Genetic Variation In Natural Populations Research Articles

Modeling the genetic footprint of fluctuating balancing selection: from the local to the genomic scale.

Natural selection not only affects the actual loci under selection but also leaves "footprints" in patterns of genetic variation in linked genetic regions. This offers exciting opportunities for inferring selection and for understanding the processes shaping levels of genetic variation in natural populations. Here, we develop analytical approximations based on coalescent theory to characterize the genetic footprint of a complex, but potentially common type of natural selection: balancing selection with seasonally fluctuating allele frequencies. As we show analytically and confirm with stochastic simulations, seasonal allele frequency fluctuations can have important (and partly unexpected) consequences for the genetic footprint of balancing selection. Fluctuating balancing selection generally leads to an increase in genetic diversity close to the selected site, the effect of balancing selection, but reduces diversity further away from the selected site, which is a consequence of the allele-frequency fluctuations effectively producing recurrent bottlenecks of allelic backgrounds. This medium- and long-range reduction usually outweighs the short-range increase when averaging diversity levels across the entire chromosome. Strong fluctuating balancing selection even induces a loss of genetic variation in unlinked regions, e.g. on different chromosomes. If many loci in the genome are simultaneously under fluctuating balancing selection this can lead to substantial genome-wide reductions in genetic diversity, even when allele-frequency fluctuations are small and local footprints are difficult to detect. Thus, together with genetic drift, selective sweeps and background selection, fluctuating selection could be a major force shaping levels of genetic diversity in natural populations.

Structure and molecular genetic diversity in natural populations and active germplasm banks of Passiflora cincinnata Mast.

Structure and molecular genetic diversity in natural populations and active germplasm banks of Passiflora cincinnata Mast.

Ecological niche, genetic variation in natural populations, and harvest maturity of Senegalia macrostachya (Rchb. ex DC) Kayl. & Boatwr., a promising wild and perennial edible-seeded crop

Senegalia macrostachya is a wild, perennial, and promising legume that can help alleviate food insecurity in sub-Saharan Africa’s drought-prone regions. However, it has been for a long time overlooked, underutilized, and scarcely studied. This study shed light on its ecological niche, genetic variation in natural populations, and seeds’ harvest maturity. Three populations of S. macrostachya were selected along an environmental gradient, and their structures, based on their plants’ pod characteristics (i.e., unique morphological differentiation trait amongst the plants), were assessed. Then, the seeds’ development was investigated following their morphological transformation, mass accumulation, and the mobilization of their proteins and secondary metabolites. S. macrostachya has revealed low genetic variation and fitness to poor soils, warm and semi-arid climates in sub-Saharan Africa, prone to droughts and low to medium agricultural productivity. The maturation of the seeds involved the accumulation of specific late embryogenesis abundant proteins (60, 48, and 14 kDa), identified as chilling-responsive dehydrins, and the degradation of the chlorophylls and carotenoids, which could be used as biochemical landmarks of the harvest maturity. Besides, an aging symptom (high seed abortion rate (14–20%)) was observed in the study populations. This work provides unprecedented information that will assist in predicting the eco-climate suitability and climate resilience, identifying the conservation strategies, and planning the harvesting, reforestation programs, and domestication of S. macrostachya. In parallel, the dehydrins identified from S. macrostachya can be tapped into for drought-resistant crop development. Further research is needed to evaluate the impacts of the mother plants’ aging and larger climate gradient on the performance (i.e., seed productivity and regeneration ability) of S. macrostachya.

