Evans BJ et al. (2015), Genetics, Morphology, Advertisement Calls, and ...

XB-ART-51652

PLoS One 2015 Dec 16;1012:e0142823. doi: 10.1371/journal.pone.0142823.

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Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from West and Central Africa.

Evans BJ , Carter TF , Greenbaum E , Gvoždík V , Kelley DB , McLaughlin PJ , Pauwels OS , Portik DM , Stanley EL , Tinsley RC , Tobias ML , Blackburn DC .

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African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness of these new species. We resurrect Xenopus calcaratus from synonymy of Xenopus tropicalis and refer populations from Bioko Island and coastal Cameroon (near Mt. Cameroon) to this species. To facilitate comparisons to the new species, we also provide comments on the type specimens, morphology, and distributions of X. epitropicalis, X. tropicalis, and X. fraseri. This includes significantly restricted application of the names X. fraseri and X. epitropicalis, the first of which we argue is known definitively only from type specimens and possibly one other specimen. Inferring the evolutionary histories of these new species allows refinement of species groups within Xenopus and leads to our recognition of two subgenera (Xenopus and Silurana) and three species groups within the subgenus Xenopus (amieti, laevis, and muelleri species groups).

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Species referenced: Xenopus tropicalis
Genes referenced: ids psmd6 rag1 rag2 tbx2

