Survival and divergence in a small group: the extraordinary genomic history of the endangered Apennine brown bear stragglers 2 AbstractAbout 100 km east of Rome, in the Central Apennine mountains, a critically endangered population of approximately fifty brown bears live in complete isolation. Mating outside this population is prevented by several hundred kilometers of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. First, we found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In Central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show non-random peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles a) can be an important driver of divergence in isolation, b) can be tolerated when balancing selection prevents random loss of variation at important genes and c) is followed by or results directly in favorable behavioral changes. SignificanceA small and relict population of brown bears lives in complete isolation in the Italian Apennine mountains, providing a unique opportunity to study the impact of drift and selection on the genomes of a large endangered mammal and to reconstruct the phenotypic consequences and the conservation implications of such evolutionary processes. The Apennine bear is highly inbred and harbors very low genomic variation. Several deleterious mutations have been accumulated by drift. We found evidence that this is a consequence of habitat fragmentation in the Neolithic, when human expansion and land clearance shrank its habitat, and that retention of variation at immune system and olfactory receptor genes, as well as changes in diet and behavior, prevented the extinction of the Apennine bear.

The objectives of this study were to determine genetic variation and to analyze population structure of 6 Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 birds belonging to 6 breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pépoi, Padovana, and Polverara; a commercial layer cross was used as reference. One hundred twelve alleles were detected in the overall population, with a mean number of 5.6 +/- 2.1 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.240 to a maximum of 0.413 and from 0.243 to 0.463 for the Pépoi and Polverara breeds, respectively. Deviation from Hardy-Weinberg equilibrium was observed in 5 breeds and in the commercial cross. The overall population heterozygote deficiency was 0.427, the average inbreeding coefficient was 0.097, and the heterozygote deficiency due to breed subdivisions was 0.437. Reynolds' distances were used to draw an unrooted neighbor-joining tree, which topology gave information on the genetic origin of these breeds and confirmed their known history. The estimated molecular kinship within a breed ranged from 0.559 to 0.769, evidencing high coancestry. Structure analysis was performed to detect the presence of population substructures. Inferred clusters corresponded to the different breeds, without presence of admixture. The exception was the Polverara breed, for which a more complex genetic structure was found. The results supported the decision of safeguarding these breeds as an important reservoir of genetic diversity and confirmed the usefulness of microsatellite markers to characterize and to monitor genetic variability in local chicken breeds.

Defining reliable demographic models is essential to understand the threats of ongoing environmental change. Yet, in the most remote and threatened areas, models are often based on the survey of a single population, assuming stationarity and independence in population responses. This is the case for the Emperor penguin Aptenodytes forsteri, a flagship Antarctic species that may be at high risk continent-wide before 2100. Here, using genome-wide data from the whole Antarctic continent, we reveal that this top-predator is organized as one single global population with a shared demography since the late Quaternary. We refute the view of the local population as a relevant demographic unit, and highlight that (i) robust extinction risk estimations are only possible by including dispersal rates and (ii) colony-scaled population size is rather indicative of local stochastic events, whereas the species' response to global environmental change is likely to follow a shared evolutionary trajectory.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.

The genetic variability and presence of population substructures in 4 native Northern Italian sheep breeds, Alpagota, Brogna, Foza, and Lamon, undergoing in situ conservation, and 1 widespread Italian breed, Bergamasca, were studied by investigating 19 microsatellite markers. The breeds showed considerable genetic variability in terms of number of alleles and heterozygosity, with the exception of Alpagota, which was the least variable (0.607). Nevertheless, a significant deficit of heterozygotes was observed in each breed due to rather increased levels of inbreeding or to the presence of population substructures, probably caused by increased genetic variation in the founder populations. The analyses evidenced clear genetic differentiation (F(ST) = 0.085), reduced levels of admixture, and presence of private alleles among the breeds, confirming their genetic uniqueness. In particular, according to Reynolds genetic distances, Alpagota was the most differentiated, perhaps because it had been bred mostly in a rather isolated area. Loss of any of the investigated breeds would result in a loss of genetic diversity ranging from 0.5 to 1.6% of the total observed gene diversity. Results supported the decision to safeguard these breeds as important reservoirs of genetic diversity and suggested breeding and mating practices to maintain variability and to overcome within-breed substructures.

