Genomes From 117 Vertebrate Species Reveal Rapidly Evolving Segmental-Duplication Landscapes

Abstract. Segmental duplications are major drivers of evolutionary innovation; yet, their dynamics across vertebrates remain poorly understood. Here, we id

academic.oup.com

Wrong but useful: Bombyx silkworm W chromosome assemblies are flawed but still capture strongly reduced diversity of repetitive DNA

Degenerate sex chromosomes ( e.g., the Y or W) remain among the most difficult regions of eukaryotic genomes to assemble because they are highly repetitive and structurally complex. While many recent ...

biorxiv.org

Evidence of two centromeres in the germline-restricted chromosome (GRC): insights from zebra finch lampbrush chromosomes

The germline-restricted chromosome (GRC) of the zebra finch Taeniopygia guttata represents a well-established model of programmed DNA elimination in vertebrates. Although the DNA composition of the GR...

biorxiv.org

Second-chance speciation in the Clouded Apollo butterfly

Lancho-Silva et al. reveal two successive contacts between butterfly populations that capture the surprisingly rapid emergence of reproductive isolation driven by selection for chemical differences, a...

cell.com

piRNA loss unleashes episodic transposition bursts

In Metazoa, transposon expression is suppressed by the piRNA pathway, and disruption of this pathway leads to rampant transposon expression. However, it remains unclear whether increased transposon ex...

biorxiv.org

Scientists Found That Bean Plants Can Summon Wasps to Fight Their Battles

Researchers found that the plants can identify caterpillar attacks and summon wasps to the scene to protect them.

vice.com

Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation

Abstract. Habitat loss contributes to extinction risk in multiple ways. Genetically, small populations can face an ‘extinction vortex’—a positive feedback

doi.org

Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution - BMC Biology

Background Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialized mammalian clades, yet the genomic basis of their adaptations remains poorly understood. Here, we present chromosome-level genomes for the two-toed sloth (Choloepus didactylus) and the southern anteater (Tamandua tetradactyla) and investigate how retrotransposon-mediated gene duplications (retrocopies) have shaped genome evolution in these and other species in Xenarthra. Results Comparative analyses revealed that the xenarthran genomes analyzed here harbour the highest number of retrocopies reported among mammals, with lineage-specific insertion dynamics. Anteater and armadillo genomes contain older LINE1 repertoires and species-specific older retrocopy insertions. In contrast, sloths retain both an abundance of young LINE1s and thousands of young retrocopies, alongside a large shared set that originated from an evolutionary burst of retroduplication in the branch leading to their last common ancestor (~ 30 Mya). In C. didactylus, 49% of retrocopies were found to be expressed in five tissues, compared with 27% in Dasypus novemcinctus in three tissues. Evolutionary analyses identified 38 retrocopies with strong hallmarks of domestication in C. didactylus. Many of these retrocopies derive from parental genes involved in mitochondrial and metabolic processes, suggesting a potential genomic contribution to the physiological specializations of sloths. Conclusions Altogether, our findings identify retrotransposition as a major contributor to the genomic architecture of the xenarthrans presented here and highlight retrocopy origination as a mechanism for generating lineage-specific novelty and, possibly, distinctive biological specializations.

doi.org

A sibling study of variation in parental mutation rates

People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098

biorxiv.org

Hybridization and speciation*

Abstract. Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow a

academic.oup.com

Genomics helps resolve allopatric COI (Cytochrome c oxidase subunit I) divergences in selected alpine Lepidoptera and allows for a taxonomic revision of the Symmoca signella species-complex (Autostich...

Abstract. European Lepidoptera have been subject of dense sampling for their DNA barcodes because of several active regional DNA barcoding initiatives. Thi

academic.oup.com

When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species

Post-glacial recolonisation of Fennoscandia created secondary contact zones in many species, offering opportunities to study how gene flow and selection contribute to their establishment and maintena....

onlinelibrary.wiley.com

Coalescence and translation: A language model for population genetics | PNAS

Probabilistic models such as the sequentially Markovian coalescent have long provided a powerful framework for population genetic inference, enabli...

pnas.org

From ancient catalytic folds to retrotransposons and retroviruses

This review constitutes an evolutionary journey that begins with the emergence of reverse transcriptase and other ancient catalytic folds that shape retroelements (Class I transposable elements) and ends with the appearance of retroviruses and their subsequent or simultaneous endogenization. This path comprises milestones such as the formation of prokaryotic retroelements, their appropriation by eukaryotes, which resulted in the occurrence of non-long terminal repeat (non-LTR) retroelements, the mosaic formation of LTR retroelements by utilizing components of non-LTR retroelements and DNA transposons, and the acquisition of new domains that led to the emergence of retroviruses. We present here a comprehensive recounting of all evolutionary events that took place from the formation of primordial enzymes to the origin of retroviruses and their endogenization.

dlvr.it