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Data from: Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: evidence from community metabarcoding

Citation

Gálvez-Reyes, Nancy et al. (2021), Data from: Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: evidence from community metabarcoding, Dryad, Dataset, https://doi.org/10.5061/dryad.wh70rxwkw

Abstract

Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.

Methods

Please, See Material & Methods.

Usage Notes

Data to use in scripts of metabarcoding arthropods

This dataset includes the sequences aligned, ASVs tables and ASVs with Threshold generated from 42 whole-communities of biodiversity soups in Nevado de Toluca. For additional information on the sample codes and scripts please see at Git-hub repository https://github.com/AliciaMstt/Multihierarchical_NevadoToluca. For the raw data please see at SRA project: PRJNA743572.

Data content:

`1AlignedSeq`: contains the results of `0.4Searching_Stop_Codons.txt`. This file contents each ASV dataset was aligned in Geneious for searching codon stops. After, each fasta file you can use in `0.5to_get_ASV_tables.sh`script.

`2ASVs_Table`: contains the results of the `0.5to_get_ASV_tables.sh` analysis. Each community table was generated with read-counts (haplotype abundance) of each retained ASV for the eight orders by matching ASVs against the complete collection of reads. After, each ASV tables you can use in `0.6to_get_UPGMAtree_GMYC_MH_lineages_All.r` and `3.to_get_conservative_threhold_on_original_all.r`

`3ASVThresholdCommunities`: contains all matrix tables used in `4.to_get_Diversity_All.r` and `6.to_get_BetaDiversity_DistanceDecay_IBD_IBR.r`scripts.

Funding

Consejo Nacional de Ciencia y Tecnología, Award: 178245

Spanish Agencia Estatal de Investigación co-financed by FEDER, Award: CGL2017-85718-P

MINECO/FEDER, Award: CGL2015-74178-JIN

Spanish Agencia Estatal de Investigación co-financed by FEDER, Award: CGL2017-85718-P

MINECO/FEDER, Award: CGL2015-74178-JIN