Raziskava obravnava genetsko variabilnost, genetsko raznolikost in genetsko diferenciacijo bukve ... more Raziskava obravnava genetsko variabilnost, genetsko raznolikost in genetsko diferenciacijo bukve (Fagus sylvatica L.) v Sloveniji. S pomočjo izoencimske analize smo pregledali 13 avtohtonih bukovih populacij. Polimorfizem smo odkrili na 11 od 12 analiziranih izoencimskih lokusih, 9 lokusov je polimorfnih v vseh populacijah. Opazen je rahel trend naraščanja genetske variabilnosti v smeri od severa proti jugu, medtem ko povprečna ugotovljena heterozigotnost Ho od severa proti jugu upada. Genetska diferenciranost je razmeroma majhna, med populacijami pa nismo odkrili diferenciranosti, ki bi ji lahko pripisali jasno geografsko pogojenost.The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations. The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations. The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations
SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean isla... more SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1–7.There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8×-11.6×) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the ...
Internal transcribed spacer (ITS) sequence was tested in Acer ibericum for its suitability as a b... more Internal transcribed spacer (ITS) sequence was tested in Acer ibericum for its suitability as a barcoding as well as population genetic marker. The marker was reliably used to identify A. ibericum as well as to gain preliminary insights into the genetic diversity of Georgian populations. MegaBLAST searches of studied samples against the GenBank database revealed that all studied accessions could be considered Acer ibericum. Populations from Vashlovani National Park revealed the presence of unique ribotypes, and together with the population from Shavi Mountain, they were identified as the most genetically diverse ones. Based on presented data the populations from Eastern Georgia should be prioritized if conservation measures are planned.
The phylogeography of the European wild boar was mainly determined by postglacial recolonization ... more The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East‐Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the ...
AimClimatic changes during the Late Pleistocene had major impacts on populations of plant and ani... more AimClimatic changes during the Late Pleistocene had major impacts on populations of plant and animal species. Brown bears and other large mammals are likely to have experienced analogous ecological pressures and phylogeographical processes. Here, we address several unresolved issues regarding the Late Pleistocene demography of brown bears: (1) the putative locations of refugia; (2) the direction of migrations across Eurasia and into North America; and (3) parallels with the demographic histories of other wild mammals and modern humans.LocationEurasia and North America.MethodsWe sequenced 110 complete mitochondrial genomes from Eurasian brown bears and combined these with published sequences from 138 brown bears and 33 polar bears. We used a Bayesian approach to obtain a joint estimate of the phylogeny and evolutionary divergence times. The inferred mutation rate was compared with estimates obtained using two additional methods.ResultsBayesian phylogenetic analysis identified seven c...
Proceedings of the National Academy of Sciences of the United States of America, Nov 7, 2017
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population ... more 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 extr...
Tab separated value file containing genotypes of studied populations. The genotypes were obtained... more Tab separated value file containing genotypes of studied populations. The genotypes were obtained from 8 nuclear microsatellite loci as part of the study, the loci themselves were identified in previous works, cited in the paper. Column 'Sample ID' contains arbitrary codes that identify individual trees. Informations about populations identified by column 'Site ID' are located in supplementary material provided with the paper. Each locus has two columns ('_1' and '_2') that contain the unphased diploid data. Missing data are indicated by the string 'NA', allelle names approximately reflect the size of allelle in basepairs, and homozygotes contain the same value in both columns
<strong>Fsylvatica.csv</strong>: individual tree measurements by trial and provenance... more <strong>Fsylvatica.csv</strong>: individual tree measurements by trial and provenance of origin. <strong>Trials_coords.csv</strong>: geographical coordinates of the trials <strong>Prov_coords.cvs</strong>: geographical coordinates of the provenances <strong>BeechCOSTe52_metadata_descriptor.docx</strong>: description of the fields of Fsylvatica.csv, Trials_coords.csv and Prov_coords.cvs databases. <strong>Prov_means.xlsx</strong>: means, average and number of trees per population and trial for each phenotypic measurement. <strong>Subset_by_trial.R: </strong>R script to subset the original database (<strong>Fsylvatica.csv</strong>) by trial <strong>Merge_trial_prov-coords_individualmeasurements.R</strong>: R script to merge the coordinates of trials and provenances (<strong>Trials_coords.csv </strong>and<strong> Prov_coords.cvs</strong>) with the phenotypic measurements (<strong>Fsylvatica.csv)</strong>. <strong>Plot_Trial-Prov_locations.R:</strong> R script to map trial and provenance locations. <strong>Hplot.R</strong>: R script to map tree height variation across provenances and trials. <strong>Subset_by_trait.R: </strong>R script to subset the original database (Fsylvatica.csv) by trait (H, DBH, mortality, spring and autumn phenology. <strong>Check_mortality.R</strong>: R script to check mortality. <strong>Fagus_sylvatica_EUFORGEN.X:</strong> Shape files containing the distribution of Fagus sylvatica from EUFORGEN (http://www.euforgen.org) <strong>Additional information</strong>: pdf files containing the description of the trials.
