Browsing by Subject "1181 Ecology, evolutionary biology"

Sort by: Order: Results:

Now showing items 21-40 of 2005
  • Walton, Stephanie; Livermore, Laurence; Dillen, Mathias; De Smedt, Sofie; Groom, Quentin; Koivunen, Anne; Phillips, Sarah (2020)
    We compare different approaches to transcribing natural history data and summarise the advantages and disadvantages of each approach using six case studies from four different natural history collections. We summarise the main cost considerations when planning a transcription project and discuss the limitations we current have in understanding the costs behind transcription and data quality.
  • Murillo-Ramos, Leidys; Sihvonen, Pasi; Brehm, Gunnar; Rios-Malaver, Indiana C.; Wahlberg, Niklas (2021)
    Background Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs -Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015-2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only. New information We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoologia of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.
  • Opedal, Oystein H.; Martins, Adriana A.; Marjakangas, Emma-Liina (2020)
    Euglossine bees are an ecologically important group, which due to their diverse resource needs act as pollinators of many neotropical plants. Male euglossines collect fragrant compounds used in mating displays from diverse sources, including the flowers of orchids and other plants. This aspect of euglossine biology has proven exceptionally useful for studies of euglossine bee populations, because male bees can be readily attracted to fragrance baits deployed in natural habitats. We synthesise the data accumulated over the 50 years since the introduction of euglossine bee baiting inventories and make these data openly available in the EUGCOMM database. By fitting hierarchical joint species distribution models to presence-absence and abundance data, we reveal that the assemblages of bees attracted depend on the baits used in interaction with species-specific fragrance preferences and that bee assemblages are most diverse at sites in landscapes characterised by partial but not complete forest cover. We suggest that these results reflect the diverse resource needs of euglossine bees and are consistent with the hypothesis that male euglossines establish home ranges incorporating multiple habitat types. These results may have important consequences for the design of nature reserves in the tropics, if these iconic pollinators are to be conserved for the future.
  • Macias-Hernandez, Nuria; Ramos, Cândida; Domènech, Marc; Febles, Sara; Santos, Irene; Arnedo, Miquel A.; Borges, Paulo A. V.; Emerson, Brent C.; Cardoso, Pedro (2020)
    Background There is an increasing demand for databases including species trait information for biodiversity and community ecology studies. The existence of trait databases is useful for comparative studies within taxa or geographical regions, but there is low availability of databases for certain organisms. Here we present an open access functional trait database for spiders from Macaronesia and the Iberian Peninsula, recording several morphological and ecological traits related to the species life histories, microhabitat and trophic preferences. New information We present a database that includes 12 biological traits for 506 spider species present in natural forests of the Iberian Peninsula (Spain) and three Macaronesian archipelagoes (Azores, Madeira and Canary Islands). The functional trait database consists of two sections: 1. individual-level data for six morphological traits (total body size, prosoma length, prosoma width, prosoma height, tibia I length and fang length), based on direct measurements of 2844 specimens of all spider species; and 2. species-level aggregate data for 12 traits (same 6 morphological traits as in the previous section plus dispersal ability, vertical stratification, circadian activity, foraging strategy, trophic specialization and colonization status), based on either the average of the direct measurements or bibliographic searches. This functional trait database will serve as a data standard for currently ongoing analyses that require trait and functional diversity statistics.
  • Gashev, Sergey; Belyaeva, Fania; Sorokina, Natalya; Bykova, Elena; Kurhinen, Juri (2020)
  • Crespo, L.C.; Domenech, M; Enguídanos, A.; Malumbres-Olarte, Jagoba; Cardoso, Pedro; Moya-Larano, J; Frias-Lopez, Cristina; Macias Hernandez, Nuria Esther; de Mas, Eva; Mazzuca, Paola; Mora, E.; Opatova, Vera; Planas, Enric; Ribera, Carles; Roca-Cusachs, M.; Ruiz, D.; Sousa, Pedro; Tonzo, V.; Arnedo, M.A. (2018)
    Background A large scale semi-quantitative biodiversity assessment was conducted in white oak woodlands in areas included in the Spanish Network of National Parks, as part of a project aimed at revealing biogeographic patterns and identify biodiversity drivers. The semi-quantitative COBRA sampling protocol was conducted in sixteen 1-ha plots across six national parks using a nested design. All adult specimens were identified to species level based on morphology. Uncertain delimitations and identifications due to either limited information of diagnostic characters or conflicting taxonomy were further investigated using DNA barcode information. New information We identified 376 species belonging to 190 genera in 39 families, from the 8,521 adults found amongst the 20,539 collected specimens. Faunistic results include the discovery of 7 new species to the Iberian Peninsula, 3 new species to Spain and 11 putative new species to science. As largely expected by environmental features, the southern parks showed a higher proportion of Iberian and Mediterranean species than the northern parks, where the Palearctic elements were largely dominant. The analysis of approximately 3,200 DNA barcodes generated in the present study, corroborated and provided finer resolution to the morphologically based delimitation and identification of specimens in some taxonomically challenging families. Specifically, molecular data confirmed putative new species with diagnosable morphology, identified overlooked lineages that may constitute new species, confirmed assignment of specimens of unknown sexes to species and identified cases of misidentifications and phenotypic polymorphisms.
