Phylogenomics within the Anthonotha clade (Detarioideae, Leguminosae) reveals a high diversity in floral trait shifts and a general trend towards organ number reduction

AbstractDetarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. The genus Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity.

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Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽

10.3390/v13040545 ◽

2021 ◽

Vol 13 (4) ◽

pp. 545

Author(s):

Gédéon Prince Manouana ◽

Paul Alvyn Nguema-Moure ◽

Mirabeau Mbong Ngwese ◽

C.-Thomas Bock ◽

Peter G. Kremsner ◽

...

Keyword(s):

Genetic Diversity ◽

Preventive Measures ◽

Phylogenetic Analyses ◽

Enteric Viruses ◽

Study Cohort ◽

Viral Agent ◽

A Genome ◽

Stool Samples ◽

Pcr Techniques ◽

High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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Loose Ends in the Cortinarius Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American Nothofagaceae

Life ◽

10.3390/life11050420 ◽

2021 ◽

Vol 11 (5) ◽

pp. 420

Author(s):

María Eugenia Salgado Salomón ◽

Carolina Barroetaveña ◽

Tuula Niskanen ◽

Kare Liimatainen ◽

Matthew E. Smith ◽

...

Keyword(s):

New Species ◽

Current Knowledge ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Global Scale ◽

South American ◽

Edible Fungi ◽

Rdna Its ◽

Morphological And Molecular Data ◽

High Diversity

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American Cortinarius (Pers.) Gray. Cortinarius is among the most widely distributed and species-rich basidiomycete genera occurring with South American Nothofagaceae and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, Cortinarius species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected Cortinarius belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling Cortinarius specimens in Patagonian Nothofagaceae forests and comparing them to reference collections (including holotypes), we propose five new species of Cortinarius in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and RPB1 sequences failed to place these new species into known Cortinarius sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American Nothofagaceae forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American Cortinarius diversity needs to be discovered and described in order to understand the evolutionary history of Cortinarius on a global scale.

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Morph-specific correlations between floral traits in a distylous Ophiorrhiza napoensis (Rubiaceae) population in southern China

Journal of Tropical Ecology ◽

10.1017/s0266467401001535 ◽

2001 ◽

Vol 17 (5) ◽

pp. 719-728 ◽

Cited By ~ 17

Author(s):

HIROSHI KUDOH ◽

TAKASHI SUGAWARA ◽

SUGONG WU ◽

JIN MURATA

Keyword(s):

Southern China ◽

Principal Component ◽

Corolla Tube ◽

Floral Traits ◽

Evergreen Forest ◽

Tube Length ◽

Multiple Traits ◽

Floral Trait ◽

Subtropical Evergreen Forest ◽

Positive Correlations

Floral trait correlations were compared between the two flower morphs of a distylous Ophiorrhiza napoensis population in a subtropical evergreen forest at the Defu Natural Animal Preserve, Guangxi, China. Common principal component analyses indicated that overall patterns in correlations among floral traits were morph specific in the study population. Strong positive correlations (r > 0.9) between anther height and corolla-tube length were found in both morphs. Stigma height correlated positively with corolla-tube length in the long-styled morph (r = 0.843), but not in the short-styled morph (r = −0.018). Flower-morph-specific correlation suggests that natural selection by pollinators has moulded trait covariance among floral traits. Because morph-specific correlations are expressed as the patterns of within-morph variation among multiple traits, putative genes responsible for the stigma-corolla tube correlation should not link to the supergene for sex-organ reciprocity between the morphs, but their expression is limited in the long-styled morph.

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Micromorphological, anatomical and molecular study of Hedera species (Araliaceae) in Iran

Acta Biologica Szegediensis ◽

10.14232/abs.2019.2.91-101 ◽

2020 ◽

Vol 63 (2) ◽

pp. 91-101

Author(s):

Elham Amini ◽

Fatemeh Nasrollahi ◽

Ali Sattarian ◽

Mahboobeh Haji Moradkhani ◽

Sohrab Boozarpour ◽

...

Keyword(s):

North Africa ◽

Phylogenetic Analyses ◽

Molecular Study ◽

Molecular Characteristics ◽

Nrdna Its ◽

Anticlinal Wall ◽

Data Set ◽

Phylogenetic Methods ◽

Extant Species ◽

Qualitative Characters

Hedera, with 12 extant species, is a genus of evergreen climbers native to Europe, north Africa, and south Asia. In this study, the micromorphological, anatomical structure and molecular evidences of 11 populations from two species of Hedera (H. helix and H. pastuchovii) have been considered to evaluate the relationships in Hedera. In total, seven quantitative and qualitative characters of pollen were selected and measured. Based on this study, the anticlinal wall and surface sculpturing of seed support for separation of two species of Hedera. Micromorphology of epidermis illustrated two types of epidermal cells: puzzle-shaped and polygonal cells. Using nuclear (nrDNA ITS) marker, we reconstructed phylogenetic relationships within two species of Hedera. This data set was analyzed by phylogenetic methods including Bayesian inference, maximum likelihood, and maximum parsimony. In phylogenetic analyses, all members of two species formed a well-supported clade (PP = 1; ML/BS = 100/100) and divided into two major clades (A and B). Neighbor Net diagram demonstrated separation of the studied populations. The results showed that these taxa differ in taxonomically important micromorphological, anatomical and molecular characteristics and these data provide reliable evidence for separation of these two species.

