Fossil pollen from early Palaeogene sediments in western India provides phylogenetic insights into divergence history and pollen character evolution in the pantropical family Ebenaceae

2021 ◽  
Author(s):  
Mahi Bansal ◽  
Shivaprakash K Nagaraju ◽  
Ashish Kumar Mishra ◽  
Jeyakumar Selvaraj ◽  
Rajeev Patnaik ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Character Evolution ◽  
Fossil Pollen ◽  
Western India ◽  
Geological Time ◽  
Posterior Density ◽  
Origin And Evolution ◽  
Pollen Characters ◽  
The Family ◽  
Highest Posterior Density

Abstract Many plant families lack substantive fossil records, limiting our understanding of their origin and evolution. The abundance and preservation potential of pollen through geological time have helped to overcome such limitations and have provided reliable fossils for reconstructing biogeographical history and character evolution in many angiosperm families. Here, using scanning electron microscopy, we identified six Ebenaceae-type fossil pollen grains from early Palaeogene sediments of western India. Phenetic and phylogenetic analyses using pollen characters of fossil and extant taxa reavealed affinities of these fossils to three genera of Ebenaceae (Euclea, Royena and Diospyros). Furthermore, our divergence dating analysis using these fossils as priors suggested a Gondwanan origin for the family during the mid-Cretaceous [c. 107 Mya, 95% highest posterior density (HPD): 100–112 Mya] and supports the boreotropical and ‘out of India’ dispersal hypotheses as the most probable explanations for the present global distribution of the family. The study also supports the dispersal of the family into India, from Africa, through the Kohistan–Ladakh Arc during the Palaeocene. Finally, comparative phylogenetic analyses suggest significant synapomorphic and phylogenetic signals for a few selected pollen characters in Ebenaceae. Our findings have important implications for understanding the biogeography and evolution of the highly diverse and ecologically and economically important family Ebenaceae.

scholarly journals Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

2020 ◽  
Vol 194 (3) ◽  
pp. 271-289 ◽  
Author(s):  
Jerome Chave ◽  
Cynthia Sothers ◽  
Amaia Iribar ◽  
Uxue Suescun ◽  
Mark W Chase ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Large Fraction ◽  
Posterior Density ◽  
Base Pairs ◽  
Plastid Genomes ◽  
Single Clade ◽  
History Of ◽  
Rapid Diversification ◽  
Almost All ◽  
Highest Posterior Density

Abstract We studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the nearly complete DNA sequence matrix, with reliable fossils, was used to estimate a phylogenetic tree. Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density, 95% HPD: 34.2–43.9 Mya). A single clade containing almost all Neotropical species arose after a single dispersal event from the Palaeotropics into the Amazonian biome c. 29.1 Mya (95% HPD: 25.5–32.6 Mya), with subsequent dispersals into other Neotropical biomes. All Neotropical genera diversified from 10 to 14 Mya, lending clear support to the role of Andean orogeny as a major cause of diversification in Chrysobalanaceae. In particular, the understory genus Hirtella diversified extremely rapidly, producing > 100 species in the last 6 Myr (95% HPD: 4.9–7.4 Myr). Our study suggests that a large fraction of the Amazonian tree flora has been assembled in situ in the last 15 Myr.

scholarly journals The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4409 ◽  
Author(s):  
‘Ale‘alani Dudoit ◽  
Matthew Iacchei ◽  
Richard R. Coleman ◽  
Michelle R. Gaither ◽  
William E. Browne ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Population Expansion ◽  
Global Scale ◽  
Genetic Connectivity ◽  
Marine Biodiversity ◽  
Posterior Density ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Highest Posterior Density

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.

scholarly journals Origin of microbial biomineralization and magnetotaxis during the Archean

2017 ◽  
Vol 114 (9) ◽  
pp. 2171-2176 ◽  
Author(s):  
Wei Lin ◽  
Greig A. Paterson ◽  
Qiyun Zhu ◽  
Yinzhao Wang ◽  
Evguenia Kopylova ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Geochemical Processes ◽  
Geological Time ◽  
Environmental Pressures ◽  
Origin And Evolution ◽  
Planetary Environments ◽  
Evolutionary Advantage ◽  
Dating Method ◽  
Phylogenetic Divergence ◽  
Molecular Clock Dating