Genetic differentiation of grey wolf ( Canis lupus ) populations from the Balkans (Serbia and Bul... more Genetic differentiation of grey wolf ( Canis lupus ) populations from the Balkans (Serbia and Bulgaria) and the Western Carpathians was studied by means of using tissue and bone samples from legally hunted wolves. In total, 339 samples of tissues and bones and small number of feaces, blood and urine samples were used. Genotyping was based on 15 microsatellites of nuclear DNA. Genetic differentiation was studied using Bayesian approach (structure software). Obtained results showed the differenetiation between the Balkan and the Carpathian populations as well as between the Bulgarian population and both populations from Serbia and Slovakia. There are indications of migration towards west. Although these results are based on the nuclear markers, it would be advised to reanalyze the samples using mtDNA markers.
Raziskava obravnava genetsko variabilnost, genetsko raznolikost in genetsko diferenciacijo bukve ... more Raziskava obravnava genetsko variabilnost, genetsko raznolikost in genetsko diferenciacijo bukve (Fagus sylvatica L.) v Sloveniji. S pomočjo izoencimske analize smo pregledali 13 avtohtonih bukovih populacij. Polimorfizem smo odkrili na 11 od 12 analiziranih izoencimskih lokusih, 9 lokusov je polimorfnih v vseh populacijah. Opazen je rahel trend naraščanja genetske variabilnosti v smeri od severa proti jugu, medtem ko povprečna ugotovljena heterozigotnost Ho od severa proti jugu upada. Genetska diferenciranost je razmeroma majhna, med populacijami pa nismo odkrili diferenciranosti, ki bi ji lahko pripisali jasno geografsko pogojenost.The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations. The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations. The study investigates the genetic variability, genetic diversity and genetic differentiation of the beech (Fagus sylvatica L.) in Slovenia. On the basis ofisozyme analysis, 13 indigenous beech populations were examined. Polymorphism was revealed in 11 isozyme loci, 9 loci show polymorphism in all treated populations. The trend of slight north-south increase of genetic variability is present, while mean observed heterozygosity Ho decreases in thenorth-south direction. Genetic differentiation is relatively weak and we revealed no geographically conditioned differentiation among the populations
SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean isla... more SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s) 1–7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM) 8,9, until human persecutions led them to extinction 1–7.There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspecies Canis lupus cristaldii10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8×-11.6×) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM 11, around 17 kya, we explored the possibility that the ...
Internal transcribed spacer (ITS) sequence was tested in Acer ibericum for its suitability as a b... more Internal transcribed spacer (ITS) sequence was tested in Acer ibericum for its suitability as a barcoding as well as population genetic marker. The marker was reliably used to identify A. ibericum as well as to gain preliminary insights into the genetic diversity of Georgian populations. MegaBLAST searches of studied samples against the GenBank database revealed that all studied accessions could be considered Acer ibericum. Populations from Vashlovani National Park revealed the presence of unique ribotypes, and together with the population from Shavi Mountain, they were identified as the most genetically diverse ones. Based on presented data the populations from Eastern Georgia should be prioritized if conservation measures are planned.
The phylogeography of the European wild boar was mainly determined by postglacial recolonization ... more The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East‐Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the ...