VARIABILIDADE GENÉTICA DE POPULAÇÕES DE Parkia platycephala: SUBSÍDIO PARA DEFINIR ÁREAS DE COLETA DE SEMENTES

ABSTRACT Loss of genetic variability in natural populations affects negatively the adaptive and evolutive process of plant species. In this context, the objective of this work was to evaluate the existing genetic variability between and within natural populations of P. platycephala, using biometric characters of fruits and seeds and physiological characters of seeds and seedlings, and, thus, assess the potential for selection of mother trees, indicate areas for seed collection and use, and generate support for conservation and pre-breeding of plant species. A completely randomized experimental design was used, with 45 treatments (progenies) and four replications of 25 seeds. The progenies were evaluated in laboratory, using seeds collected from 45 mother trees sampled in three natural populations. The following characters were evaluated: seed germination percentage, germination speed index, and mean germination time; shoot and main root lengths; and seedling shoot and root dry weights. The data were subjected to RELM/BLUP analysis for estimating genetic parameters and correlations and to analyses of genetic divergence (UPGMA). The populations present genetic differences to each other and a significant variation between progenies for all characters evaluated, and the variation was greater within the populations. The characters evaluated present high genetic control; therefore, they can be used in analysis of genetic variability of populations and progenies of P. platycephala, thus assisting in the identification of areas for seed collection, conservation programs, and pre-breeding of the species.

A conservation genetics perspective on supportive breeding: A case study of the common nase (Chondrostoma nasus)

Abstract Supportive breeding programmes are becoming increasingly crucial for the conservation of many declining freshwater fishes such as the European common nase, Chondrostoma nasus. However, small relict populations are genetically highly vulnerable, and supportive breeding can have a detrimental impact on the genetic composition of the cultured offspring (e.g. as a result of inbreeding, genetic drift, and adaptation to captivity). This study monitored the genetic effects of a continuing supportive breeding programme of common nase by comparing the genetic diversity of two wild spawning populations with the respective wild offspring and the progeny from captive breeding originating from spawners of the two wild populations, considering genetic variability, genetic differentiation, and inbreeding effects using nine microsatellite markers. Despite low genetic differentiation, the offspring from captive breeding and from one of the natural populations (River Sims) were remarkably different genetically, as indicated by pairwise analyses of genetic divergence (FST from 0.028 to 0.070; Jost's DEST from 0.080 to 0.205) and the discriminant analysis of principal components. The mean number of alleles and mean allelic richness in the captive‐bred offspring and also in the wild offspring of the River Sims were lower than for wild populations of spawners and natural offspring of the River Mangfall, and signs of inbreeding effects were detected (F = 0.106 for captive bred and 0.048 for natural offspring). The observed effects can probably be attributed to the limited number of spawners (two females and three males) used for captive breeding. In addition, the results support previous evidence on recruitment problems of the Sims population, such as a reduced hatching success. Collecting fertilized eggs from the wild and rearing them in captivity (repatriation approach) could be an alternative to stripping a limited number of spawners and thereby to improve the conservation of genetic diversity of natural populations.

Genetic Diversity and Fine-Scale Spatial Genetic Structure of the Endangered Shrub Birch (Betula humilis Schrk.) Populations in Protected and Unprotected Areas

The genetic diversity of natural populations is a key factor in the success of long-term ecosystem protection. We studied the genetic diversity and spatial genetic structure (SGS) in three endangered shrub birch (Betula humilis) populations using seven nuclear microsatellite loci. The highest genetic variation was found in the restored Szuszalewo population in Biebrza National Park, where active prevention of thicket forest succession was recently conducted. The results of bottleneck tests were not statistically significant in each locality, although a genetic indication for population reduction was detected in the Rospuda stand, which is not actively protected. The Bayesian clustering, principal coordinates analysis, and FST estimates revealed the greatest difference between Magdzie Bagno and Rospuda samples. SGS was found in all B. humilis stands; however, it was the strongest in the Rospuda locality, where pollen and seed dispersal was limited by dense clusters of shrub birch ramets scattered among forest and brushwood plants. The weakest SGS, also supported by finding some sibling pairs in distant locations, was observed in the Szuszalewo population. The aforementioned results indicate that the active protection practices may impose an immediate beneficial effect on the restoration and maintenance of the B. humilis populations.

