Publications by authors named "Alexander Suh"

51 Publications

Author Correction: Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2021 Apr 8. Epub 2021 Apr 8.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

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http://dx.doi.org/10.1038/s41586-021-03473-8DOI Listing
April 2021

Genetic barriers to historical gene flow between cryptic species of alpine bumblebees revealed by comparative population genomics.

Mol Biol Evol 2021 Apr 6. Epub 2021 Apr 6.

Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Evidence is accumulating that gene flow commonly occurs between recently-diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that co-localize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely-related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (dXY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.
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http://dx.doi.org/10.1093/molbev/msab086DOI Listing
April 2021

Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish.

BMC Biol 2021 Mar 19;19(1):52. Epub 2021 Mar 19.

Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.

Background: Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested.

Results: Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed > 30× more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction.

Conclusions: Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
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http://dx.doi.org/10.1186/s12915-021-00991-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7976721PMC
March 2021

Meiosis and beyond - understanding the mechanistic and evolutionary processes shaping the germline genome.

Biol Rev Camb Philos Soc 2021 Jan 1. Epub 2021 Jan 1.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, U.K.

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro-evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post-meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge.
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http://dx.doi.org/10.1111/brv.12680DOI Listing
January 2021

Genome size reduction and transposon activity impact tRNA gene diversity while ensuring translational stability in birds.

Genome Biol Evol 2021 Feb 3. Epub 2021 Feb 3.

Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, 171 77, Sweden.

As a highly diverse vertebrate class, bird species have adapted to various ecological systems. How this phenotypic diversity can be explained genetically is intensively debated and is likely grounded in differences in the genome content. Larger and more complex genomes could allow for greater genetic regulation that results in more phenotypic variety. Surprisingly, avian genomes are much smaller compared to other vertebrates but contain as many protein-coding genes than other vertebrates. This supports the notion that the phenotypic diversity is largely determined by selection on non-coding gene sequences. Transfer RNA (tRNAs) represent a group of non-coding genes. However, the characteristics of tRNA genes across bird genomes have remained largely unexplored. Here we exhaustively investigated the evolution and functional consequences of these crucial translational regulators within bird species and across vertebrates. Our dense sampling of 55 avian genomes representing each bird order revealed an average of 169 tRNA genes with at least 31% being actively used. Unlike other vertebrates, avian tRNA genes are reduced in number and complexity but are still in line with vertebrate wobble pairing strategies and mutation-driven codon usage. Our detailed phylogenetic analyses further uncovered that new tRNA genes can emerge through multiplication by transposable elements. Together, this study provides the first comprehensive avian and cross-vertebrate tRNA gene analyses and demonstrates that tRNA gene evolution is flexible albeit constrained within functional boundaries of general mechanisms in protein translation.
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http://dx.doi.org/10.1093/gbe/evab016DOI Listing
February 2021

Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats.

BMC Biol 2020 12 21;18(1):199. Epub 2020 Dec 21.

Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.

Background: Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the "repeatome", are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution.

Results: We obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex.

Conclusion: This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.
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http://dx.doi.org/10.1186/s12915-020-00925-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7754599PMC
December 2020

Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759463PMC
November 2020

New Environment, New Invaders-Repeated Horizontal Transfer of LINEs to Sea Snakes.

Genome Biol Evol 2020 12;12(12):2370-2383

School of Biological Sciences, University of Adelaide, Australia.

Although numerous studies have found horizontal transposon transfer (HTT) to be widespread across metazoans, few have focused on HTT in marine ecosystems. To investigate potential recent HTTs into marine species, we searched for novel repetitive elements in sea snakes, a group of elapids which transitioned to a marine habitat at most 18 Ma. Our analysis uncovered repeated HTTs into sea snakes following their marine transition. The seven subfamilies of horizontally transferred LINE retrotransposons we identified in the olive sea snake (Aipysurus laevis) are transcribed, and hence are likely still active and expanding across the genome. A search of 600 metazoan genomes found all seven were absent from other amniotes, including terrestrial elapids, with the most similar LINEs present in fish and marine invertebrates. The one exception was a similar LINE found in sea kraits, a lineage of amphibious elapids which independently transitioned to a marine environment 25 Ma. Our finding of repeated horizontal transfer events into marine snakes greatly expands past findings that the marine environment promotes the transfer of transposons. Transposons are drivers of evolution as sources of genomic sequence and hence genomic novelty. We identified 13 candidate genes for HTT-induced adaptive change based on internal or neighboring HTT LINE insertions. One of these, ADCY4, is of particular interest as a part of the KEGG adaptation pathway "Circadian Entrainment." This provides evidence of the ecological interactions between species influencing evolution of metazoans not only through specific selection pressures, but also by contributing novel genomic material.
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http://dx.doi.org/10.1093/gbe/evaa208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846101PMC
December 2020

Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes.

