Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets

Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions

Gene flow analysis method, the D-statistic, is robust in a wide parameter space

Background: We evaluated the sensitivity of the D-statistic, a parsimony-like method widely used to detect gene flow between closely related species. This method has been applied to a variety of taxa with a wide range of divergence times. However, its parameter space and thus its applicability to a wide taxonomic range has not been systematically studied. Divergence time, population size, time of gene flow, distance of outgroup and number of loci were examined in a sensitivity analysis. Result: The sensitivity study shows that the primary determinant of the D-statistic is the relative population size, i.e. the population size scaled by the number of generations since divergence. This is consistent with the fact that the main confounding factor in gene flow detection is incomplete lineage sorting by diluting the signal. The sensitivity of the D-statistic is also affected by the direction of gene flow, size and number of loci. In addition, we examined the ability of the f-statistics, fˆGf^G and fˆhomf^hom, to estimate the fraction of a genome affected by gene flow; while these statistics are difficult to implement to practical questions in biology due to lack of knowledge of when the gene flow happened, they can be used to compare datasets with identical or similar demographic background. Conclusions: The D-statistic, as a method to detect gene flow, is robust against a wide range of genetic distances (divergence times) but it is sensitive to population size. The D-statistic should only be applied with critical reservation to taxa where population sizes are large relative to branch lengths in generations

Pangolin genomes offer key insights and resources for the world's most trafficked wild mammals

DATA AVAILABILITY : Draft genomes (Manis culionensis, M. crassicaudata, Phataginus tetradactyla, Smutsia temminckii) and the hybrid assembled, annotated reference genome with associated metadata (S. gigantea) are available in the GenBank Nucleotide Database (BioProject: PRJNA795390). The associated sequence read data have also been deposited in Genbank (SRA: SRR17702824-SRR17702828) for the aforementioned genomes (except for S. temminckii). The accession numbers or links for all accessed genomic data are listed in supplementary table S1, Supplementary Material online. A database containing the list genes ranked by diversity amongst all eight pangolin species has been deposited at Zenodo and is publicly available (supplementary Database S1, Supplementary Material online: https://doi.org/10.5281/zenodo.7517409). All original code in the form of custom scripts for processing the genomics data in this study have also been deposited at Zenodo and are publicly available (Custom scripts 1–3: https://doi.org/10.5281/zenodo.7517409). Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.The Agence Nationale de la Recherche, European Research Council, Mohamed bin Zayed Species Conservation Fund, the National Research Foundation of South Africa and the National Natural Science Foundation of China.https://academic.oup.com/mbehj2024Mammal Research InstituteZoology and EntomologySDG-15:Life on lan

Diversification Across a Dynamic Landscape: Phylogeography and Riverscape Genetics of Speckled Dace (Rhinichthys osculus) in Western North America

Evolution occurs at various spatial and temporal scales. For example, speciation may occur in historic time, whereas localized adaptation is more contemporary. Each is required to identify and manage biodiversity. However, the relative abundance of Speckled Dace (Rhinichthys osculus), a small cyprinid fish in western North America (WNA) and the study species for this dissertation, establishes it an atypical conservation target, particularly when contrasted with the profusion of narrowly endemic forms it displays. Yet, the juxtaposition of ubiquity versus endemism provides an ideal model against which to test hypotheses regarding the geomorphic evolution of WNA. More specifically, it also allows the evolutionary history of Speckled Dace to be contrasted at multiple spatial and temporal scales, and interpreted in the context of contemporary anthropogenic pressures and climatic uncertainty. Chapter II dissects the broad distribution of Speckled Dace and quantifies how its evolution has been driven by hybridization/ introgression. Chapter III narrows the geographic focus by interpreting Speckled Dace distribution within two markedly different watersheds: The Colorado River and the Great Basin. The former is a broad riverine habitat whereas the latter is an endorheic basin. Two biogeographic models compare and contrast the tempo and mode of evolution within these geologically disparate habitats. Chapter IV employs a molecular clock to determine origin of Speckled Dace lineages in Death Valley (CA/NV), and to contrast these against estimates for a second endemic species, Devil’s Hole Pupfish (Cyprinodon diabolis). While palaeohydrology served to diversify Rhinichthys, its among-population connectivity occurred contemporaneously. These data also provide guidance for assessing the origin of the Devil’s Hole Pupfish, a topic of considerable contention. The final two chapters present bioinformatic software that facilitates the analysis of single-nucleotide-polymorphism (SNP) DNA data (used herein). Chapter V describes COMP-D, a program designed to assess introgression among lineages, whereas Chapter VI presents programmatic modifications to BAYESASS that allow migration to be quantified from SNP datasets. These five studies provide an in-depth understanding of contemporary and historical processes that shape aquatic biodiversity in environments prone to anthropogenic disturbance. They also highlight the complexities of evolutionary mechanisms and their implications for conservation in a changing world

