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Genomic Resources for Global and Local Ancestry Estimation in a Captive Baboon Colony

VCF files mapped to Panubis1.0 with 881 olive (Papio anubis) and yellow (Papio cynocephalus) baboons from the Southwest National Primate Research Center. VCF files were generated in two separate pipelines, first using Beagle 4.1 and Beagle 5.4 and additionally SHAPEIT5/IMPUTE5 to test if a pedigree-aware software reduced the number of evident phase switch errors. VCFs here have been phased and imputed in their respective pipelines, filtered for imputation accuracy with markers with less than 0.7 confidence removed using BCFTools, and then phase switch corrected using Tractor. Genomic resources (AIMs and Fixed markers) are based off of Panubis1.0 coordinates. Local ancestry estimation completed by RFMix and then phase-switch-corrected using Tractor.

Figure 3 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 3. Karyotypes of (A) Hymenochirus boettgeri (IVB-H-CG17-356, male) with 18 homologous chromosome pairs, and (B) Hymenochirus sp. (IVB-H-Hsp06, female) with 10 pairs of A chromosomes and one B chromosome, arranged from Giemsa-stained chromosomes. Chromosomes were cut from metaphase spreads on the left. Long lines in karyotype arrangements indicate the position of chromosome centromere. Short vertical and horizontal lines correspond to the scale = 10 μm.

Figure 4 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 4. Hymenochirus boettgeri (IVB-H-CG17-356, male), sequential fluorescent chromosome mapping—DAPI, CMA3, C-banding, ribosomal DNA (rDNA) FISH, small nuclear DNA (snDNA) FISH; and non-sequential whole-genome painting on metaphase spread. A, DAPI (black and white, B&W) consistently stains all 36 chromosomes. B, CMA3 banding in green shows nucleolar secondary constriction (NOR locus) on the p arm of chromosome 4 that co-localizes with 28S. C, C-banding (B&W, brighter staining) highlights heterochromatic blocks on telomeric and pericentromeric regions of seven homologous chromosomes (14 arrows). D, FISH with 28S (red) ribosomal probes shows the p arm of chromosome 4. E, FISH with U1 (red) and U2 (green) snDNA probes shows very weak signals. The U1 probe maps to the q arm of chromosome 1, the U2 probe maps to the q arm of chromosome 8. F, genomic in situ hybridization (GISH) with Hymenochirus sp. whole-genome painting DNA probe that hybridizes to all 36 chromosomes with different intensity. Arrows show the less intensely painted chromosome pair. Scale bars represent 10 μm.

Figure 6 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 6. Schematic representation of the chromosomal location of the U1 (red) and U2 (green) snDNAs, 5S (dark blue) and 28S (yellow) rDNAs, and C-bands (dark grey) in H. boettgeri (Congo) and Hymenochirus sp. (captive population). The haploid A chromosome set of each species, 18 chromosomes in H. boettgeri and 10 chromosomes in Hymenochirus sp., is arranged in descending order of size. The B chromosome of Hymenochirus sp. is depicted separately from the A chromosomes and is entirely covered in grey, as revealed by C-banding. The 5S rDNA locus was not detected in H. boettgeri and is only depicted in the Hymenochirus sp. karyotype. Mapping of the U1 snDNA locus identified a pericentric inversion or copy number reduction/expansion visible on non-homologous regions of chromosome 1. Created with BioRender.com.

