Corresponding author: Wayne Maddison (
Academic editor: J. Miller
We present the first genome-wide molecular phylogeny of jumping spiders (
Maddison WP, Evans SC, Hamilton CA, Bond JE, Lemmon AR, Lemmon EM (2017) A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment. ZooKeys 695: 89–101.
Understanding the relationships of jumping spiders (
Our goal here is to answer remaining questions about broad salticid relationships, using data from across the genome. An efficient method to obtain data on hundreds of genes is Anchored Hybrid Enrichment (
Specimens sampled are listed in Table
When multiple specimens from a single genus (e.g. two
Voucher specimens are preserved in the Spencer Entomological Collection of the Beaty Biodiversity Museum (vouchers whose IDs in Table
Specimens were preserved in 95% ethanol, and stored between two months and 10 years before use. DNA extractions were done using the Qiagen DNEazy blood and tissue kit, using the protocol for <10 mg samples. The second through fourth pairs of legs were used if they provided sufficient sample volume; otherwise, the carapace and sometimes the distal part of the abdomen was added.
Library preparation, enrichment, and sequencing were conducted at the Center for Anchored Phylogenomics at Florida State University (
Specimens from which Anchored Hybrid Enrichment data were obtained. A “+” at the start of a row indicates that that specimen’s DNA was combined with that of the previous specimen for sequencing, to yield a single analyzed terminal taxon.
Species | Voucher ID | Sex | Locality | Latitude - longitude |
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SCE0002 | m | Malaysia: Sarawak: Mulu Nat. Pk. |
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+ |
SCE0035 | f | Malaysia: Sarawak: Mulu Nat. Pk. |
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SCE0016 | m | China: Guangxi: Ningming County |
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SCE0008 | m | Papua New Guinea: S. Highlands Prov.: Tualapa |
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SCE0022 | m | Ecuador: Orellana: Yasuní Res. Stn. |
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SCE0044 | m | China: Guangxi: Ningming County |
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SCE0005 | m | Papua New Guinea: S. Highlands Prov.: Putuwé |
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SCE0015 | m | U.S.A.: Mississippi: Holmes County State Park |
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SCE0009 | m | Ecuador: Orellana: Río Bigal Reserve |
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+ |
SCE0057 | m | Ecuador: Orellana: SE of Río Bigal Reserve | 0.53-5°S 77.42°W |
SCE0012 | m | Ecuador: Orellana: Yasuní Res. Stn. |
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SCE0065 | m | Canada: British Columbia: Furry Creek |
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SCE0029 | m | Malaysia: Sarawak: Kubah Nat. Pk. | 1.605-6°N 110.185-7°E | |
SCE0011 | m | Singapore: Labrador Park |
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+ |
SCE0049 | m | China: Guangxi: Tianlin County |
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SCE0039 | m | Spain: Albacete: Villa de Chinchilla |
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SCE0031 | f | Malaysia: Sarawak: Mulu Nat. Pk. |
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SCE0020 | m | Ecuador: Esmeraldas: Reserva Canandé |
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SCE0003 | m | Malaysia: Sarawak: Lambir Hills Nat. Pk. | 4.197-8°N 114.040°E | |
+ |
SCE0058 | f | Malaysia: Sarawak: Lambir Hills Nat. Pk. | 4.203°N 114.028-9°E |
+ |
SCE0059 | f | Malaysia: Sarawak: Lambir Hills Nat. Pk. |
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SCE0018 | m | U.S.A.: Mississippi: Wall Doxey State Park |
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SCE0021 | m | Malaysia: Sarawak: Mulu Nat. Pk. |
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SCE0053,4 | m | Malaysia: Pahang: Tanah Rata |
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SCE0038 | m | Canada: Muskoka Dist.: Port Cunnington |
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SCE0023 | m | Ecuador: Orellana: Yasuní Res. Stn. |
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SCE0047 | f | China: Guangxi: Fangchenggang City |
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+ |
SCE0048 | f | China: Guangxi: Ningming County |
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SCE0040 | f | Malaysia: Sarawak: Lambir Hills Nat. Pk. |
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+ |
SCE0041 | f | Malaysia: Sarawak: Lambir Hills Nat. Pk. |
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SCE0024 | m | U.S.A.: Oregon: Mt. Hebo |
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SCE0045 | m | Canada: British Columbia: Kelowna |
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AUMS16070 | m | U.S.A.: Alabama: Elmore Co. |
