scholarly journals Minimal effects of latitude on present-day speciation rates in New World birds

2015 ◽  
Vol 282 (1809) ◽  
pp. 20142889 ◽  
Author(s):  
Daniel L. Rabosky ◽  
Pascal O. Title ◽  
Huateng Huang
Keyword(s):  
Phylogenetic Trees ◽  
New World ◽  
Evolutionary Dynamics ◽  
Cohort Analysis ◽  
Speciation Rate ◽  
Species Formation ◽  
Speciation Rates ◽  
History Of ◽  
New World Birds ◽  
The Tropics

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.

scholarly journals Comparative Analysis of Chlamydia psittaci Genomes Reveals the Recent Emergence of a Pathogenic Lineage with a Broad Host Range

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Timothy D. Read ◽  
Sandeep J. Joseph ◽  
Xavier Didelot ◽  
Brooke Liang ◽  
Lisa Patel ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
New World ◽  
Evolutionary Dynamics ◽  
Chlamydia Psittaci ◽  
South American ◽  
Content Type ◽  
Sexually Transmitted ◽  
Genome Wide ◽  
Life Threatening ◽  
History Of

ABSTRACT Chlamydia psittaci is an obligate intracellular bacterium. Interest in Chlamydia stems from its high degree of virulence as an intestinal and pulmonary pathogen across a broad range of animals, including humans. C. psittaci human pulmonary infections, referred to as psittacosis, can be life-threatening, which is why the organism was developed as a bioweapon in the 20th century and is listed as a CDC biothreat agent. One remarkable recent result from comparative genomics is the finding of frequent homologous recombination across the genome of the sexually transmitted and trachoma pathogen Chlamydia trachomatis. We sought to determine if similar evolutionary dynamics occurred in C. psittaci. We analyzed 20 C. psittaci genomes from diverse strains representing the nine known serotypes of the organism as well as infections in a range of birds and mammals, including humans. Genome annotation revealed a core genome in all strains of 911 genes. Our analyses showed that C. psittaci has a history of frequently switching hosts and undergoing recombination more often than C. trachomatis. Evolutionary history reconstructions showed genome-wide homologous recombination and evidence of whole-plasmid exchange. Tracking the origins of recombinant segments revealed that some strains have imported DNA from as-yet-unsampled or -unsequenced C. psittaci lineages or other Chlamydiaceae species. Three ancestral populations of C. psittaci were predicted, explaining the current population structure. Molecular clock analysis found that certain strains are part of a clonal epidemic expansion likely introduced into North America by South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. IMPORTANCE Chlamydia psittaci is classified as a CDC biothreat agent based on its association with life-threatening lung disease, termed psittacosis, in humans. Because of the recent remarkable findings of frequent recombination across the genome of the human sexually transmitted and ocular trachoma pathogen Chlamydia trachomatis, we sought to determine if similar evolutionary dynamics occur in C. psittaci. Twenty C. psittaci genomes were analyzed from diverse strains that may play a pathogenic role in human disease. Evolution of the strains revealed genome-wide recombination occurring at a higher rate than for C. trachomatis. Certain strains were discovered to be part of a recent epidemic clonal expansion originating in South America. These strains may have been introduced into the United States from South American bird traders, suggesting that psittacosis is a recently emerged disease originating in New World parrots. Our analyses indicate that C. psittaci strains have a history of frequently switching hosts and undergoing recombination.

scholarly journals A Laurasian origin for a pantropical bird radiation is supported by genomic and fossil data (Aves: Coraciiformes)

2019 ◽  
Vol 286 (1910) ◽  
pp. 20190122 ◽  
Author(s):  
Jenna M. McCullough ◽  
Robert G. Moyle ◽  
Brian T. Smith ◽  
Michael J. Andersen
Keyword(s):  
Evolutionary Dynamics ◽  
Species Tree ◽  
Old World ◽  
Avian Order ◽  
History Of ◽  
The Tropics ◽  
Fossil Data ◽  
Old World Tropics ◽  
New Framework

The evolution of pantropically distributed clades has puzzled palaeo- and neontologists for decades regarding the different hypotheses about where they originated. In this study, we explored how a pantropical distribution arose in a diverse clade with a rich fossil history: the avian order Coraciiformes. This group has played a central role in the debate of the biogeographical history of Neoaves. However, the order lacked a coherent species tree to inform study of its evolutionary dynamics. Here, we present the first complete species tree of Coraciiformes, produced with 4858 ultraconserved elements, which supports two clades: (1) Old World-restricted bee-eaters, rollers and ground-rollers; and (2) New World todies and motmots, and cosmopolitan kingfishers. Our results indicated two pulses of diversification: (1) major lineages of Coraciiformes arose in Laurasia approximately 57 Ma, followed by independent dispersals into equatorial regions, possibly due to tracking tropical habitat into the lower latitudes—the Coracii (Coraciidae + Brachypteraciidae) into the Afrotropics, bee-eaters throughout the Old World tropics, and kingfishers into the Australasian tropics; and (2) diversification of genera in the tropics during the Miocene and Pliocene. Our study supports the important role of Laurasia as the geographical origin of a major pantropical lineage and provides a new framework for comparative analyses in this charismatic bird radiation.