Figure 5 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 5. Hymenochirus sp. (IVB-H-Hsp06, female), sequential fluorescent chromosome mapping (DAPI, CMA3, C-banding, rDNA FISH), non-sequential snDNA FISH, and whole-genome painting on metaphase spread. A, DAPI (B&W) counter-stained metaphase spread shows all 21 chromosomes. B, CMA3 banding in green shows NOR locus on the p arm of chromosome 4. CMA3 signal co-localizes with 28S locus. C, C-banding (B&W, brighter staining) highlights heterochromatic blocks on telomeric and pericentromeric regions of almost all chromosomes. In addition, the whole B chromosome is intensely banded (arrow). D, 5S (green) and 28S (red) rDNA loci are located on the q arm of chromosome 6 and p arm of chromosome 4, respectively. The 5S rDNA is situated on two different chromosomal loci within the single q arm. E, the snDNA loci U1 (red) and U2 (green) are located on the p arm of chromosome 1 and the q arm of chromosome 8, respectively. F, the GISH experiment of the H. boettgeri whole-genome painting probe, which hybridizes on Hymenochirus sp. chromosomes. All chromosomes are painted (red) except one, B chromosome, which shows no GISH signal and is DAPI-positive (arrow). Scale bars represent 10 μm.

Figure 2 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 2. Phylogenetic trees of dwarf clawed frogs. Maximum likelihood mtDNA (16S, left) and nDNA (rag1, right) trees showing the positions of karyotyped individuals (in bold) in the context of available molecular sampling retrieved from GenBank (acc. nos. listed). For sampling details, see Supporting Information, Table S1.

Figure 1 in Tetraploidy in the Boettger's dwarf clawed frog (Pipidae: Hymenochirus boettgeri) from the Congo indicates non-conspecificity with the captive population

Figure 1. Dwarf clawed frogs, Hymenochirus sp. (captive population) and H. boettgeri. A, Hymenochirus sp., female (IVB-H-Hsp06) and male (IVB-H-Hsp02) in amplexus. B, Hymenochirus sp., female in dorsolateral view (IVB-H-Hsp04). In (A) and (B), note the relatively smooth flanks and hindlegs with homogeneous, unenlarged tubercles. C, Hymenochirus boettgeri from the north-western part of the Republic of the Congo (male, IVB-H-CG17-356). D, holotype of H. boettgeri, female (ZMB 11521). The area marked by the red rectangle is detailed in (E). F, Hymenochirus boettgeri from the same locality as the karyotyped individual (IVB-H-CG17-112, male). In (C–F), note the enlarged and spiny tubercles on the flanks and hindlegs typical for H. boettgeri.

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Data from: Captive birds exhibit greater foraging efficiency and vigilance after anti-predator training

Rearing animals in captivity for conservation translocation is a complex undertaking that demands interdisciplinary management tactics. The maladapted behaviors that captive animals can develop create unique problems for wildlife managers seeking to release these animals into the wild. Often, released captive animals show decreased survival due to predation and their inability to display appropriate anti-predator, vigilance, and risk-analysis behaviors. Additionally, released animals may have poor foraging skills, further increasing their vulnerability to predation. Often conservation translocation programs use anti-predator training to ameliorate these maladapted behaviors before release but find mixed results in behavioral responses. The behavioral scope of analyzing the effect of anti-predator trainings is frequently narrow; the effect of this training on an animal's risk-analysis competency, or ability to assess the predation risk of a foraging patch and subsequently adjust its behavior, remains unstudied. Using a captive reared passerine species, the American robin (Turdus migratorius) (46 individuals), we applied an experimental giving up density test (GUD) to analyze the effect of anti-predator training on the robins' vigilance/risk-analysis behaviors, patch choice, and the GUD of food left behind after one foraging session. Robins moved and foraged freely between three foraging patches of differing predation risk before and after a hawk silhouette was presented for one minute. Results indicate that after anti-predator training, robins displayed increased vigilance across most foraging patches and better foraging efficiency (higher vigilance and latency to forage with simultaneous lower GUD) in the safest patch. These results can have positive survival implications post-release, however, more research on this training is needed because anti-predator training has the potential to elicit indiscriminate increased vigilance to the detriment of foraging gains. Further research is required to standardize GUD's application in translocation programs with multigenerational captive-bred animals to fully comprehend its effectiveness in identifying and correcting maladaptive behaviors. GUD tests combined with behavioral analysis should be used by conservation translocation managers to examine the need for anti-predator and foraging trainings, the effects of trainings, and a group's suitability for release.

