| 1. |
- Árnason, Úlfur, et al.
(författare)
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The reversal of human phylogeny : Homo left Africa as erectus, came back as sapiens sapiens
- 2020
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Ingår i: Hereditas. - : Springer Science and Business Media LLC. - 0018-0661 .- 1601-5223. ; 157:1
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Forskningsöversikt (refereegranskat)abstract
- Background: The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25–30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo. The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades. Results: The direction of evolution in the phylogenetic tree of modern humans (Homo sapiens sapiens, Hss) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor ≈ 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans) ≈ 800,000 YBP, an mtDNA introgression from Hss into Hsnn* ≈ 500,000 YBP and an Eurasian divergence among the ancestors of extant Hss ≈ 250,000 YBP at the exodus of Mbuti/San into Africa. Conclusions: The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.
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| 2. |
- Arnason, Ulfur
(författare)
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50 years after - examination of some circumstances around the establishment of the correct chromosome number of man
- 2006
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Ingår i: Hereditas. - : Springer Science and Business Media LLC. - 1601-5223 .- 0018-0661. ; 143:1, s. 202-211
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Tidskriftsartikel (refereegranskat)abstract
- Three authors, Levan (1975, 1978), Tjio (1978) and Hulten (2002)have independently described the establishment of the correct chromosome number of man Tjio and Levan 1956 and the background to that study. However, the three authors provide strikingly different accounts of this historical discovery. In this study I have examined the consistency between these accounts and details provided by the logbook kept at Cancer Chromosome Laboratory, University of Lund. For complementary details I have also consulted several persons that were active at the Institute of Genetics, Univ. of Lund, at the time of the discovery. Levan's (1975)Levan's (1978)accounts are both written in a modest way compared to the more self-centered narratives of Tjio and Hulten. His accounts are also consistent with all details that can be collected from the logbook. However, and most unfortunately, Levan is not explicit with respect to the dates of what might be different cytogenetic observations related to the determination of the correct chromosome number of man. The logbook leaves no room for various temporal details given by Tjio, which, if correct, might substantiate his account. Also Tjio's introduction of an alter ego into the narrative is apt to lessen the general credibility of his account. Tjio's (1978)contention of having made his human chromosome preparations at 2 a.m. on December 22nd or 23rd would be consistent with his claim that he arrived from Spain in early December 1955. His account of this crucial issue is incorrect, however, as he did not arrive at the Cancer Chromosome Laboratory until December 19. Hulten's claim of involvement becomes highly questionable in the light of her fading recollections of both the localities at the Institute of Genetics and the persons working there. Her temporal account, like that of Tjio, remains unsupported by the logbook. Examination of the logbook for temporal details relating to the establishment of the correct chromosome number of man suggests that Levan made his first preliminary 2n=46 human chromosome counts around December 20th - 23rd, 1955, and that Tjio made his first conclusive preparations two-three weeks after his arrival from Spain, that is in early January 1956.
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| 3. |
- Árnason, Úlfur
(författare)
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The out of Africa hypothesis and the ancestry of recent humans : Cherchez la femme (et l'homme)
- 2016
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Ingår i: Gene. - : Elsevier BV. - 1879-0038 .- 0378-1119. ; 585:1, s. 9-12
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Tidskriftsartikel (refereegranskat)abstract
- The out of Africa hypothesis (OOAH) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. However, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. The palaeontological progress relates to early Homo finds in the Caucasus, Denisova finds in the Altai Mountains and Neanderthal finds in a wide range of localities from the Altai Mountains, the Caucasus, the Levant, Asia Minor, southern and Central Europe and the Iberian Peninsula. The Eurasian location of these finds and recognition of the principle of Last common ancestor lend no support to OOAH. The same conclusion is drawn from genomic findings, which (a) have revealed the presence of Denisovan and Neanderthal nuclear DNA, primarily in the genomes of recent Eurasians and (b) have shown genomic introgression from early modern humans into Neanderthals in the Altai Mountains. Similarly, archaeological finds in Sulawesi and the discovery of ≈100,000years old human teeth in southern China constitute strong independent challenges to OOAH. The genomic and palaeogenomic results and the new palaeontological and archaeological discoveries suggest (a) that the ancestors of modern humans had their origin in a Eurasian (largely Asian) biogeographic region which may also have extended into NE Africa, and (b) that the founders of basal African lineages became separated, geographically and genetically, in the westernmost part of this region and spread from there to different parts of the African continent.
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| 4. |
- Douglas, Desiree, et al.
(författare)
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Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia).
- 2009
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 52, s. 784-796
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Tidskriftsartikel (refereegranskat)abstract
- Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The application of different treatments to the data showed that the removal of the fastest evolving sites in snakes improved phylogenetic signal in the dataset. Basal divergences remained, nevertheless, poorly resolved. The proportion of both fast-evolving and conserved sites in the squamate mt genomes relative to sites with intermediate rates of evolution suggests rapid early divergences among squamate taxa and at least partly explains the short internal relative to external branches in the squamate tree. Thus, mt and nuclear trees may never reach full agreement because of the short branches characterizing these divergences.
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| 5. |
- Krettek, Alexandra, 1968-, et al.
