Every shrimp everywhere all at once: phylogenomics reveals the intricate history of the most diverse group inside Atyidae (Crustacea: Decapoda)
Data files
Jul 11, 2026 version files 875.38 MB
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16S_ML_Supertee_Atyidae.pdf
206 KB
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Alignment.fasta
313.83 MB
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Alignment(reduced90).fasta
262.41 MB
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BayArea_with_coord.txt
176.81 KB
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BGB_BA_J.txt
298.06 KB
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BI_reduced90.tre
217.91 KB
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CompleteAlignment.nex
297.56 MB
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IQTREE_full.contree
20.06 KB
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IQTREE_reduced90.contree
19.25 KB
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ML_geneconcfac.tre
12.46 KB
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README.md
7.58 KB
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Supplementary_Table_1_(unformatted).csv
13.88 KB
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Supplementary_Table_1.xlsx
22.78 KB
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Supplementary_Table_2.csv
344 B
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Supplementary_Table_3.csv
6.06 KB
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SupplementaryFigure_1.pdf
274.06 KB
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SupplementaryFigure_2.pdf
306.09 KB
Abstract
The Atyidae is a diverse and old freshwater shrimp family distributed across all continents bar Antarctica. It is particularly speciose in the Indo-Pacific, the domain of its most diverse group, the so-called Caridella group, which includes the largest and taxonomically challenging genus, Caridina. By using a time-calibrated genomic framework, we reconstructed the biogeographic history of the Caridella group. We show that although their evolution is intimately tied to the geological history of the Tethys Ocean, a slow periodic expansion westward provided multiple invasions of Africa. Knowledge gap about African species is further covered by linking the divergence between East and West African taxa to the East African Rift. Meanwhile, sea level oscillations and landscape changes seem to be the major factors responsible for splits within the Indo-Pacific. We show that amphidromy is ancestral and that landlocked species and clades originated through multiple isolations followed by diversification, which might be related to the numerous species complexes found in this group. Constant diversification rates could reinforce this dispersal-isolation-diversification pattern. Our results also provide the basis for an overdue re-assessment of the systematics of the Caridella group.
Dataset DOI: 10.5061/dryad.5hqbzkhjr
Description of the data and file structure
This dataset contains both the data used and produced in Bernardes et al. (in review) to achieve a time-calibrated phylogeny of the Atyidae (Crustacea: Decapoda), specifically the Caridella group. This data includes different alignments used in different analyses, including the complete partitioned alignment (CompleteAlignment.nex), an equivalent alignment in FASTA (Alignment.fasta) and a reduced alignment with a higher capture rate threshold (Alignment(reduced90).fasta). All phylogenetic trees generated by this data are also included: Bayesian (time-calibrated) (BI_reduced90.tre); maximum likelihood with the complete alignment (IQTREE_full.contree); and maximum likelihood with reduced alignment (IQTREE_reduced90.contree). Finally, we included all the data used and produced by the ancestral area reconstruction analyses: the distribution file (distribution.csv); Bayarea results using RASP (BayArea_with_coord.txt); and bayarealike results using BioGeoBEARS (BGB_BA+J.txt). These last files are readable in tree format using RASP.
Files and variables
File: BayArea_with_coord.txt
Description: Result of the ancestral area reconstruction under the Bayarea model in RASP. The results can be opened on RASP in the form of a time-calibrated phylogeny.
Variables
- Species (scientific name)
- Coded area of occurrence
- Time-calibrated phylogeny
- Reconstructed ancestral area of occurrence and biogeographic events (dispersal, vicariance, cladogenesis etc) with respective probabilities
File: BGB_BA_J.txt
Description: Result of the ancestral area reconstruction under the Bayarealike model in BioGeoBEARS. The results can be opened on RASP in the form of a time-calibrated phylogeny.
Variables
- Species (scientific name)
- Coded area of occurrence
- Time-calibrated phylogeny
- Reconstructed ancestral area of occurrence and biogeographic events (dispersal, vicariance, cladogenesis etc) with respective probabilities
File: BI_reduced90.tre
Description: Time-calibrated phylogetic tree obtained within a Bayesian framework using BEAST2.