FIG. 12 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 12. Inflation in Tetraodontiformes. Orange indicates presence of inflation behavior. (A) Inflation has three steps when optimized on the topology of Arcila and Tyler (2017; 16 loci and morphology). (B) Inflation has three steps when optimized on the topology of Betancur-R. et al. (2017; nuclear and mitochondrial loci). (C) Inflation has three steps when optimized on the topology of Ghezelayagh et al. (2022; ultraconserved elements). Data on the occurrence of inflation are summarized in Table 2.

FIG. 11 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 11. Pelvic-fan flaring in Tetraodontiformes. Blue indicates presence of pelvic-fan flaring behavior. (A) Pelvic-fan flaring has two steps when optimized on the topology of Arcila and Tyler (2017; 16 loci and morphology). (B) Pelvic-fan flaring has two steps when optimized on the topology of Betancur-R. et al. (2017; nuclear and mitochondrial loci). (C) Pelvic-fan flaring has two steps when optimized on the topology of Ghezelayagh et al. (2022; ultraconserved elements). Data on the occurrence of pelvic-fan flaring are summarized in Table 2.

FIG. 7 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 7. Dissection of branchiostegal rays and muscles of Triodon macropterus (NSMT P93783, 343 mm SL). The specimen was photographed using high-energy royal-blue light to differentiate autofluorescing alizarin-stained bones and scales from muscles (see Smith et al., 2018). (A) Overview to show position of branchiostegal rays. Rectangular box indicates area shown in part B. (B) Higher magnification view to show relative size of branchiostegal 1 in comparison with branchiostegals 2–6 and the position and size of the hyohyoidei abductores (numbers on photograph indicate branchiostegal rays).

FIG. 4. Frames from a in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 4. Frames from a video of Triodon macropterus, Fish 3 (320 mm SL), recorded during the night (1900–0400 hours) of 16 to 17 November 2020 at the Okinawa Churaumi Aquarium. Frames A–U show behaviors that occurred during a 1:11 minute interval that included 13 buccal cavity expansions and 11 pump-like expansions and retractions of the pelvic fan. We term this behavior pump flaring. No inflation occurred. Supplemental Video 2 (see Data Accessibility) was the basis for this figure.

FIG. 3 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 3. Kinematics of pelvic-fan flaring and inflation in two individuals of Triodon macropterus at the Okinawa Churaumi Aquarium during six handling trials. Shaded gray boxes behind the bars indicate when the fish was held in hand; at other times during the trials the fish was free swimming. Brackets show periods of ultrasound examination. Numbers and letters in circles for parts D and F link figure numbers to the kinematic analysis. (A, B) Trials 1 and 2 of Fish 1 (308 mm SL). Fish 1 flared its pelvic fan in response to being handled but did not inflate in either trial. Fish 1 had been handled during routine care during 16 months in the aquarium. (C–F) Trials 1–4 of Fish 2 (376 mm SL). Fish 2 flared its pelvic fan and inflated in all four trials in response to handling; it had been handled at the aquarium but was a relatively new resident (3 months) at the time of the trials.

FIG. 10 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 10. Photographs of digestive tract removed from Triodon macropterus, NMST P93783, 343 mm SL, anterior to left. (A) Digestive tract from esophagus to pseudocloaca showing the rectangular-shaped stomach with the bile duct entering the body of the stomach. The thin-walled pyloric region of the stomach is where most of the inflation occurs. (B) Lining of anterior region of digestive tract. (C) Lining of posterior half of the digestive tract.

FIG. 9 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 9. Dissection of Triodon macropterus, NSMT P0110597, 360 mm SL. Black dashed lines indicate cut edges. (A) Skin of the pelvic fan and abdomen removed to show muscles of the pelvic fan. (B) Dissection to show the viscera and extent of the ventral abdominal recess (white dashed line). Postcleithral bones removed to view abdominal cavity. The abdominal cavity has small ventral peritoneal folds. The stomach in this specimen everted into the buccal cavity because of barotrauma. It tore away from its connection with the intestine at the pyloric region; the rest of the intestinal tract, including Tyler's pouch, is in place as in life.

