The effect of inbreeding rate on fitness, inbreeding depression and heterosis over a range of inbreeding coefficients

Fitness consequences of population bottlenecks in an invasive blowfly

Invasive species often undergo demographic bottlenecks that cause a decrease in genetic diversity and associated reductions in population fitness. Despite this, they manage to thrive in novel environments. Investigating the effects of inbreeding and genetic bottlenecks on population fitness for invasive species is, therefore, key to understanding how they may survive in new environments. We used the blowfly Calliphora vicina (Sciences, Mathématiques et Physique, 1830, 2, 1), which is native to Europe and was introduced to Australia and New Zealand, to examine the effects of genetic diversity on population fitness. We first collected 59 samples from 15 populations across New Zealand and one in Australia, and used 20,501 biallelic SNPs to investigate population genomic diversity, structure and admixture. We then explored the impacts of repeated experimental bottlenecks on population fitness by creating inbred and outbred lines of C. vicina and measuring a variety of fitness traits. In wild-caught samples, we found low overall genetic diversity, signals of genetic admixture and limited (<3%) genetic differentiation between North and South Island populations, with genetic links between the South Island and Australia. Following experimental bottlenecks, we found significant reductions in fitness for inbred lines. However, fitness effects were not felt equally across all phenotypic traits. Moreover, they were not enough to cause population collapse in any experimental line, suggesting that C. vicina (when under relaxed selection, as in laboratory settings) may be able to compensate for population bottlenecks even when highly inbred. Our results demonstrate the value of a tractable experimental system for investigating processes that may facilitate or hamper biological invasion.

Experimental evolution suggests rapid assembly of the 'selfing syndrome' from standing variation in Mimulus guttatus

Ecological and evolutionary changes are likely to occur rapidly when outcrossing populations experience pollinator loss. However, the number and identify of plant traits that will respond to this form of selection, as well as the overall predictability of evolutionary responses, remain unclear. We experimentally evolved 20 large replicate populations of Mimulus guttatus for 10 generations under three treatments: pure outcrossing, mixed mating (10% outcrossing) and pure selfing. These populations were founded from the same genetically diverse and outcrossing natural population. After 10 generations, all measured traits evolved with flower size, phenology, and reproductive traits diverging consistently among mating system treatments. Autogamy increased dramatically in the selfing treatment, but the magnitude of adaptation only becomes clear once inbreeding depression is factored out. Selfing treatment plants evolved reduced stigma-anther separation, and also exhibited declines in flower size and per-flower reproductive capacity. Flower size also declined in selfing populations but this was driven mainly by inbreeding depression and cannot be attributed to adaptation towards the selfing syndrome. Generally, the mixed mating populations evolved trait values intermediate to the fully selfing and outcrossing populations. Overall, our experimental treatments reiterated differences that have been documented in interspecific comparisons between selfing and outcrossing species pairs. Given that such contrasts involve species separated by thousands or even millions of generations, it is noteworthy that large evolutionary responses were obtained from genetic variation segregating within a single natural population.

Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

Biological Fitness Cost, Demographic Growth Characteristics, and Resistance Mechanism in Alpha-Cypermethrin-Resistant Musca domestica (Diptera: Muscidae)

