64 research outputs found
Genetic variability in Peregrine Falcon populations of the Western Palaearctic region
We analysed variation in ten polymorphic microsatellite loci and a portion of cytochrome bgeneof
mitochondrial
DNA
in
65 samples
from
four populations
of
Peregrine Falcon
(Falco
peregrinus
peregrinus
and
F.
p.
brookei)
breeding
in Northern
and Southern
Italy,
Northern
Spain
and
the
Czech
Republic
to assess genetic diversity in the poorly investigated Western
Palearctic region. We
added to our cytochrome
b
sequences a dataset of previously published mtDNA
sequences of other populations and subspecies to outline
genetic
variation
in
the
region
on
a
worldwide
basis.
Regarding
mtDNA
we
identified
12
haplotypes
from
our
65
Peregrine
Falcon samples, nine of which were new and three already known. The
52% of our samples, including
all
Italian
and
Czech
specimens,
belonged
to
the
previously
identified
HI
haplotype,
another
22%
of
the
samples,
most of which were from Sicily,
showed the new H1 haplotype, while the remaining 26% of the sample partitioned
among the other 10 haplotypes. Allelic
patterns and genetic structuring of microsatellites were similar to
those
of other European populations. Genetic differentiation
in both mtDNA
and microsatellites loci is almost absent
and it
is not
possible
to
distinguish
geographical groups according to taxonomic designation
at
the subspecies
level
First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus):a collaborative approach
Additional file 8: Table S7. Allelic patterns in 2000–2010 (pop1 - pre-arctos) and 2011–2017 (pop2 - arctos & post arctos). Na number of different alleles, Na Freq. ≥5% number of alleles with a frequency ≥ 5%, Ne number of effective alleles, I Shannon Information Index, No. Private Alleles number of private alleles, Ho observed heterozygosity and He expected heterozygosity
A rapid and reliable detection procedure of Atlantic trout introgression at the diagnostic lactate dehydrogenase chain-1 gene
The Italian-native Mediterranean brown trout (Salmo ghigii) is a seriously threatened freshwater fish, especially by anthropogenic hybridisation with the domestic strains of Atlantic origin that have been repeatedly released into the wild for angling. A PCR-restriction fragment length polymorphism (RFLP) assay of the diagnostic lactate dehydrogenase chain-1 (LDH-C1) gene sequences has been routinely applied to distinguish exotic from native brown trout lineages and detect Atlantic introgression signals in the Mediterranean wild populations. Here, we used dermal swab DNA obtained from 28 wild trout to improve laboratory procedures to genetically characterise trout samples at the LDH-C1gene through (1) a capillary electrophoresis analysis of the RFLP fragments and (2) the optimisation of a diagnostic single nucleotide polymorphism analysable through mini-sequencing approaches. The developed methods were fully consistent with those obtained through the traditional approach, but their analytical process is almost entirely automated and digitalised, thus improving result readability and accuracy in the detection of alien introgressed traces in wild Mediterranean brown trout populations
Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization
In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement
Exploring the Gut Microbiome Alteration of the European Hare (Lepus europaeus) after Short-Term Diet Modifications
This study aimed to characterise the gut microbiome composition of European hares (Lepus europaeus) and its potential changes after a short-term diet modification. The high sensitivity of European hare to habitat changes makes this species a good model to analyse possible alterations in gut microbiome after the introduction of additional nourishment into the diet. In total, 20 pairs were chosen for the experiments; 10 pairs formed the control group and were fed with standard fodder. The other 10 pairs represented the experimental group, whose diet was integrated with apples and carrots. The DNA from fresh faecal pellets collected after 4 days from the start of the experiment was extracted and the V3-V4 hypervariable regions were amplified and sequenced using the Illumina MiSeq® platform. The obtained amplicon sequence variants were classified into 735 bacterial genera belonging to 285 families and 36 phyla. The control and the experimental groups appeared to have a homogenous dispersion for the two taxonomic levels analysed with the most abundant phyla represented by Bacteroidetes and Firmicutes. No difference between control and experimental samples was detected, suggesting that the short-term variation in food availability did not alter the hares’ gut microbiome. Further research is needed to estimate significant time threshold
Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field
Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization
n the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was en-acted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and as-sess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immi-gration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad- scale geographic origin assignment using nuclear markers to support law enforcement
A reduced SNP panel to trace gene flow across southern European wolf populations and detect hybridization with other Canis taxa
[EN] Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (Canis lupus) are affected by hybridization, particularly in southern Europe, where ongoing recolonization of historic ranges is augmenting gene flow among divergent populations. Our aim was to provide diagnostic canid markers focused on the long-divergent Iberian, Italian and Dinaric wolf populations, based on existing genomic resources. We used 158 canid samples to select a panel of highly informative single nucleotide polymorphisms (SNPs) to (i) distinguish wolves in the three regions from domestic dogs (C. l. familiaris) and golden jackals (C. aureus), and (ii) identify their first two hybrid generations. The resulting 192 SNPs correctly identified the five canid groups, all simulated first-generation (F1) hybrids (0.482≤Qi≤0.512 between their respective parental groups) and all first backcross (BC1) individuals (0.723≤Qi≤0.827 to parental groups). An assay design and test with invasive and non-invasive canid samples performed successfully for 178 SNPs. By separating natural population admixture from inter-specific hybridization, our reduced panel can help advance evolutionary research, monitoring, and timely conservation management.We thank S. Czarnomska, A. Galov, J. Harmoinen, E. Velli, D. Battilani, P. Aragno, P. Genovesi, and the Mam-
mal Research Institute, Polish Academy of Sciences, for their assistance. We are also grateful to two anonymous
reviewers for their constructive feedback that greatly improved our manuscript. Funding was provided to ISPRA
by the Italian Ministry of Environment (MATTM; Direzione Tutela della Natura) and Regione Emilia Romagna
(Assessorato Agricoltura) within a multi-year collaborative project to genotype and monitor the Italian wolf population. AVS was supported by a senior postdoctoral fellowship from Insubria University, Italy. RG was sup-
ported by a research contract from the Portuguese Foundation for Science and Technolog
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