Artificial Selection Pressure Research Articles

Rescue or murder? The effect of prey adaptation to the predator subjected to fisheries.

The concept of "indirect evolutionary rescue" refers to the evolutionary adaptation of an interacting species that can save a focal species from extinction in an unfavorable environment. Although theories suggest that indirect evolutionary rescue may have essential impacts on catchments in the context of fisheries where artificial selection pressure from fishing can drive evolution, its generality and conditions remain uncertain. In this study, by investigating how prey adaptation affects the persistence of a predator subjected to selective harvest with an eco-evolutionary predator-prey model, we find that prey adaptation tends to deteriorate (facilitate) predator persistence when predator's evolvability is high (low). In the system where the predator possesses high evolvability, selection by fisheries inhibits a predator's adaptation to prey, allowing the prey to escape predation by adaptation. Prey adaptation will affect predator persistence negatively, leading to evolutionary murder. Conversely, in the system where the predator's evolvability is low, the removal of predator individuals by fisheries relaxes predation pressure on prey, making the prey less defensive. Vulnerable prey affects predator persistence positively, resulting in indirect evolutionary rescue. The context-dependent response of natural resources to fisheries identified in this study suggests that the eco-evolutionary interplay should be considered for better natural resource management.

Genomic Insights into Pig Domestication and Adaptation: An Integrated Approach Using Genome-Wide Selection Analysis and Multiple Public Datasets.

As a global focus of animal husbandry, pigs provide essential meat resources for humans. Therefore, analyzing the genetic basis of adaptability, domestication, and artificial selection in pigs will contribute to further breeding. This study performed a genome-wide selection sweep analysis to identify candidate genes related to domestication and adaptive selection via data from 2413 public genotypes. Two complementary statistical analyses, FST (fixation index) and XP-EHH (cross-population extended haplotype homozygosity) were applied. The results revealed that numerous candidate genes were associated with high-altitude adaptability (e.g., SIRPA, FRS2, and GRIN2B) and habitat temperature adaptability (e.g., MITF, PI3KC2A, and FRS2). In addition, candidate genes related to the domestic genetic imprint of indigenous pigs (e.g., TNR, NOCT, and SPATA5) and strong artificial selection pressure in commercial breeds (e.g., ITPR2, HSD17B12, and UGP2) were identified in this study. Specifically, some MHC-related genes (e.g., ZRTB12, TRIM26, and C7H6orf15) were also under selection during domestication and artificial selection. Additionally, a phylogenetic comparative analysis revealed that the genetic divergence between populations does not fully follow the geographical distribution and management history in the major histocompatibility complex region/major histocompatibility complex II haplotypes, unlike that of the genome-wide genotypes. Furthermore, the higher heterozygosity and haplotype alleles of MHC reduce the differences between populations. Briefly, this study not only helps promote the relative theoretical understanding of environmental adaptive selection and domestication but also provides a theoretical reference for disease-resistant breeding in pigs.

Genetic structure analysis of yak breeds and their response to adaptive evolution

Yaks are crucial genetic resources in the Tibetan Plateau and surrounding regions. Throughout the long process of domestication, natural and artificial selection pressures have enabled yaks to demonstrate adaptive characteristics to the environment in terms of physiological structure and genetic molecules, but no systematic cell analysis has been carried out on this phenomenon of yaks. Here, the population structure and genetic diversity of yak were studied by WGRS, and the genes related to yak adaptability were excavated. Combined with scRNA-seq method, the transcription map of yak lung tissue and skin tissue was constructed, which provided a new comprehensive insight into yak adaptability. The analysis of yak population structure showed that there was obvious genetic differentiation between TZ _ yak and other seven yak populations, while there was significant genetic exchange between PL _ yak and SB _ yak at high altitude. WGRS and scRNA-seq analysis revealed that the gene HIF1A related to high altitude adaptation was expressed in various cell types, while EPAS1 was predominantly expressed in epithelial and endothelial cells of yak lung tissue. Endothelial cells play a critical role in hypoxia-adapted VEGF signaling, which correlates closely with the high expression of KDR and VEGFA genes in endothelial cells and monocytes. Furthermore, in the selection signal of High _ yak vs Low _ yak, 19.8 % of the genes overlapped with the genes screened by skin scRNA-seq, including genes related to coat color such as RORA, BNC2, and KIT. Notably, BNC2 is a gene associated with melanin deposition and shows high expression levels in HS cells. Additionally, GRN in melanocytes and SORT1 in IRS play an important role in cell communication between melanocytes and IRS. These findings offer new insights into the natural polymorphism of yaks and provide a valuable reference for future research on high-altitude mammals, and potentially even human genetics.

