Dataset Information

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.

ABSTRACT: About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ?50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. 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 nonrandom 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 (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.

SUBMITTER: Benazzo A

PROVIDER: S-EPMC5692547 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.

Benazzo Andrea A Trucchi Emiliano E Cahill James A JA Maisano Delser Pierpaolo P Mona Stefano S Fumagalli Matteo M Bunnefeld Lynsey L Cornetti Luca L Ghirotto Silvia S Girardi Matteo M Ometto Lino L Panziera Alex A Rota-Stabelli Omar O Zanetti Enrico E Karamanlidis Alexandros A Groff Claudio C Paule Ladislav L Gentile Leonardo L Vilà Carles C Vicario Saverio S Boitani Luigi L Orlando Ludovic L Fuselli Silvia S Vernesi Cristiano C Shapiro Beth B Ciucci Paolo P Bertorelle Giorgio G

Proceedings of the National Academy of Sciences of the United States of America 20171024 45

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and f ...[more]

PMID: 29078308

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Project description:Many large carnivore populations are expanding into human-modified landscapes and the subsequent increase in coexistence between humans and large carnivores may intensify various types of conflicts. A proactive management approach is critical to successful mitigation of such conflicts. The Cantabrian Mountains in Northern Spain are home to the last remaining native brown bear (Ursus arctos) population of the Iberian Peninsula, which is also amongst the most severely threatened European populations, with an important core group residing in the province of Asturias. There are indications that this small population is demographically expanding its range. The identification of the potential areas of brown bear range expansion is crucial to facilitate proactive conservation and management strategies towards promoting a further recovery of this small and isolated population. Here, we used a presence-only based maximum entropy (MaxEnt) approach to model habitat suitability and identify the areas in the Asturian portion of the Cantabrian Mountains that are likely to be occupied in the future by this endangered brown bear population following its range expansion. We used different spatial scales to identify brown bear range suitability according to different environmental, topographic, climatic and human impact variables. Our models mainly show that: (1) 4977 km2 are still available as suitable areas for bear range expansion, which represents nearly half of the territory of Asturias; (2) most of the suitable areas in the western part of the province are already occupied (77% of identified areas, 2820 km2), 41.4% of them occurring inside protected areas, which leaves relatively limited good areas for further expansion in this part of the province, although there might be more suitable areas in surrounding provinces; and (3) in the eastern sector of the Asturian Cantabrian Mountains, 62% (2155 km2) of the land was classified as suitable, and this part of the province hosts 44.3% of the total area identified as suitable areas for range expansion. Our results further highlight the importance of increasing: (a) the connectivity between the currently occupied western part of Asturias and the areas of potential range expansion in the eastern parts of the province; and (b) the protection of the eastern sector of the Cantabrian Mountains, where most of the future population expansion may be expected.

Project description:BackgroundSperm selection methods such as Single Layer Centrifugation (SLC) have been demonstrated to be a useful tool to improve the quality of sperm samples and therefore to increase the efficiency of other artificial reproductive techniques in several species. This procedure could help to improve the quality of genetic resource banks, which is essential for endangered species. In contrast, these sperm selection methods are optimized and focused on farm animals, where the recovery task is not as important as in endangered species because of their higher sperm availability. The aim of this study was to evaluate two centrifugation methods (300 x g/20 min and 600 x g/10 min) and three concentrations of SLC media (Androcoll-Bear -80, 65 and 50%) to optimise the procedure in order to recover as many sperm with the highest quality as possible. Sperm morphology could be important in the hydrodynamic relationship between the cell and centrifugation medium and thus the effect of sperm head morphometry on sperm yield and its hydrodynamic relationship were studied.ResultsThe samples selected with Androcoll-Bear 65% showed a very good yield (53.1 ± 2.9) although the yield from Androcoll-Bear 80% was lower (19.3 ± 3.3). The latter showed higher values of motility than the control immediately after post-thawing selection. However, both concentrations of colloid (65 and 80%) showed higher values of viable sperm and viable sperm with intact acrosome than the control. After an incubation of 2 h at 37 °C, the samples from Androcoll-Bear 80% had higher kinematics and proportion of viable sperm with intact acrosome. In the morphometric analysis, the sperm selected by the Androcoll-Bear 80% showed a head with a bigger area which was more elongated than the sperm from other treatments.ConclusionsWe conclude that sperm selection with Androcoll-Bear at either 65% or 80% is a suitable technique that allows a sperm population with better quality than the initial sample to be obtained. We recommend the use of Androcoll-Bear 65% since the yield is better than Androcoll-Bear 80%. Our findings pave the way for further research on application of sperm selection techniques to sperm banking in the brown bear.

Project description:BackgroundThe low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes.ResultsWe examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping.ConclusionsThe proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.

Dataset Information

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.

Publications

Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers.

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