RAPD (Random Amplified Polymorphic DNA) profiles of ten macaque species

Here, we report on the RAPD profiles of 61 individuals belonging to 10 macaque species. We used 23 different PCR primers on each sample and found an average of 17 bands per primer. The RAPD profiles appear to be highly reproducible because we found no differences in the amplification patterns produced by the DNA extracted from hair or blood. Strikingly, each species had a unique RAPD pattern homogeneously shared by all individuals. Comparisons between taxa showed that variability in the RAPD pattern was low, and the Sm index was below 0.601. Cluster analysis led to a division of the macaques into two main clusters: One with M. sylvanus and M. silenus and the other with M. arctoides, mulatta, fascicularis, nemestrina, tonkeana and fuscata. Macaca nigra and M. radiata were positioned outside of these clusters. Gene flow may explain the zoogeographic pattern present in the RAPD profiles. The lack of within-specie s variability suggests the operation of founder effects and strong genetic drift, which may have been particularly strong in the case of peripherally placed species such as M. radiata, fuscata and nigra. The position of M. tonkeana is divergent from all the commonly accepted taxonomic and phylogenetic schemes. This result suggests that the RAPD technique is not always able to reveal the "true" phylogenetic relationships within the genus Macaca. The nature of genetic variation uncovered by the RAPD method is still unclear, and prudence should guide inferences about nucleotide divergence, population structure and phylogeny based solely on RAPD markers

Ancient DNA from speleothems: opportunity or challenge?

Ancient environmental DNA retrieved from sedimentary records (sedaDNA) can complement fossil-morphological approaches for characterizing Quaternary biodiversity changes. PCR-based DNA metabarcoding is so far the most widely used method in environmental DNA studies, including sedaDNA. However, degradation of ancient DNA and potential contamination, together with the PCR amplification drawbacks, have to be carefully considered. Here we tested this approach on speleothems from an Alpine cave that, according to a previous palynomorphological study, have shown to contain abundant pollen grains. This offers a unique opportunity for comparing the two methods and, indirectly, trying to validate DNA-based results. The plant taxa identified by sedaDNA are fewer than those by pollen analysis, and success rate of PCR replicates is low. Despite extensive work performed following best practice for sedaDNA, our results are suboptimal and accompanied by a non-negligible uncertainty. Our preliminary data seem to indicate that paleoenvironmental DNA may be isolated from speleothems, but the intrinsic weakness of PCR-based metabarcoding poses a challenge to its exploitation. We suggest that newly developed methods such as hybridization capture, being free from PCR drawbacks and offering the opportunity to directly assess aDNA authenticity, may overcome these limitations, allowing a proper exploitation of speleothems as biological archive

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

First genome-wide data from Italian European beech (Fagus sylvatica L.): strong and ancient differentiation between Alps and Apennines

The European beech (Fagus sylvatica L.) is one of the most widespread forest trees in Europe whose distribution and intraspecific diversity has been largely shaped by repeated glacial cycles. Previous studies, mainly based on palaeobotanical evidence and a limited set of chloroplast and nuclear genetic markers, highlighted a complex phylogeographic scenario, with southern and western Europe characterized by a rather heterogeneous genetic structure, as a result of recolonization from different glacial refugia. Despite its ecological and economic importance, the genome of this broad-leaved tree has only recently been assembled, and its intra-species genomic diversity is still largely unexplored. Here, we performed whole-genome resequencing of nine Italian beech individuals sampled from two stands located in the Alpine and Apennine mountain ranges. We investigated patterns of genetic diversity at chloroplast, mitochondrial and nuclear genomes and we used chloroplast genomes to reconstruct a temporally-resolved phylogeny. Results allowed us to test European beech differentiation on a whole-genome level and to accurately date their divergence time. Our results showed comparable, relatively high levels of genomic diversity in the two populations and highlighted a clear differentiation at chloroplast, mitochondrial and nuclear genomes. The molecular clock analysis indicated an ancient split between the Alpine and Apennine populations, occurred between the Günz and the Riss glaciations (approximately 660 kyrs ago), suggesting a long history of separation for the two gene pools. This information has important conservation implications in the context of adaptation to ongoing climate change

Impact of forest disturbance on microarthropod communities depends on underlying ecological gradients and species traits

Windstorms and salvage logging lead to huge soil disturbance in alpine spruce forests, potentially affecting soil-living arthropods. However, the impacts of forest loss and possible interactions with underlying ecological gradients on soil microarthropod communities remain little known, especially across different environmental conditions. Here we used DNA metabarcoding approach to study wind-induced disturbances on forest communities of springtails and soil mites. In particular, we aimed to test the effect of forest soil disturbance on the abundance, richness, species composition, and functional guilds of microarthropods. We sampled 29 pairs of windfall-forest sites across gradients of elevation, precipitation, aspect and slope, 2 years after a massive windstorm, named Vaia, which hit North-Eastern Italy in October 2018. Our results showed that wind-induced disturbances led to detrimental impacts on soil-living communities. Abundance of microarthropods decreased in windfalls, but with interacting effects with precipitation gradients. Operative Taxonomic Units (OTU) richness strongly decreased in post-disturbance sites, particularly affecting plant-feeder trophic guilds. Furthermore, species composition analyses revealed that communities occurring in post-disturbance sites were different to those in undisturbed forests (i.e., stands without wind damage). However, variables at different spatial scales played different roles depending on the considered taxon. Our study contributes to shed light on the impacts on important, but often neglected arthropod communities after windstorm in spruce forests. Effects of forest disturbance are often mediated by underlying large scale ecological gradients, such as precipitation and topography. Massive impacts of stronger and more frequent windstorms are expected to hit forests in the future; given the response we recorded, mediated by environmental features, forest managers need to take site-specific conservation measures

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

Analisi della biodiversità genetica di alcune specie microalgali responsabili di fioriture tossiche nel Mar Mediterraneo

In this study a genetic diversity of the main Mediterranean dinoflagellate HAB species has been analysed using the phylogeographic based approach. Different microalgal species isolates were characterized by phylogenetic, phylogeographic and population genetic aspects using different molecular markers and genetic analyses.S

The coalition for conservation genetics: working across organizations to build capacity and achieve change in policy and practice

The Coalition for Conservation Genetics (CCG) brings together four eminentorganizations with the shared goal of improving the integration of geneticinformation into conservation policy and practice. We provide a historicalcontext of conservation genetics as a field and reflect on current barriers toconserving genetic diversity, highlighting the need for collaboration acrosstraditional divides, international partnerships, and coordinated advocacy. Wethen introduce the CCG and illustrate through examples how a coalitionapproach can leverage complementary expertise and improve the organiza-tional impact at multiple levels. The CCG has proven particularly successfulat implementing large synthesis-type projects, training early-career scientists,and advising policy makers. Achievements to date highlight the potential forthe CCG to make effective contributions to practical conservation policy andmanagement that no one“parent”organization could achieve on its own.Finally, we reflect on the lessons learned through forming the CCG, and ourvision for the futur

Ancient and historical DNA in conservation policy

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (N-e), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.Peer reviewe