AimClimatic changes during the Late Pleistocene had major impacts on populations of plant and ani... more AimClimatic changes during the Late Pleistocene had major impacts on populations of plant and animal species. Brown bears and other large mammals are likely to have experienced analogous ecological pressures and phylogeographical processes. Here, we address several unresolved issues regarding the Late Pleistocene demography of brown bears: (1) the putative locations of refugia; (2) the direction of migrations across Eurasia and into North America; and (3) parallels with the demographic histories of other wild mammals and modern humans.LocationEurasia and North America.MethodsWe sequenced 110 complete mitochondrial genomes from Eurasian brown bears and combined these with published sequences from 138 brown bears and 33 polar bears. We used a Bayesian approach to obtain a joint estimate of the phylogeny and evolutionary divergence times. The inferred mutation rate was compared with estimates obtained using two additional methods.ResultsBayesian phylogenetic analysis identified seven c...
Proceedings of the National Academy of Sciences of the United States of America, Nov 7, 2017
About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population ... more 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 extr...
Tab separated value file containing genotypes of studied populations. The genotypes were obtained... more Tab separated value file containing genotypes of studied populations. The genotypes were obtained from 8 nuclear microsatellite loci as part of the study, the loci themselves were identified in previous works, cited in the paper. Column 'Sample ID' contains arbitrary codes that identify individual trees. Informations about populations identified by column 'Site ID' are located in supplementary material provided with the paper. Each locus has two columns ('_1' and '_2') that contain the unphased diploid data. Missing data are indicated by the string 'NA', allelle names approximately reflect the size of allelle in basepairs, and homozygotes contain the same value in both columns
<strong>Fsylvatica.csv</strong>: individual tree measurements by trial and provenance... more <strong>Fsylvatica.csv</strong>: individual tree measurements by trial and provenance of origin. <strong>Trials_coords.csv</strong>: geographical coordinates of the trials <strong>Prov_coords.cvs</strong>: geographical coordinates of the provenances <strong>BeechCOSTe52_metadata_descriptor.docx</strong>: description of the fields of Fsylvatica.csv, Trials_coords.csv and Prov_coords.cvs databases. <strong>Prov_means.xlsx</strong>: means, average and number of trees per population and trial for each phenotypic measurement. <strong>Subset_by_trial.R: </strong>R script to subset the original database (<strong>Fsylvatica.csv</strong>) by trial <strong>Merge_trial_prov-coords_individualmeasurements.R</strong>: R script to merge the coordinates of trials and provenances (<strong>Trials_coords.csv </strong>and<strong> Prov_coords.cvs</strong>) with the phenotypic measurements (<strong>Fsylvatica.csv)</strong>. <strong>Plot_Trial-Prov_locations.R:</strong> R script to map trial and provenance locations. <strong>Hplot.R</strong>: R script to map tree height variation across provenances and trials. <strong>Subset_by_trait.R: </strong>R script to subset the original database (Fsylvatica.csv) by trait (H, DBH, mortality, spring and autumn phenology. <strong>Check_mortality.R</strong>: R script to check mortality. <strong>Fagus_sylvatica_EUFORGEN.X:</strong> Shape files containing the distribution of Fagus sylvatica from EUFORGEN (http://www.euforgen.org) <strong>Additional information</strong>: pdf files containing the description of the trials.
Genetic differentiation of grey wolf ( Canis lupus ) populations from the Balkans (Serbia and Bul... more Genetic differentiation of grey wolf ( Canis lupus ) populations from the Balkans (Serbia and Bulgaria) and the Western Carpathians was studied by means of using tissue and bone samples from legally hunted wolves. In total, 339 samples of tissues and bones and small number of feaces, blood and urine samples were used. Genotyping was based on 15 microsatellites of nuclear DNA. Genetic differentiation was studied using Bayesian approach (structure software). Obtained results showed the differenetiation between the Balkan and the Carpathian populations as well as between the Bulgarian population and both populations from Serbia and Slovakia. There are indications of migration towards west. Although these results are based on the nuclear markers, it would be advised to reanalyze the samples using mtDNA markers.
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