Four main challenges that can underpin ongoing, intransigent debates about species limits in birds are reviewed: allopatry (population subdivision vs. speciation), geographically widespread introgression of mitochondrial DNA (mtDNA), recent speciation, and selection. Examples from birds of the Australian region show how these challenges, their interplay, and the molecular-phenotypic discordance they generate can clarify or mislead species limits. Examples of how phylogenetic frameworks help reject or retain hypotheses of species limits under these challenges are given. Although mtDNA’s strengths and limitations are well known, an underappreciated limitation of mtDNA is geographically widespread introgression that homogenizes mtDNA diversity across species, subspecies, or population boundaries and across hundreds of kilometers. The resulting discordance between mtDNA and phenotype can be profound. If undetected, the setting of species limits and evolutionarily significant units are misled. An example shows how recent genomic analyses can detect and solve the problem. Other examples concern legacy mtDNA-only datasets. These are often essentially unfinished studies leaving residual uncertainty in species limits. Examples illustrate when the possibility of large-scale introgression across species boundaries needs to be considered, and how genomic scale data offer solutions. Researchers must carefully parse 3 questions: has there been introgression of mtDNA and, if so, which population genetics-based driver has caused introgression, and do species limits need altering? Understanding of allopatry, mtDNA introgression, recent speciation, and selection must be properly integrated if species limits are to be robustly understood and applied with maximum benefit in downstream applications such as conservation and management.

中文翻译：

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鸟类的物种限制：澳大利亚对异源性、线粒体 DNA 渗入、近期物种形成和选择的相互关联挑战的看法

回顾了四个主要挑战，这些挑战可以支撑关于鸟类物种限制的持续、顽固的辩论：异种（种群细分与物种形成）、线粒体DNA（mtDNA）在地理上广泛的基因渗入、最近的物种形成和选择。来自澳大利亚地区鸟类的例子显示了这些挑战、它们的相互作用以及它们产生的分子表型不一致如何澄清或误导物种限制。给出了系统发育框架如何帮助拒绝或保留在这些挑战下的物种限制假设的示例。尽管 mtDNA 的优势和局限性是众所周知的，但 mtDNA 的一个未被充分认识的局限性是地理上广泛的基因渗入，它使跨物种、亚种或种群边界以及跨越数百公里的 mtDNA 多样性均质化。mtDNA 和表型之间由此产生的不一致可能是深刻的。如果未被发现，物种限制和具有进化意义的单位的设定就会被误导。一个例子显示了最近的基因组分析如何检测和解决问题。其他示例涉及遗留的仅 mtDNA 数据集。这些通常是基本上未完成的研究，在物种限制中留下了剩余的不确定性。示例说明何时需要考虑跨物种边界大规模渗入的可能性，以及基因组规模数据如何提供解决方案。研究人员必须仔细分析 3 个问题：mtDNA 是否存在基因渗入，如果存在，是哪个基于种群遗传学的驱动因素导致了基因渗入，物种限制是否需要改变？了解异源性、mtDNA 渗入、最近的物种形成、