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Fig. 3. Consensus maximum likelihood tree for combined 16S in Cryptic multicolored lizards in the Polychrus marmoratus Group (Squamata: Sauria: Polychrotidae) and the status of Leiolepis auduboni Hallowell

Fig. 3. Consensus maximum likelihood tree for combined 16S and COI sequence data from seventeen Polychrus tissue samples (1,035 bp total). Bootstrap support values are indicated at each node, if greater than 50%. Samples are indicated by their museum accession number and country of origin, if known. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. For details of analysis, see text.

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Global contemporary effective population sizes across taxonomic groups

Effective population size (Ne) is a particularly useful metric for conservation as it affects genetic drift, inbreeding and adaptive potential within populations. Current guidelines recommend a minimum Ne of 50 and 500 to avoid short-term inbreeding and to preserve long-term adaptive potential, respectively. However, the extent to which wild populations reach these thresholds globally has not been investigated, nor has the relationship between Ne and human activities. Through a quantitative review, we generated a dataset with 4610 georeferenced Ne estimates from 3829 unique populations, extracted from 723 articles. These data show that certain taxonomic groups are less likely to meet 50/500 thresholds and are disproportionately impacted by human activities; plant, mammal, and amphibian populations had a <54% probability of reaching = 50 and a <9% probability of reaching = 500. Populations listed as being of conservation concern according to the IUCN Red List had a smaller median than unlisted populations, and this was consistent across all taxonomic groups. was reduced in areas with a greater Global Human Footprint, especially for amphibians, birds, and mammals, however relationships varied between taxa. We also highlight several considerations for future works, including the role that gene flow and subpopulation structure plays in the estimation of in wild populations, and the need for finer-scale taxonomic analyses. Our findings provide guidance for more specific thresholds based on Ne and help prioritize assessment of populations from taxa most at risk of failing to meet conservation thresholds.

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Рис. 3. ЧисΛо яиц в цистах Heterodera glycines разных размерных групп в 2018 и 2019 гг. Fig. 3. Number of eggs in cysts of Heterodera glycines of different size groups in 2018 and 2019 in Reproductive potential of Soybean Cyst Nematode Heterodera glycines - quarantine pest of soybean - in Primorsky Region conditions

Рис. 3. ЧисΛо яиц в цистах Heterodera glycines разных размерных групп в 2018 и 2019 гг. Fig. 3. Number of eggs in cysts of Heterodera glycines of different size groups in 2018 and 2019

Fig. 4 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 4. Ordinations summarizing species variation in shape using the first two axes of (a) a conventional PCA (total variance in parentheses) or (b) those of a bgPCA (between group variance in parentheses).

Fig. 3 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 3. Visualizations of species by sex interactions using group means.a. Mean CS profile plot. For size, males are on average slightly larger than females, but the difference is small and roughly similar in all species. Thus, lines are approximately parallel in the profile plot. b. Phenogram of mean shapes. In the phenogram, with the exception of the Alaskan marmot (bro) (whose sampling error is huge, having only eight individuals of known sex), female and male means are paired within each species with almost identical shape distances between sexes in each species. The similarity of SDM shape distances provides an information equivalent, in terms of the magnitude of the sex differences, to that of the parallel lines in the CS profile plot (Fig. 3a).

Fig. 7 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 7. UPGMA phenogram of Procrustes mean shape distances for the random, mutually exclusive, species subsamples. Shape variation (magnified five times, relative to the grand mean of all species) is illustrated using the six species mean shapes (all specimens included) with wireframes and thin-plate spline deformation grids (drawn in Morpheus et al. - Slice 1999) - but equivalent to those made using MorphoJ or the TPS Series).

Fig. 6 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 6. PC1–PC2 of mean shapes for the random, mutually exclusive, species subsamples. Shape variation (magnified five times) at the opposite extremes of each PC is shown using wireframes, as well as deformation grids and expansion factors computed in PAST using the thin plate spline interpolation. (In these wireframes, unlike those in MorphoJ, the mental foramen is also connected by a line to its neighbouring landmarks, as PAST constrains users to link all landmarks: the difference is, however, minimal and purely visual).

Fig. 5 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 5. Example of visualization of shape change: hoary marmot SDM illustrated using (a) superimposed shapes (male mean, in black, and grand mean of female and male means, in grey) or separate diagrams for male (b) and female (c) mean shapes. Focusing on the coronoid region, the violet arrow shows the potentially misleading effect of the superimposition, suggesting a backward 'movement' of the tip of the coronoid in males. Separate diagrams (b–c), in contrast, correctly suggest that change happens in the region whose boundary are marked by the landmarks, with the rostral margin of the coronoid becoming longer (red arrow) in males and shorter (blue arrows) in females.

Fig. 9 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 9. Divergent allometries and their effect on size-corrected shape. (a) PLS1 summarizing allometries (35% of variance in allometric predictions) vs CS. The vertical lines emphasize the scores of speciesspecific predicted allometric shapes for either the smallest mandible of all North American marmots (CS = 56 mm, emphasized with a vertical yellow line and arrows to show the extrapolations of the allometric trajectories to CS = 56 mm) or the mean CS of all species (CS = 77 mm, emphasized with a light grey vertical line). (b1) Scatterplot of bgPC1–2 (percentages of between group shape variance in parentheses) for the size-corrected shapes predicted using species-specific allometries (i.e., separate slopes) and CS = 56 mm as 'common' size. (b2, inset) Scatterplot of bgPC1–2 of size-corrected shapes using independent trajectories (as in b1) and CS = 77 mm: if differences in slopes were negligible, b1 and b2 should be almost identical.

