Multimodal mimicry of hosts in a radiation of parasitic finches

This is the author accepted manuscript. The final version is available on open access from Wiley via the DOI in this recordData accessibility: Datasets and scripts used in the analyses in this paper have been uploaded to Dryad (doi:10.5061/dryad.tqjq2bvwf)Brood parasites use the parental care of others to raise their young and sometimes employ mimicry to dupe their hosts. The brood-parasitic finches of the genus Vidua are a textbook example of the role of imprinting in sympatric speciation. Sympatric speciation is thought to occur in Vidua because their mating traits and host preferences are strongly influenced by their early host environment. However, this alone may not be sufficient to isolate parasite lineages, and divergent ecological adaptations may also be required to prevent hybridisation collapsing incipient species. Using pattern recognition software and classification models, we provide quantitative evidence that Vidua exhibit specialist mimicry of their grassfinch hosts, matching the patterns, colours and sounds of their respective host's nestlings. We also provide qualitative evidence of mimicry in postural components of Vidua begging. Quantitative comparisons reveal small discrepancies between parasite and host phenotypes, with parasites sometimes exaggerating their host's traits. Our results support the hypothesis that behavioural imprinting on hosts has not only enabled the origin of new Vidua species, but also set the stage for the evolution of host-specific, ecological adaptations. This article is protected by copyright. All rights reserved.Leverhulme TrustRoyal SocietyBiotechnology and Biological Sciences Research Council (BBSRC)Natural Environment Research Council (NERC

Quantification of the groundwater-surface water interaction by analysing temperature gradients in the streambed of the Aa river, Belgium

The aim of this research is to gain better insight in the diverse physical and biological processes in margins, inundation areas and the hyporheic zone of water courses on a local scale. Data and results presented are from a multidisciplinary study on exchange processes in river ecosystems in which biologists, hydrologists, ecologists and engineers cooperate.Groundwater and eco-biochemical models are integrated in order to determine the exchange of water, dissolved compounds and particulate matter. Several of these processes occur simultaneously and result in feedback to other processes; hence most of the investigations aim to determine net rates of exchange. GIS is used for data management, while FEMME (Soetaert et al., 2002) serves as a platform for the integration of the different models such as MODFLOW, DAFLOW, Delft3D, and WetSpa.An innovative but cost-effective method for field investigation is the measurement of streambed temperatures profiles, which lead to a delineation and quantification of the groundwater discharge on a local scale. For the Aa River site in Belgium, a typical low land river system, combinations of longitudinal and cross-sectional measurements of temperature profiles have been conducted. Along a 1400 m long section, 5 vertical measurements of up to 80-100 cm deep into the river bottom have been performed bi-monthly between August 2004 and February 2007 at 14 measurement points and 5 cross-sections. With this information we assessed the vertical component of the groundwater flux and the spatial and temporal variability of the groundwater-surface water exchange.A streambed temperature survey does not lead directly to an estimation of the groundwater flux. Additional information, especially thermodynamic parameters of the soilwater matrix are necessary.The groundwater fluxes were calculated as point values at the measurement locations on basis of an analytical solution presented by Arriaga et al. (2006), and which is solved with the help of Microsoft Excel Solver and MATLAB. The fundamental heat flow equation was also introduced in a diagenetic model, setup in FEMME and used to compare with the Arriaga et al. (2006) solution. Interpolation of the point estimates results in net groundwater fluxes on the scale of the surveyed area. These results show discharge as well as recharge dependent on the location along the section and the season. The upper reach shows in general higher discharge rates and no change in direction of the groundwater flow, whereas the lower reach is characterized by lower flow rates and a change of direction of flow

Whole-chromosome hitchhiking driven by a male-killing endosymbiont.

Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.info:eu-repo/semantics/publishedVersio