Phylogeny of beech in western Eurasia as inferred by approximate Bayesian computation

The Fagus sylvatica L. species complex in Europe and Western Asia comprises two commonly recognized subspecies, F. sylvatica subsp. sylvatica [= F. sylvatica sensu stricto (s. str.)] and F. sylvatica subsp. orientalis (= F. orientalis), and two putatively hybridogenous or intermediate taxa, “F. moesiaca” and “F. taurica”. The present study aimed to examine the demographic history of this species complex using 12 allelic loci of nine allozymes scored in 279 beech populations in western Eurasia. Three sets of phylogenetic scenarios were tested by approximate Bayesian computation: one dealing with the divergence of subspecies and/or regional populations within the whole taxonomical complex, and two others focusing on the potential hybrid origin of “F. moesiaca” and “F. taurica”. The best-supported scenario within the first set placed the time of divergence of regional populations of F. orientalis in the Early Pleistocene (1.18–1.87 My BP). According to this scenario, the Iranian population was the ancestral lineage, whereas F. sylvatica s. str. was the lineage that diverged most recently. “Fagus taurica” was found to have originated from hybridization between the Caucasian population of F. orientalis and F. sylvatica s. str. at 144 ky BP. In contrast, there was no evidence of a hybrid origin of “F. moesiaca”. The best-supported scenario suggested that the Balkan lineage is a part of F. sylvatica s. str., which diverged early from F. orientalis in Asia Minor (817 ky BP), while both the Italian and Central-European lineages diverged from the Balkan one later, at the beginning of the last (Weichselian) glacial period

Unexpected presence of Fagus orientalis complex in Italy as inferred from 45,000-year-old DNA pollen samples from Venice lagoon

<p>Abstract</p> <p>Background</p> <p>Phylogeographic analyses on the Western Euroasiatic <it>Fagus </it>taxa (<it>F. orientalis</it>, <it>F. sylvatica</it>, <it>F. taurica </it>and <it>F. moesiaca</it>) is available, however, the subdivision of <it>Fagus </it>spp. is unresolved and there is no consensus on the phylogeny and on the identification (both with morphological than molecular markers) of <it>Fagus </it>Eurasiatic taxa.</p> <p>For the first time molecular analyses of ancient pollen, dated at least 45,000 years ago, were used in combination with the phylogeny analysis on current species, to identify the <it>Fagus </it>spp. present during the Last Interglacial period in Italy.</p> <p>In this work we aim at testing if the <it>trn</it>L-<it>trn</it>F chloroplast DNA (cpDNA) region, that has been previously proved efficient in discriminating different <it>Quercus </it>taxa, can be employed in distinguishing the <it>Fagus </it>species and in identifying the ancient pollen.</p> <p>Results</p> <p>86 populations from 4 Western Euroasistic taxa were sampled, and sequenced for the <it>trn</it>L-<it>trn</it>F region to verify the efficiency of this cpDNA region in identifying the <it>Fagus </it>spp.. Furthermore, <it>Fagus crenata </it>(2 populations), <it>Fagus grandifolia </it>(2 populations), <it>Fagus japonica</it>, <it>Fagus hayatae</it>, <it>Quercus </it>species and <it>Castanea </it>species were analysed to better resolve the phylogenetic inference.</p> <p>Our results show that this cpDNA region harbour some informative sites that allow to infer relationships among the species within the Fagaceae family. In particular, few specific and fixed mutations were able to discriminate and identify all the different <it>Fagus </it>species.</p> <p>Considering a short fragment of 176 base pairs within the <it>trn</it>L intron, 2 transversions were found able in distinguishing the <it>F. orientalis </it>complex taxa (<it>F. orientalis</it>, <it>F. taurica </it>and <it>F. moesiaca</it>) from the remaining <it>Fagus </it>spp. (<it>F. sylvatica</it>, <it>F. japonica</it>, <it>F. hayataea</it>, <it>F. crenata </it>and <it>F. grandifolia</it>). This permits to analyse this fragment also in ancient samples, where DNA is usually highly degraded.</p> <p>The sequences data indicate that the DNA recovered from ancient pollen belongs to the <it>F. orientalis </it>complex since it displays the informative sites characteristic of this complex.</p> <p>Conclusion</p> <p>The ancient DNA sequences demonstrate for the first time that, in contrast to current knowledge based on palynological and macrofossil data, the <it>F. orientalis </it>complex was already present during the Tyrrhenian period in what is now the Venice lagoon (Italy).</p> <p>This is a new and important insight considering that nowadays West Europe is not the natural area of <it>Fagus orientalis </it>complex, and up to now nobody has hypothesized the presence during the Last Interglacial period of <it>F. orientalis </it>complex in Italy.</p

Anatomy Transfer

Characters with precise internal anatomy are important in film and visual effects, as well as in medical applications. We propose the first semi-automatic method for creating anatomical structures, such as bones, muscles, viscera and fat tissues. This is done by transferring a reference anatomical model from an input template to an arbitrary target character, only defined by its boundary representation (skin). The fat distribution of the target character needs to be specified. We can either infer this information from MRI data, or allow the users to express their creative intent through a new editing tool. The rest of our method runs automatically: it first transfers the bones to the target character, while maintaining their structure as much as possible. The bone layer, along with the target skin eroded using the fat thickness information, are then used to define a volume where we map the internal anatomy of the source model using harmonic (Laplacian) deformation. This way, we are able to quickly generate anatomical models for a large range of target characters, while maintaining anatomical constraints

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

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

Tracing the origin of Oriental beech stands across Western Europe and reporting hybridization with European beech : implications for assisted gene flow

The benefits and risks of human-aided translocation of individuals within the species range, assisted gene flow (AGF), depend on the genetic divergence, on the rate and direction of hybridization, and on the climate transfer distance between the host and donor populations. In this study, we explored the use of Oriental beech (Fagus sylvatica subsp. orientalis), growing from Iran to the Balkans, for AGF into European beech populations (F. sylvatica subsp. sylvatica) that increasingly suffer from climate warming. Using samples from natural populations of Oriental and European beech and microsatellite loci, we identified 5 distinct genetic clusters in Oriental beech with a divergence (FST) of 0.15 to 0.25 from European beech. Using this knowledge, we traced the origin of 11 Oriental beech stands in Western Europe established during the 20th century. In two stands of Greater Caucasus origin, we found evidence for extensive hybridization, with 18% and 41% of the offspring having hybrid status. Climate data revealed higher seasonality with warmer and drier summers across the native Oriental beech sites in comparison to the planting sites in Western Europe. Accordingly, we found that bud burst of Oriental beech occurred four days earlier than in European beech. Overall, our results suggest that AGF of Oriental beech could increase the genetic diversity of European beech stands and may foster introgression of variants adapted to expected future climatic conditions. Our study showcases the evaluation of the benefits and risks of AGF and call for similar studies on other native tree species

Article The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, rela-tionships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s–1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37–50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environmen