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Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs) on plant genomes, few data are available on copy number variation (CNV). Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV) for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

Human-driven changes in land cover and use can significantly impact species ants community structures, often leading to a decline in taxonomic diversity or species homogenization. Ant morphology, used as a proxy for ecological function, offers a valuable framework for understanding the effects of anthropogenic disturbances on ant diversity. This study explored the morphological diversity of ant assemblages in agricultural ecosystems and secondary forests in Italy and the Brazilian Amazon, analyzing how these communities are structured and adapted to different environments. The research aims to understand the ecological interactions and the role of ants in maintaining biodiversity in these contexts. The study was conducted in the Ticino River Natural Park, Italy, and the Paragominas mosaic in Pará, Brazil. The ants were sampled using epigean pitfall traps at 15 agricultural and 13 forest sites. In the secondary forests, the species richness was significantly higher in both countries compared to agricultural areas. In general, the Community Weighted Mean (CWM) of the selected traits (head length, head width, interocular distance, mandible length, eye width, Weber's length, and tibia length) of Brazilian ants was higher than those of Italian. However, the CWM of agricultural areas of the two countries was more similar. We noticed the convex hull (i.e., the volume of an assemblage in the morphological space) of Brazilian secondary forests was still larger than Italian secondary forests when both assemblages have the same number of species. Morphological homogenization was more pronounced in agricultural settings, whereas secondary forests showed more variability, highlighting the role of environmental filtering in shaping ant communities across land use types.

The biodiversity impacts of agricultural deforestation vary widely across regions. Previous efforts to explain this variation have focused exclusively on the landscape features and management regimes of agricultural systems, neglecting the potentially critical role of ecological filtering in shaping deforestation tolerance of extant species assemblages at large geographical scales via selection for functional traits. Here we provide a large-scale test of this role using a global database of species abundance ratios between matched agricultural and native forest sites that comprises 71 avian assemblages reported in 44 primary studies, and a companion database of 10 functional traits for all 2,647 species involved. Using meta-analytic, phylogenetic and multivariate methods, we show that beyond agricultural features, filtering by the extent of natural environmental variability and the severity of historical anthropogenic deforestation shapes the varying deforestation impacts across species assemblages. For assemblages under greater environmental variability-proxied by drier and more seasonal climates under a greater disturbance regime-and longer deforestation histories, filtering has attenuated the negative impacts of current deforestation by selecting for functional traits linked to stronger deforestation tolerance. Our study provides a previously largely missing piece of knowledge in understanding and managing the biodiversity consequences of deforestation by agricultural deforestation., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

The potential for climate change to affect animal behaviour is widely recognized, yet its possible consequences on aggressiveness are still unclear. If warming and drought limit the availability of food resources, climate change may elicit an increase of intraspecific conflicts stemming from resource competition. By measuring aggressivity indices in a group-living, herbivorous mammal (the Apennine chamois Rupicapra pyrenaica ornata) in two sites differing in habitat quality, and coupling them with estimates of plant productivity, we investigated whether harsh climatic conditions accumulated during the growing season influenced agonistic contests at feeding via vegetation-mediated effects, and their interaction with the site-specific habitat quality. We focused on females, which exhibit intra-group contest competition to access nutritious food patches. Accounting for confounding variables, we found that (1) the aggression rate between foraging individuals increased with the warming accumulated over previous weeks; (2) the probability to deliver more aggressive behaviour patterns toward contestants increased with decreasing rainfall recorded in previous weeks; (3) the effects of cumulative warming and drought on aggressivity indices occurred at time windows spanning 15-30 days, matching those found on vegetation productivity; (4) the effects of unfavourable climatic conditions via vegetation growth on aggressivity were independent of the site-specific habitat quality. Simulations conducted on our model species predict a ~50 % increase in aggression rate following the warming projected over the next 60 years. Where primary productivity will be impacted by warming and drought, our findings suggest that the anticipated climate change scenarios may trigger bottom-up consequences on intraspecific animal conflicts. This study opens the doors for a better understanding of the multifactorial origin of aggression in group-living foragers, emphasising how the escalation of agonistic contests could emerge as a novel response of animal societies to ongoing global warming., Competing Interests: Declaration of competing interest The authors declare no competing interests., (Copyright © 2023 Elsevier B.V. All rights reserved.)