Musca domestica L., a pest of animals and humans, has developed resistance to alpha-cypermethrin, a pyrethroid insecticide commonly used to control medically important pests in many countries, including Saudi Arabia. We investigated the mechanism underlying the development of alpha-cypermethrin resistance and life history characteristics of alpha-cypermethrin-susceptible (Alpha-SS) and alpha-cypermethrin-resistant (Alpha-RS) M. domestica using the age-stage, two-sex life table theory, which is crucial for developing a future rational management strategy and minimizing the negative effects of alpha-cypermethrin on the environment. Our results showed that Alpha-RS M. domestica had a 405.93-fold increase in resistance to alpha-cypermethrin relative to Alpha-SS M. domestica. This increase in the resistance toward insecticide was attributed to metabolic enzymes, such as glutathione S-transferases, specific esterases, and cytochrome P450 monooxygenases. Furthermore, Alpha-RS M. domestica exhibited lower relative fitness (0.50), longevity, survival rate, life expectancy, reproductive values, intrinsic rate of increase, net reproductive rate, fecundity, maternity, and finite rate of increase, along with shorter larval, female preadult, and adult durations than Alpha-SS M. domestica, indicating fitness costs associated with most parameters. However, no significant differences were found between the strains in the following parameters: egg, pupa, and male preadult durations; adult preoviposition, total preoviposition, and oviposition periods; female ratio; and total generation time. Additionally, Alpha-RS M. domestica had a markedly lower intrinsic rate of increase, net reproductive rate, and finite rate of increase than Alpha-SS M. domestica. The results of this study suggest that alpha-cypermethrin resistance may lead to dominant fitness costs in M. domestica. Overall, these findings will aid in the development of rational control strategies for M. domestica as well as help to reduce pesticide pollution.

Portrait of autosomal recessive diseases in the French-Canadian founder population of Saguenay-Lac-Saint-Jean

The population of the Saguenay-Lac-Saint-Jean (SLSJ) region, located in the province of Quebec, Canada, is recognized as a founder population, where some rare autosomal recessive diseases show a high prevalence. Through the clinical and molecular study of 82 affected individuals from 60 families, this study outlines 12 diseases identified as recurrent in SLSJ. Their carrier frequency was estimated with the contribution of 1059 healthy individuals, increasing the number of autosomal recessive diseases with known carrier frequency in this region from 14 to 25. We review the main clinical and molecular features previously reported for these disorders. Five of the studied diseases have a potential lethal effect and three are associated with intellectual deficiency. Therefore, we believe that the provincial program for carrier screening should be extended to include these eight disorders. The high-carrier frequency, together with the absence of consanguinity in most of these unrelated families, suggest a founder effect and genetic drift for the 12 recurrent variants. We recommend further studies to validate this hypothesis, as well as to extend the present study to other regions in the province of Quebec, since some of these disorders could also be present in other French-Canadian families.

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θ π and estimated the coalescent or ancestral effective population size (N e), which ranged from 12,030 to 15,513. When compared to the census size, N C, the endangered Gaspésie Mountain caribou population had the highest ancestral N e:N C ratio which is consistent with recent work suggesting high ancestral N e:N C is of conservation concern. In contrast, values of contemporary N e, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e:N C ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral N e and Tajima's D into management decisions.

Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review

Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.

Are genetic variation and demographic performance linked?

Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ S) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re-census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.

Genomic insights into the conservation and population genetics of two Chinese native goat breeds

Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats.

A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep

Background

The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change.

Results

We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h² = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response.

Conclusions

Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00682-7.

Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds

There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

Effects of inbreeding on performance traits in Karan Fries crossbred cattle

Present study includes the effect of inbreeding on expected genetic gain and estimation of regression with respect to first lactation production, reproduction and lifetime traits in Karan Fries crossbred cattle maintained at ICAR-NDRI, Karnal. Out of total, only 36.97% were found to be inbred with an average inbreeding coefficient 3.68%. Overall least squares mean for reproduction traits (days) AFC, SP, DP and CI were 1020.41 ± 5.49, 141.42± 3.86, 74.54 ± 2.04 and 421.20 ± 3.81 respectively. For production traits (kg) were 305MY, LL, LTMY, FY and SNFY were 3169.15 ± 37.87, 353.25 ± 4.18, 3686.10 ± 55.10, 266.19 ± 4.66 and 127.81 ± 2.26 respectively and lifetime traits like LTMY and stayability were 14588.47 ± 486.09 (kg) and 2444.69 ± 41.26 (days) respectively. Among reproduction traits (days), AFC increased by +3.70, DP +3.66 and CI +68.44 however SP decreased by -0.85 d and production traits (kg), 305MY decreased by -10.2 TMY -16.09, LL -1.23 d, 305FY -1.75, 305SNFY - 0.26, LTMY 202.02 and stayability -17.37 days per unit increase in the inbreeding coefficient. Although there was no inbreeding depression in any of the traits except AFC. The expected genetic gain of AFC increased two folds in IBL2 (Fx >5%) as compared to IBL1 (Fx<5) group that is not desirable, so in future, to maintain the optimum genetic gain we should keep inbreeding at optimum level and so more precise pedigree recording and planned mating strategies should be adopted to avoid inbreeding depression in next generation.