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from theNitrospiraephylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between theNitrospiraeandProteobacteria. This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth’s dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

Bacterial genome chimaerism and the origin of mitochondria

2011 ◽  
Vol 57 (1) ◽  
pp. 49-61 ◽  
Author(s):  
Ankur Abhishek ◽  
Anish Bavishi ◽  
Ashay Bavishi ◽  
Madhusudan Choudhary
Keyword(s):  
Rhodospirillum Rubrum ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Bacterial Genome ◽  
Sister Group ◽  
Rickettsia Prowazekii ◽  
Origin And Evolution ◽  
The Family ◽  
Related Proteins ◽  
Similarity Searches

Many studies have sought to determine the origin and evolution of mitochondria. Although the Alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. Some have argued that mitochondria originated from ancestors of the order Rickettsiales, or more specifically of the Rickettsiaceae family, while others believe that ancestors of the family Rhodospirillaceae are also equally likely the progenitors. To resolve some of these disputes, sequence similarity searches and phylogenetic analyses were performed against mitochondria-related proteins in Saccharomyces cerevisiae . The 86 common matches of 5 Alphaproteobacteria ( Rickettsia prowazekii , Rhodospirillum rubrum , R hodopseudomonas palustris , Rhodobacter sphaeroides , and Ochrobactrum anthropi ) to yeast mitochondrial proteins were distributed fairly evenly among the 5 species when sorted by highest identity or score. Moreover, exploratory phylogenetic analyses revealed that among these common matches, 44.19% (38) had branched most closely with O. anthropi, while only 34.88% (30) corresponded with Rickettsia prowazekii. More detailed phylogenetic analyses with additional Alphaproteobacteria and including genes from the mitochondria of Reclinomonas americana found matches of mitochondrial genes to those of members of the Rickettsiaceae, Anaplasmataceae, and Rhodospirillaceae families. The results support the idea that notable bacterial genome chimaerism has occurred en route to the formation of mitochondria.

scholarly journals Phylodynamics of SARS-CoV-2 transmission in Spain

2020 ◽  
Author(s):  
Francisco Díez-Fuertes ◽  
María Iglesias-Caballero ◽  
Sara Monzón ◽  
Pilar Jiménez ◽  
Sarai Varona ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Posterior Density ◽  
Whole Genome Analysis ◽  
Most Recent Common Ancestor ◽  
Highest Posterior Density ◽  
The City ◽  
Hpd Interval

AbstractObjectivesSARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe.MethodsMaximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2.ResultsPhylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai.ConclusionsMultiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.

scholarly journals Year-Round Influenza a Virus Surveillance in Mallards (Anas platyrhynchos) Reveals Genetic Persistence During the Under-Sampled Spring Season

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 632
Author(s):  
Sarah E. Lauterbach ◽  
Dillon S. McBride ◽  
Brendan T. Shirkey ◽  
Jacqueline M. Nolting ◽  
Andrew S. Bowman
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
The United States ◽  
Recent Common Ancestor ◽  
Spring Season ◽  
Posterior Density ◽  
Most Recent Common Ancestor ◽  
Highest Posterior Density

Active influenza A virus (IAV) surveillance in wild waterfowl in the United States has revolved around convenience-based sampling methods, resulting in gaps in surveillance during the spring season. We conducted active IAV surveillance in mallards continuously from July 2017 to July 2019 in the coastal marshes of Lake Erie near Port Clinton, Ohio. We aimed to understand ecological and evolutionary dynamics of IAV across multiple seasons, including the under-sampled spring season. We collected 2096 cloacal swabs and estimated a 6.1% (95% confidence interval (CI): 0.050–0.071) prevalence during the study period. Prevalence was lowest during spring (1.0%, 95% CI: 0.004–0.015). Time-stamped phylogenetic analyses revealed local persistence of genetic lineages of multiple gene segments. The PA segment consists of a lineage detected in multiple seasons with a time to most recent common ancestor of 2.48 years (95% highest posterior density: 2.16–2.74). Analysis of the H3 and H6 segments showed close relation between IAVs detected in spring and the following autumn migration. Though the mechanisms behind viral persistence in a single location are not well understood, we provide evidence that viruses can persist across several seasons. Current surveillance methods should be evaluated to ensure they are capturing the breadth of genetic diversity of IAV in waterfowl and prepare for IAV outbreaks in both animals and humans.

