| 1. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 2. |
- Hartstone-Rose, Adam, et al.
(författare)
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A new species of fox from the Australopithecus sediba type locality, Malapa, South Africa
- 2013
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Ingår i: Transactions of the Royal Society of South Africa. - 0035-919X .- 2154-0098. ; 68, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- The 1.977 Ma site of ‘Malapa’ (Gauteng, South Africa) has yielded important new fossils, including the type specimens of the new hominin species Australopithecus sediba. Recently, we reported the first Carnivora specimens to have been recovered from the site. That sample included members of Felidae, Herpestidae and Hyaenidae. That first report also included three associated small canid specimens (an M2, a rib and a posterior mandibular fragment including the P4, M1, coronoid, condylar and angular processes) that we attributed to Vulpes cf. V. chama. In this paper, we compare these specimens to a broad sample of modern and fossil foxes and conclude that these specimens are distinct enough to be referred to a new species, here described and named Vulpes skinneri.
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| 3. |
- Hartstone-Rose, Adam, et al.
(författare)
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The Plio-Pleistocene ancestor of wild dogs, Lycaon sekowei n. sp.
- 2010
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Ingår i: Journal of Paleontology. - 0022-3360 .- 1937-2337. ; 84, s. 299-308
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Tidskriftsartikel (refereegranskat)abstract
- African wild dogs (Lycaon pictus) occupy an ecological niche characterized by hypercarnivory and cursorial hunting. Previous interpretations drawn from a limited, mostly Eurasian fossil record suggest that the evolutionary shift to cursorial hunting preceded the emergence of hypercarnivory in the Lycaon lineage. Here we describe 1.9–1.0 ma fossils from two South African sites representing a putative ancestor of the wild dog. The holotype is a nearly complete maxilla from Coopers Cave, and another specimen tentatively assigned to the new taxon, from Gladysvale, is the most nearly complete mammalian skeleton ever described from the Sterkfontein Valley, Gauteng, South Africa. The canid represented by these fossils is larger and more robust than are any of the other fossil or extant sub-Saharan canids. Unlike other purported L. pictus ancestors, it has distinct accessory cusps on its premolars and anterior accessory cuspids on its lower premolars–a trait unique to Lycaon among living canids. However, another hallmark autapomorphy of L. pictus, the tetradactyl manus, is not found in the new species; the Gladysvale skeleton includes a large first metacarpal. Thus, the anatomy of this new early member of the Lycaon branch suggests that, contrary to previous hypotheses, dietary specialization appears to have preceded cursorial hunting in the evolution of the Lycaon lineage. We assign these specimens to the taxon Lycaon sekowei n. sp.
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| 4. |
- Kuhn, Brian F., et al.
(författare)
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Carnivoran remains from the Malapa hominin site, South Africa
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:11, s. e26940-
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Tidskriftsartikel (refereegranskat)abstract
- Recent discoveries at the new hominin-bearing deposits of Malapa, South Africa, have yielded a rich faunal assemblage associated with the newly described hominin taxon Australopithecus sediba. Dating of this deposit using U-Pb and palaeomagnetic methods has provided an age of 1.977 Ma, being one of the most accurately dated, time constrained deposits in the Plio-Pleistocene of southern Africa. To date, 81 carnivoran specimens have been identified at this site including members of the families Canidae, Viverridae, Herpestidae, Hyaenidae and Felidae. Of note is the presence of the extinct taxon Dinofelis cf. D. barlowi that may represent the last appearance date for this species. Extant large carnivores are represented by specimens of leopard (Panthera pardus) and brown hyaena (Parahyaena brunnea). Smaller carnivores are also represented, and include the genera Atilax and Genetta, as well as Vulpes cf. V. chama. Malapa may also represent the first appearance date for Felis nigripes (Black-footed cat). The geochronological age of Malapa and the associated hominin taxa and carnivoran remains provide a window of research into mammalian evolution during a relatively unknown period in South Africa and elsewhere. In particular, the fauna represented at Malapa has the potential to elucidate aspects of the evolution of Dinofelis and may help resolve competing hypotheses about faunal exchange between East and Southern Africa during the late Pliocene or early Pleistocene.
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| 5. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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