Detecting purging of inbreeding depression by a slow rate of inbreeding for various traits: the impact of environmental and experimental conditions

Inbreeding depression (ID) has since long been recognized as a significant factor in evolutionary biology. It is mainly the consequence of (partially) recessive deleterious mutations maintained by mutation-selection balance in large random mating populations. When population size is reduced, recessive alleles are increasingly found in homozygous condition due to drift and inbreeding and become more prone to selection. Particularly at slow rates of drift and inbreeding, selection will be more effective in purging such alleles, thereby reducing the amount of ID. Here we test assumptions of the efficiency of purging in relation to the inbreeding rate and the experimental conditions for four traits in D. melanogaster. We investigated the magnitude of ID for lines that were inbred to a similar level, F ≈ 0.50, reached either by three generations of full-sib mating (fast inbreeding), or by 12 consecutive generations with a small population size (slow inbreeding). This was done on two different food media. We observed significant ID for egg-to-adult viability and heat shock mortality, but only for egg-to-adult viability a significant part of the expressed inbreeding depression was effectively purged under slow inbreeding. For other traits like developmental time and starvation resistance, however, adaptation to the experimental and environmental conditions during inbreeding might affect the likelihood of purging to occur or being detected. We discuss factors that can affect the efficiency of purging and why empirical evidence for purging may be ambiguous.

Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed

With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (F_ROH ) = 0.16; pedigree-based (F_PED ) = 0.008; and a method based on excess homozygosity (F_HOM ) = 0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0-2 Mbps, with 92.78% of the observations. In the ROHet results, only the 0-2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg²⁺ /Mn²⁺ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.

M. Groenen M, Madsen O. Genetic consequences of long-term small effective population size in the critically endangered pygmy hog

Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far-reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole-genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long-term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.

Fitness cost of imidacloprid resistance in the cotton-staining bug, Dysdercus koenigii

Dysdercus koenigii, a serious cotton-staining insect pest in many countries, has shown high resistance to imidacloprid, a systemic neonicotinoid insecticide used to control sap-sucking pests. With the aim of creating an effective management strategy, the biological traits of susceptible (SS) and imidacloprid-resistant (Imida-RS) D. koenigii, as well as their reciprocal crosses (CR1 and CR2), were investigated here using a life table established on age, stage, and two-sex patterns. Compared with SS D. koenigii, Imida-RS and CR1 strains had lower relative fitness (0.80 and 0.47, respectively) and fecundity (eggs per female); prolonged egg duration and a prolonged adult preoviposition period; shorter nymphal duration, male/female total longevity, and oviposition days, and a shorter total preoviposition period. However, there were no differences among strains in nymphal survival rates and female ratio. The CR2 D. koenigii had similar relative fitness value (1.09), suggested no fitness cost in most of the parameters. Demographic parameters, including net reproductive rate, were lower in the Imida-RS strain than in SS and CR2 D. koenigii. Similarly, the Imida-RS and CR1 strains had shorter generation time and doubling time, lower reproductive value and life expectancy relative to the SS and CR2 D. koenigii. In addition, age-specific fecundity was negatively affected in the CR1 strain compared with the other strains. These findings could help facilitate the development of rational D. koenigii control strategies.

