scholarly journals Evolutionary origins and diversification of proteobacterial mutualists

2014 ◽  
Vol 281 (1775) ◽  
pp. 20132146 ◽  
Author(s):  
Joel L. Sachs ◽  
Ryan G. Skophammer ◽  
Nidhanjali Bansal ◽  
Jason E. Stajich
Keyword(s):  
Diversification Rate ◽  
Ancestral State ◽  
Free Living ◽  
Evolutionary Diversification ◽  
Evolutionary Conservatism ◽  
Evolutionary Origins ◽  
Eukaryotic Species ◽  
Beneficial Traits ◽  
Bacterial Lineages

Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34–39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.

scholarly journals Ciliates as Symbionts

2021 ◽  
Author(s):  
Rosaura Mayén-Estrada ◽  
Roberto Júnio Pedroso Dias ◽  
Mireya Ramírez-Ballesteros ◽  
Mariana Rossi ◽  
Margarita Reyes-Santos ◽  
...  
Keyword(s):  
Molecular Data ◽  
Life Cycles ◽  
Diversification Rate ◽  
Ancestral State ◽  
Free Living ◽  
New Approaches ◽  
Integrative Study

Although many ciliates are free-living, more than 140 families of ciliates (Alveolata, Ciliophora) include symbiotic species of animals. Symbiosis, defined as an interaction between two species, is analyzed in this chapter to show a wide diversity of symbiotic systems in ciliates (epibiosis, commensalism, mutualism, and parasitism), providing some data about ciliate strategies showing their success as symbionts. Some species are free-living as well symbionts, facultative symbionts, and obligate symbionts. Analysis of reconstructions of ancestral state evidence that the parasitism arose numerous times and independently among the lineages of ciliates. At least three evolutionary routes can be traced: (1) transition from free-living to mutualism and parasitism, (2) transition from free-living to parasitism, and (3) regression from parasitism to free-living. The evolution of the symbiosis in ciliates demonstrates a higher diversification rate concerning free-living ciliates. The analysis of the evolution of the life cycles complexity, exploring molecular data of the phases of the ciliate cycle in their hosts is also essential. We propose new approaches for an integrative study of symbiotic ciliates.

scholarly journals Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Elisabeth Hehenberger ◽  
Javier del Campo ◽  
Noriko Okamoto ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Phylogenetic Position ◽  
Rrna Gene ◽  
Ancestral State ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Free Living ◽  
Surface Ocean ◽  
Lsu Rrna Gene ◽  
Important Host ◽  
Copepod Eggs

ABSTRACTSpores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

scholarly journals Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria

mBio ◽  
2013 ◽  
Vol 4 (4) ◽  
Author(s):  
Haiwei Luo ◽  
Miklós Csűros ◽  
Austin L. Hughes ◽  
Mary Ann Moran
Keyword(s):  
Life History ◽  
Life Histories ◽  
Scale Up ◽  
Carbon Mineralization ◽  
Life History Strategies ◽  
Free Living ◽  
Heterotrophic Bacterioplankton ◽  
Evolutionary Origins ◽  
Eukaryotic Phytoplankton ◽  
Microbial Groups

ABSTRACT Marine bacteria in the Roseobacter and SAR11 lineages successfully exploit the ocean habitat, together accounting for ~40% of bacteria in surface waters, yet have divergent life histories that exemplify patch-adapted versus free-living ecological roles. Here, we use a phylogenetic birth-and-death model to understand how genome content supporting different life history strategies evolved in these related alphaproteobacterial taxa, showing that the streamlined genomes of free-living SAR11 were gradually downsized from a common ancestral genome only slightly larger than the extant members (~2,000 genes), while the larger and variably sized genomes of roseobacters evolved along dynamic pathways from a sizeable common ancestor (~8,000 genes). Genome changes in the SAR11 lineage occurred gradually over ~800 million years, whereas Roseobacter genomes underwent more substantial modifications, including major periods of expansion, over ~260 million years. The timing of the first Roseobacter genome expansion was coincident with the predicted radiation of modern marine eukaryotic phytoplankton of sufficient size to create nutrient-enriched microzones and is consistent with present-day ecological associations between these microbial groups. We suggest that diversification of red-lineage phytoplankton is an important driver of divergent life history strategies among the heterotrophic bacterioplankton taxa that dominate the present-day ocean. IMPORTANCE One-half of global primary production occurs in the oceans, and more than half of this is processed by heterotrophic bacterioplankton through the marine microbial food web. The diversity of life history strategies that characterize different bacterioplankton taxa is an important subject, since the locations and mechanisms whereby bacteria interact with seawater organic matter has effects on microbial growth rates, metabolic pathways, and growth efficiencies, and these in turn affect rates of carbon mineralization to the atmosphere and sequestration into the deep sea. Understanding the evolutionary origins of the ecological strategies that underlie biochemical interactions of bacteria with the ocean system, and which scale up to affect globally important biogeochemical processes, will improve understanding of how microbial diversity is maintained and enable useful predictions about microbial response in the future ocean.

