Fishing in troubled waters: Revealing genomic signatures of local adaptation in response to freshwater pollutants in two macroinvertebrates

Weigand, Hannah; Weiss, Martina; Cai, Huimin; Li, Yongping; Yu, Lili; Zhang, Christine; Leese, Florian

doi:10.1016/j.scitotenv.2018.03.109

Cited by 16 publications

(18 citation statements)

References 97 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The genome presented here is the first high-quality draft genome of a retreat-building caddisfly. With a known diversity of more than 16,000 species, caddisflies are important members of freshwater ecological communities, and their species have been shown to be effective indicators of freshwater health [35, 81, 82]. The research of a host of researchers in freshwater biology and entomology will be positively impacted by the availability of a high-quality draft genome.…”

Section: Discussionmentioning

confidence: 99%

“…This discrepancy may reflect the differences in the two algorithms or it may imply possible redundant contigs that were not identified by our filtering procedures. The comparisons among the five available Trichoptera genome assemblies (including Glossosoma conforme [35] , Glyphotaelius pellucidus [36], Limnephilus lunatus provided by i5K [37], and Sericostoma sp. HW-2014 [38]) are shown in Table 1.…”

Section: Data Descriptionmentioning

confidence: 99%

“…The genome source: G. conforme [35], G. pellucidus [36], L. lunatus from i5K project [37], and Sericostoma sp. HW-2014 [38].…”

Section: Data Descriptionmentioning

confidence: 99%

See 2 more Smart Citations

The genome of an underwater architect, the caddisflyStenopsyche tienmushanensisHwang (Insecta: Trichoptera)

et al. 2018

View full text Add to dashboard Cite

Background Caddisflies (Insecta: Trichoptera) are a highly adapted freshwater group of insects split from a common ancestor with Lepidoptera. They are the most diverse (>16,000 species) of the strictly aquatic insect orders and are widely employed as bio-indicators in water quality assessment and monitoring. Among the numerous adaptations to aquatic habitats, caddisfly larvae use silk and materials from the environment (e.g., stones, sticks, leaf matter) to build composite structures such as fixed retreats and portable cases. Understanding how caddisflies have adapted to aquatic habitats will help explain the evolution and subsequent diversification of the group. Findings We sequenced a retreat-builder caddisfly Stenopsyche tienmushanensis Hwang and assembled a high-quality genome from both Illumina and Pacific Biosciences (PacBio) sequencing. In total, 601.2 M Illumina reads (90.2 Gb) and 16.9 M PacBio subreads (89.0 Gb) were generated. The 451.5 Mb assembled genome has a contig N50 of 1.29 M, has a longest contig of 4.76 Mb, and covers 97.65% of the 1,658 insect single-copy genes as assessed by Benchmarking Universal Single-Copy Orthologs. The genome comprises 36.76% repetitive elements. A total of 14,672 predicted protein-coding genes were identified. The genome revealed gene expansions in specific groups of the cytochrome P450 family and olfactory binding proteins, suggesting potential genomic features associated with pollutant tolerance and mate finding. In addition, the complete gene complex of the highly repetitive H-fibroin, the major protein component of caddisfly larval silk, was assembled. Conclusions We report the draft genome of Stenopsyche tienmushanensis , the highest-quality caddisfly genome so far. The genome information will be an important resource for the study of caddisflies and may shed light on the evolution of aquatic insects.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Data Descriptionmentioning

confidence: 99%

See 1 more Smart Citation

The genome of an underwater architect, the caddisflyStenopsyche tienmushanensisHwang (Insecta: Trichoptera)

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The database comprised in silico translated gene‐prediction sequences of genomic data of four Trichoptera species: Stenopsyche tienmushanensis (Luo, Tang, Frandsen, Stewart, & Zhou, ), Glossosoma conformis (Weigand et al, ), Sericostoma personatum (Weigand et al, ) and Limnephilus lunatus (Poelchau et al, ). Predicted protein sequence data were downloaded from respective repositories and fasta files concatenated using command‐line tool cat (Unix).…”

