Spatial genetic structure in the Eurasian otter (Lutra lutra) meta-population from its core range in Italy

We characterized the genetic structure of the Eurasian otter (Lutra lutra) meta-population living in the core of its Italian distribution range providing results from 191 fresh spraints, collected from 24 watercourses included in Southern Italy. Furthermore, according to ecological corridors and barriers, we discuss the likely ways of movement and possible evolutionary fate of these populations. We genotyped 136 samples using 11 Lut microsatellite nuclear markers amplified from faecal dna. Microsatellites were moderately variable (Ho = 0.45; He = 0.46), with a total number of alleles and average number of alleles per locus in the meta-population of 50 and 4.54, respectively. No significant heterozygosity excess was observed in meta-population suggesting no recent population bottlenecks. Bayesian clustering discriminated a sub-structuring of the meta-population in five putative clusters, indicating that local populations are genetically differentiated: three of these seem to be identifiable with geographically defined sub-populations (from the Cilento, Agri and Basento river basins). The fourth is represented by multiple sub-populations with admixed genotype, that include genotypes from the Lao, Sinni and Abatemaco river basins, living in a landscape with the higher environmental permeability. Landscape genetic analysis could provide evidence of an unexpected ecological corridor: the seacoast, highlighted, for the first time as a new way for the dispersion of the South-Italian otters. Deepening the knowledge of these perspectives is crucial to identify solid strategies aimed at the future health of the populations of the Italian otters, by restoring dispersal corridors and managing the watercourses.

The impact of bottlenecks and inbreeding on the genome of the endangered Pyrenean desman

The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. The complete genome of the Pyrenean desman was assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. A severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created the lowest genomic heterozygosity ever recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective that need to be genetically variable, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. These results allow us to characterize important genomic health indicators for each individual, information that may be crucial for the conservation and management of the species.

The protected tree Dimorphandra wilsonii (Fabaceae) is a population of inter-specific hybrids: recommendations for conservation in the Brazilian Cerrado/Atlantic Forest ecotone

Backgrounds and Aims Dimorphandra wilsonii Rizzini, a critically endangered and protected tree, has a restricted distribution in the ecotone between the Cerrado and the Atlantic Forest in south-eastern Brazil. In this area, it co-occurs with D. mollis Benth., a common tree from the Cerrado, and D. exaltata Schott., a rare tree from the Atlantic Forest. Previous studies of D. wilsonii indicated heterozygosity excess at the individual level. Field observation of some intermediate phenotypes between D. wilsonii and both congeners suggests hybridization of D. wilsonii with D. mollis and/or D. exaltata. Here, we tested the hypothesis that D. wilsonii may have originated from hybridization between D. exaltata and D. mollis. We also performed cytogenetic analysis to examine if the heterozygosity excess could be explained by polyploidy in D. wilsonii. Methods We evaluated the genetic diversity and population structure of D. wilsonii using 11 nuclear simple sequence repeats (SSRs) genotyped in 152 individuals sampled across the taxon’s range. We performed comparative genetic analyses using overlapping SSR markers between D. wilsonii and previously published SSR data in D. mollis and D. exaltata to subsequently perform a series of allelic comparisons, multivariate and Bayesian analysis. Key Results Our results suggest that D. wilsonii individuals are most likely to correspond to F1 hybrids between D. exaltata and D. mollis. Cytogenetic analysis indicated that D. wilsonii is diploid with the same chromosome number as D. mollis (2n = 2x = 28). Conclusions Our study raises questions about the taxonomic status and the evolutionary future of D. wilsonii. We suggest that the conservation and management strategy for D. wilsonii should be revised and that it should take into account both parental Dimorphandra species in the ecotone, with special emphasis on the threatened D. exaltata. Finally, this study highlights the value of genetic information for the design of conservation strategies.

Polymorphism, Allelic and Genotypic Frequencies of κ-Casein and β-LG genes in Egyptian Buffaloes

With a view to detecting the genotypes of both κ-CN and β-LG genes in native populations of Egyptian buffalo using PCR-RFLP technique, 80 randomly, individuals were selected from five geographical locations of some Egyptian provinces. Also, to estimate the population genetic parameters such as, allelic and genotypic frequencies, heterozygosity, and inbreeding coefficient (FIS) of these studied genes. For genotyping, 453 bp PCR product of κ-CN was digested with AcuI and HpyCH4IV (Isoschizomer for MaeII) restriction enzymes while the 247 bp PCR product of β-LG was digested with HaeIII restriction enzyme. PCR-RFLP results discovered polymorphism at the level of κ-CN gene in all studied Egyptian buffaloes with two distinct alleles “A” and “B”. PCR-RFLP analysis for κ-CN gene using both restriction enzymes successfully detected that polymorphic status of the studied populations. We recommended using AcuI enzyme which was more capable for differentiating between homozygous (17%) and heterozygous (83%) individuals than HpyCH4IV enzyme which defined only 4% of homozygous individuals and the remaining was heterozygous (96%) individuals. Existence of heterozygosity excess in all studied populations referred to higher degree of genetic variability between individuals within these populations. On contrary, results of PCR-RFLP at the level of β-LG gene revealed a monomorphic pattern of Egyptian buffaloes and genotyped as “AA” animals which signified that PCR-RFLP assay with HaeIII enzyme for β-LG gene failed to discover any evidence of polymorphism in Egyptian buffalo under the circumstances of this study or all studied animals possess only one allele.

A New Viewpoint on Genetic Diversity in Prestice Black-Pied Pig: Did the Breed Suffer from a Bottleneck?

