scholarly journals Connecting the past, present and future: A population genomic study of Australasian snapper (Chrysophrys auratus) in New Zealand

2021 ◽  
Author(s):  
◽  
Tom Oosting
Keyword(s):  
New Zealand ◽  
Fisheries Management ◽  
Divergent Selection ◽  
Whole Genome ◽  
Glacial Cycles ◽  
Population Genomic ◽  
Genomic Study ◽  
Large Populations ◽  
Scale Population ◽  
Genomic Regions

<p><b>Advances in genomic methods now enable the study of wild populations and their evolutionary history at an unprecedented level. The genotyping of many thousands of genetic markers across the genome provides high statistical resolution. This enables the identification of adaptive genetic variation, providing novel insights into population demography and the processes driving population divergence. Marine fish are ideal candidates to study the processes driving evolutionary divergence because selection works efficiently in large populations, and marine populations can be distributed over large spatial ranges and occupy a range of environmental conditions. This thesis used whole-genome variant data to study the Australasian snapper (Chrysophrys auratus, tāmure) in New Zealand. Snapper is one of New Zealand’s largest inshore fisheries and has experienced significant population reductions. The aims of this thesis were to investigate the genome-wide variation in snapper in New Zealand and 1) assess the neutral and adaptive population genetic structure, 2) reconstruct the demographic history, and 3) identify genomic regions, genes and their functions that show signs of selection.</b></p> <p>Population genomic structure was assessed using whole-genome resequencing data from 350 individuals, and this data set resulted in 167,543 assumed neutrally evolving loci (SNPs). It was found that levels of genetic diversity were not significantly different between populations, suggesting that fishing pressure has not lead to local reductions in genetic variation. Levels of genetic differentiation between sampled populations was low, with significant evidence for isolation by distance (R2 = 0.75, p = 0.002). Pairwise FST estimates and PCA/DAPC showed the presence of two genetic clusters, one containing the northern and one containing the southern populations. Genetic disjunctions combined with mixing between the clusters was detected around the Mahia peninsula and Cape Reinga. The identification of adaptive loci enabled the identification of fine-scale population structure, reflecting currently recognized stocks. The ability to differentiate between stocks is fundamental for fisheries management. The patterns detected here show promising results for future implementation into fisheries management of snapper stocks.</p> <p>Contemporary and ancient mitochondrial genomes were used to assess the demographic, and phylogeographic history of snapper. Analyses indicated that haplotype diversity was high (0.968-0.982), which is commonly observed in species with large populations sizes. Mitochondrial genomes showed the presence of two lineages that diverged approximately 650,000 (490,000 – 840,000) years ago. The separation was likely linked to reductions in sea level during glacial cycles. Estimates of changes in population size show strong support for an exponential population size increase after the last glacial maximum (LGM). Changes in population abundance based on the Bayesian Skyline plot indicated a strong population increase approximately 10,000 years ago. The steep increase in new branches in the phylogenetic tree suggests population sizes increase approximately 20,000 (7,000-35,000) years ago. A post-glacial expansion is the most likely explanation for the observed increase in population abundance. During this period, sea levels rose which presumably reconnected fragmented populations, and subsequent increased sea temperatures allowed for southward expansion.</p> <p>Whole-genome sequences from contemporary snapper populations were used to identify genes under selection. Analyses were conducted to detect selection in a single genetic cluster (divergent selection), or both genetic clusters (nation-wide selection). In total, 101 genomic regions containing 253 different genes showed evidence for selection. Two genomic regions showed strong evidence for divergent selection between the northern and southern cluster (FST > 0.2). The regions contained two genes associated with glycolysis which are linked to (cell-) growth (i.e. mast2 and hk2). The regions containing hk2 showed a lack of rare alleles (TD > 2) in the southern cluster, consistent with balancing selection maintaining multiple alleles in the population. Variation in growth rate may be maintained throughout the genetic cluster because of a latitudinal gradient in sea temperature. Strong evidence for selective sweeps were detected in two genomic regions on a nation-wide level. Both regions contained genes associated with angiogenesis (mydgf and rnf213a), which has been shown to affect maturation in species of fish. While tentative, it is possible that intense size-selective fishing is selecting for early maturation in snapper, a life life-history commonly associated with fishing-induced evolution. A selection scan contrasting the population Tasman Bay and Karamea Bight was performed to test for evidence of adaption to cold stress. Selection was detected in 123 genomic regions containing 296 genes, of which 197 potentially experience divergent selection. Two genes were located in regions that showed significant evidence of selection (camk2g and ksr2). Both genes have been associated with cold stress in previous studies, suggesting the Karamea Bight could represent an adaptive front at the southern range of the distribution of snapper.</p> <p>This thesis presents the first population genomic study of Australasian snapper in New Zealand, a species with a diverse genetic landscape and a rich evolutionary history. The detection of fine-scale population structure through adaptive differences between populations highlights the promising application of genomics in fisheries management. The study of mitochondrial lineages showed the effect of glacial cycles, providing insights into how New Zealand’s marine fauna has been affected by major changes in global climate. Finally, the identification of genes and associated biological traits under selection has provided fundamental new insights regarding the environmental conditions that drive adaptive change and act on phenotypes. Snapper is an ideal species for developing and integrating genomics into New Zealand fisheries management. A detailed understanding of fish stock demography and adaptive potential is critical to support improvement to fisheries management as wild stocks continue to face strong anthropogenic pressures (e.g. climate change and overexploitation). Genomics provides valuable insights into how stock assessments and harvesting levels can be better set to match the natural biological units of a species that are determined by gene flow and adaptive variation.</p>