scholarly journals Evolutionary origins of metabolic compartmentalization in eukaryotes

2010 ◽  
Vol 365 (1541) ◽  
pp. 847-855 ◽  
Author(s):  
William Martin
Keyword(s):  
Protein Targeting ◽  
Protein Product ◽  
Eukaryotic Cells ◽  
Evolutionary Time ◽  
Free Living ◽  
Evolutionary Origins ◽  
Dual Targeting ◽  
Targeting Signals ◽  
A Minor ◽  
Host Genes

Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary ‘homing device’ that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a ‘minor mistargeting’ mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.

scholarly journals Parallel evolution of mound-building and grass-feeding in Australian nasute termites

2017 ◽  
Vol 13 (2) ◽  
pp. 20160665 ◽  
Author(s):  
Daej A. Arab ◽  
Anna Namyatova ◽  
Theodore A. Evans ◽  
Stephen L. Cameron ◽  
David K. Yeates ◽  
...  
Keyword(s):  
Parallel Evolution ◽  
Molecular Dating ◽  
Ancestral State ◽  
Termite Mounds ◽  
Evolutionary Origins ◽  
Functional Aspects ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Nesting Habits ◽  
Ideal Group

Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6–8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes.

scholarly journals The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Min Zhang ◽  
Chengqi Wang ◽  
Jenna Oberstaller ◽  
Phaedra Thomas ◽  
Thomas D. Otto ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Heat Shock ◽  
Large Scale ◽  
Artemisinin Resistance ◽  
Free Living ◽  
Artemisinin Derivatives ◽  
Evolutionary Origins ◽  
Algal Endosymbiont ◽  
Phenotype Screen ◽  
Artemisinin Combination Therapies

AbstractThe emergence and spread of Plasmodium falciparum parasites resistant to front-line antimalarial artemisinin-combination therapies (ACT) threatens to erase the considerable gains against the disease of the last decade. Here, we develop a large-scale phenotypic screening pipeline and use it to carry out a large-scale forward-genetic phenotype screen in P. falciparum to identify genes allowing parasites to survive febrile temperatures. Screening identifies more than 200 P. falciparum mutants with differential responses to increased temperature. These mutants are more likely to be sensitive to artemisinin derivatives as well as to heightened oxidative stress. Major processes critical for P. falciparum tolerance to febrile temperatures and artemisinin include highly essential, conserved pathways associated with protein-folding, heat shock and proteasome-mediated degradation, and unexpectedly, isoprenoid biosynthesis, which originated from the ancestral genome of the parasite’s algal endosymbiont-derived plastid, the apicoplast. Apicoplast-targeted genes in general are upregulated in response to heat shock, as are other Plasmodium genes with orthologs in plant and algal genomes. Plasmodium falciparum parasites appear to exploit their innate febrile-response mechanisms to mediate resistance to artemisinin. Both responses depend on endosymbiont-derived genes in the parasite’s genome, suggesting a link to the evolutionary origins of Plasmodium parasites in free-living ancestors.

scholarly journals Evolutionary position of breviate amoebae and the primary eukaryote divergence

2008 ◽  
Vol 276 (1657) ◽  
pp. 597-604 ◽  
Author(s):  
Marianne A. Minge ◽  
Jeffrey D Silberman ◽  
Russell J.S Orr ◽  
Thomas Cavalier-Smith ◽  
Kamran Shalchian-Tabrizi ◽  
...  
Keyword(s):  
Sequence Data ◽  
Protein Sequences ◽  
Mitochondrial Genes ◽  
The Other ◽  
Ancestral State ◽  
Free Living ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Eukaryote Evolution ◽  
Key Questions

Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema , which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically ‘nomadic’ species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.

scholarly journals Comparison of NF-κB from the protists Capsaspora owczarzaki and Acanthoeca spectabilis reveals extensive evolutionary diversification of this transcription factor

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Leah M. Williams ◽  
Sainetra Sridhar ◽  
Jason Samaroo ◽  
Jada Peart ◽  
Ebubechi K. Adindu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Functional Characterization ◽  
Evolutionary Diversification ◽  
Evolutionary Origins ◽  
Dna Binding Specificity ◽  
Higher Taxa ◽  
Rel Homology Domain

