Competitive history shapes rapid evolution in a seasonal climate

Eco-evolutionary dynamics will play a critical role in determining species’ fates as climatic conditions change. Unfortunately, we have little understanding of how rapid evolutionary responses to climate play out when species are embedded in the competitive communities that they inhabit in nature. We tested the effects of rapid evolution in response to interspecific competition on subsequent ecological and evolutionary trajectories in a seasonally changing climate using a field-based evolution experiment with Drosophila melanogaster. Populations of D. melanogaster were either exposed, or not exposed, to interspecific competition with an invasive competitor, Zaprionus indianus, over the summer. We then quantified these populations’ ecological trajectories (abundances) and evolutionary trajectories (heritable phenotypic change) when exposed to a cooling fall climate. We found that competition with Z. indianus in the summer affected the subsequent evolutionary trajectory of D. melanogaster populations in the fall, after all interspecific competition had ceased. Specifically, flies with a history of interspecific competition evolved under fall conditions to be larger and have lower cold fecundity and faster development than flies without a history of interspecific competition. Surprisingly, this divergent fall evolutionary trajectory occurred in the absence of any detectible effect of the summer competitive environment on phenotypic evolution over the summer or population dynamics in the fall. This study demonstrates that competitive interactions can leave a legacy that shapes evolutionary responses to climate even after competition has ceased, and more broadly, that evolution in response to one selective pressure can fundamentally alter evolution in response to subsequent agents of selection.

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The evolutionary history of a gammaretrovirus currently colonizing the mule deer genome is marked by extensive recombination

10.1101/2021.02.24.432774 ◽

2021 ◽

Author(s):

Lei Yang ◽

Raunaq Malhotra ◽

Rayan Chikhi ◽

Daniel Elleder ◽

Theodora Kaiser ◽

...

Keyword(s):

Evolutionary History ◽

Evolutionary Dynamics ◽

De Novo ◽

Mule Deer ◽

Endogenous Retrovirus ◽

Host Population ◽

Endogenous Retroviruses ◽

Genomic Diversity ◽

Evolutionary Trajectory ◽

History Of

AbstractBackgroundAll vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although it is clear that endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term co-evolution of ERV and host. Newly colonized ERVs are thought unlikely to contribute to host genome evolution because germline infections are rare and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed.Here we investigate the history of cervid endogenous retrovirus (CrERV) acquisition and expansion in the mule deer genome to determine the potential impact of endogenizing retroviruses on host genomic diversity.MethodsA mule deer genome was de novo assembled from short and long insert mate pair reads. Scaffolds were further assembled using reference assisted chromosome assembly (RACA) to provide spatial orientation of CrERV insertion sites and to facilitate assembly of CrERV sequences. We applied phylogenetic and coalescent approaches to non-recombinant genomes to determine CrERV evolutionary history, augmenting ancestral divergence estimates with the prevalence of each CrERV locus in a population of mule deer. Recombination history was investigated on partial genome alignments.ResultsThe CrERV composition and diversity in the mule deer genome has recently measurably increased by horizontal acquisition of a new retroviruses lineage and because of recombination with existing CrERV. Resulting interlineage recombinants also endogenized and subsequently retrotransposed. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion by retrotransposition of one recombinant CrERV lineage.ConclusionsThere has been a burst of CrERV integrations during a recent retrovirus epizootic that increased genomic CrERV burden and has resulted in extensive insertional polymorphism in contemporary mule deer genomes. Recombination is a defining feature of CrERV evolutionary dynamics driven by this colonization, increasing CrERV burden and CrERV genetic diversity. These data support that retroviral colonization during an epizootic provides a burst of genomic diversity to the host population.

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How phenotypic convergence arises in experimental evolution

10.1101/579524 ◽

2019 ◽

Cited By ~ 2

Author(s):

Pedro Simões ◽

Inês Fragata ◽

Josiane Santos ◽

Marta A. Santos ◽

Mauro Santos ◽

...

Keyword(s):

Experimental Evolution ◽

Evolutionary Dynamics ◽

Short Term ◽

Common Environment ◽

Evolutionary Trajectory ◽

Trajectory Approach ◽

Evolutionary Trajectories ◽

Core Issue ◽

Evolutionary Convergence ◽

Phenotypic Convergence

AbstractEvolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a “real-time” or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment?Drosophila subobscurapopulations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short-term (∼20 generations) laboratory adaptation. Here we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics between populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after sixty generations of evolution in a common environment. We found substantial variation in longer-term evolutionary trajectories and differences between short and longer-term evolutionary dynamics. Though we observed pervasive patterns of convergence towards the character values of long-established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer-term studies for understanding convergent evolution.