Fig. 1 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 1. Box and jitter-plots of CS, for each species. a. Separate plots for females, males and unknown individuals. b. Plots with pooled sexes. As in part A, as well as shown in Table 1, species names in all figures are abbreviated using the first three letters of the scientific name (e.g., caligata = cal) and F for female, M for male, and U for individuals of unknown sex.

Fig. 2 in A practical, step-by-step, guide to taxonomic comparisons using Procrustes geometric morphometrics and user-friendly software (part B): group comparisons

Fig. 2. Visualization of shape SDM in relation to interspecific differences using a bgPCA. In this, and other Figures, percentages of variance in the scatterplots of multivariate shape are shown in parentheses, below the label for the corresponding axis. On bgPC1–2, which together account for almost all between group variance (94%), there is a large overlap between females and males within each species, whereas, between species, the separation is clear.

Fig. 15 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 15. Underwater photographs of Rhinogobius aonumai ishigakiensis taken at Ishigaki-jima Island, the Ryukyu Islands, Japan. Sakutagawa River: A (male, about 40 mm SL) and B (female, about 40 mm SL). Photographed by N. Oseko.

Fig. 17. Soft X in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 17. Soft X-ray nagatives of holotypes of two subspecies of Rhinogobius aonumai. A: Rhinogobius aonumai aonumai, B: Rhinogobius aonumai ishigakiensis. Red and yellow spots indicate abdominal and caudal vertebrae, respectively; white arrows show anteriormost two pterygiophores (proximal radials) of second dorsal fin. Photographed and annotated by T. Suzuki.

Fig. 14 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 14. Freshly-collected paratypes of Rhinogobius aonumai ishigakiensis from Ishigaki-jima Island, the Ryukyu Islands, Japan. Miyaragawa River: A (OMNH-P 40912, male, 38.0 mm SL) and B (OMNH-P 40914, female, 38.4 mm SL); Sakuta-gawa River: C (KPM-NI 65588, male, 55.9 mm SL) and D (SPMN-PI 49270, female, 40.5 mm SL); Sokobaru-gawa River: E (OMNH-P 40911, male, 39.9 mm SL) and F (OMNH-P 40913, female, 33.3 mm SL). Photographed by T. Suzuki.

Fig. 11 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 11. Ventral view of pelvic fin (A) and dorsal view of head (B), in Rhinogobius aonumai ishigakiensis stained with Alizarin Red S. OMNH-P 48923, paratype, male, 35.5 mm SL, Sakuta-gawa River. White lines indicate position where proximal most segment of each branch alignes transversely with the fifth segmented ray. Black wedge indicates slits between branches. Black circles with black letters H′, K′, and L′ indicate sensory-canal pores. P1, P2, and P3 indicate anteriormost point of anterior extension of scaly area along predorsal midline, anteriormost point of anterior extensions of scaly area on temporal region, and greatest concaved point of scaly area between P1 and P2, respectively. Photographed and annotated by T. Suzuki.

Fig. 10 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 10. Female paratype of Rhinogobius aonumai ishigakiensis (SPMN-PI 49270, female, 45.0 mm SL) collected from Sakutagawa River, Ishigaki-jima Island, the Yaeyama Group of the Ryukyu Islands, Japan. A and B: freshly-collected; C: alcoholpreserved. Photographed by T. Suzuki.

Fig. 12 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 12. Lateral view of body (A) and ventral view of belly (B) in Rhinogobius aonumai ishigakiensis stained with Alizarin Red S. OMNH-P 48923, paratype, male, 35.5 mm SL, Sakuta-gawa River. Yellow spots indicate the lateral anterior margin of ctenoid scale area. Photographed and annotated by T. Suzuki.

Fig. 9 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 9. Holotype of Rhinogobius aonumai ishigakiensis (SPMN-PI 49269, male, 51.5 mm SL) collected from Sakuta-gawa River, Ishigaki-jima Island, the Yaeyama Group of the Ryukyu Islands, Japan. A and B: freshly-collected; C: alcohol-preserved. Photographed by T. Suzuki.

Fig. 6 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 6. Freshly-collected paratypes of Rhinogobius aonumai aonumai from Iriomote-jima Island, the Ryukyu Islands, Japan. Airagawa River: A (OMNH-P 40852, male, 47.5 mm SL) and B (OMNH-P 40849, female, 42.3 mm SL); Geta-gawa River: C (OMNH-P 40832, male, 58.0 mm SL) and D (OMNH-P 40836, female, 40.5 mm SL); Hinai-gawa River: E (NSMT-P 138485, male, 56.0 mm SL) and F (NSMT-P 138486, female, 55.5 mm SL); Kuira-gawa River G: (KPM-NI 59985, male, 35.9 mm SL) and H (KPM-NI 59984, female, 38.5 mm SL); Kura-gawa River: I (OMNH-P 43162, male, 42.0 mm SL) and J (OMNH-P 43165, female, 36.0 mm SL). Photographed by T. Suzuki.

Fig. 8 in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan

Fig. 8. Underwater photographs of Rhinogobius aonumai aonumai taken at Iriomote-jima Island, the Ryukyu Islands, Japan. Hinaigawa River: A (male, about 60 mm SL) and B (female, about 45 mm SL); Urauchi-gawa River: C (male, about 50 mm SL) and D (female, about 40 mm SL). Photographed by M. Suzuki.