Massive bursts of transposable element activity in Drosophila

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.

Download Full-text

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

mBio ◽

10.1128/mbio.00604-12 ◽

2013 ◽

Vol 4 (2) ◽

Cited By ~ 49

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.

Download Full-text

Genome - wide variation and demographic history of small cats with a focus on Felis species

Canadian Journal of Biotechnology ◽

10.24870/cjb.2017-a3 ◽

2017 ◽

Vol 1 (Special Issue) ◽

pp. 15-15

Author(s):

Anubhab Khan ◽

Rithvik Vinekar ◽

Prachi Thatte ◽

Uma Ramakrishnan

Keyword(s):

Demographic History ◽

Genome Wide ◽

History Of

Download Full-text

Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

10.1101/077958 ◽

2016 ◽

Cited By ~ 3

Author(s):

Champak R. Beeravolu ◽

Michael J. Hickerson ◽

Laurent A.F. Frantz ◽

Konrad Lohse

Keyword(s):

Demographic History ◽

Composite Likelihood ◽

Model Organisms ◽

Secondary Contact ◽

Parameter Estimates ◽

Genome Sequences ◽

Frequency Spectra ◽

Genome Wide ◽

Complex Population ◽

History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

Download Full-text

Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) grown on indigenous Māori land

10.22541/au.161912114.47713005/v1 ◽

2021 ◽

Author(s):

Emily Koot ◽

Elise Arnst ◽

Melissa Taane ◽

Kelsey Goldsmith ◽

Peri Tobias ◽

...

Keyword(s):

New Zealand ◽

Demographic History ◽

Gene Pools ◽

Phylogenetic Studies ◽

Aotearoa New Zealand ◽

Genome Wide ◽

History Of ◽

Demographic Modelling ◽

Management And Conservation ◽

Leptospermum Scoparium

Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9 –12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.

Download Full-text

Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago

Molecular Biology and Evolution ◽

10.1093/molbev/msu230 ◽

2014 ◽

Vol 31 (11) ◽

pp. 2929-2940 ◽

Cited By ~ 30

Author(s):

Takehiro Sato ◽

Shigeki Nakagome ◽

Chiaki Watanabe ◽

Kyoko Yamaguchi ◽

Akira Kawaguchi ◽

...

Keyword(s):

Population Structure ◽

Demographic History ◽

Snp Analysis ◽

Japanese Archipelago ◽

Genome Wide ◽

History Of ◽

The Japanese Archipelago

Download Full-text

Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

Scientific Reports ◽

10.1038/s41598-020-66953-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Guilherme Debortoli ◽

Cristina Abbatangelo ◽

Francisco Ceballos ◽

Cesar Fortes-Lima ◽

Heather L. Norton ◽

...

Keyword(s):

Demographic History ◽

Genome Wide ◽

Genome Wide Data ◽

History Of ◽

Caste Groups

Download Full-text

Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

PLoS ONE ◽

10.1371/journal.pone.0088568 ◽

2014 ◽

Vol 9 (2) ◽

pp. e88568 ◽

Cited By ~ 37

Author(s):

Rachit K. Saxena ◽

Eric von Wettberg ◽

Hari D. Upadhyaya ◽

Vanessa Sanchez ◽

Serah Songok ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Genome Wide ◽

History Of

Download Full-text

A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds

Genetics Selection Evolution ◽

10.1186/s12711-016-0229-6 ◽

2016 ◽

Vol 48 (1) ◽

Cited By ~ 29

Author(s):

Arianna Manunza ◽

Antonia Noce ◽

Juan Manuel Serradilla ◽

Félix Goyache ◽

Amparo Martínez ◽

...

Keyword(s):

Demographic History ◽

Genome Wide ◽

A Genome ◽

History Of ◽

Wide Perspective ◽

Spanish Goat

Download Full-text

The genomic landscape of Mexican Indigenous populations brings insights into the peopling of the Americas

Nature Communications ◽

10.1038/s41467-021-26188-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Humberto García-Ortiz ◽

Francisco Barajas-Olmos ◽

Cecilia Contreras-Cubas ◽

Miguel Ángel Cid-Soto ◽

Emilio J. Córdova ◽

...

Keyword(s):

Demographic History ◽

Indigenous Populations ◽

South American ◽

Genome Wide Analysis ◽

Genome Wide ◽

Genomic Landscape ◽

A Genome ◽

Peopling Of The Americas ◽

History Of ◽

Genetic Makeup

AbstractThe genetic makeup of Indigenous populations inhabiting Mexico has been strongly influenced by geography and demographic history. Here, we perform a genome-wide analysis of 716 newly genotyped individuals from 60 of the 68 recognized ethnic groups in Mexico. We show that the genetic structure of these populations is strongly influenced by geography, and our demographic reconstructions suggest a decline in the population size of all tested populations in the last 15–30 generations. We find evidence that Aridoamerican and Mesoamerican populations diverged roughly 4–9.9 ka, around the time when sedentary farming started in Mesoamerica. Comparisons with ancient genomes indicate that the Upward Sun River 1 (USR1) individual is an outgroup to Mexican/South American Indigenous populations, whereas Anzick-1 was more closely related to Mesoamerican/South American populations than to those from Aridoamerica, showing an even more complex history of divergence than recognized so far.

Download Full-text

Competitive history shapes rapid evolution in a seasonal climate

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015772118 ◽

2021 ◽

Vol 118 (6) ◽

pp. e2015772118

Author(s):

Tess Nahanni Grainger ◽

Seth M. Rudman ◽

Paul Schmidt ◽

Jonathan M. Levine

Keyword(s):

Interspecific Competition ◽

Evolutionary Dynamics ◽

Critical Role ◽

Rapid Evolution ◽

Climatic Conditions ◽

Phenotypic Change ◽

Evolutionary Trajectory ◽

History Of ◽

Evolutionary Trajectories ◽

Faster Development

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.

Download Full-text