Multi-year evidence of unbiased sex ratios in hatchery and wild-reared age-0 lake sturgeon (Acipenser fulvescens)

Assessment of population sex ratios allows managers to forecast recruitment dynamics and loss of genetic diversity in natural populations and is important when the focal population is in low abundance and subject to demographic stochasticity. If levels of natural or artificial selection differ for males and females and levels of mortality likewise vary, lower levels of population recruitment, loss of genetic diversity, and genetic drift can occur. Lake sturgeon (Acipenser fulvescens) are a species of conservation concern, where restoration efforts increasingly rely on hatchery supplementation. Raising larvae to the juvenile stage can increase survival during important early life stages; however, knowledge is lacking concerning effects of artificial rearing environments on differential sex-specific survival before release. We genetically determined the sex of 1459 age-0 lake sturgeon from three cohorts (2016 through 2018) using PCR assays of the ALLWSex2 acipenserid sexing marker. Sexed individuals represented three groups: (1) wild-captured dispersing larvae that died during hatchery rearing, (2) wild-captured dispersing larvae that survived hatchery rearing to release, and (3) wild-captured, wild-raised age-0 individuals. Sex ratios of wild-captured larvae (dead + live) were nearly 50:50 in all years surveyed. We observed slight, but non-significant, directionality in sex ratios in the live and dead hatchery-reared larvae and in wild-captured age-0 individuals. Genetic sexing methods allow for analyses during prolonged pre-reproductive periods and associated variable environmental and demographic circumstances, in situations where physical determination of sex is not possible.

Impacts of Chronic Habitat Fragmentation on Genetic Diversity of Natural Populations of Prunus persica in China.

Wild peach is an important resource for improving existing peach varieties. However, the extant populations of wild peach show fragmented distribution due to human disturbance and geographic isolation. In this study, we used natural populations (or wild populations) of Prunus persica (Rosaceae) to assess the genetic effects of habitat fragmentation. A total of 368 individuals sampled from 16 natural populations were analyzed using 23 polymorphic simple sequence repeat (SSR) markers. Prunus persica maintained low within-population genetic variation and high level of genetic differentiation. Two genetic clusters were revealed based on three different methods (UPGMA, PCoA, and STRUCTURE). All populations showed a significant heterozygosity deficiency and most extant populations experienced recent reduction in population size. A significant isolation by distance (IBD) was observed with Mantel’s test. Compared to historical gene flow, contemporary gene flow was restricted among the studied populations, suggesting a decrease in gene flow due to habitat fragmentation. Habitat fragmentation has impacted population genetic variation and genetic structure of P. persica. For breeding and conservation purpose, collecting as many individuals as possible from multiple populations to maximize genetic diversity was recommended during the process of germplasm collection. In addition, populations from central China had higher genetic diversity, suggesting these populations should be given priority for conservation and germplasm collection.

Molecular characterization of mahogany tree (Swietenia macrophylla King, Meliaceae) in the remnant natural forest of Ecuador

ABSTRACT The Swietenia macrophylla King (Meliaceae) mahogany tree is widely spread in the neotropics. In Ecuador, it has a wide distribution range from the coastal zone to the Amazon. The mahogany tree is an endangered species due the overexploitation of the high commercial value of its wood. This study is aimed to characterize the Simple Sequence Repeat (SSR) variability of 123 trees selected from six provinces of Ecuador. The results showed that the natural mahogany population had a low level of genetic diversity (A = 6.9; Ho = 0.39; He = 0.43) and a significant heterozygous deficit inbreeding coefficient (F = 0.16). The probability of identity (PI) of the 12 microsatellite markers was low 4.3 × 10−9 and the cumulative exclusion probability of 99.99%. Additionally, the relatedness coefficient among individuals was −0.010 (se = 0.004). The genetic diversity among populations was moderate (ΦST = 8%). In addition, the structure analysis showed two genetic groups; however, it was possible to distinguish admixture within the entire range evaluated. These results show the need to establish strategies that allow the recovery and increase of the genetic diversity in natural populations, especially with the selection of trees to harvest seeds, as well as crossing the tree genetic pool to recombine their diversity.

