scholarly journals Target Capture Sequencing Unravels Rubus Evolution

2019 ◽  
Author(s):  
Katherine A. Carter ◽  
Aaron Liston ◽  
Nahla V. Bassil ◽  
Lawrence A. Alice ◽  
Jill M. Bushakra ◽  
...  
Keyword(s):  
North America ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Long Distance ◽  
Ploidy Levels ◽  
Most Recent Common Ancestor ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

AbstractBackgroundRubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to: estimate the phylogeny of 94 geographically diverse species and 3 cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification.ResultsTarget capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene.ConclusionsRubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. Target capture sequencing confirmed that most subgenera are para- or polyphyletic. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus taxonomic and phylogenetic research.

scholarly journals A new time tree reveals Earth history’s imprint on the evolution of modern birds

2015 ◽  
Vol 1 (11) ◽  
pp. e1501005 ◽  
Author(s):  
Santiago Claramunt ◽  
Joel Cracraft
Keyword(s):  
Dna Sequences ◽  
Plate Tectonics ◽  
Common Ancestor ◽  
Fossil Birds ◽  
Recent Common Ancestor ◽  
Avian Evolution ◽  
Most Recent Common Ancestor ◽  
Global Cooling ◽  
Basic Features ◽  
New Time

Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth’s dynamics.

Huehuecanauhtlus tiquichensis, a new hadrosauroid dinosaur (Ornithischia: Ornithopoda) from the Santonian (Late Cretaceous) of Michoacán, Mexico

2012 ◽  
Vol 49 (2) ◽  
pp. 379-395 ◽  
Author(s):  
Angel Alejandro Ramírez-Velasco ◽  
Mouloud Benammi ◽  
Albert Prieto-Márquez ◽  
Jesús Alvarado Ortega ◽  
René Hernández-Rivera
Keyword(s):  
North America ◽  
Late Cretaceous ◽  
Common Ancestor ◽  
Cladistic Analysis ◽  
Lateral View ◽  
Occlusal Plane ◽  
Recent Common Ancestor ◽  
Vicariant Event ◽  
Most Recent Common Ancestor ◽  
Caudal Vertebrae

Huehuecanauhtlus tiquichensis gen. et sp. nov. is the southernmost diagnostic basal hadrosauroid in the Americas. The holotype and referred material of this taxon came from Santonian strata in the Michoacán State, southwestern Mexico. Huehuecanauhtlus tiquichensis is diagnosed on the basis of a combination of dental, axial, and appendicular characters, including the following: at least two teeth exposed on the occlusal plane of the dentary and maxilla; seven sacral vertebrae; tall neural spines of caudal vertebrae; supraacetabular process long; and short and trapezoidal (in lateral view) postacetabular process. It differs from other hadrosauroids in having an ilium with extreme ventral deflection of the preacetabular process. Maximum parsimony cladistic analysis placed H. tiquichensis as a closely related outgroup to Hadrosauridae. The occurrence of H. tiquichensis in the Santonian of North America may be explained as a dispersal event from Asia to North America that occurred no later than the Albian or, alternatively, as a vicariant event of a most recent common ancestor widespread in both landmasses.

scholarly journals Progressive vowel height harmony in Proto-Kikongo and Proto-Bantu

2019 ◽  
Vol 40 (1) ◽  
pp. 23-73 ◽  
Author(s):  
Heidi Goes ◽  
Koen Bostoen
Keyword(s):  
Common Ancestor ◽  
Recent Common Ancestor ◽  
Long Distance ◽  
Systematic Comparison ◽  
Bantu Languages ◽  
Most Recent Common Ancestor ◽  
Focal Area ◽  
Different Types ◽  
Historical Comparative ◽  
Vowel Height

AbstractThe systematic comparison of the different types of progressive Vowel Height Harmony (pVHH) attested within the Kikongo Language Cluster (KLC) leads to the conclusion that this common Bantu process of long-distance assimilation cannot be reconstructed to Proto-Kikongo. The ‘(a)symmetric-pVHH’ and ‘back-pVHH’ patterns, the two main and structurally different kinds of pVHH within the KLC, emerged independently and relatively late within two distinct subgroups, viz. South Kikongo and North Kikongo respectively. Moreover, the ‘(a)symmetric-pVHH’ pattern further spread from a South Kikongo focal area coinciding with the heartland of the Kongo kingdom to other parts of the KLC through contact-induced dialectal diffusion. Furthermore, the historical-comparative evidence from the KLC suggests that neither symmetric nor asymmetric pVHH should be reconstructed to Proto-Bantu, the most recent common ancestor of all Bantu languages.