scholarly journals Three tree priors and five datasets

2018 ◽  
Vol 8 (2) ◽  
pp. 182-218 ◽  
Author(s):  
Taraka Rama
Keyword(s):  
Model Comparison ◽  
Bayes Factor ◽  
Phylogenetic Analyses ◽  
Language Family ◽  
European Language ◽  
Posterior Density ◽  
Phylogenetic Methods ◽  
Highest Posterior Density ◽  
Origin Hypothesis ◽  
European Family

Abstract The age of the root of the Indo-European language family has received much attention since the application of Bayesian phylogenetic methods by Gray and Atkinson (2003). With the application of new models, the root age of the Indo-European family has tended to decrease from an age that supported the Anatolian origin hypothesis to an age that supports the Steppe origin hypothesis (Chang et al., 2015). However, none of the published work in Indo-European phylogenetics has studied the effect of tree priors on phylogenetic analyses of the Indo-European family. In this paper, I intend to fill this gap by exploring the effect of tree priors on different aspects of the Indo-European family’s phylogenetic inference. I apply three tree priors—Uniform, Fossilized Birth-Death (FBD), and Coalescent—to five publicly available datasets of the Indo-European language family. I evaluate the posterior distribution of the trees from the Bayesian analysis using Bayes Factor, and find that there is support for the Steppe origin hypothesis in the case of two tree priors. I report the median and 95 % highest posterior density (HPD) interval of the root ages for all three tree priors. A model comparison suggests that either the Uniform prior or the FBD prior is more suitable than the Coalescent prior to the datasets belonging to the Indo-European language family.

How old are the eucalypts? A review of the microfossil and phylogenetic evidence

2016 ◽  
Vol 64 (8) ◽  
pp. 579 ◽  
Author(s):  
Mike Macphail ◽  
Andrew H. Thornhill
Keyword(s):  
Upper Cretaceous ◽  
Phylogenetic Analyses ◽  
Fossil Pollen ◽  
Early Eocene ◽  
Primary Reason ◽  
Pollen Type ◽  
Origin And Evolution ◽  
Eastern Australia ◽  
Review Current ◽  
Age Estimates

Molecular age estimates for the Eucalypteae (family Myrtaceae) suggest that the eucalypts, possibly associated with fire, have been present for ~65 million years. In contrast, macrofossils and fossil pollen attributable to three important eucalypt genera (Angophora, Corymbia and Eucalyptus) in the Eucalypteae date to ~51–53 million years ago (mid-Early Eocene) in Patagonia, eastern Antarctica and south-eastern Australia. At present, there is no fossil evidence to show that eucalypts had evolved before this epoch, i.e. when Australia was part of eastern Gondwana, although this seems probable on the basis of molecular-dated phylogenetic analyses. The primary reason is the absence of macrofossils, whereas the earliest fossil eucalypt-type pollen recorded (Myrtaceidites tenuis) is attributed to Angophora and Corymbia, not Eucalyptus. This pollen type is recorded in Australia and Antarctica but not in New Zealand or South America. The only Myrtaceidites morphospecies found in Upper Cretaceous and Paleocene deposits in Australia is M. parvus, whose affinity lies with multiple extant Myrtaceae groups other than the Eucalypteae. In the present paper, we review current phylogenetic and microfossil databases for the eucalypts and assess this evidence to develop a ‘consensus’ position on the origin and evolution of the eucalypts in the Australian region.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

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