Polygamy and Purifying Selection in Birds

Good genes theories of sexual selection predict that polygamy will be associated with more efficient removal of deleterious alleles (purifying selection), due to the alignment of sexual selection with natural selection. On the other hand, runaway selection theories expect no such alignment of natural and sexual selection, and may instead predict less efficient purifying selection in polygamous species due to higher reproductive variance. In an analysis of polymorphism data extracted from 150-bird genome assemblies, we show that polygamous species carry significantly fewer nonsynonymous polymorphisms, relative to synonymous polymorphisms, than monogamous bird species (p = .0005). We also show that this effect is independent of effective population size, consistent with the alignment of natural selection with sexual selection and “good genes” theories of sexual selection. Further analyses found no impact of polygamy on genetic diversity, while polygamy in females (polyandry) had a marginally significant impact (p = .045). We also recapitulate previous findings that smaller body mass and greater geographic range size are associated with more efficient purifying selection, more intense GC-biased gene conversion, and greater genetic diversity

Impacts of herbivory by ecological replacements on an island ecosystem

The use of ecological replacements (analogue species to replace extinct taxa) to restore ecosystem functioning is a promising conservation tool. However, this approach is controversial, in part due to a paucity of data on interactions between analogue species and established taxa in the ecosystem. We conducted ecological surveys, comprehensively DNA barcoded an ecosystem's flora and inferred the diet of the introduced Aldabra giant tortoise, acting as an ecological replacement, to understand how it might have modified island plant communities on a Mauritian islet. Through further dietary analyses, we investigated consequential effects on the threatened endemic Telfair's skink. Dietary overlap between tortoises and skinks was greater than expected by chance. However, there was a negative correlation between tortoise and skink preferences in herbivory and minimal overlap in the plants most frequently consumed by the reptiles. Changes in the plant community associated with 7 years of tortoise grazing were characterised by a decrease in the percentage cover of native herbs and creepers, and an increase in the cover of an invasive herb when compared to areas without tortoises. However, tortoise dietary preferences themselves did not directly drive changes in the plant community. Tortoises successfully dispersed the seeds of an endemic palm, which in time may increase the extent of unique palm-rich habitat. We found no evidence that tortoises have increased the extent of plant species hypothesised to be part of a lost Mauritian tortoise grazed community. Synthesis and applications. Due to a negative correlation in tortoise and skink dietary preferences and minimal overlap in the most frequently consumed taxa, the presence of tortoises is unlikely to have detrimental impacts on Telfair's skinks. Tortoise presence is likely to be beneficial to skinks in the long term by increasing the extent of palm-rich habitat. Although tortoises are likely to play a role in controlling invasive plants, they are not a panacea for this challenge. After 7 years, tortoises have not resurrected a lost tortoise grazed community that we hypothesise might have existed in limited areas on the islet, indicating that further interventions may be required to restore this plant community

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Nucleic Acids Res 2018 Jan 4; 46(D1):D221-D228

Toward community standards in the quest for orthologs

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: [email protected]