scholarly journals Connecting the past, present and future: A population genomic study of Australasian snapper (Chrysophrys auratus) in New Zealand

2021 ◽  
Author(s):  
◽  
Tom Oosting
Keyword(s):  
New Zealand ◽  
Fisheries Management ◽  
Divergent Selection ◽  
Whole Genome ◽  
Glacial Cycles ◽  
Population Genomic ◽  
Genomic Study ◽  
Large Populations ◽  
Scale Population ◽  
Genomic Regions

<p><b>Advances in genomic methods now enable the study of wild populations and their evolutionary history at an unprecedented level. The genotyping of many thousands of genetic markers across the genome provides high statistical resolution. This enables the identification of adaptive genetic variation, providing novel insights into population demography and the processes driving population divergence. Marine fish are ideal candidates to study the processes driving evolutionary divergence because selection works efficiently in large populations, and marine populations can be distributed over large spatial ranges and occupy a range of environmental conditions. This thesis used whole-genome variant data to study the Australasian snapper (Chrysophrys auratus, tāmure) in New Zealand. Snapper is one of New Zealand’s largest inshore fisheries and has experienced significant population reductions. The aims of this thesis were to investigate the genome-wide variation in snapper in New Zealand and 1) assess the neutral and adaptive population genetic structure, 2) reconstruct the demographic history, and 3) identify genomic regions, genes and their functions that show signs of selection.</b></p> <p>Population genomic structure was assessed using whole-genome resequencing data from 350 individuals, and this data set resulted in 167,543 assumed neutrally evolving loci (SNPs). It was found that levels of genetic diversity were not significantly different between populations, suggesting that fishing pressure has not lead to local reductions in genetic variation. Levels of genetic differentiation between sampled populations was low, with significant evidence for isolation by distance (R2 = 0.75, p = 0.002). Pairwise FST estimates and PCA/DAPC showed the presence of two genetic clusters, one containing the northern and one containing the southern populations. Genetic disjunctions combined with mixing between the clusters was detected around the Mahia peninsula and Cape Reinga. The identification of adaptive loci enabled the identification of fine-scale population structure, reflecting currently recognized stocks. The ability to differentiate between stocks is fundamental for fisheries management. The patterns detected here show promising results for future implementation into fisheries management of snapper stocks.</p> <p>Contemporary and ancient mitochondrial genomes were used to assess the demographic, and phylogeographic history of snapper. Analyses indicated that haplotype diversity was high (0.968-0.982), which is commonly observed in species with large populations sizes. Mitochondrial genomes showed the presence of two lineages that diverged approximately 650,000 (490,000 – 840,000) years ago. The separation was likely linked to reductions in sea level during glacial cycles. Estimates of changes in population size show strong support for an exponential population size increase after the last glacial maximum (LGM). Changes in population abundance based on the Bayesian Skyline plot indicated a strong population increase approximately 10,000 years ago. The steep increase in new branches in the phylogenetic tree suggests population sizes increase approximately 20,000 (7,000-35,000) years ago. A post-glacial expansion is the most likely explanation for the observed increase in population abundance. During this period, sea levels rose which presumably reconnected fragmented populations, and subsequent increased sea temperatures allowed for southward expansion.