scholarly journals Positive association between population genetic differentiation and speciation rates in New World birds

2017 ◽  
Vol 114 (24) ◽  
pp. 6328-6333 ◽  
Author(s):  
Michael G. Harvey ◽  
Glenn F. Seeholzer ◽  
Brian Tilston Smith ◽  
Daniel L. Rabosky ◽  
Andrés M. Cuervo ◽  
...  
Keyword(s):  
Population Differentiation ◽  
New World ◽  
Bird Species ◽  
Positive Association ◽  
Tropical Species ◽  
Implicit Assumption ◽  
Speciation Rate ◽  
Population Genetic Differentiation ◽  
Evolutionary Diversification ◽  
Speciation Rates

An implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, but its significance as a rate-limiting control on phylogenetic speciation dynamics remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. By pairing population genetics datasets from 173 New World bird species (>17,000 individuals) with phylogenetic estimates of speciation rate, we show that the population differentiation rates within species are positively correlated with their speciation rates over long timescales. Although population differentiation rate explains relatively little of the variation in speciation rate among lineages, the positive relationship between differentiation rate and speciation rate is robust to species-delimitation schemes and to alternative measures of both rates. Population differentiation occurs at least three times faster than speciation, which suggests that most populations are ephemeral. Speciation and population differentiation rates are more tightly linked in tropical species than in temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest that the processes responsible for population differentiation are tied to those that underlie broad-scale patterns of diversity.

scholarly journals Angiosperm speciation speeds up near the poles

2019 ◽  
Author(s):  
J. Igea ◽  
A. J. Tanentzap
Keyword(s):  
Species Richness ◽  
Environmental Change ◽  
Species Turnover ◽  
Undescribed Species ◽  
Opposite Pattern ◽  
Speciation Rate ◽  
Diversity Gradient ◽  
Speciation Rates ◽  
Angiosperm Species ◽  
The Tropics

AbstractRecent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results from higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. These results were consistently retrieved using two other methods to test the association between occupancy of tropical habitats and speciation rates. Our speciation rate estimates were robust to the effects of both undescribed species and missing taxa. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness. Greater ecological opportunity in the temperate zones, stemming from less saturated communities, higher species turnover or greater environmental change, may ultimately explain these results.

scholarly journals The first eukaryotic kinome tree illuminates the dynamic history of present-day kinases

2020 ◽  
Author(s):  
Leny M. van Wijk ◽  
Berend Snel
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Cell Signalling ◽  
Eukaryotic Cell ◽  
Functional Information ◽  
Last Eukaryotic Common Ancestor ◽  
History Of ◽  
Human Kinome

AbstractEukaryotic Protein Kinases (ePKs) are essential for eukaryotic cell signalling. Several phylogenetic trees of the ePK repertoire of single eukaryotes have been published, including the human kinome tree. However, a eukaryote-wide kinome tree was missing due to the large number of kinases in eukaryotes. Using a pipeline that overcomes this problem, we present here the first eukaryotic kinome tree. The tree reveals that the Last Eukaryotic Common Ancestor (LECA) possessed at least 92 ePKs, much more than previously thought. The retention of these LECA ePKs in present-day species is highly variable. Fourteen human kinases with unresolved placement in the human kinome tree were found to originate from three known ePK superfamilies. Further analysis of ePK superfamilies shows that they exhibit markedly diverse evolutionary dynamics between the LECA and present-day eukaryotes. The eukaryotic kinome tree thus unveils the evolutionary history of ePKs, but the tree also enables the transfer of functional information between related kinases.

