ORCID Profile
0000-0001-8714-0812
Current Organisation
Uppsala University
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Publisher: Springer Science and Business Media LLC
Date: 18-01-2017
Publisher: Oxford University Press (OUP)
Date: 04-05-2012
Abstract: The platypus (Ornithorhynchus anatinus) is the sole survivor of a previously widely distributed and erse lineage of ornithorhynchid monotremes. Its dependence on healthy water systems imposes an inherent sensitivity to habitat degradation and climate change. Here, we compare genetic ersity at the major histocompatibility complex (MHC) Class II-DZB gene and 3 MHC-associated microsatellite markers with ersity at 6 neutral microsatellite markers in 70 platypuses from across their range, including the mainland of Australia and the isolated populations of Tasmania, King Island, and Kangaroo Island. Overall, high DZB ersity was observed in the platypus, with 57 DZB β1 alleles characterized. Significant positive selection was detected within the DZB peptide-binding region, promoting variation in this domain. Low levels of genetic ersity were detected at all markers in the 2 island populations, King Island (endemic) and Kangaroo Island (introduced), with the King Island platypuses monomorphic at the DZB locus. Loss of MHC ersity on King Island is of concern, as the population may have compromised immunological fitness and reduced ability to resist changing environmental conditions.
Publisher: Wiley
Date: 29-05-2018
DOI: 10.1002/ECE3.4163
Publisher: Springer Science and Business Media LLC
Date: 27-05-2016
DOI: 10.1007/S00251-016-0919-9
Abstract: The cane toad has gained notoriety for its invasion across the Australian landscape, with significant impacts on the native Australian fauna. The invasion has accelerated over time, with invading cane toads adapted for highly dispersive traits. This, however, has come at the cost of the immune system, with lower investment in some immune functions. To investigate the cane toad's immunogenetics, we characterized four major histocompatibility complex (MHC) class IIA and three MHC class IIB loci. Preliminary observations suggest very low allelic ersity at all loci. We also observed various splice isoforms. One isoform seen at one class IIA and two class IIB loci was missing exon 2, which is essential to peptide binding and presentation. The other isoform, observed at a class IIA locus, is likely to be a soluble MHC product. These results may suggest a significant role of alternative splicing of MHC loci in the Australian cane toad.
Publisher: Springer Science and Business Media LLC
Date: 07-05-2021
DOI: 10.1038/S41437-021-00438-5
Abstract: The use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish ( Silurus glanis ), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for ex le due to loss of genetic ersity, and may thus require conservation actions. We sequenced in iduals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic ersity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. In iduals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.
Publisher: Cold Spring Harbor Laboratory
Date: 20-09-2018
DOI: 10.1101/421768
Abstract: Experimental intercrosses between outbred founder populations are powerful resources for mapping loci contributing to complex traits (Quantitative Trait Loci or QTL). Here, we present an approach and accompanying software for high-resolution genotype imputation in such populations using whole-genome high coverage sequence data on founder in iduals (∼30×) and low coverage sequence data on intercross in iduals (∼0.4×). The method is illustrated in a large F 2 pedigree between lines of chickens that have been ergently selected for 40 generations for the same trait (body weight at 8 weeks of age). Described is how hundreds of in iduals were whole-genome sequenced in a cost- and time-efficient manner using a Tn5 -based library preparation protocol optimized for this application. In total, 7.6M markers segregated in this pedigree and 10.0 to 13.7% were informative for imputing the founder line genotypes within the F 0 -F 2 families. The genotypes imputed from low coverage sequence data were consistent with the founder line genotypes estimated using SNP and microsatellite markers both at in idual imputed sites (92%) and across the genome of in idual chickens (93%). The resolution of the recombination breakpoints was high with 50% being resolved within kb. A method for genotype imputation from low-coverage whole-genome sequencing in outbred intercrosses is described and evaluated. By applying it to an outbred chicken F 2 cross it is illustrated that it provides high quality, high-resolution genotypes in a time and cost efficient manner.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.3382/PS/PEX383
Abstract: Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for ergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.
Publisher: Oxford University Press (OUP)
Date: 11-07-2017
Abstract: The ability of a population to adapt to changes in their living conditions, whether in nature or captivity, often depends on polymorphisms in multiple genes across the genome. In-depth studies of such polygenic adaptations are difficult in natural populations, but can be approached using the resources provided by artificial selection experiments. Here, we dissect the genetic mechanisms involved in long-term selection responses of the Virginia chicken lines, populations that after 40 generations of ergent selection for 56-day body weight display a 9-fold difference in the selected trait. In the F15 generation of an intercross between the ergent lines, 20 loci explained >60% of the additive genetic variance for the selected trait. We focused particularly on fine-mapping seven major QTL that replicated in this population and found that only two fine-mapped to single, bi-allelic loci the other five contained linked loci, multiple alleles or were epistatic. This detailed dissection of the polygenic adaptations in the Virginia lines provides a deeper understanding of the range of different genome-wide mechanisms that have been involved in these long-term selection responses. The results illustrate that the genetic architecture of a highly polygenic trait can involve a broad range of genetic mechanisms, and that this can be the case even in a small population bred from founders with limited genetic ersity.
