The continuous decline in Earth’s biodiversity represents a major crisis and challenge for the 21st century, and there is international political agreement to slow down or halt this decline. The challenge is in large part impeded by the lack of knowledge on the state and distribution of biodiversity – especially since the majority of species on Earth are un-described by science. All conservation efforts to save biodiversity essentially depend on the monitoring of species and populations to obtain reliable distribution patterns and population size estimates. Such monitoring has traditionally relied on physical identification of species by visual surveys and counting of individuals. However, traditional monitoring techniques remain problematic due to difficulties associated with correct identification of cryptic species or juvenile life stages, a continuous decline in taxonomic expertise, non-standardized sampling, and the invasive nature of some survey techniques. Hence, there is urgent need for alternative and efficient techniques for large-scale biodiversity monitoring. Environmental DNA (eDNA) – defined here as: genetic material obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material – is an efficient, non-invasive and easy-to-standardize sampling approach. Coupled with sensitive, cost-efficient and ever-advancing DNA sequencing technology, it may be an appropriate candidate for the challenge of biodiversity monitoring. Environmental DNA has been obtained from ancient as well as modern samples and encompasses single species detection to analyses of ecosystems. The research on eDNA initiated in microbiology, recognizing that culture-based methods grossly misrepresent the microbial diversity in nature. Subsequently, as a method to assess the diversity of macro-organismal communities, eDNA was first analyzed in sediments, revealing DNA from extinct and extant animals and plants, but has since been obtained from various terrestrial and aquatic environmental samples. Results from eDNA approaches have provided valuable insights to the study of ancient environments and proven useful for monitoring contemporary biodiversity in terrestrial and aquatic ecosystems. In the future, we expect the eDNA-based approaches to move from single-marker analyses of species or communities to meta-genomic surveys of entire ecosystems to predict spatial and temporal biodiversity patterns. Such advances have applications for a range of biological, geological and environmental sciences. Here we review the achievements gained through analyses of eDNA from macro-organisms in a conservation context, and discuss its potential advantages and limitations for biodiversity monitoring.No Full Tex

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

DNA barcoding should provide rapid, accurate and automatable species identifications by using a standardized DNA region as a tag. Based on sequences available in GenBank and sequences produced for this study, we evaluated the resolution power of the whole chloroplast trn L (UAA) intron (254–767 bp) and of a shorter fragment of this intron (the P6 loop, 10–143 bp) amplified with highly conserved primers. The main limitation of the whole trn L intron for DNA barcoding remains its relatively low resolution (67.3% of the species from GenBank unambiguously identified). The resolution of the P6 loop is lower (19.5% identified) but remains higher than those of existing alternative systems. The resolution is much higher in specific contexts such as species originating from a single ecosystem, or commonly eaten plants. Despite the relatively low resolution, the whole trn L intron and its P6 loop have many advantages: the primers are highly conserved, and the amplification system is very robust. The P6 loop can even be amplified when using highly degraded DNA from processed food or from permafrost samples, and has the potential to be extensively used in food industry, in forensic science, in diet analyses based on feces and in ancient DNA studies.