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Insights into the Evolutionary History of an Emerging Livestock Pathogen: Porcine Circovirus 2

Journal of Virology ◽

10.1128/jvi.01719-09 ◽

2009 ◽

Vol 83 (24) ◽

pp. 12813-12821 ◽

Cited By ~ 146

Author(s):

Cadhla Firth ◽

Michael A. Charleston ◽

Siobain Duffy ◽

Beth Shapiro ◽

Edward C. Holmes

Keyword(s):

Evolutionary Dynamics ◽

Postweaning Multisystemic Wasting Syndrome ◽

High Rate ◽

Porcine Circovirus ◽

Dna Viruses ◽

Wasting Syndrome ◽

Porcine Circovirus 2 ◽

History Of ◽

Evolutionary Trajectories ◽

Swine Diseases

ABSTRACT Porcine circovirus 2 (PCV2) is the primary etiological agent of postweaning multisystemic wasting syndrome (PMWS), one of the most economically important emerging swine diseases worldwide. Virulent PCV2 was first identified following nearly simultaneous outbreaks of PMWS in North America and Europe in the 1990s and has since achieved global distribution. However, the processes responsible for the emergence and spread of PCV2 remain poorly understood. Here, phylogenetic and cophylogenetic inferences were utilized to address key questions on the time scale, processes, and geographic diffusion of emerging PCV2. The results of these analyses suggest that the two genotypes of PCV2 (PCV2a and PCV2b) are likely to have emerged from a common ancestor approximately 100 years ago and have been on independent evolutionary trajectories since that time, despite cocirculating in the same host species and geographic regions. The patterns of geographic movement of PCV2 that we recovered appear to mimic those of the global pig trade and suggest that the movement of asymptomatic animals is likely to have facilitated the rapid spread of virulent PCV2 around the globe. We further estimated the rate of nucleotide substitution for PCV2 to be on the order of 1.2 × 10−3 substitutions/site/year, the highest yet recorded for a single-stranded DNA virus. This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide.

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Massive bursts of transposable element activity in Drosophila

10.1101/010231 ◽

2014 ◽

Cited By ~ 1

Author(s):

Robert Kofler ◽

Viola Nolte ◽

Christian Schlötterer

Keyword(s):

Transposable Element ◽

Genome Evolution ◽

South African ◽

Evolutionary Dynamics ◽

Demographic History ◽

Rapid Evolution ◽

Activity Levels ◽

Genome Wide ◽

History Of ◽

Element Activity

The evolutionary dynamics of transposable element (TE) insertions have been of continued interest since TE activity has important implications for genome evolution and adaptation. Here, we infer the transposition dynamics of TEs by comparing their abundance in natural D. melanogaster and D. simulans populations. Sequencing pools of more than 550 South African flies to at least 320-fold coverage, we determined the genome wide TE insertion frequencies in both species. We show that 46 (49%) TE families in D. melanogaster and 44 (47%) in D. simulans experienced a recent burst of activity. The bursts of activity affected different TE families in the two species. While in D. melanogaster retrotransposons predominated, DNA transposons showed higher activity levels in D. simulans. We propose that the observed TE dynamics are the outcome of the demographic history of the two species, with habitat expansion triggering a period of rapid evolution.

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Predator coevolution and prey trait variability determine species coexistence

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.0245 ◽

2019 ◽

Vol 286 (1902) ◽

pp. 20190245 ◽

Cited By ~ 5

Author(s):

Thomas Scheuerl ◽

Johannes Cairns ◽

Lutz Becks ◽

Teppo Hiltunen

Keyword(s):

Evolutionary Dynamics ◽

Biological Diversity ◽

Species Coexistence ◽

Ecological Interactions ◽

Trait Variation ◽

Ecological Processes ◽

History Of ◽

Evolutionary Trajectories ◽

Ecological Mechanisms

Predation is one of the key ecological mechanisms allowing species coexistence and influencing biological diversity. However, ecological processes are subject to contemporary evolutionary change, and the degree to which predation affects diversity ultimately depends on the interplay between evolution and ecology. Furthermore, ecological interactions that influence species coexistence can be altered by reciprocal coevolution especially in the case of antagonistic interactions such as predation or parasitism. Here we used an experimental evolution approach to test for the role of initial trait variation in the prey population and coevolutionary history of the predator in the ecological dynamics of a two-species bacterial community predated by a ciliate. We found that initial trait variation both at the bacterial and ciliate level enhanced species coexistence, and that subsequent trait evolutionary trajectories depended on the initial genetic diversity present in the population. Our findings provide further support to the notion that the ecology-centric view of diversity maintenance must be reinvestigated in light of recent findings in the field of eco-evolutionary dynamics.