</p> <p>Whole-genome sequences from contemporary snapper populations were used to identify genes under selection. Analyses were conducted to detect selection in a single genetic cluster (divergent selection), or both genetic clusters (nation-wide selection). In total, 101 genomic regions containing 253 different genes showed evidence for selection. Two genomic regions showed strong evidence for divergent selection between the northern and southern cluster (FST > 0.2). The regions contained two genes associated with glycolysis which are linked to (cell-) growth (i.e. mast2 and hk2). The regions containing hk2 showed a lack of rare alleles (TD > 2) in the southern cluster, consistent with balancing selection maintaining multiple alleles in the population. Variation in growth rate may be maintained throughout the genetic cluster because of a latitudinal gradient in sea temperature. Strong evidence for selective sweeps were detected in two genomic regions on a nation-wide level. Both regions contained genes associated with angiogenesis (mydgf and rnf213a), which has been shown to affect maturation in species of fish. While tentative, it is possible that intense size-selective fishing is selecting for early maturation in snapper, a life life-history commonly associated with fishing-induced evolution. A selection scan contrasting the population Tasman Bay and Karamea Bight was performed to test for evidence of adaption to cold stress. Selection was detected in 123 genomic regions containing 296 genes, of which 197 potentially experience divergent selection. Two genes were located in regions that showed significant evidence of selection (camk2g and ksr2). Both genes have been associated with cold stress in previous studies, suggesting the Karamea Bight could represent an adaptive front at the southern range of the distribution of snapper.</p> <p>This thesis presents the first population genomic study of Australasian snapper in New Zealand, a species with a diverse genetic landscape and a rich evolutionary history. The detection of fine-scale population structure through adaptive differences between populations highlights the promising application of genomics in fisheries management. The study of mitochondrial lineages showed the effect of glacial cycles, providing insights into how New Zealand’s marine fauna has been affected by major changes in global climate. Finally, the identification of genes and associated biological traits under selection has provided fundamental new insights regarding the environmental conditions that drive adaptive change and act on phenotypes. Snapper is an ideal species for developing and integrating genomics into New Zealand fisheries management. A detailed understanding of fish stock demography and adaptive potential is critical to support improvement to fisheries management as wild stocks continue to face strong anthropogenic pressures (e.g. climate change and overexploitation). Genomics provides valuable insights into how stock assessments and harvesting levels can be better set to match the natural biological units of a species that are determined by gene flow and adaptive variation.</p>

scholarly journals Genomic signatures of rapid adaptive divergence in a tropical montane species

