Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Rutschmann, Sereina; Detering, Harald; Simon, Sabrina; Funk, David H.; Gattolliat, Jean‐Luc; Hughes, Samantha Jane; Raposeiro, Pedro M.; DeSalle, Rob; Sartori, Michel; Monaghan, Michael T.

doi:10.1101/063859

Cited by 6 publications

(12 citation statements)

References 101 publications

(111 reference statements)

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“…The use of the marker set for C. dipterum developed here resulted in a fully resolved phylogenetic tree in contrast to the mitochondrial tree of Rutschmann et al (2014). The phylogeny of the Cloeon-species complex presented here also is in complete agreement with species tree reconstructions based on 59 nDNA markers (Rutschmann et al, 2016).…”

Section: Resultssupporting

confidence: 67%

discomark: nuclear marker discovery from orthologous sequences using draft genome data

Rutschmann

Detering

Simon

et al. 2016

Molecular Ecology Resources

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High‐throughput sequencing has laid the foundation for fast and cost‐effective development of phylogenetic markers. Here we present the program discomark, which streamlines the development of nuclear DNA (nDNA) markers from whole‐genome (or whole‐transcriptome) sequencing data, combining local alignment, alignment trimming, reference mapping and primer design based on multiple sequence alignments to design primer pairs from input orthologous sequences. To demonstrate the suitability of discomark, we designed markers for two groups of species, one consisting of closely related species and one group of distantly related species. For the closely related members of the species complex of Cloeon dipterum s.l. (Insecta, Ephemeroptera), the program discovered a total of 78 markers. Among these, we selected eight markers for amplification and Sanger sequencing. The exon sequence alignments (2526 base pairs) were used to reconstruct a well‐supported phylogeny and to infer clearly structured haplotype networks. For the distantly related species, we designed primers for the insect order Ephemeroptera, using available genomic data from four sequenced species. We developed primer pairs for 23 markers that are designed to amplify across several families. The discomark program will enhance the development of new nDNA markers by providing a streamlined, automated approach to perform genome‐scale scans for phylogenetic markers. The program is written in Python, released under a public licence (GNU GPL version 2), and together with a manual and example data set available at: https://github.com/hdetering/discomark.

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Section: Resultssupporting

confidence: 67%

discomark: nuclear marker discovery from orthologous sequences using draft genome data

Rutschmann

Detering

Simon

et al. 2016

Molecular Ecology Resources

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“…These specimens fit Sowa's (1975) concept of Cloeon cognatum Stephens 1835, where C. cognatum is generally treated as a junior synonym of C. dipterum. Under this broad concept, genetic analysis of C. dipterum has recently shown that it includes ≥4 species in Europe, 2 of which are now also present in eastern North America (Rutschmann et al 2017). Specimens used in our study were referred to as species IS1 by Rutschmann et al (2017).…”

Section: Study Animalsmentioning

confidence: 99%

Why adult mayflies ofCloeon dipterum(Ephemeroptera:Baetidae) become smaller as temperature warms

et al. 2018

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We reared Cloeon dipterum from egg hatch to adult at 10 constant temperatures (12.1-33.57C) to test 3 hypotheses (thermal equilibrium hypothesis, temperature size rule [TSR], and O 2 -and capacity-limited thermal tolerance [OCLTT]) that account for variation in life-history traits across thermal gradients. Male and female adult size declined~67 and 78% and larval development time declined~88% with warming; chronic survivorship (thermal limit for population growth) was highest from 16.2 to 23.97C (mean 5 85%) and declined to 0 at 33.57C; thresholds for 0 growth and development were 10.0 and 10.77C, respectively; peak rate of population increase (r) occurred at 27.87C; rates of growth and development were maximal at 307C; fecundity was greatest at 12.17C; and between 14.3 and 307C, growth and development rates increased linearly and the number of degree days (>10.77C) to complete development was nearly constant (mean 5 271). Acute survivorship during short-term thermal ramping was 0 at 407C. Warming temperature caused development rate to increase proportionately faster than growth rate; male and female adult size to decrease as per TSR, with adult females~5Â larger at 12.1 than 31.77C; adult size to decrease proportionately more for females than males; and fecundity to decrease proportionately more than adult female size. TSR was related to differences in the responses of growth and development rates at temperatures above thresholds rather than to thresholds for growth or development per se. Respirometry suggested that OCLTT is more applicable to acute than chronic thermal limits. Cloeon dipterum appears to have a thermal 'acclimation zone' between 14.3 and 307C where development and growth rates change linearly and degree-day requirements to complete metamorphosis are constant. The optimum temperature is~27.87C where r is maximum. We propose 5 hypotheses to explain these patterns. Figure 4. Per capita rate of population increase (r) for female Cloeon dipterum across a range of rearing temperatures.