The research was aimed at determination of genetic variability of Prestice Black-Pied (PC) pig breed (Czech national breed and genetic resource) and to evaluate possible presence of recent bottleneck in this closed small pig population. One hundred and eighty of breeding boars were analysed by eleven tetramer Short Tandem Repeats (STR) panel specifically developed for the genotyping of breeding livestock. Despite the fact that appearance of rare alleles, which may be relatively increased after recent bottleneck, was discovered, the heterozygosity excess was not significant. The PC breed has not undergone recent bottleneck and remained at mutation-drift equilibrium.

Genetic variability in a population of Astyanax scabripinnis: recent bottleneck and the possible influence of individuals with B chromosomes

Access the genetic variability of endangered and isolated populations has become an important conservation tool. Astyanax scabripinnis is a well-known fish model for genetic studies, forming very isolated populations in headwaters. Besides that, this species frequently presents supernumerary chromosomes, which elevates the interest on genetic studies. Genetic diversity of an Astyanax scabripinnis population from the Atlantic Forest (Serra da Mantiqueira region, Brazil) was assessed with microsatellite markers for the first time. Since microsatellite markers are not described for this species, we tested markers described for a related species for transferability to A. scabripinnis. Six polymorphic loci were sufficiently reliable for population genetic analysis. We found that this population passed through a recent bottleneck because of the presence of an excess of heterozygotes, low allelic diversity, heterozygosity excess, and small effective population size. Individuals with and without B chromosomes were previously identified in this population and our study found private alleles in the individuals without B chromosomes. Furthermore, when individuals without B chromosomes were removed from the analysis, the population did not present heterozygosity excess, suggesting that the bottleneck event was driven by individuals with B chromosomes. Our results provide an insight into the value of microsatellite markers as molecular tools and is the first genetic study using molecular data of A. scabripinnis from this area.

Genetic bottleneck studies in five duck (Anas platyrhynchos) populations of India

The data of 24 microsatellite loci were generated for 4 indigenous duck populations and 1 commercial breed (Khakhi Campbell). The data were subjected to statistical analysis to test for heterozygosity excess or deficiency since any bottlenecked population would undergo transient heterozygosity excess. Three tests, viz. Sign-rank test, Standardised differences test and Wilcoxon test were utilised in each of the three models of mutations, IAM, SMM and TPM. SMM, which is the most suited model for evolution of microsatellites did not reveal any bottleneck in the last few generations. In our present study the heterozygosity excess is not evident in any of the 5 duck populations and thus the duck populations of India under study are in mutation drift equilibrium. The rejection of null hypothesis in the duck populations is attributed to heterozygotic deficiency.

A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection ecology approach and compare the genetic and phenotypic divergence of temporally sampled seed progenies of Ipomoeapurpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that this bottleneck may have occurred prior to 2003. Further, a greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.

On some genetic consequences of social structure, mating systems, dispersal, and sampling

Many species are spatially and socially organized, with complex social organizations and dispersal patterns that are increasingly documented. Social species typically consist of small age-structured units, where a limited number of individuals monopolize reproduction and exhibit complex mating strategies. Here, we model social groups as age-structured units and investigate the genetic consequences of social structure under distinct mating strategies commonly found in mammals. Our results show that sociality maximizes genotypic diversity, which contradicts the belief that social groups are necessarily subject to strong genetic drift and at high risk of inbreeding depression. Social structure generates an excess of genotypic diversity. This is commonly observed in ecological studies but rarely reported in population genetic studies that ignore social structure. This heterozygosity excess, when detected, is often interpreted as a consequence of inbreeding avoidance mechanisms, but we show that it can occur even in the absence of such mechanisms. Many seemly contradictory results from ecology and population genetics can be reconciled by genetic models that include the complexities of social species. We find that such discrepancies can be explained by the intrinsic properties of social groups and by the sampling strategies of real populations. In particular, the number of social groups and the nature of the individuals that compose samples (e.g., nonreproductive and reproductive individuals) are key factors in generating outbreeding signatures. Sociality is an important component of population structure that needs to be revisited by ecologists and population geneticists alike.

Assessment of recent bottlenecks and estimation of effective population size in the Ethiopian wild sorghum using simple sequence repeat allele diversity and mutation models

Since the immediate wild relatives ofSorghum bicolor(L.) Moench are indigenous to Ethiopia, studying their population biology is timely for undertaking conservation measures. A study was conducted to investigate the occurrence of population bottlenecks and to estimate the long-term effective population size (Ne) in wild relatives of sorghum. For this, 40 samples of wild sorghum were collected from two remotely located populations that were allopatric to the cultivated sorghum. The presence of bottlenecks was investigated using heterozygosity excess/deficiency, mode shift and allelic diversity based on nine polymorphic simple sequence repeat (SSR) loci. We also estimated theNeof the studied populations using two different methods employing SSR mutation models. The expected heterozygosity was found to be 0.41 and 0.71 and allelic richness was 3.0 and 4.9, in Awash and Gibe populations, respectively. Neither the heterozygosity excess nor the mode-shift methods detected signatures of bottlenecks in the studied populations. The effective size of the two wild sorghum populations studied also showed no risk of population reduction in these regions of Ethiopia. Therefore, these allopatric wild sorghum populations can survive by occupying patches by the roadsides and fences, areas within abandoned farm lands, forests, etc., which shows that their wild characteristics of adaptation have been adequate for them to survive from extinction despite extensive deforestation of their habitat for modern agriculture and frequent grazing by livestock. However, this does not guarantee the survival of these species for the future andex situconservation measures or policies could help maintain their diversity.