at finer spatial scales within the context of natural biogeography.

scholarly journals Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders

2007 ◽  
Vol 274 (1612) ◽  
pp. 919-928 ◽  
Author(s):  
John J Wiens ◽  
Gabriela Parra-Olea ◽  
Mario García-París ◽  
David B Wake
Keyword(s):  
Species Richness ◽  
Dna Sequences ◽  
Phylogenetic Diversity ◽  
Strong Relationship ◽  
Biodiversity Patterns ◽  
Number Of Species ◽  
Elevational Distribution ◽  
History Of ◽  
Elevational Variation

Elevational variation in species richness is ubiquitous and important for conservation, but remains poorly explained. Numerous studies have documented higher species richness at mid-elevations, but none have addressed the underlying evolutionary and biogeographic processes that ultimately explain this pattern (i.e. speciation, extinction and dispersal). Here, we address the evolutionary causes of the mid-elevational diversity hump in the most species-rich clade of salamanders, the tropical bolitoglossine plethodontids. We present a new phylogeny for the group based on DNA sequences from all 13 genera and 137 species. Using this phylogeny, we find no relationship between rates of diversification of clades and their elevational distribution, and no evidence for a rapid ‘species pump’ in tropical montane regions. Instead, we find a strong relationship between the number of species in each elevational zone and the estimated time when each elevational band was first colonized. Mid-elevation habitats were colonized early in the phylogenetic history of bolitoglossines, and given similar rates of diversification across elevations, more species have accumulated in the elevational zones that were inhabited the longest. This pattern may be widespread and suggests that mid-elevation habitats may not only harbour more species, but may also contain more phylogenetic diversity than other habitats within a region.

scholarly journals RecPD: A Recombination-Aware Measure of Phylogenetic Diversity

2021 ◽  
Author(s):  
Cedoljub Bundalovic-Torma ◽  
Darrell Desveaux ◽  
David S Guttman
Keyword(s):  
Pseudomonas Syringae ◽  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
Evolutionary Dynamics ◽  
Gene Families ◽  
Ancestral State ◽  
History Of ◽  
Preliminary Study ◽  
Potential Impact ◽  
Study Type

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) underlying traits or outcomes of interest is assessing their diversity and distribution. Accurate assessments of these patterns are essential for linking features to traits or outcomes and understanding their functional impact. Consequently, it is of crucial importance that the metrics employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard metrics used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity metric for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive a number of related metrics from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably identifies evolutionary histories under diverse recombination and loss scenarios. We then apply RecPD in a real-world scenario in a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and demonstrate that prevalence is an inadequate metric that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.

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 Taxonomy of Bacteria Nodulating Legumes

2009 ◽  
Vol 2 ◽  
pp. MBI.S3137 ◽  
Author(s):  
Raúl Rivas ◽  
Paula García-Fraile ◽  
Encarna Velázquez
Keyword(s):  
Nitrogen Fixation ◽  
Phylogenetic Diversity ◽  
Nitrogen Fixing ◽  
Rhizobial Species ◽  
History Of

Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.

scholarly journals Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids’ di-symbiotic systems

2019 ◽  
Author(s):  
Alejandro Manzano-Marín ◽  
Armelle Coeur d’acier ◽  
Anne-Laure Clamens ◽  
Céline Orvain ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Essential Amino Acids ◽  
B Vitamins ◽  
Restricted Diet ◽  
Symbiotic System ◽  
Biosynthetic Genes ◽  
Obligate Symbiont ◽  
Related Bacterium ◽  
B Vitamin

ABSTRACTMany insects with a nutrient-restricted diet depend on obligate mutualistic bacteria for the provisioning of essential nutrients lacking from their food source, namely essential amino acids and B vitamins. Most aphids (Hemiptera: Aphididae), whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera for the supply of the aforementioned compounds. However, in some aphid lineages Buchnera have lost the capability of producing these nutrients and thus the symbiotic consortium has accommodated an extra bacterial partner to supplement Buchnera’s deficiencies. In this work, we explore the di-symbiotic nutritional endosymbiosis of a group of Cinara aphids which has been found to harbour both Buchnera and an Erwinia-related symbiont. Using fluorescence in situ hybridisation, we have located this symbiont to the bacteriome where it inhabits its own bacteriocytes. Through whole-genome sequencing of the endosymbionts of 9 species of Erwinia-associated Cinara aphids, we have found that Ewrinia genomes are highly syntenic and all show significant genome reduction. Additionally, Erwinia symbionts display phylogenetic congruency with Buchnera, suggesting long-term co-divergence. Most significantly, we found that not only is Erwinia capable of complementing Buchnera’s auxotrophies, but that the genes involved in the biosynthesis of two B vitamins have actually been horizontally acquired from a Sodalis-related bacterium. Finally, this B-vitamin biosynthetic genes have been further transferred to a new Hamiltonella co-obligate symbiont in a specific Cinara lineage, thus displaying a tri-symbiotic system. These results highlight the important role horizontal gene transfer plays in the establishment of new obligate nutritional symbionts.

Phylogenetic diversity, types of endemism and the evolutionary history of New World bats

Ecography ◽  
2018 ◽  
Vol 41 (12) ◽  
pp. 1955-1966 ◽  
Author(s):  
Camilo López-Aguirre ◽  
Suzanne J. Hand ◽  
Shawn W. Laffan ◽  
Michael Archer
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Diversity ◽  
New World ◽  
History Of
Sign in / Sign up

Export Citation Format

Share Document