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SCE0046 | m | Ecuador: Napo: Estación Biológica Jatun Sacha |
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AUMS16722 | f | U.S.A.: Washington: Northcreek |
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SCE0060,1,2 | m | French Guiana: Commune Règina, les Nourages |
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SCE0028 | m | Canada: Ontario: Burlington |
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SCE0050 | f | Malaysia: Sarawak: Lambir Hills Nat. Pk. |
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+ |
SCE0051 | f | Malaysia: Sarawak: Mulu Nat. Pk. |
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+ |
SCE0052 | f | Malaysia: Sarawak: Mulu Nat. Pk. |
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SCE0055,6 | f | Brazil: Pará: Algodoal |
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SCE0017 | f | Gabon: Woleu-Ntem:Tchimbélé |
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SCE0042,3 | j | Poland: Kozki |
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G1765 | f | U.S.A.: California: Torrey Pines S.P. |
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G1699 | f | U.S.A.: Arkansas: Stone Co., S. Calico Rock |
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G1048 | m | U.S.A.: California: San Diego Co., Lake Murray |
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AUMS16708 | f | U.S.A.: Washington: Stella |
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AUMS11918 | f | U.S.A.: California: Imperial Co. | — | |
AUMS16717 | — | U.S.A.: Washington: Bear Canyon |
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AUMS19518 | — | U.S.A.: Tennessee: Heck Hollow Road |
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ARA0192 | f | Switzerland: Grison Alps, Alp Flix, Salatinas: |
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AUMS16731 | m | U.S.A.: Alabama: Lee Co., Auburn |
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SCE0063 | m | U.S.A.: Arizona: Tumacacori |
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AUMS16723 | f | U.S.A.: Washington: Little Rock Road |
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ARA1365 | f | Slovenia: Ljubljana |
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Prior to assembly, overlapping paired reads were merged following
Divergent reference assembly was used to map reads to the probe regions and extend the assembly into the flanking regions (see
Orthology was determined among the homologous consensus sequences at each locus following
For all samples except
Sequences in each orthologous cluster were aligned using MAFFT v7.023b (
In preparation for phylogenetic analyses, the 447 trimmed
We inferred the phylogeny for the 46 taxa using Maximum Likelihood, parsimony, and SVDQuartets applied to a concatenated supermatrix of the 447 aligned loci, and using ASTRAL (a coalescent-based approach, like SVDQuartets) applied to
Two Maximum Likelihood (
We present as our primary result the best-scoring
Parsimony bootstrap analysis was performed by PAUP* version 4.0a151 (
We also used two methods based on the multi-species coalescent model to infer the species phylogeny, SVDQuartets (
Hybrid enrichment results are shown in the Supplementary Table. The 447 loci obtained in the final filtered data set represent for most taxa about 80 kb of nucleotide sequence. We were less successful at obtaining data for two taxa, with
Fig.
Maximum likelihood phylogeny from the partitioned concatenated matrix of 447 loci captured by Anchored Hybrid Enrichment. Numbers indicate percentage of likelihood bootstrap replicates showing the clade. Half circle indicates clades supported also in the results of
This first genome-wide analysis of salticids resolves the group’s phylogeny with greater confidence than previous studies, confirming and extending those results based on far fewer genes (
The relationships among the subfamilies, previously poorly resolved (
A novel result is the placement of
Within the
The relationships among the four major subgroups of
Within the Simonida, the
Given the strength of this broad data set and its concordance with previous results, we can now be reasonably confident in our current phylogenetic classification (
For assistance in collecting specimens we thank especially Edyta Piascik, Mauricio Vega, and Junxia Zhang. This work was supported by an NSERC Discovery grant to W. Maddison (RGPIN 261352-2013); National Science Foundation Doctoral Dissertation Improvement Grant – DEB-1311494 to CAH; an Auburn University Cellular and Molecular Biosciences Peaks of Excellence Research Fellowship (CAH).
Supplementary table of assembly statistics
Microsoft Excel Worksheet (.xlsx)
Statistics describing raw reads, loci, sequence lengths, and other aspects of sequencing assembly for each of the 34 salticid taxa and 12 outgroup taxa.