Biology subjects

Wu, F. L.

Publications and source records attributed to Wu, F. L..

4 recordsLinked to original sources

bioRxiv2026

Estimating self-fertilization rates from the diploid genotype spectrum

The distribution of self-fertilization across the tree of life remains poorly characterized. Here we present the diploid genotype spectrum (DGS) as a useful genomic data summary for characterizing populations undergoing partial self-fertilization (selfing). This statistic provides a straightforward baseline for estimating selfing rates from population genomic data. At every segregating site across a genome, the diploid genotype configuration records the numbers of homozygous ancestral, heterozygous, and homozygous derived individuals, and the DGS compiles the counts of these configurations across sites. We show that the expected relative frequencies of DGS configurations among segregating sites can be computed under the standard coalescent approximation for partial selfing. We present two methods for doing this, one that is an intuitive recursion through possible states of the model, and one that is a more efficient combinatorial version. We give a worked example, validate the analytical expectations using forward simulations, and introduce a software package that estimates population selfing rates from diploid SNP data. The computations here mechanistically link selfing to observed patterns of diploid genotype configurations.

genomics↗

bioRxiv2026

Unmasking the large and highly repetitive genome of Phlox reveals a complex evolutionary history of speciation with gene flow

The large size and high repetitive content of many plant genomes have hindered elucidation of how the fundamental processes of evolution give rise to speciation. Here we present chromosome-level assemblies of 6 gigabase genomes for four closely related Phlox wildflower species. We generate extensive population genetic data for the three well-studied annual species P. drummondii, P. cuspidata, and P. roemeriana, including structural variation from whole-genome long-read resequencing data. The whole-genome assemblies reveal extensive differences in amount and distribution of genetic variation within and between species, reflective of differences in life-history strategies, mating systems, and edaphic specialization. The population genetic data exposes a history of widespread and consistent gene flow between all three annual Phlox species throughout their divergence and speciation. Our unmasking of structural variants and repetitive elements exposes rich and dynamic forms of genetic variation that show strong phylogenetic signal and pervasive patterns of gene flow. Our results lay a foundation for untangling the highly complex genomes of plants to make advancements in our understanding of the processes of speciation and divergence.

evolutionary biology↗

bioRxiv2022

A paternal bias in germline mutation is widespread across amniotes and can arise independently of cell divisions

In humans and other mammals, germline mutations are more likely to arise in fathers than in mothers. Although this sex bias has long been attributed to DNA replication errors in spermatogenesis, recent evidence from humans points to the importance of mutagenic processes that do not depend on cell division, calling into question our understanding of this basic phenomenon. Here, we infer the ratio of paternal-to-maternal mutations, , in 42 species of amniotes, from putatively neutral substitution rates of sex chromosomes and autosomes. Despite marked differences in gametogenesis, physiologies and environments across species, fathers consistently contribute more mutations than mothers in all the species examined, including mammals, birds and reptiles. In mammals, is as high as 4 and correlates with generation times; in birds and snakes, appears more stable around 2. These observations are consistent with a simple model, in which mutations accrue at equal rates in both sexes during early development and at a higher rate in the male germline after sexual differentiation, with a conserved paternal-to-maternal ratio across species. Thus, may reflect the relative contributions of two or more developmental phases to total germline mutations, and is expected to depend on generation time even if mutations do not track cell divisions.

evolutionary biology↗

bioRxiv2019

A comparison of humans and baboons suggests germline mutation rates do not track cell divisions

In humans, most germline mutations are inherited from the father. This observation is widely interpreted as resulting from the replication errors that accrue during spermatogenesis. If so, the male bias in mutation should be substantially lower in a closely related species with similar rates of spermatogonial stem cell divisions but a shorter mean age of reproduction. To test this hypothesis, we resequenced two 3-4 generation nuclear families (totaling 29 individuals) of olive baboons (Papio anubis), who reproduce at ~10 years of age on average. We inferred sex-specific mutation rates by analyzing the data in parallel with three three-generation human pedigrees (26 individuals). The mutation rate per generation in baboons is 0.55x10-8 per base pair, approximately half that of humans. Strikingly, however, the degree of male mutation bias is approximately 3:1, similar to that of humans; in fact, a similar male bias is seen across mammals that reproduce months, years or decades after birth. These results echo findings in humans that the male bias is stable with parental ages and cast further doubt on the assumption that germline mutations track cell divisions. Our mutation rate estimates for baboons raise a further puzzle in suggesting a divergence time between apes and Old World Monkeys of 67 My, too old to be consistent with the fossil record; reconciling them now requires not only a slowdown of the mutation rate per generation in humans but also in baboons.

evolutionary biology↗