  • Ramage, Thibault; Martins-Simoes, Patricia; Mialdea, Gladys; Allemand, Roland; Duplouy, Anne; Rousse, Pascal; Davies, Neil; Roderick, George K.; Charlat, Sylvain (2017)
    We report here on the taxonomic and molecular diversity of 10 929 terrestrial arthropod specimens, collected on four islands of the Society Archipelago, French Polynesia. The survey was part of the 'SymbioCode Project' that aims to establish the Society Islands as a natural laboratory in which to investigate the flux of bacterial symbionts (e.g., Wolbachia) and other genetic material among branches of the arthropod tree. The sample includes an estimated 1127 species, of which 1098 included at least one DNA-barcoded specimen and 29 were identified to species level using morphological traits only. Species counts based on molecular data emphasize that some groups have been understudied in this region and deserve more focused taxonomic effort, notably Diptera, Lepidoptera and Hymenoptera. Some taxa that were also subjected to morphological scrutiny reveal a consistent match between DNA and morphology-based species boundaries in 90% of the cases, with a larger than expected genetic diversity in the remaining 10%. Many species from this sample are new to this region or are undescribed. Some are under description, but many await inspection by motivated experts, who can use the online images or request access to ethanol-stored specimens.
  • Nichols, Hazel J.; Arbuckle, Kevin; Sanderson, Jennifer L.; Vitikainen, Emma I. K.; Marshall, Harry H.; Thompson, Faye J.; Cant, Michael A.; Wells, David A. (2021)
    Personality traits, such as the propensity to cooperate, are often inherited from parents to offspring, but the pathway of inheritance is unclear. Traits could be inherited via genetic or parental effects, or culturally via social learning from role models. However, these pathways are difficult to disentangle in natural systems as parents are usually the source of all of these effects. Here, we exploit natural 'cross fostering' in wild banded mongooses to investigate the inheritance of cooperative behaviour. Our analysis of 800 adult helpers over 21 years showed low but significant genetic heritability of cooperative personalities in males but not females. Cross fostering revealed little evidence of cultural heritability: offspring reared by particularly cooperative helpers did not become more cooperative themselves. Our results demonstrate that cooperative personalities are not always highly heritable in wild, and that the basis of behavioural traits can vary within a species (here, by sex).
  • Silva, Sofia Marques; Townsend Peterson, A.; Carneiro, Lincoln; Tortola Burlamaqui, Tiberio Cesar; Ribas, Camila C.; Sousa-Neves, Tiago; Miranda, Leonardo S.; Fernandes, Alexandre M.; d'Horta, Fernando M.; Araujo-Silva, Lucas Eduardo; Batista, Romina; Bandeira, Cinthia H. M. M.; Dantas, Sidnei M.; Ferreira, Mateus; Martins, Denise M.; Oliveira, Joiciane; Rocha, Taina C.; Sardelli, Carla H.; Thom, Gregory; Rego, Pericles Sena; Santos, Marcos Persio; Sequeira, Fernando; Vallinoto, Marcelo; Aleixo, Alexandre (2019)
    The Amazon is the primary source of Neotropical diversity and a nexus for discussions on processes that drive biotic diversification. Biogeographers have focused on the roles of rivers and Pleistocene climate change in explaining high rates of speciation. We combine phylogeographic and niche-based paleodistributional projections for 23 upland terra firme forest bird lineages from across the Amazon to derive a new model of regional biological diversification. We found that climate-driven refugial dynamics interact with dynamic riverine barriers to produce a dominant pattern: Older lineages in the wetter western and northern parts of the Amazon gave rise to lineages in the drier southern and eastern parts. This climate/drainage basin evolution interaction links landscape dynamics with biotic diversification and explains the east-west diversity gradients across the Amazon.
  • Cornetti, Luca; Fields, Peter D.; Van Damme, Kay; Ebert, Dieter (2019)
    In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system.