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Floral trait variation and links to climate in the mixed-mating annual Clarkia pulchella

Botany ◽

10.1139/cjb-2017-0234 ◽

2018 ◽

Vol 96 (7) ◽

pp. 425-435 ◽

Cited By ~ 2

Author(s):

Devin E. Gamble ◽

Megan Bontrager ◽

Amy L. Angert

Keyword(s):

Mating System ◽

Common Garden ◽

Moisture Stress ◽

Floral Traits ◽

Mixed Mating ◽

Floral Trait ◽

Local Climate ◽

Self Fertilization ◽

Clarkia Pulchella ◽

Watering Treatment

The benefits of self-fertilization can vary across environments, leading to selection for different reproductive strategies and influencing the evolution of floral traits. Although stressful conditions have been suggested to favour self-pollination, the role of climate as a driver of mating-system variation is generally not well understood. Here, we investigate the contributions of local climate to intraspecific differences in mating-system traits in Clarkia pulchella Pursh in a common-garden growth chamber experiment. We also tested for plastic responses to soil moisture with watering treatments. Herkogamy (anther–stigma spacing) correlated positively with dichogamy (timing of anther–stigma receptivity) and date of first flower, and northern populations had smaller petals and flowered earlier in response to experimental drought. Watering treatment alone had little effect on traits, and dichogamy unexpectedly decreased with annual precipitation. Populations also differed in phenological response to watering treatment, based on precipitation and winter temperature of their origin, indicating that populations from cool and dry sites have greater plasticity under different levels of moisture stress. While some variation in floral traits is attributable to climate, further investigation into variation in pollinator communities and the indirect effects of climate on mating system can improve our understanding of the evolution of plant mating.

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Novel Cell-Virus-Virophage Tripartite Infection Systems Discovered in the Freshwater Lake Dishui Lake in Shanghai, China

Journal of Virology ◽

10.1128/jvi.00149-20 ◽

2020 ◽

Vol 94 (11) ◽

Cited By ~ 1

Author(s):

Shengzhong Xu ◽

Liang Zhou ◽

Xiaosha Liang ◽

Yifan Zhou ◽

Hao Chen ◽

...

Keyword(s):

Green Algae ◽

Green Alga ◽

Phylogenetic Analyses ◽

Freshwater Lake ◽

Metagenomic Data ◽

Data Sets ◽

Data Set ◽

Dna Viruses ◽

Oligonucleotide Frequency ◽

Dsdna Viruses

ABSTRACT Virophages are small parasitic double-stranded DNA (dsDNA) viruses of giant dsDNA viruses infecting unicellular eukaryotes. Except for a few isolated virophages characterized by parasitization mechanisms, features of virophages discovered in metagenomic data sets remain largely unknown. Here, the complete genomes of seven virophages (26.6 to 31.5 kbp) and four large DNA viruses (190.4 to 392.5 kbp) that coexist in the freshwater lake Dishui Lake, Shanghai, China, have been identified based on environmental metagenomic investigation. Both genomic and phylogenetic analyses indicate that Dishui Lake virophages (DSLVs) are closely related to each other and to other lake virophages, and Dishui Lake large DNA viruses are affiliated with the micro-green alga-infecting Prasinovirus of the Phycodnaviridae (named Dishui Lake phycodnaviruses [DSLPVs]) and protist (protozoan and alga)-infecting Mimiviridae (named Dishui Lake large alga virus [DSLLAV]). The DSLVs possess more genes with closer homology to that of large alga viruses than to that of giant protozoan viruses. Furthermore, the DSLVs are strongly associated with large green alga viruses, including DSLPV4 and DSLLAV1, based on codon usage as well as oligonucleotide frequency and correlation analyses. Surprisingly, a nonhomologous CRISPR-Cas like system is found in DSLLAV1, which appears to protect DSLLAV1 from the parasitization of DSLV5 and DSLV8. These results suggest that novel cell-virus-virophage (CVv) tripartite infection systems of green algae, large green alga virus (Phycodnaviridae- and Mimiviridae-related), and virophage exist in Dishui Lake, which will contribute to further deep investigations of the evolutionary interaction of virophages and large alga viruses as well as of the essential roles that the CVv plays in the ecology of algae. IMPORTANCE Virophages are small parasitizing viruses of large/giant viruses. To our knowledge, the few isolated virophages all parasitize giant protozoan viruses (Mimiviridae) for propagation and form a tripartite infection system with hosts, here named the cell-virus-virophage (CVv) system. However, the CVv system remains largely unknown in environmental metagenomic data sets. In this study, we systematically investigated the metagenomic data set from the freshwater lake Dishui Lake, Shanghai, China. Consequently, four novel large alga viruses and seven virophages were discovered to coexist in Dishui Lake. Surprisingly, a novel CVv tripartite infection system comprising green algae, large green alga viruses (Phycodnaviridae- and Mimiviridae-related), and virophages was identified based on genetic link, genomic signature, and CRISPR system analyses. Meanwhile, a nonhomologous CRISPR-like system was found in Dishui Lake large alga viruses, which appears to protect the virus host from the infection of Dishui Lake virophages (DSLVs). These findings are critical to give insight into the potential significance of CVv in global evolution and ecology.