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	Fig 1. Mitochondrial DNA chronogram using calibration from [34]. New and resurrected species detailed here are indicated in red, possible additional new species are indicated with blue, and species with paraphyletic mtDNA are indicated with gray. Dots subtending nodes indicate posterior probabilities as indicated by the key with some values over terminal clades omitted for clarity. The scale is in units of millions of years.
	Fig 2. RAG1/ RAG2 chronogram using calibration from [34]. Labeling follows Fig 1 with the addition that tetraploid homeologs are indicated with α and β and, for octoploid and dodecaploids, each of these homeologs classes is further divided into two or three categories indicated by numbers. Homeologs of new and resurrected species are in red. Letters in circles indicate homeologous lineages inferred to be descended from six tetraploid ancestral species A–F. Data are lacking from X. petersii, X. poweri, and X. victorianus, which form a clade with X. laevis, and from X. fraseri.
	Fig 3. Summary phylogeny. A summary phylogeny inferred by comparing the mitochondrial and autosomal gene trees depicted in Figs 1 and 2. New and resurrected species described here are in red. S, A, L, and M refer to subgenus Silurana, and the amieti, laevis, and muelleri species groups within subgenus Xenopus respectively. Dotted lines indicate paternal ancestral lineages. Circles over internal nodes indicate allopolyploidization events; shapes on branch tips indicate ploidy of extant species; colored next to these shapes circles indicate call type inferred from this study and Tobias et al. [42]. Letters over red dots refer to ancestors whose homeologous lineages are labled in Fig 2. Daggers indicate lost ancestors, including up to three diploid species (assuming allotetraploidization in subgenus Xenopus) and at least three tetraploid ancestors (A, B, and C).
	“Fig. 4. External morphology of subgenera Silurana and Xenopus. Comparison of external morphology of subgenera Xenopus (left, specimen of X. victorianus CAS 250836 [DCB-202]) and Silurana (right, X. mellotropicalis NCSM 78871) including in Silurana rougher skin, relatively smaller eyes, relatively shorter subocular tentacle (in comparison to sympatric Xenopus species), and relatively less of eye covered by lower eyelid (top), relatively shorter feet (middle), and ventrally fused cloacal lobes, claw on prehallux, and lack of skin ridge on first pedal digit from the prehallux (bottom).” (corrected)
	Fig 5. Internal morphology of subgenera Silurana and Xenopus. Comparison of osteology of subgenera Xenopus (left, holotype specimen of Xenopus amieti, MHNG 2030.80 and Silurana (right, X. calcaratus, CAS 207759). Differences include (a) paired nasal bones in subgenus Silurana but not subgenus Xenopus, (b) absence of the vomer bones in the palate of subgenus Silurana but not subgenus Xenopus and (c) fusion of the first two presacral vertebrae in subgenus Silurana but not subgenus Xenopus.
	Fig 6. Pictures of holotypes. Pictures of type specimens of resurrected and new species including X. calcaratus ZMB 8255A (lectotype), X. mellotropicalis NCSM 76797 (holotype), X. allofraseri CAS 207765 (holotype), X. eysoole MCZ A-138016 (holotype), X. kobeli MCZ A-148037 (holotype), X. parafraseri MCZ A-148034 (holotype), and X. fischbergi CAS 255060 (holotype). Scale bar is 5 mm. This is a truncated version of Fig 6 and is meant for preview purposes. Please refer to S3–S5 Figs in the Supporting information for the full size version.
	Fig 7. Pictures in life. Pictures of resurrected and new species in life. This is a truncated version of Fig 7 and is meant for preview purposes. Please refer to S6–S8 Figs in the Supporting information for the full size version.
	Fig 8. The male vocalizations of resurrected and new species. Axes are labeled only in panel A. For some of the recorded individuals, specimen IDs are available including X. kobeli (field ID: BJE 3073), X. allofraseri (MCZ A-148176), X. parafraseri (CAS 249961), X. eysoole (MCZ A-148129 or MCZ A-148130), and X. calcaratus (field ID: VG09-368 or VG09-369).
	Fig 9. Karyotypes of new and resurrected species. (A) X. calcaratus, NMP6V 74746 (VG05-S; female) from Cameroon, (B) X. mellotropicalis, CAS 255058 (BJE 3652) from Republic of Congo, (C) X. fischbergi non-vouchered sample (BJE 3873), (D) X. parafraseri, CAS 249961 (BJE 3060) from Cameroon, (E) X. allofraseri, MCZ A-148162 (BJE 3486) from Bioko Island, Equatorial Guinea, (F) X. kobeli, MCZ A-148038 (BJE 3076) from Cameroon, (G) X. eysoole, MCZ A-148097 (BJE 3220), from Cameroon.
	Fig 10. Distributions of new species. Type localities with black dots inside symbols. For X. fischbergi white circles with slashes indicate specimens from which we have genetic data (including the holotype), unfilled circles are specimens from Tinsley et al. [1] and those other collections from which we lack genetic data, including one field sample from Uganda–indicated by a hexagon–in which the X. fischbergi-specific parasite Protopolystoma occidentalis was detected (J. A. Jackson & RCT, unpublished).
	Fig 11. MicroCT scans of skulls of two tetraploids in subgenus Silurana and two dodecaploid in subgenus Xenopus. Dorsal view is on the left and ventral view is on the right, including the lectotype specimen of Xenopus (Silurana) calcaratus (ZMB 8255A) from Cameroon and a specimen from Bioko Island (CAS 207759), holotype of X. (S.) mellotropicalis (NCSM 76797), and the holotypes of the new dodecaploid species from subgenus Xenopus: X. eysoole (MCZ A-138016) and X. kobeli (MCZ A-148037). The type specimen of X. calcaratus was preserved with its mouth ajar
	Fig 12. MicroCT scans of skulls of four tetraploids in subgenus Xenopus. Images are of a type specimen of X. fraseri (BMNH 1947.2.24.79) and holotypes of the new tetraploid species from subgenus Xenopus: X. fischbergi (CAS 255060), X. allofraseri (CAS 207765), X. parafraseri (MCZ A-148034). Each ventral view (on right for each species) and insert shows the presence of vomerine teeth (X. fraseri and X. fischbergi) or absence of vomerine teeth (X. allofraseri and X. parafraseri).
	S1 Fig. Analysis of mitochondrial DNA data using the calibration from [9]. Labeling follows Fig 1.
	S2 Fig. Analysis of mitochondrial DNA data using the calibration from [9]. Labeling follows Fig 2. doi:10.1371/journal.pone.0142823.s002
	SFig 3. Full size version of Fig 6, part one of three. doi:10.1371/journal.pone.0142823.s003
	Supp Figure S4. Full size version of Fig 6, part two of three. doi:10.1371/journal.pone.0142823.s004
	Suppl. Figure S5. Full size version of Fig 6, part three of three. doi:10.1371/journal.pone.0142823.s005
	Suppl. Figure S6. Full size version of Fig 7, part one of three. doi:10.1371/journal.pone.0142823.s006
	Suppl. Figure S7. Full size version of Fig 7, part two of three. doi:10.1371/journal.pone.0142823.s007
	Suppl. Figure S8. Full size version of Fig 7, part three of three. doi:10.1371/journal.pone.0142823.s008
	Suppl. Figure S9. Photographs of type material from several previously described Xenopus taxa part one of six. Images include, from subgenus Silurana: X. tropicalis (BMNH 1947.2.24.83) and X. epitropicalis (BMNH 1982.462), from amieti species group: X. amieti (MHNG 2030.80), X. andrei (MHNG 2088.32), X. boumbaensis (MHNG 2080.31), X. itombwensis (MCZ A-138192), X. longipes (MHNG 2497.10), X. ruwenzoriensis (MHNG 2238.15), and X. lenduensis (MCZ A-139853), from laevis species group: X. laevis sudanensis (= X. poweri; MHNG 1017.74) and X. laevis bunyoniensis (= X. victorianus; MCZ A-14616), and X. fraseri (BMNH 1947.2.24.78). Scale bar is 5 mm. doi:10.1371/journal.pone.0142823.s009
	Suppl. Figure S10. Photographs of type material from several previously described Xenopus taxa part two of six. doi:10.1371/journal.pone.0142823.s010
	Suppl. Figure S11. Photographs of type material from several previously described Xenopus taxa part three of six. doi:10.1371/journal.pone.0142823.s011
	Suppl. Figure S12. Photographs of type material from several previously described Xenopus taxa part four of six. doi:10.1371/journal.pone.0142823.s012
	Suppl. Figure S14. Photographs of type material from several previously described Xenopus taxa part six of six. doi:10.1371/journal.pone.0142823.s014
	Suppl. Figure S15. X-ray of X. eysoole holotype (MCZ A-138016). doi:10.1371/journal.pone.0142823.s015
	Fig 4. External morphology of subgenera Silurana and Xenopus.Comparison of external morphology of subgenera Xenopus (right, specimen of X. victorianus CAS 250836 [DCB-202]) and Silurana (left, X. calcaratus CAS 207759) including in Silurana rougher skin, relatively smaller eyes, relatively shorter subocular tentacle (in comparison to sympatric Xenopus species), and relatively less of eye covered by lower eyelid (top), relatively shorter feet (middle), and ventrally fused cloacal lobes, claw on prehallux, and lack of skin ridge on first pedal digit from the prehallus (bottom).

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