AbstractWe provide a functional characterization of transcription factor NF-κB in protists and provide information about the evolution and diversification of this biologically important protein. We characterized NF-κB in two protists using phylogenetic, cellular, and biochemical techniques. NF-κB of the holozoan Capsaspora owczarzaki (Co) has an N-terminal DNA-binding domain and a C-terminal Ankyrin repeat (ANK) domain, and its DNA-binding specificity is more similar to metazoan NF-κB proteins than to Rel proteins. Removal of the ANK domain allows Co-NF-κB to enter the nucleus, bind DNA, and activate transcription. However, C-terminal processing of Co-NF-κB is not induced by IκB kinases in human cells. Overexpressed Co-NF-κB localizes to the cytoplasm in Co cells. Co-NF-κB mRNA and DNA-binding levels differ across three Capsaspora life stages. RNA-sequencing and GO analyses identify possible gene targets of Co-NF-κB. Three NF-κB-like proteins from the choanoflagellate Acanthoeca spectabilis (As) contain conserved Rel Homology domain sequences, but lack C-terminal ANK repeats. All three As-NF-κB proteins constitutively enter the nucleus of cells, but differ in their DNA-binding abilities, transcriptional activation activities, and dimerization properties. These results provide a basis for understanding the evolutionary origins of this key transcription factor and could have implications for the origins of regulated immunity in higher taxa.

scholarly journals Substantial rearrangements, single nucleotide frameshift deletion and low diversity in mitogenome of Wolbachia-infected strepsipteran endoparasitoid in comparison to its tephritid hosts

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Sharon Towett-Kirui ◽  
Jennifer L. Morrow ◽  
Markus Riegler
Keyword(s):  
Fruit Fly ◽  
Life Cycles ◽  
Trna Genes ◽  
Ancestral State ◽  
Free Living ◽  
Single Nucleotide ◽  
Translational Frameshifting ◽  
Frameshift Deletion ◽  
Low Diversity ◽  
Bacterial Endosymbionts

AbstractInsect mitogenome organisation is highly conserved, yet, some insects, especially with parasitic life cycles, have rearranged mitogenomes. Furthermore, intraspecific mitochondrial diversity can be reduced by fitness-affecting bacterial endosymbionts like Wolbachia due to their maternal coinheritance with mitochondria. We have sequenced mitogenomes of the Wolbachia-infected endoparasitoid Dipterophagus daci (Strepsiptera: Halictophagidae) and four of its 22 known tephritid fruit fly host species using total genomic extracts of parasitised flies collected across > 700 km in Australia. This halictophagid mitogenome revealed extensive rearrangements relative to the four fly mitogenomes which exhibited the ancestral insect mitogenome pattern. Compared to the only four available other strepsipteran mitogenomes, the D. daci mitogenome had additional transpositions of one rRNA and two tRNA genes, and a single nucleotide frameshift deletion in nad5 requiring translational frameshifting or, alternatively, resulting in a large protein truncation. Dipterophagus daci displays an almost completely endoparasitic life cycle when compared to Strepsiptera that have maintained the ancestral state of free-living adults. Our results support the hypothesis that the transition to extreme endoparasitism evolved together with increased levels of mitogenome changes. Furthermore, intraspecific mitogenome diversity was substantially smaller in D. daci than the parasitised flies suggesting Wolbachia reduced mitochondrial diversity because of a role in D. daci fitness.

scholarly journals Floral evolution and pollinator diversification in Hedychium J.Koenig (Zingiberaceae): one of Mr. Darwin’s tropical fantasies

2021 ◽  
Author(s):  
Ajith Ashokan ◽  
Piyakaset Suksathan ◽  
Jana Leong-Škorničková ◽  
Mark Newman ◽  
W. John Kress ◽  
...  
Keyword(s):  
Diversification Rate ◽  
Floral Traits ◽  
Tube Length ◽  
Pollination Syndromes ◽  
Bird Pollination ◽  
Evolutionary Diversification ◽  
Moth Pollination ◽  
Floral Color ◽  
Inflorescence Structure ◽  
Pollination Systems

ABSTRACTPREMISEHedychium J.Koenig (ginger lilies: Zingiberaceae) is endemic to the Indo-Malayan Realm (IMR) and is known for its fragrant flowers. Two different pollination syndromes characterize the genus: diurnal or bird pollination and nocturnal or moth pollination systems. To date, no attempt has been undertaken to understand the evolution of floral traits in this genus.METHODSWe estimated ancestral character-states, phylogenetic signals, and character correlations for thirteen discrete and eight continuous floral traits representing 75% species diversity of Hedychium. Diversification rate estimation analyses were also employed to understand trait-dependent diversification in the genus.RESULTSInflorescence structure, cincinnus capacity, and curvature of floral tubes revealed strong phylogenetic dependence, whereas number of open flowers per inflorescence per day, color of the labellum, and exertion of the stigma characterized higher ecological effects. Diversification rate estimations suggested that the labellum width, floral tube length, and labellum color played a major role in the evolutionary diversification of Hedychium.CONCLUSIONSWe identified bract type and cincinnus capacity as synapomorphies for Hedychium, while the island-specific clade III was characterized by slender cylindrical inflorescence, coiling of floral tubes, and longer bract to calyx ratio. The circum-Himalayan clade IV is the most speciose, derived, and with most variable floral traits. Although floral color and size lacked any association with pollinator-specific traits (moth and bird pollination), pale colored flowers were most common in the early diverging clades (clade I, II-el., and II-de.), indicating their ancestral nature, when compared to brightly colored flowers.

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