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Chips with Everything

10.1093/oso/9780198804079.003.0003 ◽

2017 ◽

Author(s):

David Segal

Keyword(s):

Quantum Computing ◽

Integrated Circuits ◽

Critical Role ◽

Moore’S Law ◽

Moore's Law ◽

Silicon Chips ◽

History Of ◽

Future Potential ◽

Digital Computers ◽

Dna Computer

Chapter 3 highlights the critical role materials have in the development of digital computers. It traces developments from the cat’s whisker to valves through to relays and transistors. Accounts are given for transistors and the manufacture of integrated circuits (silicon chips) by use of photolithography. Future potential computing techniques, namely quantum computing and the DNA computer, are covered. The history of computability and Moore’s Law are discussed.

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

Biomedicines ◽

10.3390/biomedicines9070808 ◽

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.

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Friends of Rose Canyon

California History ◽

10.1525/ch.2018.95.3.2 ◽

2018 ◽

Vol 95 (3) ◽

pp. 2-20 ◽

Cited By ~ 1

Author(s):

Andrew Wiese

Keyword(s):

Open Space ◽

Critical Role ◽

First Century ◽

Grassroots Politics ◽

History Of ◽

University City ◽

Participant Observer ◽

The Rose

Place-based activism has played a critical role in the history of urban and environmental politics in California. This article explores the continuing significance of environmental place making to grassroots politics through a case study of Friends of Rose Canyon, an environmental group in San Diego. Based in the fast-growing University City neighborhood, Friends of Rose Canyon waged a long, successful campaign between 2002 and 2018 to prevent construction of a bridge in the Rose Canyon Open Space Park in their community. Using historical and participant observer methodologies, this study reveals how twenty-first-century California urbanites claimed and created meaningful local places and mobilized effective politics around them. It illuminates the critical role of individual activists; suggests practical, replicable strategies for community mobilization; and demonstrates the significant impact of local activism at the urban and metropolitan scales.

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IMGs Have Played Critical Role In History of U.S. Psychiatry

Psychiatric News ◽

10.1176/pn.37.21.0018a ◽

2002 ◽

Vol 37 (21) ◽

pp. 18-44

Author(s):

David Milne

Keyword(s):

Critical Role ◽

History Of

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Late-glacial and Post-glacial history of the Chalk escarpment near Brook, Kent

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1964.0010 ◽

1964 ◽

Vol 248 (745) ◽

pp. 135-204 ◽

Cited By ~ 87

Keyword(s):

Bronze Age ◽

Iron Age ◽

Late Glacial ◽

Climatic Conditions ◽

Valley Floor ◽

Glacial Period ◽

Late Neolithic ◽

Local Conditions ◽

Arable Farming ◽

History Of

This paper describes the morphology of a small piece of the Chalk escarpment near Brook in east Kent, and reconstructs its history since the end of the Last Glaciation. The escarpment contains a number of steep-sided valleys, or coombes, with which are associated deposits of chalk debris, filling their bottoms and extending as fans over the Gault Clay plain beyond. Here the fans overlie radiocarbon-dated marsh deposits of zone II (10 000 to 8800 B.C.) of the Late-glacial Period. The debris fans were formed and the coombes were cut very largely during the succeeding zone III (8800 to 8300 B.C.). The fans are the products of frost-shattering, probably transported by a combination of niveo-fluvial action and the release of spring waters; intercalated seams of loess also occur. The molluscs and plants preserved in the Late-glacial deposits give a fairly detailed picture of local conditions. The later history of one of the coombes, the Devil’s Kneadingtrough, is reconstructed. The springs have effected virtually no erosion and have probably always emerged more or less in their present position. In the floor of the coombe the periglacial chalk rubbles of zone III are covered by Postglacial deposits, mainly hillwashes. They are oxidized and yield no pollen, but contain rich faunas of land Mollusca, which are presented in the form of histograms revealing changing local ecological and climatic conditions. During most of the Post-glacial Period, from the end of zone III until about the beginning of zone VIII, very little accumulation took place on the coombe floor. But below the springs there are marsh deposits which span much of this interval. They yield faunas of considerable zoogeographical interest. The approximate beginning of zone VII a (Atlantic Period) is reflected by a calcareous tufa, which overlies a weathering horizon, and represents an increase in spring flow. Two clearance phases are deduced from the molluscan record. The first may have taken place at least as early as the Beaker Period (Late Neolithic/earliest Bronze Age); the second is probably of Iron Age ‘A’ date. In Iron Age times the subsoil was mobilized and a phase of rapid hillwashing began. As a result the valley floor became buried by humic chalk muds. The prime cause of this process was probably the beginning of intensive arable farming on the slopes above the coombe; a possible subsidiary factor may have been the Sub-Atlantic worsening of climate. The muds yield pottery ranging in date from Iron Age ‘Kentish first A’ ( ca . 500 to ca . 300 B.C.) to Romano-British ware of the first or second centuries A.D. Evidence is put forward for a possible climatic oscillation from dry to wet taking place at about the time of Christ. In the later stages of cultivation, possibly in the Roman Era, the valley floor was ploughed and given its present-day form.

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