Fitness cost, realized heritability and stability of resistance to spiromesifen in house fly, Musca domestica L. (Diptera: Muscidae)

The house fly, Musca domestica L. (Diptera: Muscidae), is an insect pest of public health and veterinary importance. Spiromesifen is a new chemistry insecticide widely used for the management of sucking insect pests of vegetables and crops. In the present study, assessment of resistance risk and fitness costs associated with spiromesifen resistance in M. domestica was studied. Moreover, stability of resistance to spiromesifen and other tested insecticides (fipronil, spinosad, and bifenthrin) was evaluated in the spiromesifen-selected-strain (SPIRO-SEL-POP). After 7-generations of selection with spiromesifen, SPIRO-SEL-POP developed 108.76-fold resistance compared with the unselected strain (UNSEL-POP). The estimated value of realized heritability was 0.59 for spiromesifen resistance. Due to withdrawal of spiromesifen selection for five generations (F₆-F₁₀) on SPIRO-SEL-POP, a decline in LC₅₀ values against spiromesifen, spinosad and bifenthrin was 0.16, 0.14 and 0.13-folds, respectively. In biological trait experiments, larval weight of Cross₁ (SPIRO-SEL-POP♀ × UNSEL-POP♂) and SPIRO-SEL-POP was significantly lower than that of Cross₂ (SPIRO-SEL-POP♂ × UNSEL-POP♀) and UNSEL-POP. Pupal weight of SPIRO-SEL-POP was higher when compared with Cross₁ while it was similar to that of Cross₂ and UNSEL-POP. Adult emergence rate of UNSEL-POP was higher than Cross₁, but similar to the Cross₂ and SPIRO-SEL-POP. The SPIRO-SEL-POP and Cross₁ showed the lowest relative fitness when compared with USEL-POP and Cross₂. Intrinsic rate of natural increase of SPIRO-SEL-POP was much lower than that of UNSEL-POP and Cross₂ followed by Cross₁. The SPIRO-SEL-POP exhibited lower biotic potential when compared with UNSEL-POP and Cross₂ but similar to Cross₁. Fecundity and hatching rates were lower in SPIRO-SEL-POP compared to UNSEL-POP. It could be concluded that spiromesifen resistance in M. domestica comes with a cost and is instable. Therefore, spiromesifen rotation with other insecticides and withdraw of its usage for some period could help to sustain its efficacy by delaying the development of resistance.

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.

Genetic variability and relationships in nine South African cattle breeds using microsatellite markers

Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven bovine-specific microsatellite markers were used to genotype animals from each of nine South African cattle breeds: Afrikaner (N = 550), Angus (N = 550), Bonsmara (N = 550), Boran (N = 321), Brahman (N = 550), Drakensberger (N = 550), Nguni (N = 550), Simmental (N = 550), and Tuli (N = 311). These breeds were drawn from Bos taurus africanus, Bos taurus, and Bos indicus. Genetic variability estimates included unbiased heterozygosity, effective number of alleles, and inbreeding. Ranges of these parameters were 0.569-0.741, 8.818-11.455, and - 0.001-0.050, respectively. Breed private allele and breed pairwise comparison was also used to characterize the breeds. The analysis of population structure with K = 2 revealed clusters comprised of Sanga-indicine and taurine, while K = 3 included separate clusters of Sanga, indicine, and taurine, and with K = 9 showed the breeds arising from unique progenitor populations. This study broke new ground in molecular cattle genetic diversity by genotyping a large sample size per breed and using a larger number of breeds compared with similar studies that have been conducted in the recent past which have either used a smaller number of breeds or smaller sample sizes but with a larger number of marker loci. Thus, opportunities that arise to explore genetic diversity and relationships in both the livestock and wildlife industries in Southern Africa may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their extensive use for parentage verification.

