Genomic Patterns of Iberian Wild Bees Reveal Levels of Diversity, Differentiation and Population Structure, Supporting the “Refugia within Refugia” Hypothesis

Sousa, Paulo De; Henriques, André F; Silva, Sara E.; Carvalheiro, Luísa G.; Smagghe, Guy; Michez, Denis; Wood, Thomas J.; Paulo, Octávio S.

doi:10.3390/d15060746

Cited by 3 publications

(4 citation statements)

References 62 publications

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“…High genetic diversity within a nominal species might be a signal of unresolved taxonomy, cryptic diversity or a signature of evolutionary history of the group that lead to the differentiation of isolated populations within the same species. These phenomena are well known for many organisms in the Iberian Peninsula as a result of the occurrence of several refugia within the Peninsula itself, referred to as “refugia within refugia” ( Gómez and Lunt 2007 , Abellán and Svenning 2014 , de Sousa et al 2023 ). Therefore, several species that present a rather homegeneous genetic signature across their European ranges can exhibit more than one genetically differentiated population within the Iberian Peninsula, potentially resulting in the classification of specimens in more than one BIN.…”

Section: General Descriptionmentioning

confidence: 99%

“…In addition to the incomplete study, the Iberian bee fauna has also been seldom studied using genetic techniques as a way to taxonomically delineate its fauna (as opposed to focused population genetic studies or taxonomic studies on specific species, for example, Chávez‐Galarza et al (2015) , Cejas et al (2019) , de Sousa et al (2023) ) until very recently (e.g. Ghisbain et al (2021a) , Ghisbain et al (2021b) , Wood et al (2021) , Kasparek et al (2023) , Wood (2023) ).…”

Section: Introductionmentioning

confidence: 99%

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The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

Wood,

Gaspar,

Le Divelec

et al. 2024

BDJ

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Bees are important actors in terrestrial ecosystems and are recognised for their prominent role as pollinators. In the Iberian Peninsula, approximately 1,100 bee species are known, with nearly 100 of these species being endemic to the Peninsula. A reference collection of DNA barcodes, based on morphologically identified bee specimens, representing 514 Iberian species, was constructed. The "InBIO Barcoding Initiative Database: DNA Barcodes of Iberian bees" dataset contains records of 1,059 sequenced specimens. The species of this dataset correspond to about 47% of Iberian bee species diversity and 21% of endemic species diversity. For peninsular Portugal only, the corresponding coverage is 71% and 50%. Specimens were collected between 2014 and 2022 and are deposited in the research collection of Thomas Wood (Naturalis Biodiversity Center, The Netherlands), in the FLOWer Lab collection at the University of Coimbra (Portugal), in the Andreia Penado collection at the Natural History and Science Museum of the University of Porto (MHNC-UP) (Portugal) and in the InBIO Barcoding Initiative (IBI) reference collection (Vairão, Portugal). Of the 514 species sequenced, 75 species from five different families are new additions to the Barcode of Life Data System (BOLD) and 112 new BINs were added. Whilst the majority of species were assigned to a single BIN (94.9%), 27 nominal species were assigned to multiple BINs. Although the placement into multiple BINs may simply reflect genetic diversity and variation, it likely also represents currently unrecognised species-level diversity across diverse taxa, such as Amegilla albigena Lepeletier, 1841, Andrena russula Lepeletier, 1841, Lasioglossum leucozonium (Schrank, 1781), Nomada femoralis Morawitz, 1869 and Sphecodes alternatus Smith, 1853. Further species pairs of Colletes, Hylaeus and Nomada were placed into the same BINs, emphasising the need for integrative taxonomy within Iberia and across the Mediterranean Basin more broadly. These data substantially contribute to our understanding of bee genetic diversity and DNA barcodes in Iberia and provide an important baseline for ongoing taxonomic revisions in the West Palaearctic biogeographical region.

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Section: General Descriptionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

Wood,

Gaspar,

Le Divelec

et al. 2024

BDJ

Self Cite

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“…Ethanol-based sampling and storage nevertheless remains the cheapest and most practical method compared to other options such as flash freezing with liquid nitrogen, and is therefore widespread (e.g. [10][11][12]). Library preparation methods which are compatible with material collected and stored using suboptimal preservation protocols are therefore required when working with entomological specimens.…”

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

Cobb,

de Muinck,

Kollias

et al. 2024

PLoS ONE

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Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

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“…In a first run, subsample sizes for the sub-F ST estimation were kept identical to the empirical sample sizes. As an additional scenario, subsample sizes were reduced to 2 Â 35 to represent more realistic sample sizes in population genomics, comparable to sample sizes used byKahnt et al (2018),Lozier (2014) or DeSousa et al (2023).SIMUPOP simulations and plots were all prepared by adjusting the custom python and R scripts by Ben Chehida et al (2020) with reference toBailleul et al (2018).…”

mentioning

confidence: 99%

Genetic connectivity is maintained in two insect pollinators across a human‐altered landscape

Schleimer,

Wittische,

Luttringer

et al. 2024

Insect Conserv Diversity

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Population genetics is a valuable tool for assessing the impact of human‐altered landscapes on genetic connectivity in various species. However, when applied to insects, challenges arise due to potentially large effective population sizes (), high dispersal capacities and the recency of anthropogenic impacts. This study assessed the population genetic structure of two pollinators across a human‐altered landscape in Luxembourg. Samples from the ashy mining bee (Andrena cineraria, N = 201) and the greater bee fly (Bombylius major, N = 637) were genotyped at 25 microsatellite loci, including a genotyping‐by‐amplicon‐sequencing approach for A. cineraria. Despite high statistical power of > 0.002 in B. major and > 0.0025 in A. cineraria, no deviations from genetic homogeneity were detected. For both species, there was no evidence for isolation‐by‐distance or genetic clustering. Genetic homogeneity was most likely the result of high levels of gene flow that compensate for the effects of genetic drift. Estimates of ranged between several thousand to tens of thousands, although precision was low. Simulations highlighted that genetic lag times can substantially affect our ability to detect recent (<50 generations) population differentiation when is very large. Lag times were shorter with data from 25,000 simulated di‐allelic loci, but only when sample sizes remained high. Insect genetic studies should consider lag times due to large and ensure sample size and markers offer adequate power to reject the null hypothesis of no landscape effect on genetic connectivity.

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Genomic Patterns of Iberian Wild Bees Reveal Levels of Diversity, Differentiation and Population Structure, Supporting the “Refugia within Refugia” Hypothesis

Cited by 3 publications

References 62 publications

The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

The InBIO Barcoding Initiative Database: DNA barcodes of Iberian Bees

High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method

Genetic connectivity is maintained in two insect pollinators across a human‐altered landscape

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