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 Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Ana M.R. Liedke ◽  
Hudson T. Pinheiro ◽  
Sergio R. Floeter ◽  
Giacomo Bernardi
Keyword(s):  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Rocky Reef ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Network Analyses ◽  
Biogeographic Provinces ◽  
The Caribbean

ABSTRACT Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.

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 &gt; 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.

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 Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion

2018 ◽  
Author(s):  
Tanvi P. Honap ◽  
Krithivasan Sankaranarayanan ◽  
Stephanie L. Schnorr ◽  
Andrew T. Ozga ◽  
Christina Warinner ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Sensu Stricto ◽  
Metagenomic Data ◽  
Human Populations ◽  
Multiple Time ◽  
Human Gut ◽  
Recent Population Expansion ◽  
Study Population ◽  
Multiple Time Points

AbstractCrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of a recent expansion event within crAssphage. Using a Bayesian dating approach, we estimate this expansion has occurred within the past 200 years. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle. The absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.

scholarly journals Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

2021 ◽  
Author(s):  
Jay-Vee S. Mendoza ◽  
Fe M. Dela Cueva ◽  
Cris Q. Cortaga ◽  
Anand Noel C. Manohar ◽  
Roanne R. Gardoce ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Phylogenetic Analyses ◽  
Infected Plant ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
The Philippines ◽  
Recent Population Expansion ◽  
Banana Bunchy Top Virus ◽  
Reference Sequences ◽  
Genetic Structure And Diversity

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity (π) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fu′s Fs and Tajima′s D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

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 Occurrence of the genus Pseudoboletia (Echinoidea: Toxopneustidae) in the South-Western Atlantic: morphological and molecular approaches

2017 ◽  
Vol 65 (1-1) ◽  
pp. 299 ◽  
Author(s):  
Elinia M. Lopes ◽  
Carlos Eduardo L. Ferreira ◽  
Carlos Renato R. Ventura
Keyword(s):  
Sea Urchins ◽  
Population Expansion ◽  
First Record ◽  
Molecular Data ◽  
Brazilian Coast ◽  
Long Distance ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Molecular Approaches ◽  
Morphological And Molecular Data

The genus Pseudoboletia was recently reported off coast of Brazil (Trindade-Martin Vaz insular complex). This study reports the first record of this genus to southern of Brazil in Rio de Janeiro and Santa Catarina coasts. Morphological and molecular data showed that sea urchins from Brazil and São Tomé are the same species, genetically distinct of individuals from Indo-Pacific. However, taxonomic identity of Brazilian species remains as a challenge. Two hypotheses to explain the recent records of this species on Brazilian coast are discussed: a recent natural invasion by long-distance dispersal and a recent population expansion in the Brazilian coast after absence or low density period. Rev. Biol. Trop. 65(Suppl. 1): S299-S308. Epub 2017 November 01. 

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.

scholarly journals Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People’s Democratic Republic

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Maysa Tiemi Motoki ◽  
Dina Madera Fonseca ◽  
Elliott Frederic Miot ◽  
Bruna Demari-Silva ◽  
Phoutmany Thammavong ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Aedes Albopictus ◽  
Isolation By Distance ◽  
Genetic Locus ◽  
Lao Pdr ◽  
Phylogenetic Network ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
The Usa

Abstract Background The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR. Methods We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA. Results We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions. Conclusions Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.

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