Generation of Fam83h knockout mice by CRISPR/Cas9-mediated gene engineering

Family with sequence similarity 83 member H (FAM83H) protein-coding geneplay an essential role in the structural organization, calcification of developing enamel, and keratin cytoskeleton disassembly by recruiting Casein kinase 1 alpha (CSNK1A1) to keratin filaments. In this study, we have applied CRISPR Cas9 nickase (D10A) to knockout (KO) the Fam83h gene in NMRI outbred mice. We generated homozygous Fam83h KO mice ( Fam83h ^Ko/Ko ) through a premature termination codon, which was validated by Sanger sequencing in F0 generation. Next, we also bred the FAM83H KO for two generations. Reverse-transcription polymerase chain reaction and Western blot analysis approved the Fam83h KO mice. The Fam83h KO mice had evidence of normal morphology at the cervical loops, secretory and maturation stages, and mandibular molars. In comparison with the normal wild-type mice ( Fam83h ^W/W ), the F2 homozygous KO ( Fam83h ^Ko/Ko ) had sparse, scruffy coats with small body size and decreased general activity. Also, they had the natural reproductive ability and natural lifespan. In addition, delay in opening the eyes and dry eyes among infant mice were seen. The F1 heterozygous mice looked comparable to the normal wild-type mice ( Fam83h ^W/W ), which showed autosomal recessive inheritance of these phenotypes. The KO of FAM83H had controversial effects on the development of teeth and the formation of enamel. The phenotype defect in dental development and the enamel formation were seen in three mice among four generations. It can be concluded that null FAM83H in outbred mice not only showed the reported phenotypes in null inbred mouse but also showed normal lifespan and reproductive ability; dental deficiency in three homozygous mice; and the symptoms that were similar to the symptoms of dry eye syndrome and curly coat dog syndrome in all four evaluated KO generations.

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication

Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops, such as rice, maize, barley, wheat, and tomato, to non-native latitudes. Modifications in the plant architecture and branching have been selected for higher yields and easier harvests. These phenotypes are often produced by alterations in the regulation of the transition of shoot apical meristems to inflorescences, and then to floral meristems. Floral homeotic mutants are responsible for popular double-flower phenotypes in Japanese cherries, roses, camellias, and lilies. The rise of peloric flowers in ornamentals such as snapdragon and florists' gloxinia is associated with non-functional alleles that control the relative expansion of lateral and ventral petals. Mechanisms to force outcrossing such as self-incompatibility have been removed in some tree crops cultivars such as almonds and peaches. In this review, we revisit some of these important concepts from the plant domestication perspective, focusing on four topics related to the pre-fertilization mechanisms: flowering time, inflorescence architecture, flower development, and pre-fertilization self-incompatibility mechanisms.

Cryptic Lineages and a Population Dammed to Incipient Extinction? Insights into the Genetic Structure of a Mekong River Catfish

An understanding of the genetic composition of populations across management boundaries is vital to developing successful strategies for sustaining biodiversity and food resources. This is especially important in ecosystems where habitat fragmentation has altered baseline patterns of gene flow, dividing natural populations into smaller subpopulations and increasing potential loss of genetic variation through genetic drift. River systems can be highly fragmented by dams built for flow regulation and hydropower. We used reduced-representation sequencing to examine genomic patterns in an exploited catfish, Hemibagrus spilopterus, in a hotspot of biodiversity and hydropower development—the Mekong River basin. Our results revealed the presence of 2 highly divergent coexisting genetic lineages which may be cryptic species. Within the lineage with the greatest sample sizes, pairwise FST values, principal component analysis, and a STRUCTURE analysis all suggest that long-distance migration is not common across the Lower Mekong Basin, even in areas where flood-pulse hydrology has limited genetic divergence. In tributaries, effective population size estimates were at least an order of magnitude lower than in the Mekong mainstream indicating these populations may be more vulnerable to perturbations such as human-induced fragmentation. Fish isolated upstream of several dams in one tributary exhibited particularly low genetic diversity, high amounts of relatedness, and a level of inbreeding (GIS = 0.51) that has been associated with inbreeding depression in other outcrossing species. Our results highlight the importance of assessing genetic structure and diversity in riverine fisheries populations across proposed dam development sites for the preservation of these critically important resources.

