DOI: 10.5061/dryad.tk043
title: Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?

description: 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.
description: Adams_etal_Syst_Biol_unique_cytb_haplotypesMEGA file of n=277 unique cytb haplotypes (271 ingroup and 6 outgroup sequences for 602bp),Adams_etal_Syst_Biol_Supplemental_Table_1TABLE 1. Locality, collection and sample size information for mountain galaxias specimens used in the molecular studies or prepared and assessed for the morphological studies. Sites arranged according to species, Drainage Division (DD) and River Basin (RB) (AWRC 1976). Alloz = Allozymes; Cytb = Cytochrome-b sequenced; Morph – Morphometrics; Meris – Meristics. Sample sizes for each morphological assessment include the individuals used in the final analyses, plus outliers, plus those subsequently used to assess the geographic range of each species. Taxon codes follow Table 1 and Figure 5. Where provided, sites codes match those of Raadik (2011). Sites were assigned to three regions for some of the allozyme PCoAs, namely ‘northern’ (all sites within DD 2, RB 3–17 or DD 4, RB 10–22), ‘central’ (all sites within DD 2, RB 18–35 or DD 4, RB 1–12), or ‘western’ (all sites within DD 4, RB 26 or DD 5).Adams_etal_Syst_Biol_Supplemental_Table_2_allozyme_raw_dataIndividual allozyme genotypes for n=838 mountain galaxias at 54 allozyme loci. Gel# = individual allozyme code; Taxon/DD/RB/site no = as per Supplemental Table 1; Locus abbreviations as outlined in main text.Adams_etal_Syst_Biol_Supplemental_Table_3TABLE 3. Allozyme frequencies for the 15 diagnosable candidate species, as identified using stepwise PCoA. Alleles with a frequency of less than 0.5 % in any taxon are not shown. For polymorphic loci, the frequencies of all but the rarer/rarest alleles are expressed as percentages and shown as superscripts (allowing the frequency of each rare allele to be calculated by subtraction from 100 %). Alleles not separated by a comma all shared the frequency indicated. Taxon codes follow Table 1 and Figure 3. A dash indicates no genotype was assignable at this locus.Adams_etal_Syst_Biol_Supplemental_Table_4TABLE 4. Total number of diagnostic ‘characters’ among the 15 candidate species across both the allozyme and morphological datasets. The morphometric and meristic datasets were each only counted as one ‘super-character’, based on the outcomes of our multivariate analyses. In all cases, multiple univariate morphological characters were able to differentiate pairwise combinations of taxa (Raadik 2011).Adams_etal_hyper-cryptic_olidus_Syst_Biol_Supplementary_Figures_R1Powerpoint file containing Supplemental Figures 1-6. Each figure is individually captioned.Adams_etal_hyper-crpytic_olidus_Syst_Biol_Supplementary_TextSupplementary Text 1 and 2, providing additional details of the morphological analyses undertaken.