Genetic identification and diversity of stocks of the African bonytongue, Heterotis niloticus (Osteoglossiformes: Arapaiminae), in Nigeria, West Africa

Inland fisheries are an important source of protein and income for people in Africa. Their sustainable management can greatly benefit from identification of regional genetic stocks and characterization of their genetic diversity, but such information is lacking for most African freshwater fisheries. The African bonytongue, Heterotis niloticus, is an important component of inland fisheries in West Africa. Nigeria has the largest fishery for African bonytongues, representing ~ 86% of the global total. Recent declines in yields at some Nigerian locations, however, suggest current levels of exploitation may be unsustainable. Habitat degradation also may be impacting some stocks. Despite its commercial and nutritional importance, the African bonytongue has been the subject of scant genetic research to support management. We examined patterns of genetic diversity in natural populations of H. niloticus at four locations in Nigeria, including Kainji Lake, a reservoir on the Niger River in north-central Nigeria, and three southern localities (Ethiope River, Igbokoda River, and Epe Lagoon), as well fish from the Ouémé River delta near Porto Novo, Benin. Eighty-five specimens were genotyped for nine microsatellite-loci. Genetic diversity estimates were highest at Kainji Lake, and substantially lower at southern localities. High levels of genetic differentiation were detected between samples from Kainji Lake and those from southern localities. Low, yet significant FST values were observed among samples from southern Nigerian localities that were more differentiated from the sample from nearby coastal Benin. We thus recommend that African bonytongues from the five locations be considered distinct genetic stocks and managed accordingly.

Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora

Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.

Efficiency of Arbitrary and Semi Arbitrary Markers for assessing Genetic Diversity in Natural Populations of Tecomella Undulata- An Important Timber yielding Tree Species of Rajasthan

The genetic variability and relationships among one twenty Tecomella undulata individuals representing twelve natural populations of Rajasthan were analyzed using ten RAPD and twenty-two ISSR markers. RAPD markers were found to be more efficient than the ISSR assay in respect to polymorphism detection, as they detected 96.10% polymorphism as compared to 91.02% for ISSR markers. But, multiplex ration (MR), heterozygosity (h), marker index (MI), average PIC value, resolving power (RP), total number of genotype specific marker loci, H, I, Ht, Hs and GST were more for ISSR than RAPD markers. Further, the dendrogram constructed based on the ISSR marker was able to segregate the twelve populations much clear and distinct as compared to RAPD markers. Data obtained in the present study supports ISSR markers as robust marker system suitable for genetic diversity studies and is also equally effective for characterization of the populations of Tecomella undulata from different geographical regions.

Genetic diversity in natural population of Notopterus notopterus evaluated through mitochondrial DNA marker ATPase 6/8 regions and cytochrome b gene.

Population structure and genetic diversity of bronze featherback Notopterus notopterus, fish was not studied yet from Pakistan. So, genetic diversity and population structure of N. notopterus was analysed using two mitochondrial DNA genetic markers, ATPase 6/8 and Cytochrome b. 150 specimens were collected from five different rivers of Pakistan, resulting 56 haplotypes were detected for ATPase 6/8, Cytb and concatenated gene. Haplotype and nucleotide diversity for ATPase 6/8, Cytb and concatenated gene was observed below 1% among five natural populations of N. notopterus. ATPase 6/8 and Cytb genetic variance among populations was 6% and among and within individuals was 94%. Concatenated genetic variance among populations was 11%, among individual 5% and within individuals 84%. Fst value among all population was found 0.091 (p-value=0.02, p<0.05). The combined data set mean coefficient of genetic differentiation (FST) was 0.5572. The pair-wise FST was 0.000 (Chenab) to 0.88911 (Ravi). Maximum likelihood phylogeographic history of concatenated gene haplotypes showed four distinct diversified clusters. AMOVA, PCoA (Principal Coordinate Analysis) and maximum likelihood tree indicated that the natural populations of N. notopterus were comprised of four genetic stocks among five Pakistani rivers (Chenab, Indus, Jehlum, Ravi and Satluj). This study provides the higher level of genetic diversity with confirmatory proofs among genetic stocks of five natural populations of N. notopterus. The information of genetic diversity and genetic variation, from this research can be utilised to help conserve and manage the species in the wild.