  • Webster, Mike M.; Chouinard-Thuly, Laura; Herczeg, Gabor; Kitano, Jun; Riley, Riva; Rogers, Sean; Shapiro, Michael D.; Shikano, Takahito; Laland, Kevin N. (2019)
    Whether learning primarily reflects general processes or species-specific challenges is a long-standing matter of dispute. Here, we present a comprehensive analysis of public information use (PI-use) in sticklebacks (Gasterosteidae). PI-use is a form of social learning by which animals are able to assess the relative quality of resources, here prey patches, by observing the behaviour of others. PI-use was highly specific with only Pungitius and their closest relative Culaea inconstans showing evidence of PI-use. We saw no effects of ontogenetic experience upon PI-use in Pungitius pungitius. Experiments with live demonstrators and animated fish revealed that heightened activity and feeding strikes by foraging conspecifics are important cues in the transmission of PI. Finally, PI-use was the only form of learning in which P. pungitius and another stickleback, Gasterosteus aculeatus differed. PI-use in sticklebacks is species-specific and may represent an 'ecological specialization' for social foraging. Whether this reflects selection on perception, attentional or cognitive processes remains to be determined.
  • Ovaskainen, Otso; Somervuo, Panu; Finkelshtein, Dmitri (2020)
    Agent-based models are used to study complex phenomena in many fields of science. While simulating agent-based models is often straightforward, predicting their behaviour mathematically has remained a key challenge. Recently developed mathematical methods allow the prediction of the emerging spatial patterns for a general class of agent-based models, whereas the prediction of spatio-temporal pattern has been thus far achieved only for special cases. We present a general and mathematically rigorous methodology that allows deriving the spatio-temporal correlation structure for a general class of individual-based models. To do so, we define an auxiliary model, in which each agent type of the primary model expands to three types, called the original, the past and the new agents. In this way, the auxiliary model keeps track of both the initial and current state of the primary model, and hence the spatio-temporal correlations of the primary model can be derived from the spatial correlations of the auxiliary model. We illustrate the agreement between analytical predictions and agent-based simulations using two example models from theoretical ecology. In particular, we show that the methodology is able to correctly predict the dynamical behaviour of a host-parasite model that shows spatially localized oscillations.
  • Vesterinen, Eero J.; Kaunisto, Kari M.; Lilley, Thomas M. (2020)
    We report a detection of a surprising similarity in the diet of predators across distant phyla. Though just a first glimpse into the subject, our discovery contradicts traditional aspects of biology, as the earliest notions in ecology have linked the most severe competition of resources with evolutionary relatedness. We argue that our finding deserves more research, and propose a plan to reveal more information on the current biodiversity loss around the world. While doing so, we expand the recently proposed conservation roadmaps into a parallel study of global interaction networks.
  • van den Hoogen, Johan; Geisen, Stefan; Wall, Diana H.; Wardle, David A.; Traunspurger, Walter; de Goede, Ron G. M.; Adams, Byron J.; Ahmad, Wasim; Ferris, Howard; Bardgett, Richard D.; Bonkowski, Michael; Campos-Herrera, Raquel; Cares, Juvenil E.; Caruso, Tancredi; de Brito Caixeta, Larissa; Chen, Xiaoyun; Costa, Sofia R.; Creamer, Rachel; da Cunha e Castro, José Mauro; Dam, Marie; Djigal, Djibril; Escuer, Miguel; Griffiths, Bryan S.; Gutiérrez, Carmen; Hohberg, Karin; Kalinkina, Daria; Kardol, Paul; Kergunteuil, Alan; Korthals, Gerard; Krashevska, Valentyna; Kudrin, Alexey A.; Li, Qi; Liang, Wenju; Magilton, Matthew; Marais, Mariette; Martín, José Antonio Rodríguez; Matveeva, Elizaveta; Mayad, El Hassan; Mzough, E.; Mulder, Christian; Mullin, Peter; Neilson, Roy; Nguyen, T. A. Duong; Nielsen, Uffe N.; Okada, Hiroaki; Rius, Juan Emilio Palomares; Pan, Kaiwen; Peneva, Vlada; Pellissier, Loïc; da Silva, Julio Carlos Pereira; Pitteloud, Camille; Powers, Thomas O.; Powers, Kirsten; Quist, Casper W.; Rasmann, Sergio; Moreno, Sara Sánchez; Scheu, Stefan; Setälä, Heikki; Sushchuk, Anna; Tiunov, Alexei V.; Trap, Jean; Vestergård, Mette; Villenave, Cecile; Waeyenberge, Lieven; Wilschut, Rutger A.; Wright, Daniel G.; Keith, Aidan M.; Yang, Jiue-in; Schmidt, Olaf; Bouharroud, R.; Ferji, Z.; van der Putten, Wim H.; Routh, Devin; Crowther, Thomas W. (2020)
    As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
  • Marin-Gomez, Oscar H.; MacGregor-Fors, Ian (2021)
    Urbanization drives changes in acoustic communication systems in some animal species. Noise and light pollution are among the main urban factors known to disrupt the timing and structure of avian singing behaviour. Despite our understanding of the ways in which urbanization can drive variations in avian acoustic communication, our ability to generalize the underlying causes of such variation and its consequences is still limited. Here, we reviewed the literature focused on the study of avian dawn choruses in urban settings at a global scale. Our findings reveal that avian dawn chorus research has focused on the impact of anthropogenic noise on dawn chorus traits (i.e. timing, peak, song output, song frequencies); relationships between light pollution and chorus timing; the effects of temperature, cloudiness, moonlight and natural light on chorus timing; relationships between nocturnal noise and light, and dawn chorus timing; the effects of chemical pollution and supplementary feeding on dawn chorus activity; and ecological patterns of dawn choruses in soundscapes across urban-non-urban gradients. We identified important knowledge gaps in the study of avian dawn choruses in urban settings and thus suggest future research directions, including frameworks (e.g. the urbanization intensity gradient) and consideration of a wider array of urban conditions and variables. Given the complexity of urban settings, we encourage further studies to address the role that all sources of pollution can have on avian acoustic communication at dawn. Additionally, a central question to resolve is whether the function of avian dawn choruses in urban areas differs, and if so how, from non-urban counterparts. Given that most research has been performed across Holarctic cities and towns, studies from tropical and subtropical regions are needed if we aim to understand the phenomenon globally. Finally, studies at the community- and soundscape-level across cities could advance understanding of the way in which urban birds use the acoustic space during the most critical singing time period, dawn.
  • Rogers, Paul C.; Pinno, Bradley D.; Šebesta, Jan; Albrectsen, Benedicte R.; Li, Guoqing; Ivanova, Natalya; Kusbach, Antonín; Kuuluvainen, Timo; Landhäusser, Simon M.; Liu, Hongyan; Myking, Tor; Pulkkinen, Pertti; Wen, Zhongming; Kulakowski, Dominik (2020)
    Across the northern hemisphere, six species of aspen (Populus spp.) play a disproportionately important role in promoting biodiversity, sequestering carbon, limiting forest disturbances, and providing other ecosystem services. These species are illustrative of efforts to move beyond single-species conservation because they facilitate hundreds of plants and animals worldwide. This review is intended to place aspen in a global conservation context by focusing on the many scientific advances taking place in such biologically diverse systems. In this manner, aspen may serve as a model for other widespread keystone systems where science-based practice may have world implications for biodiversity conservation. In many regions, aspen can maintain canopy dominance for decades to centuries as the sole major broadleaf trees in forested landscapes otherwise dominated by conifers. Aspen ecosystems are valued for many reasons, but here we highlight their potential as key contributors to regional and global biodiversity. We present global trends in research priorities, strengths, and weaknesses based on, 1) a qualitative survey, 2) a systematic literature analysis, and 3) regional syntheses of leading research topics. These regional syntheses explore important aspen uses, threats, and research priorities with the ultimate intent of research sharing focused on sound conservation practice. In all regions, we found that aspen enhance biodiversity, facilitate rapid (re)colonization in natural and damaged settings (e.g., abandoned mines), and provide adaptability in changing environments. Common threats to aspen ecosystems in many, but not all, regions include effects of herbivory, land clearing, logging practices favoring conifer species, and projected climate warming. We also highlight regional research gaps that emerged from the three survey approaches above. We believe multi-scale research is needed that examines disturbance processes in the context of dynamic climates where ecological, physiological, and genetic variability will ultimately determine widespread aspen sustainability. Based on this global review of aspen research, we argue for the advancement of the “mega-conservation” strategy, centered on the idea of sustaining a set of common keystone communities (aspen) that support wide arrays of obligate species. This approach contrasts with conventional preservation which focuses limited resources on individual species residing in narrow niches.
