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F I G U R E 6 A in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation

F I G U R E 6 A midpoint rooted, maximum likelihood phylogeny using IQ-TREE of the 20 biological species found in this study. The phylogeny was estimated using 1000 ultrafast bootstraps (ufBS) from the three-gene concatenated sequence alignment. Coloured boxes and borders correspond to the colours used under the 5% cut-off (Figure S1). Only ufBS of 90 or greater are shown. Species sharing the same colour were found to share at least one nuclear allele.

F I G U R E 3 A 16S in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation

F I G U R E 3 A 16S neighbour-joining tree constructed under an HKY substitution model used for identifying putative species.

F I G U R E 5 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation

F I G U R E 5 TCS haplotype network coloured by putative species identified at the 4% cut-off. (a) EF1γ. (b) 28S.

F I G U R E 1 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation

F I G U R E 1 Map of sampling localities across Australia identified by putative species under the 4% threshold.

F I G U R E 4 in Assessing the diversity of Australian tarantulas (Araneae: Theraphosidae) using DNA barcoding and iterative species delimitation

F I G U R E 4 Species delimitation summary. Boxes in white represent which initial putative species specimens are assigned to as estimated under different barcode gap cut-offs. Letters within boxes represent different putative species hypotheses. Boxes in green are where the nuclear loci are consistent with being a distinct biological species, with no evidence of allele sharing. Boxes in grey are where putative species are found to share alleles of the nuclear loci. Boxes in orange are where putative species share internal haplotypes but also have alleles unique to each putative species (neotypy). Boxes in black represent the putative species found to be supported under different initial putative species thresholds.

Figure 3 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 3. Published values of percent divergence between cetacean subspecies (black bars), species (white bars), and taxa of uncertain taxonomic status (gray bars). Values are based on mtDNA control region sequence data. Not all values represent net sequence divergence. See Table 1 for list of papers corresponding to each value. Since completing this work, Sousa species have been supported ((Mendez et al. 2013) and Inia subspecies changed.

Figure 1 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 1. Sample sizes used in publications of molecular genetic studies of marine mammals at different taxonomic levels. Graphs present the proportion of studies at each taxonomic level that fall into each sample size category. (A) minimum total sample size per focal taxon; (B) maximum sample size per single sampling locality. Papers were categorized as examining taxonomic questions at: species = subspecies/species boundary; subspecies = population/subspecies boundary; uncertain = taxonomic boundary uncertain (see text).

Figure 2 in A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species

Figure 2. Types of molecular genetic data used in published studies examining questions at the species-level, subspecies-level, or undefined taxonomic level for marine mammals. Note that studies may have used more than one data type. Mitochondrial DNA sequence data (MtDNASeq), nuclear DNA sequence data (NuSeq), microsatellites (Msats), morphological data (Morph).

Figure 3 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

Figure 3. Flow diagram for subspecies delineation using combined quantitative and qualitative standards. The threshold values assume the user is evaluating a case relying on mtDNA control region data. Percent Diagnosable (PD) is the smallest strata-specific correct classification score in a given comparison (e.g., PD50 in two-strata comparisons in Archer et al. 2017). The second box in the second row (other evidence to meet subspecies definition) allows for subspecies delineation when both conditions are not met using mtDNA. This box could be used either for the case when one condition is met and one unmet or when both just barely miss meeting the standards. For example, consider the case with PD <95% and dA> 0.004. Diagnosability could be achieved with morphological data or nuclear data that are sufficient for subspecies but not for full species.

Figure 2. A in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data

Figure 2. A comparison of the pairs of populations (red triangles), subspecies (green squares) and species (blue circles) estimated by Rosel et al. (2017a). Net nucleotide divergence (dA) is shown on a natural log scale to better illustrate differences between the pairwise comparisons at low levels of divergence. Bars show the central 95th-pecentile of the estimate distributions. The solid vertical line at dA = 0.020 delimits all but one species and correctly excludes all subspecies pairs. The vertical dashed line at dA = 0.004 delimits all populations from the higher taxonomic levels and correctly delimits seven of eleven subspecies. The horizontal dashed lines are two potential thresholds for percent diagnosable (80% and 95%) that are discussed in the text.

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Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly employed for the identification of animal species, despite several challenges. Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan-level universal single-copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and employ coalescent-based species inference as well as population admixture analyses and phenetic methods. We demonstrate that metazoan USCOs well distinguish closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels. Metazoan USCOs provide a powerful and unifying framework for DNA-based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources.

Fig. 5 in Species delimitation in the genus Ochraethes Chevrolat, 1860 (Coleoptera: Cerambycidae), with description of two new species

Fig. 5. Species delimitation in Ochraethes Chevrolat, 1860. Maximum likelihood tree inferred from COI in IQ TREE. The molecular operational taxonomic units (MOTU) are separated by colour bars. Abbreviations: ABGD = ast recursive analyses; bPTP = both Maximum likelihood and Bayesian analyses; GMYC = coalescence and yule analyses; MORP = morphology.

