The Abundance of Harmful Rare Homozygous Variants in Children of Consanguineous Parents.

The children born of consanguineous union were found to have a higher incidence of recessive genetic diseases than the offspring of unrelated parents. The reason for this was predicted to be the presence of more deleterious rare homozygous genetic variants in the former compared to the latter. However, the magnitude of this difference is unknown.

Purifying Selection Influences the Comparison of Heterozygosities between Populations.

Heterozygosity is a fundamental measure routinely used to compare between populations to infer the level of genetic variation and their relative effective population sizes. However, such comparison is highly influenced by the magnitude of selection pressure on the genomic regions used. Using over 2 million Single Nucleotide Variants (SNVs) from chimpanzee and mouse populations, this study shows that the heterozygosities estimated using neutrally evolving sites of large populations were two times higher than those of small populations.

The Association between the Abundance of Homozygous Deleterious Variants and the Morbidity of Dog Breeds.

It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the load of recessive deleterious variants. Using the genomes of 392 dogs belonging to 83 breeds, we investigated the association between the abundance of homozygous deleterious variants and dog health.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island).

Genomic consequences of isolation and inbreeding in an island dingo population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island).

Genomic signatures of bottleneck and founder effects in dingoes.

Dingoes arrived in Australia during the mid-Holocene and are the top-order terrestrial predator on the continent. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. We investigated this hypothesis by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects.

Genomic footprints of bottleneck in landlocked salmon population.

At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and ponds of the Northern Hemisphere. Occasionally, the populations also got locked when the flow of rivers terminated from reaching the sea due to land upheaval. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers.

The Difference in the Proportions of Deleterious Variations within and between Populations Influences the Estimation of FST.

Estimating the extent of genetic differentiation between populations is an important measure in population genetics, ecology and evolutionary biology. The fixation index, or FST, is an important measure, which is routinely used to quantify this. Previous studies have shown that the FST estimated for selectively constrained regions was significantly lower than that estimated for neutral regions.

Deleterious protein-coding variants in diverse cattle breeds of the world.

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle breeds, their deleterious mutation load can vary.

Genomic Prediction for Whole Weight, Body Shape, Meat Yield, and Color Traits in the Portuguese Oyster .

Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, .

NMOSD and MS prevalence in the Indigenous populations of Australia and New Zealand.

Background: We studied the prevalence of neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) in Indigenous populations of Australia and New Zealand with the aim of assessing potential differences.

Methods: Cases of possible NMOSD and MS were collected from Australia and New Zealand. Clinical details, MR imaging, and serologic results were used to apply 2015 IPND diagnostic criteria for NMOSD and 2010 McDonald criteria for MS.

Harmful mutation load in the mitochondrial genomes of cattle breeds.

Objective: Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads.

The Long-Term Evolutionary History of Gradual Reduction of CpG Dinucleotides in the SARS-CoV-2 Lineage.

Recent studies suggested that the fraction of CG dinucleotides (CpG) is severely reduced in the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The CpG deficiency was predicted to be the adaptive response of the virus to evade degradation of the viral RNA by the antiviral zinc finger protein that specifically binds to CpG nucleotides. By comparing all representative genomes belonging to the genus this study examined the potential time of origin of CpG depletion.

A study on the efficacy of single layer full thickness duct to mucosa pancreatojejunostomy following pancreatoduodenectomy.

Pancreatoduodenectomy is the procedure of choice for treating periampullary and pancreatic head malignancy. The procedure has been standardized and the mortality has reduced considerably to fewer than 5% in high volume centers specializing in pancreatic surgeries. Unfortunately, the morbidity still hovers around 40%.

: a client-side software to construct population phylogeny from genome-wide SNPs.

In the past decades a number of software programs have been developed to infer phylogenetic relationships between populations. However, most of these programs typically use alignments of sequences from genes to build phylogeny. Recently, many standalone or web applications have been developed to handle large-scale whole genome data, but they are either computationally intensive, dependent on third party software or required significant time and resource of a web server.

Population size influences the type of nucleotide variations in humans.

Background: It is well known that the effective size of a population (N) is one of the major determinants of the amount of genetic variation within the population. However, it is unclear whether the types of genetic variations are also dictated by the effective population size. To examine this, we obtained whole genome data from over 100 populations of the world and investigated the patterns of mutational changes.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms.

Melioidosis-Series of Seven Cases from Madurai, Tamil Nadu, India.

Unlabelled: We describe a case series of seven culture proven melioidosis patients presenting during 2014 to 2016 in Madurai, south Tamilnadu. Skin, soft tissue, bone and joint infections were common. All of them were middle aged men except one case.

Ancient nuclear genomes enable repatriation of Indigenous human remains.

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible.

The genome of the oyster Saccostrea offers insight into the environmental resilience of bivalves.

Oysters are keystone species in estuarine ecosystems and are of substantial economic value to fisheries and aquaculture worldwide. Contending with disease and environmental stress are considerable challenges to oyster culture. Here we report a draft genome of the Sydney Rock Oyster, Saccostrea glomerata, an iconic and commercially important species of edible oyster in Australia known for its enhanced resilience to harsh environmental conditions.

Effect of genetic drift on determinants of protein evolution.

A number of previous studies reported that gene expression, tissue specificity, gene essentiality and the number of protein-protein interactions influence the rate of protein evolution. Here we investigated the influence of effective population size () on these determinants of protein evolution. For this purpose, we compared the ratio of non-synonymous-to-synonymous diversities (/) estimated for protein-coding genes of and : populations with high and low respectively.

Abundance of clinical variants in exons included in multiple transcripts.

Previous studies showed that the magnitude of selection pressure in constitutive exons is higher than that in alternatively spliced exons. The intensity of selection was also shown to be depended on the inclusion level of exons: the number of transcripts that include an exon. Here, we examined how the difference in selection pressure influences the patterns of clinical variants in human exons.

Influence of Effective Population Size on Genes under Varying Levels of Selection Pressure.

The ratio of diversities at amino acid changing (nonsynonymous) and neutral (synonymous) sites (ω = πN/πS) is routinely used to measure the intensity of selection pressure. It is well known that this ratio is influenced by the effective population size (Ne) and selection coefficient (s). Here, we examined the effects of effective population size on ω by comparing protein-coding genes from Mus musculus castaneus and Mus musculus musculus-two mouse subspecies with different Ne.

A genomic history of Aboriginal Australia.

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania).