Search results for "Assembly"

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

2017

Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic…

2019

Abstract The success of social insects is largely intertwined with their highly advanced chemical communication system that facilitates recognition and discrimination of species and nest-mates, recruitment, and division of labor. Hydrocarbons, which cover the cuticle of insects, not only serve as waterproofing agents but also constitute a major component of this communication system. Two cryptic Crematogaster species, which share their nest with Camponotus ants, show striking diversity in their cuticular hydrocarbon (CHC) profile. This mutualistic system therefore offers a great opportunity to study the genetic basis of CHC divergence between sister species. As a basis for further genome-wi…

The effects of drainage and restoration of pine mires on habitat structure, vegetation and ants

2016

Habitat loss and degradation are the main threats to biodiversity worldwide. For example, nearly 80% of peatlands in southern Finland have been drained. There is thus a need to safeguard the remaining pristine mires and to restore degraded ones. Ants play a pivotal role in many ecosystems and like many keystone plant species, shape ecosystem conditions for other biota. The effects of mire restoration and subsequent vegetation succession on ants, however, are poorly understood. We inventoried tree stands, vegetation, water-table level, and ants (with pitfall traps) in nine mires in southern Finland to explore differences in habitats, vegetation and ant assemblages among pristine, drained (30…

Experimentally induced community assembly of polypores reveals the importance of both environmental filtering and assembly history

2019

The community assembly of wood-inhabiting fungi follows a successional pathway, with newly emerging resource patches being colonised by pioneer species, followed by those specialised on later stages of decay. The primary coloniser species have been suggested to strongly influence the assembly of the later-arriving community. We created an artificial resource pulse and studied the assembly of polypores over an 11yr period to ask how the identities of the colonising species depend on the environmental characteristics and the assembly history of the dead wood unit. Our results support the view that community assembly in fungi is a highly stochastic process, as even detailed description of the …

2016

Ecological communities are structured by competitive, predatory, mutualistic and parasitic interactions combined with chance events. Separating deterministic from stochastic processes is possible, but finding statistical evidence for specific biological interactions is challenging. We attempt to solve this problem for ant communities nesting in epiphytic bird’s nest ferns (Asplenium nidus) in Borneo’s lowland rainforest. By recording the frequencies with which each and every single ant species occurred together, we were able to test statistically for patterns associated with interspecific competition. We found evidence for competition, but the resulting co-occurrence pattern was the opposit…

Fuzzy quantification of common and rare species in ecological communities (FuzzyQ)

2021

International audience; Most species in ecological communities are rare, whereas only a few are common. This distributional paradox has intrigued ecologists for decades but the interpretation of species abundance distributions remains elusive.We present Fuzzy Quantification of Common and Rare Species in Ecological Communities (FuzzyQ) as an R package. FuzzyQ shifts the focus from the prevailing species-categorization approach to develop a quantitative framework that seeks to place each species along a rarity-commonness gradient. Given a community surveyed over a number of sites, quadrats, or any other convenient sampling unit, FuzzyQ uses a fuzzy clustering algorithm that estimates a probab…

De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

2021

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was gene…

Accounting for species interactions is necessary for predicting how arctic arthropod communities respond to climate change

2021

Species interactions are known to structure ecological communities. Still, the influence of climate change on biodiversity has primarily been evaluated by correlating individual species distributions with local climatic descriptors, then extrapolating into future climate scenarios. We ask whether predictions on arctic arthropod response to climate change can be improved by accounting for species interactions. For this, we use a 14-year-long, weekly time series from Greenland, resolved to the species level by mitogenome mapping. During the study period, temperature increased by 2 degrees C and arthropod species richness halved. We show that with abiotic variables alone, we are essentially un…

Ecological response hides behind the species abundance distribution : Community response to low-intensity disturbance in managed grasslands

2017

Land-use and management are disturbance factors that have diverse effects on community composition and structure. In traditional rural grasslands, such as meadows and pastures, low-intensity management is maintained to enhance biodiversity. Maintenance of road verges, in turn, creates habitat, which may complement traditional rural grasslands. To evaluate the effect of low-intensity disturbance on insect communities, we characterized species abundance distributions (SAD) for Carabidae, Formicidae, and Heteroptera in three grassland types, which differed in management: meadows, pastures, and road verges. The shape of SAD was estimated with three parameters: abundance decay rate, dominance, a…

High-Quality Genome Assembly and Annotation of the Big-Eye Mandarin Fish (Siniperca knerii)

2020

Abstract The big-eye mandarin fish (Siniperca knerii) is an endemic species of southern China. It belongs to the family Sinipercidae, which is closely related to the well-known North American sunfish family Centrarchidae. Determining the genome sequence of S. knerii would provide a foundation for better examining its genetic diversity and population history. A novel sequenced genome of the Sinipercidae also would help in comparative study of the Centrarchidae using Siniperca as a reference. Here, we determined the genome sequence of S. knerii using 10x Genomics technology and next-generation sequencing. Paired-end sequencing on a half lane of HiSeq X platform generated 56 Gbp of raw data. R…