1. An experiment involving 60 male chickens reared in an organic production system was carried out in order to investigate carcase characteristics and qualitative meat traits of three slow-growing Italian local breeds of chicken (Ermellinata, Padovana and Pepoi). 2. Chicks were randomly selected at hatch, raised together under the same conditions, slaughtered at 190 d of age, dissected for carcase traits, and meat (breast and thigh) stored for subsequent analysis of quality parameters. 3. Ermellinata (EA) chickens were significantly different from Padovana (PA) and Pepoi (PI) chickens for live, carcase and thigh weights. Breeds were also different for breast muscle protein content (EA > PI and PA), shear force (PA < EA and PI) and cooking loss (PI > PA and EA) values. 4. The CIE system values of lightness (L*), redness (a*), and yellowness (b*) evidenced a distinctive darker meat and lighter skin colour of PA breast meat. 5. Polyunsaturated fatty acids composition of breast meat was similar among the analysed breeds. EA had significantly higher saturated but significantly lower monounsaturated fatty acid contents than the other two breeds.

The aim of this study was to analyze the variation of different genetic diversity measures in 5 Italian local chicken breeds over a 4-yr period of conservation. The local breeds were Ermellinata di Rovigo, Padovana, Pépoi, Robusta Lionata, and Robusta Maculata. A total of 368 samples were chosen for the analysis among the birds hatched in the years 2002 and 2006. Genetic variation over 30 microsatellite loci was analyzed. All 30 microsatellites were polymorphic, with a total number of alleles equal to 251, a mean (±SD) of 8.367 ± 3.378 across populations and 3.233 ± 1.338 within population. After 4 yr of conservation, a loss of alleles occurred for all the microsatellites, with the exception of 4 loci. The total number of alleles and expected heterozygosity estimates significantly decreased during the 4 yr of conservation, whereas no significant differences were detected for the microsatellites polymorphism information content or for the observed heterozygosity estimates. A decrease of the inbreeding coefficient occurred for all the breeds, with the exception of Padovana and Robusta Lionata. All populations showed evidence of a persistent significant deviation from Hardy-Weinberg equilibrium caused by an excess of homozygotes, except Robusta Maculata, which reached the equilibrium in 2006. For Pépoi, Padovana, Ermellinata di Rovigo, and Robusta Maculata, molecular coancestry increased significantly (P < 0.001) after the 4 yr of conservation. No evident genetic structures were detectable within breed, both for 2002 and for 2006 individuals. However, a slight increase in the proportion of membership for each breed had occurred in the year 2006 compared with the data obtained in the year 2002. As consequence, within breed, individuals in 2006 appear more homogeneous, producing clearer, more distinctive and separated groups. Molecular markers analysis helped us monitor the genetic variability of local breeds involved in a conservation scheme, enabling the planning of new strategies for the improvement of in situ conservation schemes.

Physical and color characteristics of chicken meat were investigated on 193 animals by directly applying a fiberoptic probe to the breast muscle and using the visible-near-infrared (NIR) spectral range from 350 to 1,800 nm. Data on pH was recorded 48 h postmortem (pH); lightness (L*), redness (a*), and yellowness (b*) 48 h postmortem; thawing and cooking losses and shear force after freezing. Partial least squares regressions were performed using untreated data, raw absorbance data (log(1/R)), and multiplicative scatter correction plus first or second derivative spectra. Models were validated using full cross-validation, and their predictive ability was determined by root mean square error of cross-validation (RMSE(CV)) and correlation coefficient of cross-validation (r(cv)). Means (±SD) of pH, L*, a*, b*, thawing loss, cooking loss, and shear force were 5.83 ± 0.13, 44.54 ± 2.42, -1.90 ± 0.62, 3.21 ± 3.28, 4.84 ± 2.44%, 19.39 ± 2.95%, and 16.08 ± 3.83 N, respectively. The best prediction models were developed using log(1/R) spectra for b* (r(cv) = 0.93; RMSE(CV) = 1.16) and a* (r(cv) = 0.88; RMSE(CV) = 0.29), while a medium predictive ability of NIR was obtained for pH, L*, and thawing and cooking losses (r(cv) from 0.69 to 0.76; RMSE(CV) from 0.01 to 1.73). Finally, predicted model for shear force (r(cv) = 0.41; RMSE(CV) = 3.18) was unsatisfactory. Results suggest that NIR is a feasible technique for the assessment of several quality traits of intact breast muscle.