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A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.

ABSTRACT: We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.

SUBMITTER: Maddison WP

PROVIDER: S-EPMC5673835 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.

Maddison Wayne P WP Evans Samuel C SC Hamilton Chris A CA Bond Jason E JE Lemmon Alan R AR Lemmon Emily Moriarty EM

ZooKeys 20170904 695

We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving ...[more]

PMID: 29134008

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Project description:BackgroundHabronattus 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.ResultsTo 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.ConclusionsOur 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.

Project description:The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribeAillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószy?ski, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola, A. sylvestris, A. cutleri, A. striatus, and A. finschi. The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 (A. dorsata, A. concolor, A. juniperi), (2) Tomis (T. welchi), and (3) Sittisax Prószy?ski, 2017 (S. ranieri). All Neotropical and Caribbean "Sitticus" are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus; the synonymy of Sitticus cabellensis Prószy?ski, 1971 with Pseudattulus kratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis. Six generic names are newly synonymized with Attulus and one with Attinella. Two Neotropical species are described as new, Jollas cupreus sp. nov. and Tomis manabita sp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X1X2Y and X1X2X3Y), some of which (Sittisax ranieri and S. saxicola) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.

Project description:The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group's genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison, gen. nov. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly delimited groups. Eighteen new species are described: Bavia nessagyna, Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I. sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus), M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P. bakau, P. kohi, P. mandai, and Stagetillus irri, all sp. nov., with taxonomic authority W. Maddison. The distinctions between baviines and the astioid Nungia ?abka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established: Bavia maurerae (Freudenschuss & Seiter, 2016), Indopadilla annamita (Simon, 1903), I. kahariana (Prószy?ski & Deeleman-Reinhold, 2013), I. sonsorol (Berry, Beatty & Prószy?ski, 1997), I. suhartoi (Prószy?ski & Deeleman-Reinhold, 2013), Maripanthus menghaiensis (Cao & Li, 2016), M. smedleyi (Reimoser, 1929), Nungia hatamensis (Thorell, 1881), N. modesta (Keyserling, 1883), N. papakula (Strand, 1911), N. xiaolonghaensis (Cao & Li, 2016), Padillothorax casteti (Simon, 1900), P. exilis (Cao & Li, 2016), P. flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillus banda (Strand, 1911), all comb. nov. One combination is restored, Bavia capistrata (C. L. Koch, 1846). Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes, emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószy?ski, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.

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A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.

Publications

A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.

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