Phylogeny and historical biogeography of the southern African lacewing genus Afroptera (Neuroptera: Nemopteridae: Nemopterinae)
Data files
Jul 18, 2024 version files 303.54 KB
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16S.fasta
13.30 KB
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18S.fasta
30.26 KB
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28S.fasta
19.86 KB
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Appendix_1__Morphological_characters_list.txt
8.72 KB
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CAD.fasta
15.34 KB
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COI.fasta
34.70 KB
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dated_tree_Afroptera.tre
4.67 KB
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morphological_molecular_combined.nex
173.32 KB
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range.data
281 B
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README.md
3.09 KB
Abstract
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.
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 ++ .
Sampling and taxon selection
a) To test the monophyly and relatedness of the Nemopterinae genera, we included as in-group taxa all known southern African Nemopterinae genera: Barbibucca, Derhynchia, Halterina, Knersvlaktia, Nemeura, Nemia, Palmipenna, Semirhynchia and Sicyoptera, as well as the Australian Chasmoptera Westwood, in addition to the newly proposed Nemopterella Banks sensu stricto, Afroptera Abdalla & Mansell, and Siccanada Abdalla & Mansell. The only genus not included in this study is Nemopistha. A representative of the subfamily Crocinae, Laurhervasia setacea (Klug), was chosen as the out-group taxon, following Sole et al (2013).
b) To study the biogeography and diversification estimate time of the genus Afroptera, we included 14 species from the genus Afroptera on the basis of availability and suitability of fresh material for DNA extraction. We also include species of two genera, Knersvlaktia (one sp.) and Palmipenna (three spp.), as these taxa were regarded as phylogenetically close to Afroptera (Sole et al. 2013) before the problematic Nemopteralla was split into three genera (Abdalla et al. 2019). Additionally, we sought an outgroup entirely distinct from the problematic Nemopterellla, which Knersvlaktia and Palmipenna fit perfectly. Of these, 12 species of Afroptera 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).