Fig. 3 in Species delimitation in the genus Ochraethes Chevrolat, 1860 (Coleoptera: Cerambycidae), with description of two new species

Fig. 3. Pubescence variation on the elytra in Ochraethes Chevrolat, 1860. A–B. Ochraethes brevicornis (Chevrolat, 1860) (♀, ♂). C–E. O. cinereolus (Bates, 1892) comb. nov. (♂, ♂, ♀). F–I. O. obliquus (Chevrolat, 1860) (♂, ♂, ♀, ♀). J–N. O. sommeri (Chevrolat, 1835) (♂, ♂, ♂, ♀, ♀). O–S. O. viridiventris (Chevrolat, 1860) (♂, ♀, ♂, ♂, ♀). T–X. O. z-littera (Chevrolat, 1860) (♂, ♂, ♂, ♀, ♀).

Fig. 2 in Species delimitation in the genus Ochraethes Chevrolat, 1860 (Coleoptera: Cerambycidae), with description of two new species

Fig. 2. Ochraethes nigroapicalis sp. nov. A–D. Holotype, ♂ (EMEC). A. Habitus, dorsal. B. Habitus, ventral. C. Habitus, lateral. D. Frons. E. Paratype, ♂ (CNIN), ventral view of male genitalia. F. Paratype, ♀ (EMEC), habitus, dorsal.

Fig. 4 in Species delimitation in the genus Ochraethes Chevrolat, 1860 (Coleoptera: Cerambycidae), with description of two new species

Fig. 4. Head, frontal view of type species of Ochraethes. A. Ochraethes brevicornis (Chevrolat, 1860), ♀. B. O. virescens (Chevrolat, 1860), ♂. C. O. cinereolus (Bates, 1892) comb. nov., ♀. D. O. octomaculata Chemsak & Noguera, 2001, ♂. E. O. obliquus (Chevrolat, 1860), ♂. F. O. zebratus Bates, 1885, ♀. G. O. sommeri (Chevrolat, 1835), ♂. H. O. circuliferus (Chevrolat, 1860) (= Ochraethes sommeri), ♀. I. Trichoxys giesberti Botero et al., 2019, ♀. J. O. viridiventris (Chevrolat, 1860), ♂. K. O. nigritus Bates, 1892 (= Ochraethes viridiventris), ♂. L. O. clerinus Bates, 1892, ♀. M. O. z-littera (Chevrolat, 1860), ♂. N. O. cristoforii (Chevrolat, 1860), ♂. O. O. litura Bates, 1885, ♀.

Fig. 1 in Species delimitation in the genus Ochraethes Chevrolat, 1860 (Coleoptera: Cerambycidae), with description of two new species

Fig. 1. Ochraethes confusus sp. nov. A–D. Holotype, ♂ (EMEC). A. Habitus, dorsal. B. Habitus, ventral. C. Habitus, lateral. D. Frons. E. Paratype, ♂ (CNIN), ventral view of male genitalia. F. Paratype, ♀ (EMEC), habitus, dorsal.

FIGURE 4 in Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes)

FIGURE 4 | Species tree inferred from the concatenated dataset of mitochondrial genes (COI, Cytb, and 16S). Nodal support values are Bayesian posterior probabilities. Non-significant speciation probabilities identified in BP&P analysis algorithm A10 (PP:<0.95) are indicate by black circles and species supported with asterisk.

FIGURE 2 in Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes)

FIGURE 2 | Map of northwestern South America showing the geographic distribution of samples used in this study and species distribution of Astroblepus reported in Global Biodiversity Information Facility (GBIF) and the California Academy of Sciences (CAS) databases.

FIGURE 1 in Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes)

FIGURE 1 | Species of Astroblepus included in this study, A. A. ardiladuartei (LBP 26696 topotype live, 4.54 mm SL), B. A. cachara (LBP 26712 topotype live, 4.23 mm SL), C. A. caquetae (CZUT-IC 18464 topotype of museum, 7.84 mm SL), D. A. curitiensis (LBP 97118 topotype live, 5.92 mm SL), E. A. homodon (CZUT-IC 18390, 6.15 mm SL), F. A. gr. grixalvii (LBP24242 topotype live, 11.70 mm SL); F'. A. gr. grixalvii (CZUT-IC 18498 specimen of Magdalena basin 6,01 mm SL); F". A. gr. grixalvii (CZUT-IC 18320 specimen of Cauca basin, 15.25 mm SL), G. A. itae (topotype live, 3.58 mm SL), H. A. latidens (topotype live, 13.40 mm SL), I. A. onzagaensis (topotype live, 7.82 mm SL), J. A. pradai (topotype live, 4.53 mm SL), K. A. trifasciatus (topotype of museum, 9.65 mm SL), K'. A. trifasciatus (topotype of museum, 9.01 mm SL), L. A. aff. trifasciatus (specimen of Magdalena basin, 7.94 mm SL), M. A. verai (topotype live, 3.51 mm SL).

FIGURE 3 in Species delimitation reveals an underestimated diversity of Andean catfishes of the family Astroblepidae (Teleostei: Siluriformes)

FIGURE 3 | Results of single-locus approaches using cytochrome oxidase c subunit I (COI) for developing preliminary species delimitation hypothesis with 42 lineages. Results are represented on the ultrametric gene tree with collapsed nodes. All nodal support values were PP>0.95. Blocks at right of the tree represent hypothesized species groups and the values in the middle indicate the number of clusters identified by ABGD, bPTP and GMYC analyses for every collapsed node. COL: Colombia, ECU: Ecuador, PER: Peru.