Genetic diversity of United States Rambouillet, Katahdin and Dorper sheep

BackgroundManaging genetic diversity is critically important for maintaining species fitness. Excessive homozygosity caused by the loss of genetic diversity can have detrimental effects on the reproduction and production performance of a breed. Analysis of genetic diversity can facilitate the identification of signatures of selection which may contribute to the specific characteristics regarding the health, production and physical appearance of a breed or population. In this study, breeds with well-characterized traits such as fine wool production (Rambouillet, N = 745), parasite resistance (Katahdin, N = 581) and environmental hardiness (Dorper, N = 265) were evaluated for inbreeding, effective population size (Ne), runs of homozygosity (ROH) and Wright’s fixation index (FST) outlier approach to identify differential signatures of selection at 36,113 autosomal single nucleotide polymorphisms (SNPs).ResultsKatahdin sheep had the largest current Ne at the most recent generation estimated with both the GONe and NeEstimator software. The most highly conserved ROH Island was identified in Rambouillet with a signature of selection on chromosome 6 containing 202 SNPs called in an ROH in 50 to 94% of the individuals. This region contained the DCAF16, LCORL and NCAPG genes that have been previously reported to be under selection and have biological roles related to milk production and growth traits. The outlier regions identified through the FST comparisons of Katahdin with Rambouillet and Dorper contained genes with known roles in milk production and mastitis resistance or susceptibility, and the FST comparisons of Rambouillet with Katahdin and Dorper identified genes related to wool growth, suggesting these traits have been under natural or artificial selection pressure in these populations. Genes involved in the cytokine-cytokine receptor interaction pathways were identified in all FST breed comparisons, which indicates the presence of allelic diversity between these breeds in genomic regions controlling cytokine signaling mechanisms.ConclusionsIn this paper, we describe signatures of selection within diverse and economically important U.S. sheep breeds. The genes contained within these signatures are proposed for further study to understand their relevance to biological traits and improve understanding of breed diversity.

Resequencing of reindeer genomes provides clues to their docile habits.

Reindeer have long been served as vital subsistence resources for inhabitants of Arctic and subarctic regions owing to their domestication. However, the evolutionary relationships and divergence times among different reindeer populations, genetic traits that distinguish domesticated reindeer, and factors that contribute to their relative docility compared with that of other Cervidae specie, remain unclear. In this study, we sequenced the genomes of 32 individuals from wild and domestic reindeer populations that inhabit Arctic and subarctic regions. We found that reindeer experienced 2 or more independent domestication events characterized by weak artificial selection pressure and limited significant differences in genomic parameters between wild and domestic populations. Alterations in conserved noncoding elements in the reindeer genomes, particularly those associated with nervous system development, may have contributed to their domestication by rendering the nervous system less responsive. Together, our results suggest that inherent species-specific traits, rather than intense artificial selection, may have played a significant role in the relatively docile behavior of reindeer and offer valuable insights into the domestication process of these animals.

Whole-genome resequencing of major populations revealed domestication-related genes in yaks

