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.近期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学界所宣称的宽泛范围下限。然而，此类近期评估均未正式探讨那个真正的“房间里的大象”——即常规分类学评估无法识别的物种占比究竟几何：这些未被辨识的隐存种（cryptic species）在通过多基因分子分析被揭示前，始终无法被纳入统计计数。本研究以澳洲淡水鱼Galaxias olidus作为模式类群，针对那些相较于研究匮乏类群或形态未分化类群而言，分类学本应已基本定型的任一生物类群，探讨所谓“超隐存种（hyper-cryptic species）”复合群的生物学意义与分布规模。我们针对该物种的广布地理范围开展了综合评估：涵盖同工酶（allozyme）分析（838尾样本，检测54个推定基因座）、线粒体DNA（mtDNA）分析（557尾样本，测序605bp的细胞色素b（cytb）基因片段）以及形态学分析（1963~3389份标本凭证（vouchers），检测17~58个形态性状）。结果显示，物种水平的生物多样性提升了1500%，且暗示仍有未被发现的类群存在。值得注意的是，尽管事后（a posteriori）通过形态学可区分全部15个候选物种，但单基因DNA条形码（DNA barcoding）作为物种鉴定的先验（a priori）方法，整体而言效果欠佳。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，超隐存种复合群很可能在众多生物类群中广泛存在；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占比估算，都不能被视为“最佳实践”。