In the Cercopithecini ancestor two chromosomes, homologous to human chromosomes 20 and 21, fused to form the Cercopithecini specific 20/21 association. In some individuals from the genus Cercopithecus, this association was shown to be polymorphic for the position of the centromere, suggesting centromere repositioning events. We set out to test this hypothesis by defining the evolutionary history of the 20/21 association in four Cercopithecini species from three different genera. The marker order of the various 20/21 associations was established using molecular cytogenetic techniques, including an array of more than 100 BACs. We discovered that five different forms of the 20/21 association were present in the four studied Cercopithecini species. Remarkably, in the two Cercopithecus species, we found individuals in which one homolog conserved the ancestral condition, but the other homolog was highly rearranged. The phylogenetic analysis showed that the heterozygosity in these two species originated about 8 million years ago and was maintained for this entire arc of time, surviving multiple speciation events. Our report is a remarkable extension of Dobzhansky's pioneering observation in Drosophila concerning the maintenance of chromosomal heterozygosity due to selective advantage. Dobzhansky's hypothesis recently received strong support in a series of detailed reports on the fruit fly genome. Our findings are first extension to primates, indeed to Old World monkeys phylogenetically close to humans of an analogous situation. Our results have important implications for hypotheses on how chromosome rearrangements, selection, and speciation are related.

Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

In temperate ecosystems, seasonality influences animal behaviour. Food availability, weather, photoperiod and endogenous factors relevant to the biological cycle of individuals have been shown as major drivers of temporal changes in activity rhythms and group size/structure of herbivorous species. We evaluated how diurnal female foraging activity and grouping patterns of a mountain herbivore, the Apennine chamois Rupicapra pyrenaica ornata, varied during a decreasing gradient of pasture availability along the summer-autumn progression (July-October), a crucial period for the life cycle of mountain ungulates. Females increased diurnal foraging activity, possibly because of constrains elicited by variation in environmental factors. Size of mixed groups did not vary, in contrast with the hypothesis that groups should be smaller when pasture availability is lower. Proportion of females in groups increased, possibly suggesting that they concentrated on patchily distributed nutritious forbs. Occurrence of yearlings in groups decreased, which may have depended on dispersal of chamois in this age class. Presence of kids in groups did not show variation through summer-autumn, suggesting a close mother-juvenile relationship even at the end of weaning and/or, possibly, low summer mortality. Both endogenous and environmental factors contribute to shape variation in foraging activity and grouping behaviour in mountain-dwelling herbivores., (Copyright © 2019 Elsevier B.V. All rights reserved.)

To counteract the negative effects of forest fragmentation on wildlife, it is crucial to maintain functional ecological networks. We identified the ecological networks for 2 mammals with very different degrees of forest specialization, the European badger Meles meles and the Roe deer Capreolus capreolus , by differentiating 4 agroforestry elements as either nodes or connectivity elements, and by defining the distance that provides the functional connectivity between fragments. Species occurrence data were collected in a wide agroecosystem in northern Italy. To test the role of hedgerows, traditional poplar cultivations, short rotation coppices, and reforestations as ecological network elements for the 2 species we applied the method of simulated species perceptions of the landscape (SSPL), comparing the ability of different SSPLs to explain the observed species distribution. All analyses were repeated considering different scenarios of species movement ability through the matrix. Model outputs seem to show that the specialist and highly mobile Roe deer has the same movement ability throughout the matrix (2 km) as the European badger, a smaller, but generalist species. The ecological network identified for the European badger was widespread throughout the area and was composed of woodlands, poplar cultivations and hedgerows as nodes and short rotation coppices as connectivity elements. Conversely, the ecological network of the Roe deer was mostly limited to the main forest areas and was composed of woodlands, poplar cultivations and reforestations as nodes and short rotation coppices and hedgerows as connectivity elements. The degree of forest specialization strongly affects both species perception of habitat and movement ability throughout the matrix, regardless of species size. This has important implications for species conservation.

Cytogenetics has historically played a key role in research on squirrel monkey (genus Saimiri) evolutionary biology. Squirrel monkeys have a diploid number of 2n = 44, but vary in fundamental number (FN). Apparently, differences in FN have phylogenetic implications and are correlated with geographic regions. A number of hypothetical mechanisms were proposed to explain difference in FN: translocations, heterochromatin, or, most commonly, pericentric inversions. Recently, an additional mechanism, centromere repositioning, was discovered, which can alter chromosome morphology and FN. Here, we used chromosome banding, chromosome painting, and BAC-FISH to test these hypotheses. We demonstrate that centromere repositioning on chromosomes 5 and 15 is the mechanism that accounts for differences in FN. Current phylogenomic trees of platyrrhines provide a temporal framework for evolutionary new centromeres (ENC) in Saimiri. The X-chromosome ENC could be up to 15 million years (my) old that on chromosome 5 as recent as 0.3 my. The chromosome 15 ENC is intermediate, as young as 2.24 my. All ENC have abundant satellite DNAs indicating that the maturation process was fairly rapid. Callithrix jacchus was used as an outgroup for the BAC-FISH data analysis. Comparison with scaffolds from the S. boliviensis genome revealed an error in the last marmoset genome release. Future research including at the sequence level will provide better understanding of chromosome evolution in Saimiri and other platyrrhines. Probably other cases of differences in chromosome morphology and FN, both within and between taxa, will be shown to be due to centromere repositioning and not pericentric inversions.

Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Background: Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies., Results: Here we propose a novel algorithm, VALOR, to discover large inversions using new sequencing methods that provide long range information such as 10X Genomics linked-read sequencing, pooled clone sequencing, or other similar technologies that we commonly refer to as long range sequencing. We demonstrate the utility of VALOR using both pooled clone sequencing and 10X Genomics linked-read sequencing generated from the genome of an individual from the HapMap project (NA12878). We also provide a comprehensive comparison of VALOR against several state-of-the-art structural variation discovery algorithms that use whole genome shotgun sequencing data., Conclusions: In this paper, we show that VALOR is able to accurately discover all previously identified and experimentally validated large inversions in the same genome with a low false discovery rate. Using VALOR, we also predicted a novel inversion, which we validated using fluorescent in situ hybridization. VALOR is available at https://github.com/BilkentCompGen/VALOR.

Endocanalar posts are necessary to build up and retain coronal restorations but they do not reinforce dental roots. It was observed that the dislodgement of post-retained restorations commonly occurs after several years of function and long-term retention may be influenced by various factors such as temperature changes. Temperature changes, in fact, produce micrometric deformations of post and surrounding tissues/materials that may generate high stress concentrations at the interface thus leading to failure. In this study we present an optical system based on the projection moiré technique that has been utilized to monitor the displacement field of endocanalar glass-fibre posts subjected to temperature changes. Measurements were performed on forty samples and the average displacement values registered at the apical and middle region were determined for six different temperature levels. A total of 480 displacement measurements was hence performed. The values of the standard deviation computed for each of the tested temperatures over the forty samples appear reasonably small which proves the robustness and the reliability of the proposed optical technique. The possible implications for the use of the system in the applicative context were discussed.

Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11. rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.

Nowadays we are seeing the largest biodiversity loss since the extinction of the dinosaurs. To conserve biodiversity it is essential to plan protected areas using a prioritization approach, which takes into account the current biodiversity value of the sites. Considering that in the Mediterranean Basin the agro-ecosystems are one of the most important parts of the landscape, the conservation of crops is essential to biodiversity conservation. In the framework of agro-ecosystem conservation, farmland birds play an important role because of their representativeness, and because of their steady decline in the last Century in Western Europe. The main aim of this research was to define if crop dominated landscapes could be useful for biodiversity conservation in a Mediterranean area in which the landscape was modified by humans in the last thousand years and was affected by the important biogeographical phenomenon of peninsula effect. To assess this, we identify the hotspots and the coldspots of bird diversity in southern Italy both during the winter and in the breeding season. In particular we used a scoring method, defining a biodiversity value for each cell of a 1-km grid superimposed on the study area, using data collected by fieldwork following a stratified random sampling design. This value was analysed by a multiple linear regression analysis and was predicted in the whole study area. Then we defined the hotspots and the coldspots of the study area as 15% of the cells with higher and lower value of biodiversity, respectively. Finally, we used GAP analysis to compare hotspot distribution with the current network of protected areas. This study showed that the winter hotspots of bird diversity were associated with marshes and water bodies, shrublands, and irrigated crops, whilst the breeding hotspots were associated with more natural areas (e.g. transitional wood/shrubs), such as open areas (natural grasslands, pastures and not irrigated crops). Moreover, the results underlined the negative effects of permanent crops, such as vineyards, olive groves, and orchards, in particular during the winter season. This research highlights the importance of farmland areas mainly for wintering species and the importance of open areas for breeding species in the Mediterranean Basin. This may be true even when the species' spatial distribution could be affected by biogeography. An important result showed that the hotspots for breeding species cannot be used as a surrogate for the wintering species, which were often not considered in the planning of protected areas.

Gibbons are small arboreal apes that display an accelerated rate of evolutionary chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes. Here we present the assembly and analysis of a northern white-cheeked gibbon (Nomascus leucogenys) genome. We describe the propensity for a gibbon-specific retrotransposon (LAVA) to insert into chromosome segregation genes and alter transcription by providing a premature termination site, suggesting a possible molecular mechanism for the genome plasticity of the gibbon lineage. We further show that the gibbon genera (Nomascus, Hylobates, Hoolock and Symphalangus) experienced a near-instantaneous radiation ∼5 million years ago, coincident with major geographical changes in southeast Asia that caused cycles of habitat compression and expansion. Finally, we identify signatures of positive selection in genes important for forelimb development (TBX5) and connective tissues (COL1A1) that may have been involved in the adaptation of gibbons to their arboreal habitat.

We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.