BackgroundThe yak is a symbol of the Qinghai-Tibet Plateau and provides important basic resources for human life on the plateau. Domestic yaks have been subjected to strong artificial selection and environmental pressures over the long-term. Understanding the molecular mechanisms of phenotypic differences in yak populations can reveal key functional genes involved in the domestication process and improve genetic breeding.Material and methodHere, we re-sequenced 80 yaks (Maiwa, Yushu, and Huanhu populations) to identify single-nucleotide polymorphisms (SNPs) as genetic variants. After filtering and quality control, remaining SNPs were kept to identify the genome-wide regions of selective sweeps associated with domestic traits. The four methods (π, XPEHH, iHS, and XP-nSL) were used to detect the population genetic separation.ResultsBy comparing the differences in the population stratification, linkage disequilibrium decay rate, and characteristic selective sweep signals, we identified 203 putative selective regions of domestic traits, 45 of which were mapped to 27 known genes. They were clustered into 4 major GO biological process terms. All known genes were associated with seven major domestication traits, such as dwarfism (ANKRD28), milk (HECW1, HECW2, and OSBPL2), meat (SPATA5 and GRHL2), fertility (BTBD11 and ARFIP1), adaptation (NCKAP5, ANTXR1, LAMA5, OSBPL2, AOC2, and RYR2), growth (GRHL2, GRID2, SMARCAL1, and EPHB2), and the immune system (INPP5D and ADCYAP1R1).ConclusionsWe provided there is an obvious genetic different among domestic progress in these three yak populations. Our findings improve the understanding of the major genetic switches and domestic processes among yak populations.

52 The Power of Pangenome Assemblies in Ruminants

Abstract High quality reference genomes are the bases of all genomic research and they have facilitated a wealth of discoveries and research tools for the improvement of livestock species. These works have enabled major advances in the fields of animal science and genetics and impacted livestock production and associated industries for the benefit of society. However, because a single reference genome fails to represent all of the genetic material present across populations, it inherently limits the ability to comprehensively evaluate all genomic variants within a species. A complete understanding of how small and large genomic variants, from single nucleotide polymorphisms (SNP) to larger structural variations (SV) including insertions/deletions (InDels) and copy number variation (CNVs), have been selected for over time for specific environments and phenotypes, remains elusive. To address this, it is necessary to generate a catalog of genomic variants in populations subjected to natural or artificial selection pressures and evaluate their relationship among phenotypic classes. The pangenome approach is a means to comprehensively identify and catalog genomic variation and representation that will make more suitable reference for mapping population sequence data for variant detection and frequency evaluation. The goal of the most pangenome projects is to provide genomic resources to represent the immense genetic diversity of this species more completely. This will increase our understanding of genetic variation and its role in dictating different phenomes, empowering scientists to predict the physiological outcomes more effectively from genomic variation towards the improvement of breeding strategies. These pangenomes can then be used to discover the underlying mechanism of biological traits and inform future breeding strategies and support sustainable production of this global source of food and fiber.

Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye.

Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method. The integrated haplotype score (iHS) statistic was utilised to reveal selection signatures within populations, whereas the cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST ) approaches were preferred to reveal differently fixed genomic regions between native Turkish and cosmopolitan cattle breeds. Selection signatures in 142 genomic regions containing 305 genes were detected within eight cattle breeds by iHS statistics. The XP-EHH and FST approaches revealed that 197 and 114 SNPs were under selection pressure, respectively, which overlapped with 144 and 190 genes, respectively. A total of 18 genes were detected by at least two approaches. Six genes related to disease resistance (TTP2), meat yield (DIAPH3 and METTL21C), meat quality (ZNF24 and ZNF397) and first calving interval (ZSCAN30) turned out to be differently fixed between native Turkish and cosmopolitan cattle breeds, as they were identified by both XP-EHH and FST approaches. In addition, the iHS approach revealed that eight genes associated with visual modality (LSGN), olfaction (MOXD2, OR4C1F and OR4C1F), and immune response (TRBV3-1 and CLDN10) were under selection pressure in both native and cosmopolitan cattle breeds. Owing to their being significantly related to survival traits, these regions may have played a key role in cattle genome evolution. Future studies utilising denser genetic data are required to obtain deeper knowledge on effects of natural and artificial selection in Anatolian cattle breeds. © 2023 Stichting International Foundation for Animal Genetics.

Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States.

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

Evolution of NLR genes in genus Arachis reveals asymmetric expansion of NLRome in wild and domesticated tetraploid species

Arachis hypogaea is an allotetraploid crop widely grown in the world. Wild relatives of genus Arachis are the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genus Arachis and performed their comparative genomics among four diploids (A. duranensis, A. ipaensis, A. cardenasii, A. stenosperma) and two tetraploid (wild: A. monticola and domesticated: A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified from A. cardenasii, A. stenosperma and A. duranensis, A. hypogaea, A. monticola and A. ipaensis respectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome of A. monticola exhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case of A. hypogaea probably due to distinct natural and artificial selection pressure. In addition, diploid species A. cardenasii revealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure. A. cardenasii and A. monticola can be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genus Arachis to identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security.

