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1. Genomic data reveal new species and the limits of mtDNA barcode diagnostics to contain a global pest species complex ( Diptera: Tephritidae: Dacinae )

   https://doi.org/10.1111/syen.12616  

   Doorenweerd, Camiel ; San Jose, Michael ; Geib, Scott ; Barr, Norman ; Rubinoff, Daniel ( November 2023 , Systematic Entomology)

   The Oriental fruit flyBactrocera dorsalis(Hendel), a global pest that can decimate regional fruit industries and elicit international quarantines, has been the subject of considerable taxonomic confusion. Previous phylogenetic work revealed thatB. dorsalisis part of a monophyletic clade containing 12 species. We present restriction site‐associated DNA sequencing (RAD‐seq) genomic data for 2,292 specimens, which unequivocally supports the delimitation of two new species, here described asBactrocera borneoensissp. n.Doorenweerd & San Jose andB. incognitasp. n.Doorenweerd & San Jose. We additionally obtained 1,985 Cytochrome C oxidase I (COI) sequences for a subset of the specimens to see which species can be diagnosed with this mtDNA marker and conclude thatB. dorsalis,B. incognita,B. carambolaeDrew & Hancock,B. raiensisDrew & Hancock,B. occipitalis(Bezzi) andB. kandiensisDrew & Hancock cannot be identified reliably using COI due to introgression—but the newly described speciesB. borneoensiscan be identified using COI. The supposed innocuous speciesB. raiensisdistribution is underestimated in Asia and Africa.Bactrocera kandiensisCOI genotypes occur in African flies, but RAD‐seq data confirm that these areB. dorsaliswith introgressedB. kandiensisCOI. The phylogenomic dataset brings new light to the extent of theB. dorsalis s.l.clade and the morphological and molecular confusion based on COI. This will have ramifications for ecological data—including host and distribution ranges—associated withB. dorsalis s.l.clade species, pest identification protocols and our understanding of the economic importance of the various species in the clade.

    

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2. Paraphyletic species no more – genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)

   https://doi.org/10.1111/syen.12415  

   Huang, Jen‐Pan ; Hill, JoVonn G. ; Ortego, Joaquín ; Knowles, L. Lacey ( January 2020 , Systematic Entomology)

   Rapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29 000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short‐winged grasshopper species complex (Melanoplus scudderigroup), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that, based on a maximum likelihood molecular phylogeny, each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent‐based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds to the morphologically defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, not only indicating that this trait is labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be primarily associated with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e. fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e. genitalic divergence).

    

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3. Comparison between p‐distance and single‐locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox 1, rbcL and ITS

   https://doi.org/10.1111/jeu.12986  

   Franco, Andréa de ; Ashworth, Matt P. ; Odebrecht, Clarisse ( September 2023 , Journal of Eukaryotic Microbiology)

   Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single‐locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partialcox1,rbcL,5.8S + ITS2,ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species ofEunotia,Seminavis, Nitzschia, SellaphoraandPseudo‐nitzschiacorresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.

    

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4. flexsdm : An r package for supporting a comprehensive and flexible species distribution modelling workflow

   https://doi.org/10.1111/2041-210X.13874  

   Velazco, Santiago José ; Rose, Miranda Brooke ; de Andrade, André Felipe ; Minoli, Ignacio ; Franklin, Janet ( August 2022 , Methods in Ecology and Evolution)
5. Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito‐nuclear discordance in two genera of a New Zealand cicada ( Hemiptera: Cicadidae ) species radiation

   https://doi.org/10.1111/syen.12613  

   Stukel, Mark ; Porczak, Alexandra E. ; Gordon, Eric R. L. ; Vailionis, Jason ; Haji, Diler ; Buckley, Thomas R. ; Lemmon, Alan R. ; Lemmon, Emily Moriarty ; Simon, Chris ( November 2023 , Systematic Entomology)

   Rapid species radiations present difficulties for phylogenetic reconstruction due to lack of phylogenetic information and processes such as deep coalescence/incomplete lineage sorting and hybridization. Phylogenomic data can overcome some of these difficulties. In this study, we use anchored hybrid enrichment (AHE) nuclear phylogenomic data and mitochondrial genomes recovered from AHE bycatch with several concatenated and coalescent approaches to reconstruct the poorly resolved radiation of the New Zealand cicada species in the generaKikihiaDugdale andMaoricicadaDugdale. Compared with previous studies using only three to five Sanger‐sequenced genes, we find increased resolution across our phylogenies, but several branches remain unresolved due to topological conflict among genes. Some nodes that are strongly supported by traditional support measures like bootstraps and posterior probabilities still show significant gene and site concordance conflict. In addition, we find strong mito‐nuclear discordance; likely the result of interspecific hybridization events in the evolutionary history ofKikihiaandMaoricicada.

    

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