V. J. Lynch

Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows (Paenungualta)

The paper identifies gene losses in regulated necrotic cell death pathways in elephants, hyraxes, and sea cows, linking these losses to traits like large body size and cancer resistance.

Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants

The paper identifies positively selected and rapidly evolving genes in elephants that may contribute to their cancer resistance.

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata)

This study uses phylogenomic data to analyze the branching order of Paenungulata, finding strong evidence for a polytomy with limited gene support for any specific resolution.

Pervasive relaxed selection on spermatogenesis genes coincident with the evolution of polygyny in gorillas

This study identifies genes under relaxed purifying selection in gorillas linked to male reproductive function, showing their association with human male infertility.

A CDKN2C retroduplication in Bowhead whales is associated with the evolution of extremely long lifespans and alerted cell cycle dynamics

This study identifies a CDKN2C retroduplication in Bowhead whales linked to long lifespan and altered cell cycle dynamics through evolutionary genomics and experimental approaches.

Parallel evolution of reduced cancer risk and tumor suppressor duplications in Xenarthra

The paper shows that Xenarthran mammals evolved reduced cancer risk alongside tumor suppressor gene duplications, similar to Afrotherians, and exhibit slow cell proliferation and low DNA damage.

Unraveling the relationship between cancer and life history traits in vertebrates

The paper analyzes cancer prevalence across vertebrates to explore its relationship with life history traits, finding low rates in turtles and high rates in squamates and mammals.

Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation

This study investigates the evolutionary changes in the cadherin-23 and protocadherin-15 protein complex, showing how sequence variations affect biophysical properties and contribute to deafness-causing mutations across vertebrates.

Transposable elements continuously remodel the regulatory landscape, transcriptome, and function of decidual stromal cells

This study shows transposable elements (TEs) remodel the transcriptome and regulatory landscape of decidual stromal cells through two waves, with latent enhancer functions unmasked by histone deacetylase inhibitors.

Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

This study uses ancestral transcriptome reconstruction to trace the evolution of pregnancy in vertebrates, finding that maternal gene expression correlates with placental invasion and suggesting an early origin of hemochorial placentation in eutherians.

Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles

This study shows that Galapagos giant tortoises evolved large body size, long lifespan, and reduced cancer risk through gene duplications and stress resistance mechanisms.

Evolutionary transcriptomics implicates new genes and pathways in human pregnancy and adverse pregnancy outcomes

The paper identifies human-specific gene expression changes in the endometrium linked to pregnancy traits and pathologies, suggesting evolutionary insights for understanding adverse pregnancy outcomes.

Return of a lost structure in the evolution of felid dentition revisited: A DevoEvo perspective on the irreversibility of evolution

The paper reevaluates the reevolution of the second lower molar in Eurasian lynx, finding support for its reevolution and proposing developmental mechanisms.

Pervasive duplication of tumor suppressors in Afrotherians during the evolution of large bodies and reduced cancer risk

This study identifies widespread tumor suppressor gene duplication in Afrotherians, suggesting it contributed to increased body size and reduced cancer risk.

Evolutionary transcriptomics implicates HAND2 in the origins of implantation and regulation of gestation length

This study identifies HAND2 as a key regulator of implantation and gestation length by analyzing its expression and regulatory networks at the maternal-fetal interface in eutherian mammals.

Cooption of polyalanine tract into a repressor domain in the mammalian transcription factor HoxA11

The paper shows that a polyalanine tract in HoxA11 evolved into a repressor domain in mammals, suggesting polyalanine tracts can function as repressor domains and contribute to transcription factor diversification.

Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage

This study shows that the progesterone receptor gene (PGR) evolved rapidly in the human stem-lineage due to relaxed selection, leading to functional divergence of PR-A and PR-B isoforms.

A zombie LIF gene in elephants is up-regulated by TP53 to induce apoptosis in response to DNA damage

The paper shows that elephants re-functionalized a pseudogene to enhance apoptosis, potentially explaining their resistance to cancer despite large body size.