Genes (Basel) 2020 Sep 30;11(10). Epub 2020 Sep 30.

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK.

The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.
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http://dx.doi.org/10.3390/genes11101153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7601716PMC
September 2020

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.

Mol Ecol Resour 2021 Jan 10;21(1):263-286. Epub 2020 Oct 10.

Department of Ecology and Genetics-Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden.

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic "dark matter") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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http://dx.doi.org/10.1111/1755-0998.13252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757076PMC
January 2021

The tuatara genome reveals ancient features of amniote evolution.

Nature 2020 08 5;584(7821):403-409. Epub 2020 Aug 5.

Ngatiwai Trust Board, Whangarei, New Zealand.

The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana-is an iconic species that is endemic to New Zealand. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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http://dx.doi.org/10.1038/s41586-020-2561-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116210PMC
August 2020

Discovery and population genomics of structural variation in a songbird genus.

Nat Commun 2020 07 7;11(1):3403. Epub 2020 Jul 7.

Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.

Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
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http://dx.doi.org/10.1038/s41467-020-17195-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7341801PMC
July 2020

Linked-read sequencing enables haplotype-resolved resequencing at population scale.

Mol Ecol Resour 2020 Sep 29;20(5):1311-1322. Epub 2020 Jun 29.

Department of Population Ecology, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany.

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences - including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps - are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high-coverage data (46-68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.
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http://dx.doi.org/10.1111/1755-0998.13192DOI Listing
September 2020

Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes.

Mob DNA 2019 12;10:49. Epub 2019 Dec 12.

2Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Background: Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected.

Results: The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. non-repetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome.

Conclusion: Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation.
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http://dx.doi.org/10.1186/s13100-019-0195-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6909575PMC
December 2019

Programmed DNA elimination of germline development genes in songbirds.

Nat Commun 2019 11 29;10(1):5468. Epub 2019 Nov 29.

Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.

In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline-soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits.
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http://dx.doi.org/10.1038/s41467-019-13427-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884545PMC
November 2019

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.

Mol Phylogenet Evol 2019 10 23;139:106568. Epub 2019 Jul 23.

Department of Population Ecology, Institute of Ecology and Evolution, Friedrich Schiller University Jena, D-07743 Jena, Germany. Electronic address:

In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.
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http://dx.doi.org/10.1016/j.ympev.2019.106568DOI Listing
October 2019

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.

Genes (Basel) 2019 04 13;10(4). Epub 2019 Apr 13.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden.

Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.
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http://dx.doi.org/10.3390/genes10040301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6523648PMC
April 2019

Genome Size Evolution: Small Transposons with Large Consequences.

Authors:
Alexander Suh

Curr Biol 2019 04;29(7):R241-R243

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden. Electronic address:

Transposable elements (TEs) heavily influence genome size variation between organisms. A new study on larvacean tunicates now shows that even non-autonomous TEs - small TEs that parasitize the enzymatic machinery of large, autonomous TEs - can have a large impact on genome size.
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http://dx.doi.org/10.1016/j.cub.2019.02.032DOI Listing
April 2019

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Nat Ecol Evol 2019 05 1;3(5):834-844. Epub 2019 Apr 1.

MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.

Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
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http://dx.doi.org/10.1038/s41559-019-0850-1DOI Listing
May 2019

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.

Gigascience 2019 05;8(5)

Department of Biodiversity and Genetics, Swedish Museum of Natural History, Frescativaegen 40, 114 18 Stockholm, Sweden.

The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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http://dx.doi.org/10.1093/gigascience/giz003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497032PMC
May 2019

Parallel plumage colour evolution and introgressive hybridization in wheatears.

J Evol Biol 2019 01 30;32(1):100-110. Epub 2018 Nov 30.

Department of Population Ecology, Institute of Ecology and Evolution, Friedrich Schiller University Jena, Jena, Germany.

Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa-pied wheatear (O. pleschanka), Cyprus wheatear (Oenanthe cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20,000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of colour phenotypes and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage colour evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.
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http://dx.doi.org/10.1111/jeb.13401DOI Listing
January 2019

How complete are "complete" genome assemblies?-An avian perspective.

Mol Ecol Resour 2018 Nov 16;18(6):1188-1195. Epub 2018 Aug 16.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

The genomics revolution has led to the sequencing of a large variety of nonmodel organisms often referred to as "whole" or "complete" genome assemblies. But how complete are these, really? Here, we use birds as an example for nonmodel vertebrates and find that, although suitable in principle for genomic studies, the current standard of short-read assemblies misses a significant proportion of the expected genome size (7% to 42%; mean 20 ± 9%). In particular, regions with strongly deviating nucleotide composition (e.g., guanine-cytosine-[GC]-rich) and regions highly enriched in repetitive DNA (e.g., transposable elements and satellite DNA) are usually underrepresented in assemblies. However, long-read sequencing technologies successfully characterize many of these underrepresented GC-rich or repeat-rich regions in several bird genomes. For instance, only ~2% of the expected total base pairs are missing in the last chicken reference (galGal5). These assemblies still contain thousands of gaps (i.e., fragmented sequences) because some chromosomal structures (e.g., centromeres) likely contain arrays of repetitive DNA that are too long to bridge with currently available technologies. We discuss how to minimize the number of assembly gaps by combining the latest available technologies with complementary strengths. At last, we emphasize the importance of knowing the location, size and potential content of assembly gaps when making population genetic inferences about adjacent genomic regions.
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http://dx.doi.org/10.1111/1755-0998.12933DOI Listing
November 2018

Improved Genome Assembly and Annotation for the Rock Pigeon ().

G3 (Bethesda) 2018 05 4;8(5):1391-1398. Epub 2018 May 4.

Department of Biology, University of Utah, Salt Lake City, UT, USA

The domestic rock pigeon () is among the most widely distributed and phenotypically diverse avian species. is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general.
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http://dx.doi.org/10.1534/g3.117.300443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940132PMC
May 2018

emergence of SINE retroposons during the early evolution of passerine birds.

Mob DNA 2017 14;8:21. Epub 2017 Dec 14.

Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.

Background: Passeriformes ("perching birds" or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

Results: Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri - songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

Conclusions: We propose that the early evolution of passerines was unusual among birds in that it was accompanied by emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.
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http://dx.doi.org/10.1186/s13100-017-0104-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729268PMC
December 2017

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis).

Mol Ecol 2018 01 9;27(2):476-492. Epub 2018 Jan 9.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that ~6.6% of the collared flycatcher genome (74.0 Mb) is spanned by ~1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations. Importantly, no less than ~71% of CE sites were nonexonic (52.6 Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a progressive cactus whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.
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http://dx.doi.org/10.1111/mec.14462DOI Listing
January 2018

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes.

Mol Ecol 2018 01 12;27(1):99-111. Epub 2017 Dec 12.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in-depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus-like LTR retrotransposon families. Then, using whole-genome resequencing data from 200 Ficedula flycatchers, we detected 11,888 polymorphic TE insertions (TE presence/absence variations, TEVs) that segregated within and among species. The density of TEVs was one every 1.5-2.5 Mb per individual, with heterozygosities of 0.12-0.16. The majority of TEVs belonged to some 10 different LTR families, most of which are specific to the flycatcher lineage. TEVs were validated by tracing the segregation of hundreds of TEVs across a three-generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species-rich group of birds.
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http://dx.doi.org/10.1111/mec.14439DOI Listing
January 2018

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

Genome Biol Evol 2017 10;9(10):2491-2505

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden.

Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.
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http://dx.doi.org/10.1093/gbe/evx163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737376PMC
October 2017

Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.

Cell Host Microbe 2017 Sep 31;22(3):387-399.e6. Epub 2017 Aug 31.

University of Heidelberg, Department of Infectious Diseases, Molecular Virology, 69120 Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras.
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http://dx.doi.org/10.1016/j.chom.2017.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604429PMC
September 2017

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

Mol Ecol 2017 Aug 5;26(16):4158-4172. Epub 2017 Jul 5.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

Recombination rate is heterogeneous across the genome of various species and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200 kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.
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http://dx.doi.org/10.1111/mec.14197DOI Listing
August 2017