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Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
<p>The known biodiversity of Asia and Australasia is continuously expanding with more focused studies on systematics of various groups and the respective biogeography. Historically, fluctuating sea-levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly-studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae, and that, alternatively, geological shifts in mainland Southeast Asia may be a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling in knowledge gaps in poorly known, but highly diverse and conceptually important groups, constituting a non-traditional model study system for understanding transitions between terrestrial, marine, and freshwater environments.</p>
FIGURE 11. Fossil larva BUB 4436, specimen 9. A. Overview dorsal side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 11. Fossil larva BUB 4436, specimen 9. A. Overview dorsal side. B. Colour-marked version of A. C. Ventral side. D. Close-up trunk end. E. Close-up on head. F. Close-up on thorax. Abbreviations: ad = abdomen; at = antenna; fe = femur; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax.
FIGURE 10. Fossil larva BUB 4436, specimen 8. A. Overview ventral side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 10. Fossil larva BUB 4436, specimen 8. A. Overview ventral side. B. Colour-marked version of C. C. Dorsal side. D. Close-up on head. E. Close-up trunk end. F. Close-up on leg. G. Close-up on tergites. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax.
FIGURE 12. Fossil larvae BUB 4436, specimens 10 and 11. A–F. Specimen 10. A. Overview dorsal side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 12. Fossil larvae BUB 4436, specimens 10 and 11. A–F. Specimen 10. A. Overview dorsal side. B. Colourmarked version of A. C. Ventral side. D. Close-up on head. E. Close-up trunk end. F. Close-up on leg. G–K. Specimen 11. G. Overview ventral side. H. Colour-marked version of G. I. Dorsal side. J. Close-up on head. K. Close-up on trunk end. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax; th = thorax; ti = tibia.
FIGURE 5. Fossil larva BUB 4436, specimen 2. A in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 5. Fossil larva BUB 4436, specimen 2. A. Overview on lateral side. B. Colour-marked version of A. C. Other side. D. Close-up on trunk end. E. Close-up on thorax. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax.
FIGURE 6. Fossil larva BUB 4436, specimen 3. A. Overview dorsal side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 6. Fossil larva BUB 4436, specimen 3. A. Overview dorsal side. B. Colour-marked version of B. C. Ventral side. D. Close-up on anterior region in ventral view. E. Close-up on head. F. Close-up on very terminal end. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax; te = trunk end.
FIGURE 8. Fossil larva BUB 4436, specimen 5. A. Overview ventral side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 8. Fossil larva BUB 4436, specimen 5. A. Overview ventral side. B. Colour-marked version of B. C. Dorsal side. D. Close-up on head. E. Close-up on leg. F. Terminal end in different contrasting to highlight setae. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; th = thorax.
FIGURE 7. Fossil larva BUB 4436, specimen 4. A. Overview dorsal side. B in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 7. Fossil larva BUB 4436, specimen 4. A. Overview dorsal side. B. Colour-marked version of B. C. Ventral side. D. Close-up on trunk end. E. Close-up on head. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; pt = prothorax; te = trunk end.
FIGURE 4. Fossil larvae BUB 4436, specimens 1 and 6. A–D. Specimen 1. A in An overview of crawling water beetle larvae and a first possible record from 100-million-years-old Myanmar amber
FIGURE 4. Fossil larvae BUB 4436, specimens 1 and 6. A–D. Specimen 1. A. View on one side. B. Colour-marked version of A. C. View on other side. D. Very terminal end, with different contrasting to highlight the setae. E–G. Specimen 6. E. Overview. F. Colour-marked version of E. G. Close-up on very terminal end. Abbreviations: ad = abdomen; at = antenna; hc = head capsule; ms = mesothorax; mt = metathorax; pt = prothorax; te = trunk end.
Fig. 2 – Specimen SNHMB.G 8109, Kachin amber. A – Ventral view. B in A modern type of ant-like stone beetle larva preserved in 99-million-year-old Kachin amber (Coleoptera: Staphylinidae, Scydmaeninae)
Fig. 2 – Specimen SNHMB.G 8109, Kachin amber. A – Ventral view. B – Detail of head, ventral. C – Colour-marked version of B. D – Detail of trunk appendage. Abbreviations: cl = claw; cx = coxa; de = distal visible element of maxillary palp; fe = femur; gl = possible galea; li = labium; lr = labrum; md = mandible; pe = proximal visible element of maxillary palp; pm = proximal region of maxilla (stipes?); ti = tibio-tarsus; tr = trochanter.