Foraging behavior of Raramuri Criollo vs. commercial crossbred cows on rangelands of the southwestern United States and Northern Mexico

Matching livestock genetics to climatically variable and nutritionally challenging environments is critical to the success of livestock ranching in the Southwest US, Northern Mexico, and arid rangelands elsewhere. We compared foraging behavior patterns of Raramuri Criollo (a heritage breed) and British beef cows at the Jornada Experimental Range (JER) in southern New Mexico, USA, and Rancho Experimental Teseachi (RET) in central Chihuahua, Mexico, during spring and fall of 2005. The study design comprised four animal monitoring weeks per site and season and each animal monitoring period consisted of four replicates, each of which included a set of six mature cows per breed equipped with a GPS tracking collar. GPS-derived movement, activity, and vegetation use variables were analyzed by sets of mixed models considering the fixed effects of breed, site, season, and all interactions (significance; P < 0.05). Compared to the British cows, Raramuri Criollo counterparts traveled further and grazed across larger areas of flat desert rangeland at JER and explored and grazed higher elevation rangelands with steeper slopes at RET. Breed differences were greatest when forages were dormant or scarce. Similarly, habitat use differed by vegetation class and breed with British cows spending more time in open grassland areas dominated by palatable herbaceous plants at JER and RET. Breed differences observed in this study likely reflected the outcomes of natural (Criollo) vs. artificial (British) selection pressure through time. Foraging behavior traits observed in Raramuri Criollo cows could be critical for adaptation of cow-calf production systems of the region to increasingly variable foraging environments caused by climate change.

Genome-wide identification, expression pattern and genetic variation analysis of SWEET gene family in barley reveal the artificial selection of HvSWEET1a during domestication and improvement.

SWEET (Sugars Will Eventually be Exported Transporter) proteins, an essential class of sugar transporters, are involved in vital biological processes of plant growth and development. To date, systematical analysis of SWEET family in barley (Hordeum vulgare) has not been reported. In this study, we genome-wide identified 23 HvSWEET genes in barley, which were further clustered into four clades by phylogenetic tree. The members belonging to the same clade showed relatively similar gene structures and conserved protein motifs. Synteny analysis confirmed the tandem and segmental duplications among HvSWEET genes during evolution. Expression profile analysis demonstrated that the patterns of HvSWEET genes varied and the gene neofunctionalization occurred after duplications. Yeast complementary assay and subcellular localization in tobacco leaves suggested that HvSWEET1a and HvSWEET4, highly expressed in seed aleurone and scutellum during germination, respectively, functioned as plasma membrane hexose sugar transporters. Furthermore, genetic variation detection indicated that HvSWEET1a was under artificial selection pressure during barley domestication and improvement. The obtained results facilitate our comprehensive understanding and further functional investigations of barley HvSWEET gene family, and also provide a potential candidate gene for de novo domestication breeding of barley.

Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens.

The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.

Novel insights into the dissemination route of Japanese apricot (Prunus mume Sieb. et Zucc.) based on genomics

