Phylogenomic Species Delimitation, Taxonomy, and ‘Bird Guide’ Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

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Abstract

Rasopone Schmidt and Shattuck is a poorly known lineage of ants that live in Neotropical forests. Informed by phylogenetic results from thousands of ultraconserved elements (UCEs) and mitochondrial DNA barcodes, we revise the genus, providing a new morphological diagnosis and a species-level treatment. Analysis of UCE data from many Rasopone samples and select outgroups revealed non-monophyly of the genus. Monophyly of Rasopone was restored by transferring several species to the unrelated genus Mayaponera Schmidt and Shattuck. Within Rasopone, species are morphologically very similar, and we provide a ‘bird guide’ approach to identification rather than the traditional dichotomous key. Species are arranged by size in a table, along with geographic range and standard images. Additional diagnostic information is then provided in individual species accounts. We recognize a total of 15 named species, of which the following are described as new species: R. costaricensis, R. cryptergates, R. cubitalis, R. guatemalensis, R. mesoamericana, R. pluviselva, R. politognatha, R. subcubitalis, and R. titanis. An additional 12 morphospecies are described but not formally named due to insufficient material. Rasopone panamensis (Forel, 1899) is removed from synonymy and elevated to species. The following species are removed from Rasopone and made new combinations in Mayaponera: M. arhuaca (Forel, 1901), M. becculata (Mackay and Mackay, 2010), M. cernua (Mackay and Mackay, 2010), M. conicula (Mackay and Mackay, 2010), M. longidentata (Mackay and Mackay, 2010), and M. pergandei (Forel, 1909).

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Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

Brant C Faircloth, John E McCormack, Nicholas G Crawford … (2012)

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.

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PHYLUCE is a software package for the analysis of conserved genomic loci.

Brant C Faircloth (2016)

Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales ( 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.

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Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Brant C Faircloth, Michael G Branstetter, Noor D. White … (2014)

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.

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Contributors

John T Longino: (View ORCID Profile)

Journal

Title: Insect Systematics and Diversity

Publisher: Oxford University Press (OUP)

ISSN (Electronic): 2399-3421

Publication date Created: March 2020

Publication date Created: March 01 2020

Publication date Other: March 2020

Publication date (Print): March 01 2020

Publication date (Electronic): April 11 2020

Volume: 4

Issue: 2

Affiliations

[1 ]Department of Biology, University of Utah, Salt Lake City, UT

[2 ]USDA-ARS Pollinating Insects Research Unit, Utah State University, Logan, UT

Article

DOI: 10.1093/isd/ixaa004

SO-VID: 4d94487b-7183-41e0-9828-70c1b141169d

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https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

Phylogenomic Species Delimitation, Taxonomy, and ‘Bird Guide’ Identification for the Neotropical Ant Genus Rasopone (Hymenoptera: Formicidae)

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Hymenoptera

Most cited references 11

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

PHYLUCE is a software package for the analysis of conserved genomic loci.

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

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