Biology subjects

Hamlin, J.

Publications and source records attributed to Hamlin, J..

3 recordsLinked to original sources

bioRxiv2026

Epidemiology of Legionella: Genome-bAsed Typing (el_gato) - a new bioinformatic tool for identifying sequence-based types of Legionella pneumophila from whole genome sequencing data

Sequence-based typing (SBT) via Sanger sequencing has been the standard for describing Legionella pneumophila relationships for two decades. SBT involves sequencing seven loci, identifying alleles using the United Kingdom Health Security Agency (UKHSA) database, and inferring the corresponding sequence type (ST). While similar SBT approaches for other organisms can be easily adapted to whole genome sequencing (WGS), L. pneumophila presents two known challenges for this adaptation: multiple copies of one locus (mompS) and extensive heterogeneity in a second locus (neuA/neuAh). Although several computational methods have been proposed to address these issues, a WGS-based replacement with equal resolution to traditional SBT has been elusive. To address this gap, we developed el_gato (Epidemiology of Legionella: Genome-bAsed Typing; https://github.com/CDCgov/el_gato), which offers several advantages over existing methods: (1) a novel approach for resolving multiple mompS alleles identified in the same isolate, (2) the ability to capture diverse neuA/neuAh alleles, (3) fast runtime with an average of 27.7 seconds per sample, (4) easy installation via Bioconda or Docker and (5) an updated database as of March 2025. el_gato works with either paired-end short reads or genome assemblies, performing more accurately with paired-end short reads at least 250 base pairs (bp) in length. We compared el_gato against two other in silico SBT tools ("mompS", hereafter referred to as mompS tool and "legsta") using a dataset of 441 isolates with sequence types (STs) previously determined by Sanger-based sequencing. el_gato correctly identified the ST for 98.9% of the test isolates, compared to 95.2% for the mompS tool and 42.2% for legsta, demonstrating a significant improvement compared to the mompS tool (adjusted p = 1.06e-3) and legsta (adjusted p = 4.24e-55) in ST identification. Furthermore, el_gatos determination of ST was not significantly different from Sanger sequencing (adjusted p = 0.442). In summary, el_gato significantly improves in silico SBT and given its growing adoption, is poised to support the public health community.

bioinformatics↗

bioRxiv2019

Spatial proximity determines post-speciation introgression in Solanum

An increasing number of phylogenomic studies have documented a clear footprint of post-speciation introgression among closely-related species. Nonetheless, systematic genome-wide studies of factors influencing the likelihood of introgression remain rare. Here, we use an a priori hypothesis-testing framework, and introgression statistics, to evaluate the prevalence and frequency of introgression. Specifically, with whole genome sequences from 32 lineages of wild tomato species, we assess the effect of three factors on introgression: genetic relatedness, geographical proximity, and mating system differences. Using multiple trios within the ABBA-BABA test, we find that one of our factors, geographic proximity, is consistently associated with evidence for recent introgression between species. Of 14 species pairs with proximate versus distant population comparisons, 12 showed evidence of introgression; in ten of these cases, this was more prevalent between geographically-closer populations. We found no evidence that introgression varies systematically with increasing genetic divergence between lineages or with mating system differences, although we have limited power to address the latter effect. While our analysis indicates that recent post-speciation introgression is frequent in this group, estimated levels of genetic exchange are modest (0.05-1.5% of the genome), so the relative importance of hybridization in shaping the evolutionary trajectories of these species could be limited. Regardless, similar clade-wide analyses of genomic introgression would be valuable for disentangling the major ecological, reproductive, and historical determinants of post-speciation gene flow, and for assessing the relative importance of introgression as a source of evolutionary change. IMPACT STATEMENTThe formation of new species is traditionally viewed as a tree-like branching process, in which species are discrete branches that no longer share an ongoing genealogical connection with other, equally discrete, species. Recently this view has been challenged by numerous studies examining genealogical patterns across entire genomes (all the DNA of an organism); these studies suggest that the exchange of genes between different species (known as introgression) is much more common than previously appreciated. This unexpected observation raises questions about which conditions are most important in determining whether species continue to exchange genes after they diverge. Factors such as physical proximity, differences in reproductive mechanisms, and time since species shared a common ancestor, might all contribute to determining the prevalence of introgression. But to evaluate the general importance of these factors requires more than individual cases; many species comparisons, that differ systematically in one or more of these conditions, are needed. Here we use whole-genome information from 32 lineages to evaluate patterns of introgression among multiple species in a single, closely related group--the wild tomatoes of south America. We contrast these patterns among pairs of lineages that differ in their geographical proximity, reproductive system, and time since common ancestry, to assess the individual influence of each condition on the prevalence of introgression. We find that only one of our factors--geographical proximity--is consistently associated with greater evidence for recent introgression, indicating that this is largely shaped by the geographical opportunity for hybridization, rather than other plausible biological processes. Our study is one of the first to systematically assess the influence of general ecological and evolutionary conditions on the frequency of post-speciation introgression. It also provides a straightforward, generalizable, hypothesis-testing framework for similar systematic analyses of introgression in groups of other organisms in the future.

evolutionary biology↗

bioRxiv2016

Two loci contribute epistastically to heterospecific pollen rejection, a postmating isolating barrier between species

Recognition and rejection of heterospecific male gametes occurs in a broad range of taxa, although the complexity and redundancy of mechanisms underlying this postmating cryptic female choice is poorly understood. In plants, the arena for these interactions is the female reproductive tract (pistil), within which heterospecific pollen tube growth can be arrested via active molecular recognition. Unilateral incompatibility (UI) is one such pistil-mediated barrier in which pollen rejection occurs in only one direction of an interspecific cross. We investigated the genetic basis of pistil-side UI between Solanum species, with the specific goal of understanding the role and magnitude of epistasis between UI QTL. Using heterospecific introgression lines (ILs) between Solanum pennellii and S. lycopersicum, we assessed the individual and pairwise effects of three chromosomal regions (ui1.1, ui3.1, and ui12.1) previously associated with interspecific UI among Solanum species. Specifically, we pyramided ui12.1 with each of ui1.1 and ui3.1, and assessed the strength of UI pollen rejection in pyramided (double introgression) lines, compared to single introgression genotypes. We found that none of the three QTL individually showed UI rejection phenotypes, but lines combining ui3.1 and ui12.1 showed significant pistil-side pollen rejection. Furthermore, double introgression lines that combined different chromosomal regions overlapping ui3.1 differed significantly in their rate of UI, consistent with at least two genetic factors on chromosome three contributing quantitatively to interspecific pollen rejection. Together, our data indicate that loci on both chromosomes 3 and 12 are jointly required for the expression of UI between S. pennellii and S. lycopersicum suggesting that coordinated molecular interactions among a relatively few loci underlying the expression of this postmating prezygotic barrier. In addition, in conjunction with previous data, at least one of these loci appears to also contribute to conspecific self-incompatibility, consistent with a partially shared genetic basis between inter- and intraspecific mechanisms of postmating prezygotic female choice.

evolutionary biology↗