Detection of barriers to dispersal is masked by long lifespans and large population sizes

Population genetic analyses of species inhabiting fragmented landscapes are essential tools for conservation. Occasionally, analyses of fragmented populations find no evidence of isolation, even though a barrier to dispersal is apparent. In some cases, not enough time may have passed to observe divergence due to genetic drift, a problem particularly relevant for long‐lived species with overlapping generations. Failing to consider this quality during population structure analyses could result in incorrect conclusions about the impact of fragmentation on the species. We designed a model to explore how lifespan and population size influence perceived population structure of isolated populations over time. This iterative model tracked how simulated populations of variable lifespan and population size were affected by drift alone, using a freshwater mussel, Quadrula quadrula (mapleleaf), as a model system. In addition to exhibiting dramatic lifespan variability among species, mussels are also highly imperiled and exhibit fragmentation by dams throughout the range of many species. Results indicated that, unless population size was small (<50 individuals) or lifespan short (<22 years), observing genetic divergence among populations was unlikely. Even if wild populations are isolated, observing population structure in long‐lived mussels from modern damming practices is unlikely because it takes longer for population structure to develop in these species than most North American dams have existed. Larger population sizes and longer lifespans increase the time needed for significant divergence to occur. This study helps illuminate the factors that influence genetic responses by populations to isolation and provides a useful model for conservation‐oriented research.

The role of genetic diversity and past-history selection pressures in the susceptibility of Chironomus riparius populations to environmental stress

Natural populations experiencing intense selection and genetic drift may exhibit limited potential to adapt to environmental change. The present study addresses the following aspects of the "genetic erosion" hypothesis in the midge Chironomus riparius: does long-term mercury (Hg) contamination affect the Hg tolerance of midge populations inhabiting such impacted areas? If so, is there any fitness cost under changing environmental conditions? And does genetic impoverishment influence the susceptibility of C. riparius to cope with environmental stressful conditions? For this end, we tested the acute and chronic tolerance to Hg and salinity in four C. riparius populations differing in their levels of genetic diversity (assessed through microsatellite markers) and past-histories of Hg exposure. Results showed that the midge population collected from a heavily Hg-contaminated site had higher Hg tolerance compared to the population collected from a closely-located reference site suggesting directional selection for Hg-tolerant traits in its native environment despite no genetic erosion in the field. No increased susceptibility under changing environmental conditions of salinity stress was observed. Moreover, results also showed that populations with higher genetic diversity performed better in the partial life-cycle assays providing evidence on the key role that genetic diversity plays as mediator of populations' susceptibility to environmental stress. Our findings are discussed in terms of the suitability of C. riparius as a model organism in evolutionary toxicology studies as well as the validity of ecotoxicological assessments using genetically eroded laboratory populations.

Genetic load, inbreeding depression, and hybrid vigor covary with population size: An empirical evaluation of theoretical predictions

Reduced population size is thought to have strong consequences for evolutionary processes as it enhances the strength of genetic drift. In its interaction with selection, this is predicted to increase the genetic load, reduce inbreeding depression, and increase hybrid vigor, and in turn affect phenotypic evolution. Several of these predictions have been tested, but comprehensive studies controlling for confounding factors are scarce. Here, we show that populations of Daphnia magna, which vary strongly in genetic diversity, also differ in genetic load, inbreeding depression, and hybrid vigor in a way that strongly supports theoretical predictions. Inbreeding depression is positively correlated with genetic diversity (a proxy for Ne ), and genetic load and hybrid vigor are negatively correlated with genetic diversity. These patterns remain significant after accounting for potential confounding factors and indicate that, in small populations, a large proportion of the segregation load is converted into fixed load. Overall, the results suggest that the nature of genetic variation for fitness-related traits differs strongly between large and small populations. This has large consequences for evolutionary processes in natural populations, such as selection on dispersal, breeding systems, ageing, and local adaptation.

Evolutionary conservation-evaluating the adaptive potential of species

Despite intense efforts, biodiversity around the globe continues to decrease. To cease this phenomenon, we urgently need a better knowledge not only of the true extent of biodiversity, but also of the evolutionary potential of species to respond to environmental change. These aims are the heart of the developing field of Evolutionary conservation. Here, after describing problems associated with implementing evolutionary perspectives into management, we outline how evolutionary principles can contribute to efficient conservation programmes. We then introduce articles from this special issue on Evolutionary conservation, outlining how each study or review provides tools and concepts to contribute to efficient management of species or populations. Ultimately, we highlight what we believe can be future research avenues for evolutionary conservation.