Data from: Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)

The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier & Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753 bp) and cytochrome b (CytB, 587 bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426 bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere.

Stomoxys Geoffroy属（双翅目Diptera；蝇科Muscidae）包含具有医学与经济重要性的寄生蝇类。本研究针对该属的10个代表物种（含多个复份标本）以及近缘属Prostomoxys Zumpt、Haematobosca Bezzi和Haematobia Lepeletier & Serville开展了系统发育分析。基于细胞色素c氧化酶亚基I（cytochrome c oxidase subunit I, COI，753 bp）、细胞色素b（cytochrome b, CytB，587 bp）线粒体基因片段以及核糖体核内转录间隔区2（nuclear ribosomal internal transcribed spacer 2, ITS2，426 bp）的序列，采用最大似然法与贝叶斯法推断系统发育关系。线粒体与核基因数据的联合分析强有力地支持Stomoxys属为并系群，原因是Prostomoxys saegerae Zumpt被归入该属。这一出人意料的结果提示Prostomoxys属应更名为Stomoxys属。此外，在亚种Stomoxys niger niger Macquart与S. niger bilineatus Grünbreg之间观测到的深度分子分化，结合现有生态数据，提示二者应被视为独立物种。贝叶斯系统发育分析支持Stomoxys属内存在3个具有显著生物地理特征的独立演化支。第一演化支仅包含分化程度较高的亚洲物种S. indicus Picard，该物种是其余所有Stomoxys物种的姊妹群。第二演化支包含所有严格分布于非洲的物种：Stomoxys inornatus Grünbreg、Stomoxys transvittatus Villeneuve、Stomoxys omega Newstead以及Stomoxys pallidus Roubaud。第三演化支则涵盖非洲分布种与分布更广的物种，例如牲畜害虫Stomoxys calcitrans Linnaeus。分化时间估算结果显示，Stomoxys属起源于渐新世晚期，距今约3000万年；其主要演化支的分化发生于中新世早期（距今2000万至1500万年），此时北半球温带森林正处于发育阶段。