  • Nevalainen, Liisa; Kivila, E. Henriikka; Luoto, Tomi P.; Rantala, Marttiina V.; Van Damme, Kay (2019)
    A long hidden chydorid (Chydoridae, Cladocera) taxon, first found as fossil specimens and recently redefined as Rhynchotalona latens (Sarmaja-Korjonen et al., Hydrobiologia 436: 165-169, 2000) is investigated for its biogeography and ecology. Late Holocene sediment sequence from Lake Sylvilampi, NE Finnish Lapland, and R. latens spatial distribution in relation to limno-climatic attributes in Finland were examined. Principal component analyses of fossil cladoceran communities showed that R. latens is mostly affiliated with Alonella excisa-Alonopsis elongata-Alonella nana species pool. Generalized linear modeling of R. latens responses to limno-climatic variation indicated that it prefers acidic, mesotrophic, humic and shallow lakes with organic sediments in NE Lapland and has a north boreal-subarctic climatic affiliation. At the northern end of its geographical distribution (NE Lapland), it reproduces with abundant gamogenesis under environmental stress. The specialized taxon is a benthic detritivore and scraper and has a Holarctic northern-alpine distribution. It is a glacial relict associated with modern analogs of periglacial aquatic environments, and it occurs in semi-aquatic wetlands, lush lake littorals and clear and cold waters. Examination of chydorids as bioindicators, especially those with restricted niches, allow us to understand biodiversity responses of lake littorals under changing limno-climatic regimes.
  • Nowell, RW; Elsworth, B; Oostra, Vicencio; Zwaan, Bas J.; Wheat, Christopher West; Saastamoinen, Marjo Anna Kaarina; Saccheri, Ilik; Van't Hof, AE; Wasik, BR; Connahs, H; Kumar, S; Challis, RJ; Aslam, L; Monteiro, Antonia; Brakefield, Paul M.; Blaxter, M (2017)
    The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
  • Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F.; Guo, Baocheng; Nederbragt, Alexander J.; Jakobsen, Kjetill S.; Merilä, Juha (2019)
    The Gasterosteidae fish family hosts several species that are important models for eco-evolutionary, genetic, and genomic research. In particular, a wealth of genetic and genomic data has been generated for the three-spined stickleback (Gasterosteus aculeatus), the "ecology's supermodel," whereas the genomic resources for the nine-spined stickleback (Pungitius pungitius) have remained relatively scarce. Here, we report a high-quality chromosome-level genome assembly of P. pungitius consisting of 5,303 contigs (N50 = 1.2Mbp) with a total size of 521 Mbp. These contigs were mapped to 21 linkage groups using a high-density linkage map, yielding a final assembly with 98.5% BUSCO completeness. A total of 25,062 protein-coding genes were annotated, and about 23% of the assembly was found to consist of repetitive elements. A comprehensive analysis of repetitive elements uncovered centromere-specific tandem repeats and provided insights into the evolution of retrotransposons. A multigene phylogenetic analysis inferred a divergence time of about 26 million years ago (Ma) between nine- and three-spined sticklebacks, which is far older than the commonly assumed estimate of 13 Ma. Compared with the three-spined stickleback, we identified an additional duplication of several genes in the hemoglobin cluster. Sequencing data from populations adapted to different environments indicated potential copy number variations in hemoglobin genes. Furthermore, genome-wide synteny comparisons between three- and nine-spined sticklebacks identified chromosomal rearrangements underlying the karyotypic differences between the two species. The high-quality chromosome-scale assembly of the nine-spined stickleback genome obtained with long-read sequencing technology provides a crucial resource for comparative and population genomic investigations of stickleback fishes and teleosts.
  • Poikane, Sandra; Birk, Sebastian; Boehmer, Juergen; Carvalho, Laurence; de Hoyos, Caridad; Gassner, Hubert; Hellsten, Seppo; Kelly, Martyn; Solheim, Anne Lyche; Olin, Mikko; Pall, Karin; Phillips, Geoff; Portielje, Rob; Ritterbusch, David; Sandin, Leonard; Schartau, Ann-Kristin; Solimini, Angelo G.; van den Berg, Marcel; Wolfram, Georg; van de Bund, Wouter (2015)
    The Water Framework Directive is the first international legislation to require European countries to establish comparable ecological assessment schemes for their freshwaters. A key element in harmonising quality classification within and between Europe's river basins is an "Intercalibration" exercise, stipulated by the WFD, to ensure that the good status boundaries in all of the biological assessment methods correspond to similar levels of anthropogenic pressure. In this article, we provide a comprehensive overview of this international comparison, focusing on the assessment schemes developed for freshwater lakes. Out of 82 lake ecological assessment methods reported for the comparison, 62 were successfully intercalibrated and included in the EC Decision on intercalibration, with a high proportion of phytoplankton (18), macrophyte (17) and benthic fauna (13) assessment methods. All the lake assessment methods are reviewed in this article, including the results of intercalibration. Furthermore, the current gaps and way forward to reach consistent management objectives for European lakes are discussed. (C) 2015 The Authors. Published by Elsevier Ltd.