Fig. 6 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 6. Vertebrae of new specimen (MPM-PV 17410) of Palaehoplophorus meridionalis Ameghino, 1904 from Meseta de Guenguel, Patagonia, Río Mayo Formation, Serravallian–Tortonian, middle–late Miocene. A. Atlas in anterior (A1), posterior (A2), and latero-external (A3) views. B. Caudal vertebra in anterior view.
Fig. 5 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 5. Osteoderms of new specimen (MPM-PV 17410) of Palaehoplophorus meridionalis Ameghino, 1904 from Meseta de Guenguel, Patagonia, Río Mayo Formation, Serravallian–Tortonian, middle–late Miocene. Anterior region: fixed (A), semi-movable (B), movable (C). Middle region: fixed (D, E), lateral margin (F). Posterior region: fixed (G, H), posterior margin (I). Caudal rings: movable (J), fixed (K). Indeterminated region: semi-movable (L). Osteoderms in lateral view (C2, L2).
Fig. 2 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 2. Stratigraphic profile of the fossil locality (photograph by LRGR, 2015). Abbreviations: c, coarse; f, fine; m, medium; vc, very coarse; vf, very fine.
Fig. 1 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 1. Map of South Argentina showing location of the studied area (A) and the fossil locality mentioned in the text (B), tablelands marked in light gray.
Fig. 7 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 7. Skeleton of new specimen (MPM-PV 17410) of Palaehoplophorus meridionalis Ameghino, 1904 from Meseta de Guenguel, Patagonia, Río Mayo Formation, Serravallian–Tortonian, middle-late Miocene. A. Ulna in anterior (A1), latero-external (A2), and distal (A3) views; B. Cuboid in latero-internal (B1), antero-ventral (B2), and dorso-lateral (B3) views. C. Ectocuneiform in proximal (C1), distal (C2), latero-internal (C3), and latero-external (C4) views. D. Ungual phalanx in dorsal (D1) and ventral (D2) views.
Fig. 3 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 3. Osteoderms of old specimens (MACN A 11137, syntype) of glyptodont Palaehoplophorus meridionalis Ameghino, 1904 from Río Fénix and Lago Blanco, Patagonia, Serravallian–Tortonian, middle–late Miocene. Osteoderms from posterior region (A–N) and caudal ring (O). Abbreviations: apf, accessory periferal figure; cf, central figure; f, foramina; s, sulci; pf, periferal figure.
Fig. 4 in Old and new specimens of a poorly known glyptodont from the Miocene of Patagonia and their biochronological implications
Fig. 4. Caudal tubes of old specimens, syntype and assigned specimens of Palaehoplophorus meridionalis Ameghino, 1904 from Río Fénix, Lago Blanco, and "Rionegrense", Patagonia, Serravallian–Tortonian, middlelate Miocene. A. MACN A 11737, syntype, in lateral (A1), distal (A2), dorsal (A3), and ventral (A4) views. B. MACN A 11132, in distal (B1), lateral B2), dorsal (B3), and ventral (B4) views.
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone. in Mortality Profiles Of Castor And Trogontherium (Mammalia: Rodentia, Castoridae), With Notes On The Site Formation Of The Mid-Pleistocene Hominin Locality Bilzingsleben Ii (Thuringia, Central Germany)
Text-fig. 3 Ternary diagram of the relative abundance (in %) of juvenile, prime adult, and old adult specimens in samples of Castor fiber (data from Table 3). The red dots indicate the Pleistocene samples of Bilzingsleben II (B), Weimar- Ehringsdorf (E), and Weimar-Taubach (T), the black dot represents an extant population from Telemark in Norway (data from Campbell 2009). Abbreviations of zones (after Discamps and Costamagno 2015): JOP – Juveniles-Old-Prime dominated zone, JPO – Juveniles-Prime-Old dominated zone, O – Old dominated zone, P – Prime dominated zone. The diagram shows the position of all three fossil samples in the prime dominated zone.
Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
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Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen
The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades, the group has been considered to consist of two species. Here, we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum and B. vulcanix. We describe three species (B. geopearlis, B. oromaia and B. vulcanix) as new and resurrect four previously synonymized names (B. ampliatum, B. lividulum, B. saturatum and B. testatum). Species diversity is highest throughout the Cascades in Oregon and Washington, and Sierra Nevada of California, where up to seven species can occur in sympatry. We resolved challenging nomenclatural issues through analysis of sequences obtained from century-old type specimens by using a novel application of rDNA copy number analysis – an approach that may prove useful for other historical specimens.
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