The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes.

The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.

A framework to model a web of linkage disequilibria for natural allotetraploid populations

Abstract Linkage disequilibrium (LD) is an important genetic parameter used to infer the genetic diversity of natural populations and their evolutionary history. Traditionally, LD is defined as the non‐random association of non‐alleles at different loci in gametes for diploids, but has a limited use for polyploids. We formulate a framework to define tetraploid‐specific LD including (a) Hardy–Weinberg disequilibria at each locus, (b) composite digenic disequilibrium, (c) trigenic disequilibrium and (d) composite quadrigenic disequilibrium at different loci. These four types of disequilibria affect population variation singly or jointly through a web. We implement the EM algorithm to estimate each disequilibrium parameter and test its significance in allotetraploid populations. We perform computer simulation to examine the statistical properties of our computational model. Through analysing a population genetic data of allotetraploid switchgrass, we chart the genomic distribution of LD on different chromosomes from which the evolutionary history of switchgrass is inferred, demonstrating the practical usefulness of the model. We have developed a statistical model for LD analysis in allotetraploids. The model can be generalized as a tool to study the population diversity and evolution of polyploid populations.

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

Genetic diversity of natural populations of Taxus mairei

Genetic diversity of natural populations of Taxus mairei

Evolutionary Genomics of Sex-Related Chromosomes at the Base of the Green Lineage.

Although sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT+ and MT− alleles, spanning 450–650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT+ and MT− alleles. We analyzed the phylogenetic profile and GC content of MT gene families in eight different genomes whose divergence has been previously estimated at up to 640 Myr, and found evidence that the divergence of the two MT alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT trans-specific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.

Molecular characterization of the spectacled caiman (Caiman crocodilus) in the upper Magdalena River basin, Colombia: Demographic and phylogeographic insights

Maintenance of high levels of genetic diversity is crucial for the recovery of overexploited species and gaining knowledge of genetic diversity of natural populations is crucial to define effective conservation strategies. Spectacled caimans (Caiman crocodilus) were unsustainably exploited for decades in Colombia causing drastic population reductions with unknown effects on genetic structure. We molecularly characterized three spectacled caiman populations from the upper Magdalena River basin (UMRB), analyzing them within the context of the trans-Andean C. c. fuscus sensu stricto lineage, assessing nucleotide and genetic diversity, demographic history, and phylogeography at different scales. Seventeen of the 23 mitochondrial haplotypes currently described for Colombia are present in the UMRB, showing high levels of genetic diversity even when compared with the trans-Andean region (uncorrected genetic distances 0.00-0.87%). Mutational steps between closest haplotypes ranged from one to four while the most differentiated haplotypes were separated by 19 mutational steps across the whole trans-Andean region. Distribution of pairwise nucleotide differences and raggedness tests showed unimodal patterns of mismatch distribution curves fitting the sudden expansion model. Average time since demographic expansion for UMRB, Colombia, and trans-Andean region were inferred as 10,540, 7,591, and 7,071 years before present, respectively, placing the latest expansion close to the Pleistocene-Holocene boundary. Intriguingly, samples from Tolima were overall more related to those collected from Panama and Costa Rica (0.34 ± 0.15%) than the ones collected across Choco (0.45 ± 0.15%), Cauca (0.70 ± 0.09%), and Nariño (0.60 ± 0.14%) departments. We discuss our genetic findings in the context of the management policies carried out in the country during the last decades (unsustainable and sustainable use, and population restocking), evaluating the implications of these events for the genetic integrity and conservation of the species.

Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle.

Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.