FIG. 6 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 6. Ultrasound recording of Triodon macropterus, Fish 2 (376 mm SL), at the Okinawa Churaumi Aquarium. The kinematic record of this trial is shown in Figure 3D. The circumference of the stomach is outlined with a yellow line. Black areas within the stomach are water; white spots are air bubbles. (A) Ultrasound image showing the circumference (13.0 cm) of the stomach and the area of one slice of the stomach (10.8 cm2) 30 seconds into the trial. (B) Ultrasound image showing increase in the circumference (15.5 cm) and the slice area of the stomach (17.3 cm2) 2:30 minutes after the image shown in Figure 6A.

FIG. 2 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 2. Photographs of Triodon macropterus showing pelvic-fan flaring and inflation. (A) Individual (collected 8 February 2007), 300 mm TL, in display tank at the Okinawa Churaumi Aquarium showing pelvic fan fully retracted and no inflation. Photograph by Atsushi Kaneko; modified from Matsuura et al. (2017). Photograph reprinted with permission from the Ichthyological Society of Japan. (B) Specimen with pelvic fan flared, abdomen uninflated, LBRC-F 00805, 324.5 mm SL, sex unknown. Caught by hook and line in the Maluku Sea, Indonesia, and purchased at a fish market, 11 July 2009. Photograph by Teguh Peristiwady; modified from Wibowo et al. (2020: fig. 2a). Photograph reprinted with permission from the Jurnal Iktiologi Indonesia (see Supplemental Figure 1D, Supplemental Table 1; see Data Accessibility). (C) Individual photographed shortly after capture with pelvic fan flared and abdomen inflated. The fish was destructively sampled for parasites (see Beveridge et al., 2014; Bray and Justine, 2014), 361 mm FL, female. Caught by hook and line off Récif Toombo, Nouméa, New Caledonia (22834.5650S, 166827.6360E), 2 July 2009. Collected and photographed by Jean-Lou Justine (see Supplemental Fig. 1H, Supplemental Table 1; see Data Accessibility).

FIG. 5. Frames from a in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 5. Frames from a video of Triodon macropterus, Fish 2 (376 mm SL), inflating underwater during handling for Trial 4 at the Okinawa Churaumi Aquarium. The kinematic record of this trial is shown in Figure 3F. During this 2:59 minute sequence, the fish buccal pumped water into the stomach for inflation. As the abdomen expanded, the position of the ocellus changed (white arrows; changes in the position of the ocellus are primarily the result of inflation and not further pelvicfan flaring). (A) At 27 seconds into the trial, Fish 2 showed no external signs of inflation. (B) At 49 seconds, external signs of inflation became visible. (C) At 01:19 minutes into being held, the fish was moderately inflated because water had been buccal pumped for inflation into the

FIG. 1 in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 1. Illustration from Breder and Clark (1947: fig. 3) showing their terminology for the viscera of Triodon macropterus (SU 13747, 391 mm SL). Gray shading indicates their interpretation of the extent of the abdominal cavity into the pelvic fan. In this paper, we revise their interpretations of anatomical structures and show that, contrary to their interpretation, T. macropterus can inflate.

FIG. 8. X in Pelvic-Fan Flaring and Inflation in the Three-Tooth Puffer, Triodon macropterus (Tetraodontiformes: Triodontidae), with Additional Observations on Their Behavior in Captivity

FIG. 8. X-rays of two specimens of Triodon macropterus showing differences in pelvic bone position related to extent of pelvic-fan flaring. The anterior tip of the long cleithrum extends to the lower-jaw joint. White stars indicate center of rotation of the pelvic bone at its connection with the cleithrum. (A) USNM 451516, 358 mm SL. Fan partially flared to ~258. Long ribs are numbered 2–7. (B) NSMT P0110597, 360 mm SL. Fan partially flared to ~458. White arrows indicate lines of actions of the muscles that flare and retract the pelvic fan. Patches of skin and scales were removed from this specimen for another study (see Matsuura et al., 2017).