SUMMARYJapanese apricot (Prunus mume) is an attractive fruit tree originating from China, and its cultivation history dates back 7000 years. In this study, we investigated the genetic diversity, population structure, and genetic relationship of Japanese apricots in different regions of China and Japan. The analyses of the genetic variation between wild and cultivated populations improved our understanding of the general mechanisms of domestication and improvement. A total of 146 accessions of Japanese apricot from different geographic locations were sequenced. The genetic diversity of wild and domesticated accessions (3.60 × 10−3 and 3.51 × 10−3, respectively) from China was high, and the effect of artificial selection pressure on domesticated accessions was small; however, the genetic diversity of artificially bred accessions decreased significantly (2.68 × 10−3) compared to domesticated accessions, which had an obvious improvement bottleneck effect. The chloroplast genome results showed that 41 haplotypes were detected, and Japanese apricots from the Yunnan region had the most haplotypes and the highest genetic diversity. The results revealed the dissemination route of Japanese apricot, not only along the Yangtze River basin system (from southwest China to Hunan, Jiangxi, and Anhui, and finally to the Jiangsu, Zhejiang, and Shanghai areas). Additionally, we discovered a second route for Japanese apricot dispersion, which was mostly in the Pearl River basin system, from southwest China to Libo of Guizhou and then to the Guangdong, Fujian, and Taiwan areas. This also showed that Japanese‐bred accessions originated from Zhejiang, China. In addition, selective sweep analysis showed that most of the high‐impact single nucleotide polymorphisms were identified in genes related to glucose metabolism, aromatic compound metabolism, flowering time, dormancy, and resistance to abiotic stress during the domestication and improvement of Japanese apricot.

The Evolutionary Consequences of Dams and Other Barriers for Riverine Fishes

AbstractDams and other anthropogenic barriers have caused global ecological and hydrological upheaval in the blink of the geological eye. In the present article, we synthesize 307 studies in a systematic review of contemporary evolution following reduced connectivity and habitat alteration on freshwater fishes. Genetic diversity loss was more commonly observed for small populations impounded in small habitat patches for many generations behind low-passability barriers. Studies show that impoundments can cause rapid adaptive evolution in migration timing, behavior, life history, temperature tolerance, and morphology, as well as reduce phenotypic variance, which can alter adaptive potential and ecological roles. Fish passage structures can restore migratory populations but also create artificial selection pressures on body size and migration. The accelerating pace of dam removals and the paucity of data for fishes other than salmonids, other vertebrates, invertebrates, and tropical and southern hemisphere organisms highlights the urgent need for more studies on the rapid evolutionary effects of dams.

Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping.

Simple SummaryWe performed SNP genotyping of indigenous goats of Mongolia to explore their demographic history in the global context and to estimate their genetic risks. Recently, these risks have become a subject of concern due to recent climatic disasters and uncontrolled massive breeding. Various clustering methods demonstrated close genetic relations among Mongolian, Russian, Chinese, and West Asian breeds. Mongolian goats themselves exhibited low to moderate estimates of genetic differentiation. We identified genetic features highlighting the distinct origin and breeding history of Mongolian goat breeds, as well as traces of artificial selection and geographic isolation. However, none of them met formal criteria to be considered as endangered.Mongolian goats are of great interest for studying ancient migration routes and domestication, and also represent a good model of adaptability to harsh environments. Recent climatic disasters and uncontrolled massive breeding endangered the valuable genetic resources of Mongolian goats and raised the question of their conservation status. Meanwhile, Mongolian goats have never been studied on genomic scale. We used Illumina Goat SNP50 to estimate genetic risks in five Mongolian goat breeds (Buural, Ulgii Red, Gobi GS, Erchim, Dorgon) and explored phylogenic relationships among these populations and in the context of other breeds. Various clustering methods showed that Mongolian goats grouped with other Asian breeds and were especially close to some neighboring Russian and Chinese breeds. The Buural breed showed the lowest estimates of inbreeding and exhibited the shortest genetic distances within the other Mongolian breeds, especially, to Ulgii Red and Gobi GS. These three breeds formed a single core group, being weakly differentiated from each other. Among them, Gobi GS displayed obvious signs of inbreeding probably resulted from artificial selection pressure. Dorgon and especially Erchim goats stand apart from the other Mongolian breeds according to various types of analyses, and bear unique features pointing to different breeding histories or distinct origins of these breeds. All populations showed strong decline in effective population size. However, none of them met formal criteria to be considered as endangered breeds. The SNP data obtained in this study improved the knowledge of Mongolian goat breeds and could be used in future management decisions in order to preserve their genetic diversity.