scholarly journals Phylogeographic analysis of Pseudogymnoascus destructans partitivirus-pa explains the spread dynamics of white-nose syndrome in North America

2021 ◽  
Vol 17 (3) ◽  
pp. e1009236
Author(s):  
Vaskar Thapa ◽  
Gregory G. Turner ◽  
Marilyn J. Roossinck
Keyword(s):  
North America ◽  
Geographic Origin ◽  
Recent Common Ancestor ◽  
Analysis Tool ◽  
Pseudogymnoascus Destructans ◽  
Long Distance ◽  
Phylogeographic Analysis ◽  
White Nose Syndrome ◽  
Most Recent Common Ancestor ◽  
Beast Analysis

Understanding the dynamics of white-nose syndrome spread in time and space is an important component for the disease epidemiology and control. We reported earlier that a novel partitivirus, Pseudogymnoascus destructans partitivirus-pa, had infected the North American isolates of Pseudogymnoascus destructans, the fungal pathogen that causes white-nose syndrome in bats. We showed that the diversity of the viral coat protein sequences is correlated to their geographical origin. Here we hypothesize that the geographical adaptation of the virus could be used as a proxy to characterize the spread of white-nose syndrome. We used over 100 virus isolates from diverse locations in North America and applied the phylogeographic analysis tool BEAST to characterize the spread of the disease. The strict clock phylogeographic analysis under the coalescent model in BEAST showed a patchy spread pattern of white-nose syndrome driven from a few source locations including Connecticut, New York, West Virginia, and Kentucky. The source states had significant support in the maximum clade credibility tree and Bayesian stochastic search variable selection analysis. Although the geographic origin of the virus is not definite, it is likely the virus infected the fungus prior to the spread of white-nose syndrome in North America. We also inferred from the BEAST analysis that the recent long-distance spread of the fungus to Washington had its root in Kentucky, likely from the Mammoth cave area and most probably mediated by a human. The time to the most recent common ancestor of the virus is estimated somewhere between the late 1990s to early 2000s. We found the mean substitution rate of 2 X 10−3 substitutions per site per year for the virus which is higher than expected given the persistent lifestyle of the virus, and the stamping-machine mode of replication. Our approach of using the virus as a proxy to understand the spread of white-nose syndrome could be an important tool for the study and management of other infectious diseases.

scholarly journals Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene

2005 ◽  
Vol 86 (5) ◽  
pp. 1467-1474 ◽  
Author(s):  
Gareth J. Hughes ◽  
Lillian A. Orciari ◽  
Charles E. Rupprecht
Keyword(s):  
North America ◽  
Rabies Virus ◽  
Common Ancestor ◽  
Recent Common Ancestor ◽  
N Gene ◽  
Primary Host ◽  
Substitution Rates ◽  
Most Recent Common Ancestor ◽  
Molecular Clock Model ◽  
Virus Adaptation

Throughout North America, rabies virus (RV) is endemic in bats. Distinct RV variants exist that are closely associated with infection of individual host species, such that there is little or no sustained spillover infection away from the primary host. Using Bayesian methodology, nucleotide substitution rates were estimated from alignments of partial nucleoprotein (N) gene sequences of nine distinct bat RV variants from North America. Substitution rates ranged from 2·32×10−4 to 1·38×10−3 substitutions per site per year. A maximum-likelihood (ML) molecular clock model was rejected for only two of the nine datasets. In addition, using sequences from bat RV variants across the Americas, the evolutionary rate for the complete N gene was estimated to be 2·32×10−4. This rate was used to scale trees using Bayesian and ML methods, and the time of the most recent common ancestor for current bat RV variant diversity in the Americas was estimated to be 1660 (range 1267–1782) and 1651 (range 1254–1773), respectively. Our reconstructions suggest that RV variants currently associated with infection of bats from Latin America (Desmodus and Tadarida) share the earliest common ancestor with the progenitor RV. In addition, from the ML tree, times were estimated for the emergence of the three major lineages responsible for bat rabies cases in North America. Adaptation to infection of the colonial bat species analysed (Eptesicus fuscus, Myotis spp.) appears to have occurred much quicker than for the solitary species analysed (Lasionycteris noctivagans, Pipistrellus subflavus, Lasiurus borealis, Lasiurus cinereus), suggesting that the process of virus adaptation may be dependent on host biology.

scholarly journals Estimating the Age of the Common Ancestor of a DNA Sample Using the Number of Segregating Sites

