Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?

Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real ‘elephant in the room’, namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called ‘hyper-cryptic’ species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605bp of cytb), and morphological (1963–3389 vouchers for 17–58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered ‘best practice’ in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity.

近年多项全球生物多样性评估研究均指出，地球现存物种总数已趋近于过去数十年间所宣称的宽泛区间的下限。然而，此类近期评估均未正式探讨真正的“房间里的大象”——即有多大比例的物种在传统分类学评估中处于“不可见”状态，这些未被鉴定的隐存种（cryptic species）因此无法被计数，直至通过多基因分子鉴定手段方能被揭示。
本研究以澳大利亚淡水鱼*Galaxias olidus*作为代理类群，用以代表相较于研究匮乏类群或形态难以区分类群而言，分类学本应已基本完善的任一生物类群，探讨了所谓“超隐存（hyper-cryptic）”物种复合群的重要性与分布范围。
我们针对该物种的广泛地理分布范围开展了全面评估：涵盖838尾个体、54个推定基因座的同工酶（allozyme）分析，557尾个体、605bp细胞色素b（cytb）基因的线粒体DNA（mtDNA）测序，以及针对1963至3389份标本凭证、17至58项形态特征的形态学鉴定。结果显示该类群的物种级生物多样性提升了1500%，且暗示仍有未被发现的类群存在。
值得注意的是，尽管15个候选物种均可通过形态特征进行回溯性区分，但单基因DNA条形码（DNA barcoding）作为物种鉴定的预判性方法，整体效果并不理想。
基于上述结果，我们得出两项与全球生物多样性评估密切相关的重要推论：其一，超隐存物种复合群大概率广泛存在于众多生物类群中；其二，在分子生物学时代，任何物种数量评估若未明确纳入隐存种与超隐存种生物多样性的估算范围，均不能被视为“最佳实践”。