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Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil

Viruses ◽

10.3390/v12010048 ◽

2019 ◽

Vol 12 (1) ◽

pp. 48 ◽

Cited By ~ 3

Author(s):

Anne-Lie Blomström ◽

Hermes R. Luz ◽

Pontus Öhlund ◽

Matthew Lukenge ◽

Paulo Eduardo Brandão ◽

...

Keyword(s):

Rna Viruses ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Blood Feeding ◽

Dominant Group ◽

Data Set ◽

Adult Feeding ◽

Viral Sequences ◽

Negative Sense ◽

Bat Guano

In this study, we describe the viral composition of adult Antricola delacruzi ticks collected in a hot bat cave in the state of Rondônia, Western Amazonia, Brazil. A. delacruzi ticks, are special, compared to many other ticks, in that they feed on both bats (larval blood feeding) and bat guano (nymphal and adult feeding) instead of feeding exclusively on vertebrate hosts (blood feeding). Considering this unique life-cycle it is potentially possible that these ticks can pick up/be infected by viruses not only present in the blood of viremic bats but also by virus shed through the bat guano. The viral metagenomic investigation of adult ticks showed that single-stranded negative-sense RNA viruses were the dominant group of viruses identified in the investigated ticks. Out of these, members of the Nairoviridae family were in clear majority constituting 88% of all viral reads in the data set. Genetic and phylogenetic analyses indicate the presence of several different orthonairoviruses in the investigated ticks with only distant relationship to previously described ones. In addition, identification of viral sequences belonging to Orthomyxoviridae, Iflaviridae, Dicistroviridae, Polycipiviridae, Reoviridae and different unclassified RNA viruses showed the presence of viruses with low sequence similarity to previously described viruses.

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The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

Insect Systematics & Evolution ◽

10.1163/1876312x-45032119 ◽

2015 ◽

Vol 46 (3) ◽

pp. 269-290 ◽

Cited By ~ 6

Author(s):

Ian J. Kitching ◽

C. Lorna Culverwell ◽

Ralph E. Harbach

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Data Set ◽

Generic Status ◽

Strong Signal ◽

Phylogenetic Studies ◽

Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

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Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

Applied and Environmental Microbiology ◽

10.1128/aem.00410-08 ◽

2008 ◽

Vol 74 (17) ◽

pp. 5422-5428 ◽

Cited By ~ 147

Author(s):

Mostafa S. Elshahed ◽

Noha H. Youssef ◽

Anne M. Spain ◽

Cody Sheik ◽

Fares Z. Najar ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Bacterial Species ◽

Rrna Gene ◽

Tall Grass ◽

Data Set ◽

Bacterial Phyla ◽

Rare Biosphere ◽

Soil Bacterial ◽

Close Relatives ◽

Taxonomic Groups

ABSTRACT Soil bacterial communities typically exhibit a distribution pattern in which most bacterial species are present in low abundance. Due to the relatively small size of most culture-independent sequencing surveys, a detailed phylogenetic analysis of rare members of the community is lacking. To gain access to the rarely sampled soil biosphere, we analyzed a data set of 13,001 near-full-length 16S rRNA gene clones derived from an undisturbed tall grass prairie soil in central Oklahoma. Rare members of the soil bacterial community (empirically defined at two different abundance cutoffs) represented 18.1 to 37.1% of the total number of clones in the data set and were, on average, less similar to their closest relatives in public databases when compared to more abundant members of the community. Detailed phylogenetic analyses indicated that members of the soil rare biosphere either belonged to novel bacterial lineages (members of five novel bacterial phyla identified in the data set, as well as members of multiple novel lineages within previously described phyla or candidate phyla), to lineages that are prevalent in other environments but rarely encountered in soil, or were close relatives to more abundant taxa in the data set. While a fraction of the rare community was closely related to more abundant taxonomic groups in the data set, a significant portion of the rare biosphere represented evolutionarily distinct lineages at various taxonomic cutoffs. We reason that these novelty and uniqueness patterns provide clues regarding the origins and potential ecological roles of members of the soil's rare biosphere.

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