The influence of hybridization on range dynamics

Hybridization can have a significant influence on the evolutionary trajectories of both plant and animal lineages, resulting in a variety of outcomes including – but not limited to – range expansion, stabilization, and decay. When early generation hybrids have high fitness, or when adaptive genetic variation is transferred between the genetic backgrounds of hybridizing taxa via so-called adaptive introgression, hybridization can facilitate the colonization of novel environments, resulting in range expansion. On the other hand, when hybrids have low fitness, or when other negative sexual interactions occur, frequent heterospecific mating can result in a reduction in parental fitness via wasting reproductive effort. One potential result of this evolutionarily unstable scenario is the evolution of reproductive characters to avoid heterospecific mating (ie. reproductive character displacement and reinforcement), which may stabilize range boundaries. Another potential result is that one of the two lineages is excluded from sympatry before reinforcement can evolve, leading to range decay. Although much attention has been paid to reinforcement due to the important implications it has for the process of speciation, relatively less is known about the factors that influence when hybridization results in range expansion and decay.The body of work presented here seeks to help fill this knowledge gap by exploring a number of ecological and evolutionary genetic factors that influence when and how hybridization leads to range expansion and decay. I focus predominantly on island systems because islands: i) offer unique eco-evolutionary contexts that may encourage heterospecific mating in secondary contact, ii) host an alarming number of biological invasions where hybridization may have influenced range dynamics and, consequently, iii) offer systems where the influence of hybridization on range dynamics may have immediate ramifications for the conservation of native species. In my first chapter, I present an ecological and evolutionary framework for understanding the causes and consequences of hybridization on islands – with particular emphasis on the influence of genetic divergence on outcomes of hybridization. In my second chapter, I use a population genetic modeling approach to generate predictions about how genetic architecture influences the contribution of hybridization to range expansion. In my third chapter, I explore the potential role of hybridization in facilitating the range expansion of invasive Psidium guajava in the Galápagos Islands. In my fourth and final chapter, I investigate whether reproductive interference with invasive guava may be contributing to the ongoing range decay of guayabillo in the Galápagos.Doctor of Philosoph

Additional file 1: of Gene flow analysis method, the D-statistic, is robust in a wide parameter space

Sensitivity and input parameters (continued). Description: The relationship of sensitivity as measured with MF80, the minimal fraction of gene flow that produces over 80% significant D-statistics, and various input parameters: A. the ratio of divergence times, T2 and T3; B. the ratio of time of gene flow (Tgf) and T2. Red points represent gene flow from H3 to H2, and green points represent gene flow from H2 to H3. (PDF 150 kb

Elucidating the past using ancient genomes and metagenomes

The recognition that DNA from long dead organisms can be extracted and sequenced from a multitude of substrates has revolutionised the field of bioarchaeology. Apart from yielding profound discoveries into the biology, migrations, and admixture of past populations based on the host DNA, some artefacts are now recognised as repositories for dietary and host- associated microbial DNA and thus hold vital clues to the health status and lifestyle of the individual. This thesis is composed of three studies on three quite distinct substrates – historic hide, fluid-preserved museum specimens, and an ancient birch “chewing gum” – where I applied population genomic and metagenomic analyses to infer the population history and microbiome compositions of past organisms. After briefly introducing the broad themes of this dissertation in Chapter 1, Chapter 2 of this dissertation explores the population history of the Honshū wolves, a poorly-understood grey wolf subspecies that was endemic to the Japanese archipelago and went extinct at the beginning of the 20th century. The nuclear genome from the museum hide of one specimen was ge at an average depth of coverage of 3.8×, and I discovered that Honshū wolves were likely the relict of a Pleistocene Siberian wolf population that was up to now believed to have gone extinct about 10,000 years ago. Chapter 3 and Chapter 4 discuss the metagenomic potential of two novel substrates. In Chapter 3 we sequenced gut samples of six historic fluid-preserved birds with the aim of capturing the host-associated microbial profile. While I was able to characterise the gut microbiome of one specimen, further research is necessary to improve the feasibility of performing metagenomic analyses on fluid-preserved samples. Finally, in Chapter 4 I analysed the DNA extracted from a 5,700 year old chewed birch bark pitch. We obtained a complete human genome at an average depth of coverage of 2.3× and found that the female who chewed the birch pitch genetically closely resembles Western hunter-gatherers. The birch “chewing gum” also proved to be a rich source of microbial and non-human eukaryotic DNA, and I was able to recover the genomes of bacterial taxa that are closely associated with the oral microbiome as well as DNA from mallard, hazelnut, and birch that are likely derived from a recent meal and the birch pitch material itself. In conclusion, this dissertation sheds light on wolf and human evolution as well as introduces two novel substrates with potential for future metagenomic analyses. These projects demonstrate that researchers must continue exploring whether unusual archaeological and historic substrates contain genetic material that can be used to resolve long standing questions, thereby unlocking new opportunities to understand the history of our world