Phylogenetics and introgression of Habronattus jumping spiders using transcriptomes (Araneae:Salticidae)

Habronattus is a diverse genus of jumping spiders with complex courtship displays and colourful ornaments in males. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved because of conflicting signals from the few genes available. While such discordant gene trees could be the result of deep coalescence in the recently diverged group, there are many indications that hybridization may have occurred and could be the source of conflict. To infer Habronattus phylogenetic relationships and to investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. We conducted a concatenated phylogenetic analysis using Maximum Likelihood for 2.41 Mb of nuclear data and for 12.33 kb of mitochondrial data. The concatenated nuclear phylogeny was resolved with high bootstrap support (95-100%) at most nodes with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, and H. oregonensis, and Pellenes cf. levii. There are several nodes of the mitochondrial phylogeny that are incongruent to the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus group, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the extent of incomplete lineage sorting (ILS) and introgression, we analyzed gene tree discordance for loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the viridipes/clypeatus/coecatus (VCC) group (517 loci) and found high levels of genetic discordance, especially in VCC group. Finally, we tested specifically for nuclear 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, and between H. sp. (ROBRT) and the clypeatus group, and more minimal nuclear introgression between the clypeatus group and the coecatus group, and between the americanus group and several distant species. Our results indicate that hybridization may have been historically common between phylogenetically distant species of Habronattus, and that reproductive isolation is yet to be complete across the Habronattus phylogeny.Science, Faculty ofZoology, Department ofGraduat

Data from: Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

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

HabronattusChromosomes2013-MaddisonLeducRobert

DNA sequences from Maddison & Hedin (2003), realigned, plus original observations on sex chromosomes and chiasma localization. Phylogenies from BEAST analysis and Maddison & Hedin 2003

Matrices of concatenated aligned sequences

5 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

Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

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.Science, Faculty ofBotany, Department ofZoology, Department ofReviewedFacult

Data from: Multiple origins of sex chromosome fusions correlated with chiasma localization in Habronattus jumping spiders (Araneae: Salticidae)

Entelegyne spiders rarely show fusions yielding neo-Y chromosomes, which M. J. D. White attributed to a constraint in spiders, namely their proximal chiasma localization acting to upset meiotic segregation in males with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have X1X20 sex chromosomes in males, 10 have X1X2Y, 15 have X1X2X3Y, 2 have X0, and one has both X1X20 and X1X2X3Y. Chromosome numbers and behavior suggest neo-Ys formed by an autosome-X fusion to make X1X2Y, with a second fusion to an autosome to make X1X2X3Y. Phylogeny shows at least 8-15 gains (or possibly some losses) of neo-Y (i.e. X-autosome fusions), a remarkable number for such a small clade. In contrast to the many X-autosome fusions, at most one autosome-autosome fusion is indicated. Origins of neo-Y are correlated significantly with distal localization of chiasmata, supporting White’s hypothesis that evolution of neo-Y systems is facilitated by looser pairing (distal chiasmata) at meiosis. However, an alternative (or contributing) explanation for the correlation is that X-autosome fusions were selected to permit isolation of male-favored alleles to the neo-Y chromosome, aided by distal chiasmata limiting recombination. This intralocus sexual conflict hypothesis could explain both the many X-autosome fusions, and the stunning complexity of male Habronattus courtship displays

NEXUS file of inferred phylogenetic trees

Inferred trees from the various analyses and partitions of the transcriptome data

Varia

Ce numéro est dédié à la mémoire de Dino Ambaglio, ami, lecteur et compagnon de voyage de toutes nos «Anabases». ἐν κοινωνίᾳ τε καὶ συμφωνί