The Tenacious Travels of the Torrid Zone and the Global Dimensions of Geographical Knowledge in the Eighteenth Century

2014 ◽  
Vol 18 (1-2) ◽  
pp. 141-172 ◽  
Author(s):  
Neil Safier
Keyword(s):  
Eighteenth Century ◽  
New World ◽  
European History ◽  
Cultural Characteristics ◽  
Geographical Knowledge ◽  
Alexander Von Humboldt ◽  
History Of ◽  
Natural Philosophers ◽  
The Tropics ◽  
Explanatory Mechanism

Abstract This article sets out to explore the longevity and tenacity of the torrid zone as an explanatory mechanism for describing the cultural characteristics of those populations living between the tropics during the seventeenth and eighteenth centuries. By examining a series of colonizing missions and scientific expeditions to the New World, it argues that long before the iconic voyage of Alexander von Humboldt, which is thought to inaugurate a modern conception of the tropics, European travelers and natural philosophers were molding earlier geographical theories in ways that extended the life of certain pejorative stereotypes about non-European peoples. As such, it represents an important example of how geographical knowledge traveled across imperial lines and, more importantly, challenges scholars to use more expansive temporal ranges that normally separate the pre-European history of the Americas from its post-conquest phase.

scholarly journals A positive association between population genetic differentiation and speciation rates in New World birds

2016 ◽  
Author(s):  
Michael G. Harvey ◽  
Glenn F. Seeholzer ◽  
Brian Tilston Smith ◽  
Daniel L. Rabosky ◽  
Andrés M. Cuervo ◽  
...  
Keyword(s):  
Population Differentiation ◽  
New World ◽  
Bird Species ◽  
Positive Association ◽  
Tropical Species ◽  
Implicit Assumption ◽  
Speciation Rate ◽  
Population Genetic Differentiation ◽  
Evolutionary Diversification ◽  
Speciation Rates

AbstractAlthough an implicit assumption of speciation biology is that population differentiation is an important stage of evolutionary diversification, its true significance remains largely untested. If population differentiation within a species is related to its speciation rate over evolutionary time, the causes of differentiation could also be driving dynamics of organismal diversity across time and space. Alternatively, geographic variants might be short-lived entities with rates of formation that are unlinked to speciation rates, in which case the causes of differentiation would have only ephemeral impacts. Combining population genetics datasets including 17,746 individuals from 176 New World bird species with speciation rates estimated from phylogenetic data, we show that the population differentiation rates within species predict their speciation rates over long timescales. Although relatively little variance in speciation rate is explained by population differentiation rate, the relationship between the two is robust to diverse strategies of sampling and analyzing both population-level and species-level datasets. Population differentiation occurs at least three to five times faster than speciation, suggesting that most populations are ephemeral. Population differentiation and speciation rates are more tightly linked in tropical species than temperate species, consistent with a history of more stable diversification dynamics through time in the Tropics. Overall, our results suggest investigations into the processes responsible for population differentiation can reveal factors that contribute to broad-scale patterns of diversity.

Scriptural Battlefields: The Old Testament, Legal Culture, and the Polemics of the Spanish New World Empire, 1492–1821

2019 ◽  
Author(s):  
Jorge Cañizares-Esguerra ◽  
Adrian Masters
Keyword(s):  
Old Testament ◽  
Social Order ◽  
New World ◽  
Legal Culture ◽  
Spanish Empire ◽  
Correct Interpretation ◽  
Group Status ◽  
History Of ◽  
New Social Order

Scholars have barely begun to explore the role of the Old Testament in the history of the Spanish New World. And yet this text was central for the Empire’s legal thought, playing a role in its legislation, adjudication, and understandings of group status. Institutions like the Council of the Indies, the Inquisition, and the monarchy itself invited countless parallels to ancient Hebrew justice. Scripture influenced how subjects understood and valued imperial space as well as theories about Paradise or King Solomon’s mines of Ophir. Scripture shaped debates about the nature of the New World past, the legitimacy of the conquest, and the questions of mining, taxation, and other major issues. In the world of privilege and status, conquerors and pessimists could depict the New World and its peoples as the antithesis of Israel and the Israelites, while activists, patriots, and women flipped the script with aplomb. In the readings of Indians, American-born Spaniards, nuns, and others, the correct interpretation of the Old Testament justified a new social order where these groups’ supposed demerits were in reality their virtues. Indeed, vassals and royal officials’ interpretations of the Old Testament are as diverse as the Spanish Empire itself. Scripture even outlasted the Empire. As republicans defeated royalists in the nineteenth century, divergent readings of the book, variously supporting the Israelite monarchy or the Hebrew republic, had their day on the battlefield itself.

scholarly journals Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 808
Author(s):  
Laura Pérez-Lago ◽  
Teresa Aldámiz-Echevarría ◽  
Rita García-Martínez ◽  
Leire Pérez-Latorre ◽  
Marta Herranz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Evolutionary Dynamics ◽  
Viral Evolution ◽  
Special Focus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
New Variant ◽  
History Of ◽  
Evolution Dynamics ◽  
The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

Sign in / Sign up

Export Citation Format

Share Document