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 829-838 ◽  
Author(s):  
Yun-Xin Fu
Keyword(s):  
Dna Sequences ◽  
Common Ancestor ◽  
Likelihood Function ◽  
Joint Probability ◽  
Recent Common Ancestor ◽  
Joint Probability Distribution ◽  
Most Recent Common Ancestor ◽  
Y Chromosomes ◽  
Point Estimators ◽  
Segregating Sites

Abstract The number of segregating sites in a sample of DNA sequences and the age of the most recent common ancestor (MRCA) of the sequences in the sample are positively correlated. The value of the former can be used to estimate the value of the latter. Using the coalescent approach, we derive in this paper the joint probability distribution of the number of segregating sites and the age of the MRCA of a sample under the neutral Wright-Fisher model. From this distribution, we are able to compute the likelihood function of the number of segregating sites and the posterior probability of the age of the MRCA of a sample. Three point estimators and one interval estimator of the age of the MRCA are developed; their relationships and properties are investigated. The estimation of the age of the MRCA of human Y chromosomes from a sample of no variation is discussed.

The genealogy of branching processes and the age of our most recent common ancestor

1995 ◽  
Vol 27 (02) ◽  
pp. 418-442 ◽  
Author(s):  
Neil O'Connell
Keyword(s):  
Dna Sequences ◽  
Branching Process ◽  
Common Ancestor ◽  
Branching Processes ◽  
Recent Common Ancestor ◽  
Time Interval ◽  
Weak Approximation ◽  
Family Tree ◽  
Exponential Law ◽  
Most Recent Common Ancestor

We obtain a weak approximation for the reduced family tree in a near-critical Markov branching process when the time interval considered is long; we also extend Yaglom's theorem and the exponential law to this case. These results are then applied to the problem of estimating the age of our most recent common female ancestor, using mitochondrial DNA sequences taken from a sample of contemporary humans.

scholarly journals Reconstruction of the Evolutionary History and Dispersal of Usutu Virus, a Neglected Emerging Arbovirus in Europe and Africa

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Dimitri Engel ◽  
Hanna Jöst ◽  
Michael Wink ◽  
Jessica Börstler ◽  
Stefan Bosch ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Public Health Problem ◽  
Migratory Bird ◽  
Recent Common Ancestor ◽  
Evolutionary Analysis ◽  
Long Distance ◽  
Genetic Traits ◽  
Usutu Virus ◽  
Most Recent Common Ancestor

ABSTRACT Usutu virus (USUV), one of the most neglected Old World encephalitic flaviviruses, causes epizootics among wild and captive birds and sporadic infection in humans. The dynamics of USUV spread and evolution in its natural hosts are unknown. Here, we present the phylogeny and evolutionary history of all available USUV strains, including 77 newly sequenced complete genomes from a variety of host species at a temporal and spatial scaled resolution. The results showed that USUV can be classified into six distinct lineages and that the most recent common ancestor of the recent European epizootics emerged in Africa at least 500 years ago. We demonstrated that USUV was introduced regularly from Africa into Europe in the last 50 years, and the genetic diversity of European lineages is shaped primarily by in situ evolution, while the African lineages have been driven by extensive gene flow. Most of the amino acid changes are deleterious polymorphisms removed by purifying selection, with adaptive evolution restricted to the NS5 gene and several others evolving under episodic directional selection, indicating that the ecological or immunological factors were mostly the key determinants of USUV dispersal and outbreaks. Host-specific mutations have been detected, while the host transition analysis identified mosquitoes as the most likely origin of the common ancestor and birds as the source of the recent European USUV lineages. Our results suggest that the major migratory bird flyways could predict the continental and intercontinental dispersal patterns of USUV and that migratory birds might act as potential long-distance dispersal vehicles. IMPORTANCE Usutu virus (USUV), a mosquito-borne flavivirus of the Japanese encephalitis virus antigenic group, caused massive bird die-offs, mostly in Europe. There is increasing evidence that USUV appears to be pathogenic for humans, becoming a potential public health problem. The emergence of USUV in Europe allows us to understand how an arbovirus spreads, adapts, and evolves in a naive environment. Thus, understanding the epidemiological and evolutionary processes that contribute to the emergence, maintenance, and further spread of viral diseases is the sine qua non to develop and implement surveillance strategies for their control. In this work, we performed an expansive phylogeographic and evolutionary analysis of USUV using all published sequences and those generated during this study. Subsequently, we described the genetic traits, reconstructed the potential pattern of geographic spread between continents/countries of the identified viral lineages and the drivers of viral migration, and traced the origin of outbreaks and transition events between different hosts.

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