DOI: 10.5061/dryad.tmpg4f56k
title: Phylogeny and historical biogeography of the southern African lacewing genus Afroptera (Neuroptera: Nemopteridae: Nemopterinae)

description: The lacewing genus Afroptera Abdalla & Mansell (Neuroptera:
 Nemopteridae: Nemopterinae) is endemic to southern Africa, predominantly
 found in the Fynbos and Succulent Karoo biomes. The taxonomy of the genus
 has been recently resolved. However, the monophyly and evolutionary
 history of the genus has never been addressed. This study employs an
 integrative phylogenetic approach, by incorporating three ribosomal genes
 (16S, 28S, and 18S) and two protein-coding genes (COI and CAD), and
 morphological data to examine the monophyly and historical biogeography of
 Afroptera. We use Bayesian, parsimony and maximum likelihood phylogenetic
 methods to assess the monophyly and relatedness of Afroptera within the
 Nemopterinae. We also use ancestral ranges reconstruction and
 diversification analysis to infer the historical biogeography of the
 genus. Our analyses reveals the genus as a monophyletic lineage. The genus
 Afroptera originated during the Pliocene (5.24–3.13 Mya) in a desert
 environment, experiencing rapid speciation during the Pleistocene,
 primarily within the Fynbos and Succulent biomes; and secondarily
 dispersed into the Nama Karoo and Savannah (Kalahari) biomes. The current
 distribution patterns of Afroptera species likely stem from intensified
 aridification in the southwest during the Plio-Pleistocene, consistent
 with the dry-adapted nature of Afroptera's ancestors. Therefore, our
 findings suggest a climatically driven diversification model for the genus
 Afroptera.
description: <strong>Sampling and taxon selection
 </strong> a)     To test the monophyly and
 relatedness of the Nemopterinae genera, we included as in-group taxa all
 known southern African Nemopterinae genera:
 <em>Barbibucca</em>, <em>Derhynchia</em>,
 <em>Halterina</em>, <em>Knersvlaktia</em>,
 <em>Nemeura</em>, <em>Nemia, Palmipenna</em>,
 <em>Semirhynchia</em> and <em>Sicyoptera,</em> as
 well as the Australian <em>Chasmoptera </em>Westwood, in
 addition to the newly proposed <em>Nemopterella</em> Banks
 <em>sensu stricto</em>, <em>Afroptera</em> Abdalla
 & Mansell<em>,</em> and <em>Siccanada</em>
 Abdalla & Mansell. The only genus not included in this study is
 <em>Nemopistha</em>. A representative of the subfamily
 Crocinae, <em>Laurhervasia setacea</em> (Klug), was chosen as
 the out-group taxon, following Sole <em>et al</em>
 (2013). b)    To study the biogeography and
 diversification estimate time of the genus <em>Afroptera</em>,
 we included 14 species from the genus <em>Afroptera </em>on
 the basis of availability and suitability of fresh material for DNA
 extraction. We also include species of two genera,
 <em>Knersvlaktia</em> (one sp.) and
 <em>Palmipenna</em> (three spp.), as these taxa were regarded
 as phylogenetically close to <em>Afroptera </em>(Sole
 <em>et al</em>. 2013) before the problematic
 <em>Nemopteralla</em> was split into three genera (Abdalla
 <em>et al</em>. 2019).<em> </em>Additionally, we
 sought an outgroup entirely distinct from the problematic
 <em>Nemopterellla,</em> which
 <em>Knersvlaktia</em> and <em>Palmipenna</em> fit
 perfectly. Of these, 12 species of <em>Afroptera</em> were
 sequenced for the first time, the remainder taxa were retrieved from
 GenBank (see Table S1). All the sequences are deposited in Genbank (see
 Table S1).
description: # Phylogeny and historical biogeography of the southern African lacewing
 genus Afroptera (Neuroptera: Nemopteridae: Nemopterinae)
 [https://doi.org/10.5061/dryad.tmpg4f56k](https://doi.org/10.5061/dryad.tmpg4f56k) The dataset comprises both raw molecular and morphological data used for phylogenetic inferences. We have also included R-code scripts for biogeographical analysis using the R package ‘BioGeoBEARS’ and diversification analysis—a plot of lineage through time (LTT) and compound Poisson process on mass extinction times (CoMET) as implemented in the R (R Core Team, 2019) package ‘TESS’.  ## Description of the data and file structure * The molecular data comprises five gene regions as follows: three ribosomal genes (16S -, 28S, and 18S) and two protein-coding genes (COI - Cytochrome Oxidase subunit I and CAD - carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase). The data are in fasta file format. Also, we have attached a list of morphological characters used to generate a matrix for combined morphological and molecular phylogenetic inferences (represented by nexus file morphological_molecular_combine.nex). The same data we used to infer the dating phylogeny is represented by the tree file dated_tree_Afroptera.tre. The same tree was used for biogeographical and diversification analyses. These tree files can be viewed in R or Fig tree programs. * For biogeographical analyses we used two data files: (range. data) contains the distribution ranges of each species. The distribution ranges are represented by letters A, B, C, D and E., as follows: (A) Desert; (B) Fynbos; (C) Savannah; (D) Succulent Karoo and (E) Nama Karoo. Here are the list of the files and respective details. a) 16S.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .\ b) 18S.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .\ c) 28S.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ . d) CAD.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ .\ e) COI.fasta - .fasta files can be viewed in a standard text editor, like notepad or notepad ++ . f) Appendix_1__Morphological_characters_list.txt - This file contains list of morphological characters used to produce phylogenetic matrix. The file can be opened in any standard text editor. g) dated_tree_Afroptera.tre - This is a dated molecular tre file used for biogeographical and diversification analyses. The .tre file queue be viewed in a standard text editor, like notepad or notepad ++, but to visualize the tree we use FigTree program. h) Morphological_molecular_combined.nex. This is a combined phylogenetic matrix of both molecular and morphological data. Nexus file can be opened in a standard text editor, like notepad or notepad ++ . j) Range.data. This file contains distribution data of the species used in the biogeographical analysis. The .data files queue be opened in a standard text editor, like notepad or notepad ++ .