File: Supplementary_Table_1.xlsx
Description: Full information about the samples used in this study, including Genbank accession numbers for the exomes and transcriptomes. Samples marked with superscript 1 (¹) are Atyidae not within the Caridella group. Samples marked with a superscript 2 (²) were used for bait design. The species Paratya caledonica is a landlocked clade, but we coded it as amphidromous in our analyses because the 'Paratya clade' comprises mostly genera that show traits that we consider amphidromous.
Variables
- Species (scientific name) and individuals
- Museum voucher (collection number_individual number (in case of lots with several individuals))
- DNA collection voucher
- Original collection site latitude in decimal degrees
- Original collection site longitude in decimal degrees
- Species distribution coded as A – Australia; B – Middle East; C – China; D – Indo-Burma; E – Indian Ocean Islands; F – Philippines; G – East Africa; H – West Africa; I – India; J – Japan and Korea; K – Polynesia; L – Sundaland; and M – Wallacea
- Life history considered in the analyses
- Genbank accession numbers.
File: Supplementary_Table_1_(unformatted).csv
Description: Same information as the file Supplementary_Table_1.xlsx in a CSV format to facilitate downstream analyses.
Variables
- Species
- Museum voucher (collection number_individual number (in case of lots with several individuals))
- DNA collection voucher
- Original collection site latitude in decimal degrees
- Original collection site longitude in decimal degrees
- Species distribution coded as A – Australia; B – Middle East; C – China; D – Indo-Burma; E – Indian Ocean Islands; F – Philippines; G – East Africa; H – West Africa; I – India; J – Japan and Korea; K – Polynesia; L – Sundaland; and M – Wallacea
- Life history considered in the analyses
- Genbank accession numbers.
File: Supplementary_Table_2.csv
Description: Results from the Model Test implemented in BioGeoBEARS.
Variables
- Model
- Likelihood (LnL)
- Calculated weight for parameters d, e and j
- Akaike Information Criterion (AIC)
- Weighted Akaike Information Criterion (AICc_wt)
File: Supplementary_Table_3.csv
Description: Distribution file used in the ancestral area reconstruction. Areas are coded following the coded presented in Figure 1 in the article.
Variables
- Sample id in the program
- Sample original ID (species and individual)
- Areas of occurence coded as A – Australia; B – Middle East; C – China; D – Indo-Burma; E – Indian Ocean Islands; F – Philippines; G – East Africa; H – West Africa; I – India; J – Japan and Korea; K – Polynesia; L – Sundaland; and M – Wallacea.
File: SupplementaryFigure_1.pdf
Description: Supplementary Figure 1. Phylogenetic range of the customised baits. The phylogeny inferred from transcriptomes was used to infer ancestral sequences, which were then combined with modern sequences to produce a comprehensive set of baits. Four nodes (N1, N3, N5 and N6) had sequences reconstructed for bait design. The clade with bold branches represents our final target (Caridella group). The Atya group transcriptomes and reconstructed nodes are represented in green, and the Caridella group is represented in purple. The designed baits and corresponding exons obtained from each node and terminal are represented in brown (note also that the number of exons refers to the number of unique exons)..
File: SupplementaryFigure_2.pdf
Description: Supplementary Figure 2. ML ancestral state reconstruction made with phytools under the Mk model. Colour coding as follows: orange = amphidromous; purple = landlocked; grey = unknown.
File: IQTREE_full.contree
Description: Phylogetic tree obtained within a maimum likelihood framework using IQ-Tree and the complete alignment using 70 % capture rate threshold.
File: IQTREE_reduced90.contree
Description: Phylogetic tree obtained within a maimum likelihood framework using IQ-Tree and the reduced alignment using 90 % capture rate threshold.
File: ML_geneconcfac.tre
Description: Phylogetic tree obtained within a maimum likelihood framework using IQ-Tree containing the gene concordance factors for all the nodes.
File: Alignment(reduced90).fasta
Description: Reduced alignment using 90 % capture rate threshold.
File: Alignment.fasta
Description: Complete alignment using 70 % capture rate threshold.
File: CompleteAlignment.nex
Description: Complete alignment using 70 % capture rate threshold containing all partition data (exon id).
File: 16S_ML_Supertee_Atyidae.pdf
Description: Phylogetic tree obtained within a maimum likelihood framework in Geneious with the FastTree plugin.
Statement on changed variables:
We have reduced precision of geographic coordinates available here to two decimal places. In the original analyses, we used up to five. The reduction on the publicly available data is due to concern to exposing endangered species to unnecessary vulnerabilities.