Section: Methodsmentioning

confidence: 99%

“…The database comprised in silico translated gene-prediction sequences of genomic data of four Trichoptera species: Stenopsyche tienmushanensis (Luo, Tang, Frandsen, Stewart, & Zhou, 2018), Glossosoma conformis (Weigand et al, 2018), Sericostoma personatum (Weigand et al, 2017) and Limnephilus lunatus (Poelchau et al, 2015).…”

Section: Construction Of a Homology-based Sequence Databasementioning

confidence: 99%

Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

2019

View full text Add to dashboard Cite

Species' ecological preferences are often deduced from habitat characteristics thought to represent more or less optimal conditions for physiological functioning. Evolution has led to stenotopic and eurytopic species, the former having decreased niche breadths and lower tolerances to environmental variability. Species inhabiting freshwater springs are often described as being stenotopic specialists, adapted to the stable thermal conditions found in these habitats. Whether due to past local adaptation these species have evolved or have lost intra‐generational adaptive mechanisms to cope with increasing thermal variability has, to our knowledge, never been investigated. By studying how the proteome of a stenotopic species changes as a result of increasing temperatures, we investigate if the absence or attenuation of molecular mechanisms is indicative of local adaptation to freshwater springs. An understanding of compensatory mechanisms is especially relevant as spring specialists will experience thermal conditions beyond their physiological limits due to climate change. In this study, the stenotopic species Crunoecia irrorata (Trichoptera: Lepidostomatidae, Curtis 1834) was acclimated to 10, 15 and 20°C for 168 hr. We constructed a homology‐based database and via liquid chromatography‐tandem mass spectrometry (LC‐MS/MS)‐based shotgun proteomics identified 1,358 proteins. Differentially abundant proteins and protein norms of reaction revealed candidate proteins and molecular mechanisms facilitating compensatory responses such as trehalose metabolism, tracheal system alteration and heat‐shock protein regulation. A species‐specific understanding of compensatory physiologies challenges the characterization of species as having narrow tolerances to environmental variability if that characterization is based on occurrences and habitat characteristics alone.

show abstract

Individual small in‐stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa

Weiss

Weigand

Leese

2022

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Water flow in river networks is frequently regulated by man‐made in‐stream barriers. These obstacles can hinder dispersal of aquatic organisms and isolate populations leading to the loss of genetic diversity. Although millions of small in‐stream barriers exist worldwide, their impact on dispersal of macroinvertebrates remains unclear. Therefore, we, therefore, assessed the effects of such barriers on the population structure and effective dispersal of five macroinvertebrate species with strictly aquatic life cycles: the amphipod crustacean Gammarus fossarum (clade 11), three snail species of the Ancylus fluviatilis species complex and the flatworm Dugesia gonocephala. We studied populations at nine weirs and eight culverts (3 pipes, 5 tunnels), built 33–109 years ago, mainly in the heavily fragmented catchment of the river Ruhr (Sauerland, Germany). To assess fragmentation and barrier effects, we generated genome‐wide SNP data using ddRAD sequencing and evaluated clustering, differentiation between populations up‐ and downstream of each barrier and effective migration rates among sites and across barriers. Additionally, we applied population genomic simulations to assess expected differentiation patterns under different gene flow scenarios. Our data show that populations of all species are highly isolated at regional and local scales within few kilometers. While the regional population structure likely results from historical processes, the strong local differentiation suggests that contemporary dispersal barriers exist. However, we identified significant barrier effects only for pipes (for A. fluviatilis II and III) and few larger weirs (>1.3 m; for D. gonocephala). Therefore, our data suggest that most small in‐stream barriers can probably be overcome by all studied taxa frequently enough to prevent fragmentation. However, it remains to be tested if the strong local differentiation is a result of a cumulative effect of small barriers, or if larger in‐stream barriers, land use, chemical pollution, urbanization, or a combination of these factors impede gene flow.

show abstract

Fishing in troubled waters: Revealing genomic signatures of local adaptation in response to freshwater pollutants in two macroinvertebrates

Cited by 16 publications

References 97 publications

The genome of an underwater architect, the caddisflyStenopsyche tienmushanensisHwang (Insecta: Trichoptera)

The genome of an underwater architect, the caddisflyStenopsyche tienmushanensisHwang (Insecta: Trichoptera)

Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

Individual small in‐stream barriers contribute little to strong local population genetic structure five strictly aquatic macroinvertebrate taxa

Contact Info

Product

Resources

About