10.5061/DRYAD.5KG33
Leduc-Robert, Geneviève
University of British Columbia
Maddison, Wayne P.
University of British Columbia
Data from: Phylogeny with introgression in Habronattus jumping spiders
(Araneae: Salticidae)
Dryad
dataset
2018
Habronattus
Harmochirina
Plexippini
Salticidae
Salticinae
Jumping spiders
2018-01-18T14:08:36Z
2018-01-18T14:08:36Z
en
https://doi.org/10.1186/s12862-018-1137-x
13276011 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: Habronattus is a diverse clade of jumping spiders with complex
courtship displays and repeated evolution of Y chromosomes. A
well-resolved species phylogeny would provide an important framework to
study these traits, but has not yet been achieved, in part because the few
genes available in past studies gave conflicting signals. Such discordant
gene trees could be the result of incomplete lineage sorting (ILS) in
recently diverged parts of the phylogeny, but there are indications that
introgression could be a source of conflict. Results: To infer Habronattus
phylogeny and investigate the cause of gene tree discordance, we assembled
transcriptomes for 34 Habronattus species and 2 outgroups. The
concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by
Maximum Likelihood (ML) with high bootstrap support (95-100%) at most
nodes, with some uncertainty surrounding the relationships of H.
icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species
tree analyses by ASTRAL and SVDQuartets gave almost completely congruent
results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial
data are incongruent with the nuclear phylogeny and indicate possible
mitochondrial introgression: the internal relationships of the americanus
and the coecatus groups, the relationship between the altanus, decorus,
banksi, and americanus group, and between H. clypeatus and the coecatus
group. To determine the relative contributions of ILS and introgression,
we analyzed gene tree discordance for nuclear loci longer than 1 kb using
Bayesian Concordance Analysis (BCA) for the americanus group (679 loci)
and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517
loci) and found signals of introgression in both. Finally, we tested
specifically for introgression in the concatenated nuclear matrix with
Patterson’s D statistics and DFOIL. We found nuclear introgression
resulting in substantial admixture between americanus group species,
between H. roberti and the clypeatus group, and between the clypeatus and
coecatus groups. Conclusions: Our results indicate that the phylogenetic
history of Habronattus is predominantly a diverging tree, but that
hybridization may have been common between phylogenetically distant
species, especially in subgroups with complex courtship displays.
Matrices of concatenated aligned sequences5 files. Three are partitions of
nuclear transcriptomes (primary matrix of 1877 genes; secondary matrices
of (MS) loci with species missing and (NL) noncoding loci. The fourth
matrix is of the mitochondrial transcriptomes; the fifth is the mix of 16s
and ND1 from the transcriptomes, and previous data from Sanger
sequencing.Leduc-Robert&Maddison_Habronattus-AlignedMatrices.tgzNEXUS file of inferred phylogenetic treesInferred trees from the various analyses and partitions of the transcriptome data.Leduc-Robert&Maddison_Habronattus-Trees.nex
North America