2021 ◽  
Vol 17 (7) ◽  
pp. 20210089
Author(s):  
Per G. P. Ericson ◽  
Martin Irestedt ◽  
Huishang She ◽  
Yanhua Qu
Keyword(s):  
Environmental Heterogeneity ◽  
Adaptive Divergence ◽  
Glacial Cycles ◽  
Genomic Signatures ◽  
Tropical Mountain ◽  
Population Genomic ◽  
Allopatric Divergence ◽  
Suitable Habitats ◽  
Genomic Regions ◽  
Two Populations

Mountain regions contain extraordinary biodiversity. The environmental heterogeneity and glacial cycles often accelerate speciation and adaptation of montane species, but how these processes influence the genomic differentiation of these species is largely unknown. Using a novel chromosome-level genome and population genomic comparisons, we study allopatric divergence and selection in an iconic bird living in a tropical mountain region in New Guinea, Archbold's bowerbird ( Amblyornis papuensis ). Our results show that the two populations inhabiting the eastern and western Central Range became isolated ca 11 800 years ago, probably because the suitable habitats for this cold-tolerating bird decreased when the climate got warmer. Our genomic scans detect that genes in highly divergent genomic regions are over-represented in developmental processes, which is probably associated with the observed differences in body size between the populations. Overall, our results suggest that environmental differences between the eastern and western Central Range probably drive adaptive divergence between them.

scholarly journals Interspecific introgression mediates adaptation to whole genome duplication

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Sarah Marburger ◽  
Patrick Monnahan ◽  
Paul J. Seear ◽  
Simon H. Martin ◽  
Jordan Koch ◽  
...  
Keyword(s):  
Gene Flow ◽  
Opposite Direction ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Levels Of Selection ◽  
Whole Genome ◽  
Interspecific Introgression ◽  
Population Genomic ◽  
Genomic Study ◽  
Arabidopsis Arenosa

AbstractAdaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.

Identification of genomic islands in Synechococcus sp. WH8102 using genomic barcode and whole-genome microarray analyses

2020 ◽  
Vol 15 ◽  
Author(s):  
Jiahui Pan ◽  
Xizi Luo ◽  
Tong Shao ◽  
Chaoying Li ◽  
Tingting Zhao ◽  
...  
Keyword(s):  
Genomic Islands ◽  
Whole Genome ◽  
Photosynthetic Organisms ◽  
Depth Study ◽  
Whole Genome Microarray ◽  
Integrated Methods ◽  
Synechococcus Sp ◽  
Intuitive View ◽  
Genomic Regions ◽  
Different Origins

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes. Results: Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain. Conclusion: Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 456
Author(s):  
Hewa Bahithige Pavithra Chathurangi Ariyarathne ◽  
Martin Correa-Luna ◽  
Hugh Thomas Blair ◽  
Dorian John Garrick ◽  
Nicolas Lopez-Villalobos
Keyword(s):  
Gene Ontology ◽  
New Zealand ◽  
Dairy Cows ◽  
Candidate Genes ◽  
Milk Fat ◽  
Crude Protein ◽  
Single Locus ◽  
Protein Utilization ◽  
Grazing Dairy Cows ◽  
Genomic Regions

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals Fast genetic mapping using insertion-deletion polymorphisms in Caenorhabditis elegans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ho-Yon Hwang ◽  
Jiou Wang
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Mapping ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Material ◽  
Mapping Method ◽  
Forward Genetics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Large Populations

AbstractGenetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.

scholarly journals Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Joseph Crispell ◽  
Ruth N. Zadoks ◽  
Simon R. Harris ◽  
Brent Paterson ◽  
Desmond M. Collins ◽  
...  
Keyword(s):  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bovine Tuberculosis ◽  
Whole Genome ◽  
Host System

46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 25-25
Author(s):  
Muhammad Yasir Nawaz ◽  
Rodrigo Pelicioni Savegnago ◽  
Cedric Gondro
Keyword(s):  
Beef Cattle ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Whole Genome ◽  
Extended Haplotype Homozygosity ◽  
Extended Haplotype ◽  
Genome Sequence Data ◽  
Genomic Regions

Abstract In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.

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