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“…Mynott, Webb, & Suter, 2011; Vogler & Monaghan, 2006), or based on the congruency between mitochondrial and nuclear DNA (e.g. Rutschmann et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-species

Gamboa

Serrana

Takemon

et al. 2019

Preprint

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23 1. Stream ecosystems are spatially heterogeneous environments due to the habitat diversity 24 that define different microhabitat patches within a single area. Despite the influence of 25 habitat heterogeneity on the biodiversity of insect community, little is known about how 26 habitat heterogeneity governs species coexistence and community assembly. Here, we 27 address the question if habitat heterogeneity may drive changes in community composition28 of the stonefly (Plecoptera, Insecta) community in different sampling locations, by 29 assessing the relative role of the habitats that explain beta biodiversity patterns (spatial 30 structure) and evolutionary processes (phylogenetic signal) in structuring communities.31 2. We sampled across seven habitats types among 20 sampling sites in Alpine rivers, and we 32 used mitochondrial DNA, cox1, and nuclear DNA, ITS, genetic markers on 21 stoneflies 33 morpho-species to estimate putative DNA-species by General Mixed Yule Coalescent 34 model (GMYC). With the use of putative DNA-species, we first analyzed the patterns of 35 variation of DNA-species richness, composition, and diversity of stonefly community 36 assessing their habitat correlates. Then, we assessed through a phylogenetic clustered 37 pattern if DNA-species with similar physiological requirements co-occur due to 38 environmental filtering.39 3. Based on 52 putative DNA-species, we found that corridors contributed to DNA-species 40 richness where the meandering corridor section displayed the highest contribution. While, 41 habitats contributed to DNA-species diversity, where glide, riffle, and pool influenced the 42 spatial structure of the stonefly community possible owed to the high species turnover 43 observed.44 4. Among the habitats, pool showed a significant phylogenetic clustering, suggesting 45 evolutionary adaptation and strong habitat filtering. This pattern of community phylogenetic 46 structure could have resulted from the long-term stability of the habitat and physiological 47 requirements of the species that cohabitate.48 5. Our study shows the importance of different habitats on the spatial and phylogenetic 49 structure of stonefly community assemblies and sheds light on the habitat-specific diversity 50 that may help improve conservation practices. 51 52 53 KEYWORDS 54 DNA-species, habitats, spatial structure, phylogenetic structure, Plecoptera 55 56 93 species based on variation in DNA sequences (DNA taxonomy; Vogler & Monaghan, 2006) 94 using Generalized Mixed Yule Coalescent model (GMYC; Pons et al., 2006) is one of the most 95 common methods employed for recognizing putative DNA-species. Briefly, GMYC identify the 96 transition rate between inter and intra-species branching events on a time-calibrated ultrametric 97 tree (distances from the root of every branch is equal), using molecular markers, as

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Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Cited by 6 publications

References 101 publications

discomark: nuclear marker discovery from orthologous sequences using draft genome data

discomark: nuclear marker discovery from orthologous sequences using draft genome data

Why adult mayflies ofCloeon dipterum(Ephemeroptera:Baetidae) become smaller as temperature warms

Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-species

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