Can domestication shape Canidae brain morphology? The accessory olfactory bulb of the red fox as a case in point

BackgroundThe accessory olfactory bulb (AOB) is the first integrative center of the vomeronasal system (VNS), and the general macroscopic, microscopic, and neurochemical organizational patterns of the AOB differ fundamentally among species. Therefore, the low degree of differentiation observed for the dog AOB is surprising. As the artificial selection pressure exerted on domestic dogs has been suggested to play a key role in the involution of the dog VNS, a wild canid, such as the fox, represents a useful model for studying the hypothetical effects of domestication on the AOB morphology. MethodsA comprehensive histological, lectin-histochemical, and immunohistochemical study of the fox AOB was performed. Anti-Gαo and anti-Gαi2 antibodies were particularly useful, as they label the transduction cascade of the vomeronasal receptor types 1 (V1R) and 2 (V2R), respectively. Other employed antibodies included those against proteins such as microtubule-associated protein 2 (MAP-2), tubulin, glial fibrillary acidic protein, growth-associated protein 43 (GAP-43), olfactory marker protein (OMP), calbindin, and calretinin. ResultsThe cytoarchitecture of the fox AOB showed a clear lamination, with neatly differentiated layers; a highly developed glomerular layer, rich in periglomerular cells; and large inner cell and granular layers. The immunolabeling of Gαi2, OMP, and GAP-43 delineated the outer layers, whereas Gαo and MAP-2 immunolabeling defined the inner layers. MAP-2 characterized the somas of AOB principal cells and their dendritic trees. Anti-calbindin and anti-calretinin antibodies discriminated neural subpopulations in both the mitral-plexiform layer and the granular cell layer, and the lectin Ulex europeus agglutinin I (UEA-I) showed selectivity for the AOB and the vomeronasal nerves. ConclusionThe fox AOB presents unique characteristics and a higher degree of morphological development compared with the dog AOB. The comparatively complex neural basis for semiochemical information processing in the fox compared with that observed in dogs suggests loss of AOB anatomical complexity during the evolutionary history of dogs and opens a new avenue of research for studying the effects of domestication on brain structures.

Versatile selective evolutionary pressure using synthetic defect in universal metabolism

The non-natural needs of industrial applications often require new or improved enzymes. The structures and properties of enzymes are difficult to predict or design de novo. Instead, semi-rational approaches mimicking evolution entail diversification of parent enzymes followed by evaluation of isolated variants. Artificial selection pressures coupling desired enzyme properties to cell growth could overcome this key bottleneck, but are usually narrow in scope. Here we show diverse enzymes using the ubiquitous cofactors nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) can substitute for defective NAD regeneration, representing a very broadly-applicable artificial selection. Inactivation of Escherichia coli genes required for anaerobic NAD regeneration causes a conditional growth defect. Cells are rescued by foreign enzymes connected to the metabolic network only via NAD or NADP, but only when their substrates are supplied. Using this principle, alcohol dehydrogenase, imine reductase and nitroreductase variants with desired selectivity modifications, and a high-performing isopropanol metabolic pathway, are isolated from libraries of millions of variants in single-round experiments with typical limited information to guide design.

Short-term effects of controlled mating and selection on the genetic variance of honeybee populations

Directional selection in a population yields reduced genetic variance due to the Bulmer effect. While this effect has been thoroughly investigated in mammals, it is poorly studied in social insects with biological peculiarities such as haplo-diploidy or the collective expression of traits. In addition to the natural adaptation to climate change, parasites, and pesticides, honeybees increasingly experience artificial selection pressure through modern breeding programs. Besides selection, many honeybee breeding schemes introduce controlled mating. We investigated which individual effects selection and controlled mating have on genetic variance. We derived formulas to describe short-term changes of genetic variance in honeybee populations and conducted computer simulations to confirm them. Thereby, we found that the changes in genetic variance depend on whether the variance is measured between queens (inheritance criterion), worker groups (selection criterion), or both (performance criterion). All three criteria showed reduced genetic variance under selection. In the selection and performance criteria, our formulas and simulations showed an increased genetic variance through controlled mating. This newly described effect counterbalanced and occasionally outweighed the Bulmer effect. It could not be observed in the inheritance criterion. A good understanding of the different notions of genetic variance in honeybees, therefore, appears crucial to interpreting population parameters correctly.

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

BackgroundPopulation history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands.ResultsA total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns.ConclusionsOverall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.