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.3382/PS/PEZ411
Publisher: Wiley
Date: 19-04-2010
Publisher: Springer Science and Business Media LLC
Date: 14-08-2019
Publisher: Public Library of Science (PLoS)
Date: 05-08-2014
Publisher: Springer Science and Business Media LLC
Date: 13-10-2022
DOI: 10.1038/S41467-022-33723-W
Abstract: Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a s ling of retroviral ersity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all s les indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Publisher: Cold Spring Harbor Laboratory
Date: 05-04-2016
DOI: 10.1101/046953
Abstract: Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation. They allow researchers to uncover the targets of selection and how these contribute to the mode and tempo of adaptation. Here we report results from a pooled genome re-sequencing study to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells. We observed wide genome involvement in response to this selection regime, with over 200 candidate sweep regions characterised by spans of high genetic differentiation ( F ST ). These sweep signatures, encompassing almost 20% of the chicken genome (208.8 Mb), are primarily the result from bidirectional selection on haplotypes present in the base population. These extensive genomic changes highlight both the extent of standing genetic variation at immune loci available at the onset of selection, as well as how the long-term selection response results from selection on a highly polygenic genetic architecture. Furthermore, we present three ex les of strong candidate genes that may have contributed to the profound phenotypic response to selection. Pooled genome data generated for this study will become available via SRA upon acceptance of manuscript
Publisher: Cold Spring Harbor Laboratory
Date: 14-11-2018
DOI: 10.1101/469049
Abstract: Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. Using pooled genome resequencing of paired generations of these lines, we reveal the within and between-line genomic signatures of selection. At 55 generations of ergent selection, 14.2% of the genome showed extreme differentiation between the selected lines were contained within 395 genomic regions. The lines often displayed a duality of the sweep signatures: an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consist of short, distinct haploblocks of variable between-line ergence. Formed during what probably was a complex history of bottlenecks, inbreeding, and introgressions, these mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.
Publisher: Proceedings of the National Academy of Sciences
Date: 13-06-2022
Abstract: Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, ersity, and prevalence provide insights into the historical dynamics of retrovirus–host interactions. In bioinformatic analyses of koala ( Phascolarctos cinereus ) whole-genome sequences, we identify a recently expanded ERV lineage ( phaCin-β ) that is related to the New World squirrel monkey retrovirus. This ERV expansion shares many parallels with the ongoing koala retrovirus (KoRV) invasion of the koala genome, including highly similar and mostly intact sequences, and polymorphic ERV loci in the s led koala population. The recent phaCin-β ERV colonization of the koala genome appears to predate the current KoRV invasion, but polymorphic ERVs and ergence comparisons between these two lineages predict a currently uncharacterized, possibly still extant, phaCin-β retrovirus. The genomics approach to ERV-guided discovery of novel retroviruses in host species provides a strong incentive to search for phaCin-β retroviruses in the Australasian fauna.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2015
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.DCI.2016.12.003
Abstract: Amphibians, as the first terrestrial vertebrates, offer a window into early major histocompatibility complex (MHC) evolution. We characterized the MHC class I of two Korean hibians, the Asiatic toad (Bufo gargarizans) and the Japanese tree frog (Hyla japonica). We found at least four transcribed MHC class I (MHC I) loci, the highest number confirmed in any anuran to date. Furthermore, we identified MHC I transcripts in terrestrial adults, and possibly in aquatic larvae, of both species. We conducted a phylogenetic analysis based on MHC I sequence data and found that B. gargarizans and H. japonica cluster together in the superfamily Nobleobatrachia. We further identified three supertypes shared by the two species. Our results reveal substantial variation in the number of MHC I loci in anurans and suggest that certain supertypes have particular physiochemical properties that may confer pathogen resistance.
Publisher: Oxford University Press (OUP)
Date: 15-05-2012
Publisher: CSIRO Publishing
Date: 2017
DOI: 10.1071/WR17055
Abstract: Context The cane toad (Rhinella marina), a native species of central and southern America, was introduced to Australia in 1935 as a biocontrol agent after a complex history of prior introductions. The population rapidly expanded and has since spread through much of the Australian landmass, with severe impacts on the endemic wildlife, primarily via toxicity to predators. The invasion process has taken its toll on the cane toad, with changes in the immunological capacity across the Australian invasive population. Aims To investigate the immunogenetic underpinnings of these changes, we studied the ersity of the Major Histocompatiblity Complex (MHC) genes in introduced cane toad populations. Methods We studied the ersity of two MHC genes (the classical class I UA locus and a class II DAB locus) and compared these with neutral microsatellite markers in toads from the Australian site of introduction and the Australian invasion front. We also included toads from Hawai’i, the original source of the Australian toads, to infer founder effect. Key results Diversity across all markers was low across Australian and Hawai’ian s les, consistent with a reduction in genetic ersity through multiple founder effects during the course of the successive translocations. In Australia, allelic ersity at the microsatellite markers and the UA locus was reduced at the invasion front, whereas all three alleles at the DAB locus were maintained in the invasion-front toads. Conclusions Loss of allelic ersity observed at the microsatellite markers and the UA locus could be the result of drift and bottlenecking along the invasion process, however, the persistence of DAB ersity warrants further investigation to disentangle the evolutionary forces influencing this locus. Implications Through the use of different molecular markers, we provide a preliminary description of the adaptive genetic processes occurring in this invasive population. The extremely limited MHC ersity may represent low immunogenetic competence across the Australian population, which could be exploited for invasive species management.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Springer Science and Business Media LLC
Date: 04-02-2019
Publisher: Cold Spring Harbor Laboratory
Date: 26-03-2022
DOI: 10.1101/2022.03.25.485756
Abstract: Endogenous retroviruses (ERVs) are inherited remnants of past retroviruses that colonized host germline over millions of years, providing a s ling of retroviral ersity across time. The utility of ERVs as markers of host genome evolution is augmented by their ability to reveal historic retrovirus-host interactions, given that ERVs are ex les of active retroviruses at the time of germline invasion. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system as a natural model for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We found shared ERVs among all s les indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggest historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, as well as across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.
Publisher: Oxford University Press (OUP)
Date: 04-2019
Abstract: Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of ergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line ergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the ex le of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.
No related grants have been discovered for Mette Lillie.