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately

Assessing population coherence and connectivity: some methods and caveats

Genetic tools have been championed as providing novel and sensitive ways to detect the otherwise cryptic movements of organisms, and their genes, in the context of landscape connectivity. A variety of statistical approaches have been developed to detect migrants and their descendants within populations of conservation concern. These methods have taken advantage of increasingly powerful molecular approaches, initially from microsatellite DNA profiling, now to whole genome resequencing1. The transition from standard molecular ecology techniques to population genomics not only allows the demographic consequences of migration and gene-flow to be better inferred, but the fitness consequences may become predictable too. Inferring movement between populations that are genetically very similar (possibly because they recently lost contact, or because gene-flow is reciprocal) has been traditionally challenging using a handful of DNA profiling markers, but the resolution of this approach will be transformed by the application of genome-wide datasets. Recent and ongoing studies, using whole genome resequencing of species benefitting from well-annotated reference genomes, have been able to shed light on likely chromosome and finer scale effects of immigration and for managed translocation/gene-flow, which potentially puts individual fitness-defining genomic variants in the hands of conservation managers. The conservation implications of this transformation in our ability to resolve connectivity and population coherence remains, however, unclear. For instance, when assessing the likely benefits of gene-flow, whether natural or by assisted translocation, the balance between genome-wide versus locus-specific management has yet to be fully assessed, especially in the context of environmental heterogeneity. One possible solution is the use of so-called landscape genomics tools that simultaneously evaluate genomic and large-scale environmental datasets2 but these methods can produce conflicting results and/or different rankings and priorities. I will discuss these problems and methods in the context of ongoing conservation initiatives in Europe and at a global level, with the aim of proposing research avenues and policy discussions that could be relevant to advancing this exciting new field. 1. Caroll EL, Bruford MW, et al (2018) Genetic and genomic monitoring with minimally invasive sampling methods. Evolutionary Applications. In press. 2. Stucki S, Orozco-terWengel P, et al (2017) High performance computation of landscape genomic models including local indicators of spatial association. Molecular Ecology Resources 17: 1072-1089.peerReviewe

Prospects for genomic monitoring using minimally invasive sampling

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g. collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically-driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy datasets and recommend how to address the challenges of moving between traditional and next generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment1. 1. Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J (2018) Genetic and genomic monitoring with minimally invasive sampling methods. Evolutionary Applications. In press.peerReviewe

The Urban Biodiversity Hub: A Webtool and Interactive Database to Connect Scientists and Practitioners

Urban biodiversity has been demonstrated to increase resilience and improve ecological and human health and well-being; however, many local governments currently lack the capacity to develop and manage urban biodiversity strategies. The Urban Biodiversity Hub (UBHub) is a new web tool that increases the capacity of cities to make decisions for urban biodiversity planning and management. One of the main goals of UBHub is to support local governments through providing resources, connections, and ultimately by funneling funding to those who most need it. In the long term, we seek to promote biodiversity mainstreaming, the integration of associated tools, and awareness of biodiversity planning. UBHub will be previewing our online platform comprising (1) a searchable map of urban biodiversity activities around the world covering over 900 activities and frameworks; (2) myHub, a tracking tool for cities to measure their progress towards urban biodiversity protection; and (3) an experts forum connecting cities, practitioners, and researchers. The platform is designed to increase the capacity of cities to plan for and manage biodiversity, and to foster the development and refinement of biodiversity indicators. UBHub was founded in 2016 at the 13th Conference of the Parties of the Convention on Biological Diversity by like-minded individuals who saw the need for a one-stop shop for all things on urban biodiversity. It has since grown into an international all-volunteer powerhouse that has produced the largest known urban biodiversity database and is developing the first customizable tool for biodiversity indicator development for local governments. Our partners include international NGOs and academic groups as well as leading cities.peerReviewe

Mitochondrial phylogenetics of UK eurytomids

The aim of this study was to investigate the taxonomic limits of species within four Eurytomid genera, namely Euratoma lliger, Tetramesa Walker, Ahtola Claridge and Sycophila (Walker). In order to further clarify the taxonomic status of the genera, including Tetramesa, Eurtoma, Ahtola and Sycophila, mitochondria1 DNA sequence analysis revealed differentiation between the above Eurytomid genera. With the sequence data, the monophyletic status of three of these genera is well supported by all methods of phylogenetic reconstruction. Only Tetramesa, which is by far the most specious taxon studied here, seems polyphyletic, but even in this case, there are certain relationships within the group that are interesting from both a morphological and host preference point of view. For example, T. periolata (Walker) and T. airae (von Schlechtendal), which are both herbivores of the grass, Deschampsia cespitosa (L.) (Beauv.) group together and two clusters contained all species that use Elymus repens (L.), i.e., T. linearis (Walker), T. hyalipenis (Walker) and T. cornuta (Walker). Another result of this analysis supports the validity of Ahtola as a separate genus, which was prcviously uncertain