A test for rate‐coupling of trophic and cranial evolutionary dynamics in New World bats

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.

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Evolutionary history of New World monkeys revealed by molecular and fossil data

10.1101/178111 ◽

2017 ◽

Cited By ~ 1

Author(s):

Daniele Silvestro ◽

Marcelo F. Tejedor ◽

Martha L. Serrano-Serrano ◽

Oriane Loiseau ◽

Victor Rossier ◽

...

Keyword(s):

Body Mass ◽

Evolutionary History ◽

New World ◽

Evolutionary Dynamics ◽

Middle Eocene ◽

Small Body ◽

Rapid Change ◽

Molecular Evidence ◽

New World Monkeys ◽

Wide Range

AbstractNew World monkeys (parvorder Platyrrhini) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, the ancestral morphology, and the evolution of the distribution of the clade. Here we integrate paleontological and molecular evidence to investigate the evolutionary dynamics of extinct and extant platyrrhines. We develop an analytical framework to infer ancestral states, the evolution of body mass, and changes in latitudinal ranges through time. Our results show that extant platyrrhines originated some 5–10 million years earlier than previously assumed, likely dating back to the Middle Eocene (∼ 43 million years ago, Ma). The estimated ancestral platyrrhine was strikingly small – weighing ∼ 0.4 kg, as compared to the largest modern species over 10 kg – matching the size of their presumed Eocene North African ancestors. Small-sized callitrichines (marmosets and tamarins) retained a small body mass throughout their evolutionary history, thus challenging the hypothesis of phyletic dwarfism as an explanation to their adaptive traits. In contrast, a rapid change in body mass range took place as the three families diverged between the Late Oligocene and the Early Miocene. That period also marks a peak in diversity of fossil platyrrhines and is associated with their widest latitudinal range, expanding as far to the South as Patagonia. This geographic expansion is temporally coincident with a significant increase in platyrrhine population size inferred from genomic data, and with warm and humid climatic conditions linked to the Miocene Climatic Optimum and the lower elevation of the Andes. These results unveil the early evolution of an iconic group of monkeys and showcase the advantages of integrating fossil and molecular data for estimating evolutionary rates and trends.

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Shifts to multiple optima underlie climatic niche evolution in New World phyllostomid bats

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blz123 ◽

2019 ◽

Vol 128 (4) ◽

pp. 1008-1020

Author(s):

Luiz H Varzinczak ◽

Mauricio O Moura ◽

Fernando C Passos

Keyword(s):

New World ◽

Evolutionary Dynamics ◽

Distribution Patterns ◽

Climate Data ◽

Niche Evolution ◽

Climatic Niche ◽

Tropical Regions ◽

Probable Role ◽

Phylogenetic Perspective ◽

Species Specific

Abstract Climate underlies species distribution patterns, especially in species where climate limits distributions, such as the phyllostomid bats, which are mostly restricted to the New World tropics. The evolutionary dynamics that shaped phyllostomid climatic niches remain unclear, and a broad phylogenetic perspective is required to uncover their patterns. We used geographical distributions and evolutionary relationships of 130 species, climate data and phylogenetic comparative methods to uncover dynamics of phyllostomid climatic niche evolution. Diversification of climatic niches began early in phyllostomid evolution (~34 Mya), with most changes taking place ~20 Mya. Although most of these bats were found in tropical regions, shifts towards different evolutionary optima were common. Shifts were mostly towards temperate climates, reflecting complexities in phyllostomid evolution highlighted by the probable role of species-specific adaptations to cope with these climates, the influence of palaeoclimatic events, and biogeographical effects related to the evolution and dispersal of clades in the New World. Our results broaden our understanding of the relationships between phyllostomid bats and climate, filling an important gap in knowledge and suggesting a complex evolution in their occupation of the climatic niche space.

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Cytoplasmic incompatibility between Old and New World populations of a tramp ant

10.1101/2020.03.13.988675 ◽

2020 ◽

Author(s):

Çiğdem Ün ◽

Eva Schultner ◽

Alejandro Manzano-Marín ◽

Laura V. Flórez ◽

Bernhard Seifert ◽

...

Keyword(s):

Reproductive Isolation ◽

New World ◽

Evolutionary Dynamics ◽

Cytoplasmic Incompatibility ◽

Isolated Populations ◽

First Case ◽

Rapid Spread ◽

Tramp Ant ◽

Globally Distributed ◽

Geographically Isolated

AbstractAs we enter the Anthropocene, the evolutionary dynamics of species will change drastically, and as yet unpredictably, due to human activity. Already today, increases in global human traffic have resulted in the rapid spread of species to new areas, leading to the formation of geographically isolated populations. These go on to evolve in allopatry, which can lead to reproductive isolation, and potentially, the formation of new species. Surprisingly, little is known about such eco-evolutionary processes in ants, even though numerous invasive ant species are globally distributed in geographically isolated populations. Here, we describe the first case of cytoplasmic incompatibility (CI) between populations of a cosmotropic distributed tramp ant with Asian roots, Cardiocondyla obscurior, which has acquired a novel Wolbachia strain in the New World. Our study uncovers the first symbiont-induced mechanism of reproductive isolation in ants, providing a novel perspective on the biology of globally distributed ants.

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Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis

10.1101/2020.06.25.171728 ◽

2020 ◽

Author(s):

César A.D. Xavier ◽

Márcio T. Godinho ◽

Talita B. Mar ◽

Camila G. Ferro ◽

Osvaldo F.L. Sande ◽

...

Keyword(s):

New World ◽

Evolutionary Dynamics ◽

Bipartite Begomoviruses ◽

Evolutionary Analysis ◽

Host Interactions ◽

Coding Regions ◽

Evolutionary Studies ◽

Genetic Clusters ◽

Complete Genome Analysis ◽

Different Levels

ABSTRACTSeveral key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of bipartite genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. We performed a parallel evolutionary analysis of the DNA-A and DNA-B components of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analyzed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both components, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate components belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and components.

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Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves:Plegadis falcinellus) into the New World

Molecular Ecology ◽

10.1111/mec.15008 ◽

2019 ◽

Vol 28 (7) ◽

pp. 1675-1691 ◽

Cited By ~ 14

Author(s):

Jessica A. Oswald ◽

Michael G. Harvey ◽

Rosalind C. Remsen ◽

DePaul U. Foxworth ◽

Donna L. Dittmann ◽

...

Keyword(s):

New World ◽

Evolutionary Dynamics ◽

Hybridization And Introgression

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Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers(Setophaga)

Molecular Ecology ◽

10.1111/mec.13180 ◽

2015 ◽

Vol 24 (10) ◽

pp. 2449-2462 ◽

Cited By ~ 6

Author(s):

Natasha I. Bloch ◽

Trevor D. Price ◽

Belinda S. W. Chang

Keyword(s):

New World ◽

Evolutionary Dynamics ◽

Accelerated Evolution

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.2889 ◽

2015 ◽

Vol 282 (1809) ◽

pp. 20142889 ◽

Cited By ~ 39

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.

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