(författare)
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Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla
- 1995
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Ingår i: Journal of Molecular Evolution. - : Springer. - 0022-2844 .- 1432-1432. ; 41:6, s. 952-957
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Tidskriftsartikel (refereegranskat)abstract
- The sequence of the mitochondrial DNA (mtDNA) molecule of the European hedgehog (Erinaceus europaeus) was determined. The length of the sequence presented is 17,442 nucleotides (nt). The molecule is thus the largest eutherian mtDNA molecule so far reported. The organization of the molecule conforms with that of other eutherians, but the control region of the molecule is exceptionally long, 1,988 nt, due to the presence of repeated motifs at two different positions in the 3' part of the control region. The length of the control region is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif TACGCA in one of the repetitive regions. The sequence presented includes 46 repeats of this type. The other repeated region is composed of different AT-rich repeats. This region was identical among four clones studied. Comparison of mitochondrial peptide-coding genes identified a separate position of the hedgehog among several mammalian orders. The concatenated protein sequence of the 13 peptide-coding genes was used in a phylogenetic study using the opossum as outgroup. The position of the hedgehog sequence was basal among the other eutherian sequences included: human, rat, mouse, cow, blue whale, harbor seal, and horse. The analysis did not resolve the relationship among carnivores, perissodactyls, and artiodactyls/cetaceans, suggesting a closer relationship among these orders than acknowledged by classical approaches.
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| 6. |
- Madsen, O, et al.
(författare)
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Molecular evolution of the mammalian alpha 2B adrenergic receptor
- 2002
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Ingår i: Molecular biology and evolution. - 0737-4038. ; 19:12, s. 2150-2160
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Tidskriftsartikel (refereegranskat)abstract
- The alpha 2B adrenergic receptor (A2AB) is a heptahelical G protein-coupled receptor for catecholamines. We compared the almost complete coding region (about 1,175 bp) of the A2AB gene from 48 mammalian species, including eight newly determined sequences, representing all the 18 eutherian and two marsupial orders. Comparison of the encoded proteins reveals that residues thought to be involved in agonist binding are highly conserved, as are the regions playing a role in G protein-coupling. The three extracellular loops are generally more variable than the transmembrane domains and two of the intracellular loops, indicating a lower functional constraint. However, the greatest variation is observed in the very long, third intracellular loop, where only a few residues and a polyglutamyl tract are preserved. Although this polyglutamyl domain displays a great variation in length, its presence in all described A2ABs confirms its proposed role in agonist-dependent phosphorylation of the third intracellular loop. Phylogenetic analyses of the A2AB data set, including Bayesian methods, recognized the superordinal clades Afrotheria, Laurasiatheria, and Euarchontoglires, in agreement with recent molecular evidence, albeit with lower support. Within Afrotheria, A2AB strongly supports the paenungulate clade and the association of the continental African otter shrew with Malagasy tenrecs. Among Laurasiatheria, A2AB confirms the nesting of whales within the artiodactyls, as a sister group to hippopotamus. Within the Euarchontoglires, there is constant support for rodent monophyly.
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| 7. |
- Moum, T, et al.
(författare)
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Mitochondrial DNA sequence evolution and phylogeny of the Atlantic Alcidae, including the extinct great auk (Pinguinus impennis)
- 2002
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Ingår i: Molecular biology and evolution. - 0737-4038. ; 19:9, s. 1434-1439
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Tidskriftsartikel (refereegranskat)abstract
- The Atlantic auk assemblage includes four extant species, razorbill (Alca torda), dovekie (Alle alle), common murre (Uria aalge), and thick-billed murre (U. lomvia), and one recently extinct species, the flightless great auk (Pinguinus impennis). To determine the phylogenetic relationships among the species, a contiguous 4.2-kb region of the mitochondrial genome from the extant species was amplified using PCR. This region included one ribosomal RNA gene, four transfer RNA genes, two protein-coding genes, the control region, and intergenic spacers. Sets of PCR primers for amplifying the same region from great auk were designed from sequences of the extant species. The authenticity of the great auk sequence was ascertained by alternative amplifications, cloning, and separate analyses in an independent laboratory. Phylogenetic analyses of the entire assemblage, made possible by the great auk sequence, fully resolved the phylogenetic relationships and split it into two primary lineages, Uria versus Alle, Alca, and Pinguinus. A sister group relationship was identified between Alca and Pinguinus to the exclusion of Alle. Phylogenetically, the flightless great auk originated late relative to other divergences within the assemblage. This suggests that three highly divergent species in terms of adaptive specializations, Alca, Alle, and Pinguinus, evolved from a single lineage in the Atlantic Ocean, in a process similar to the initial adaptive radiation of alcids in the Pacific Ocean.
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| 8. |
- Slack, Kerryn, et al.
(författare)
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Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution
- 2006
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 23:6, s. 1144-1155
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Tidskriftsartikel (refereegranskat)abstract
- Testing models of macroevolution, and especially the sufficiency of microevolutionary processes, requires good collaboration between molecular biologists and paleontologists. We report such a test for events around the Late Cretaceous by describing the earliest penguin fossils, analyzing complete mitochondrial genomes from an albatross, a petrel, and a loon, and describe the gradual decline of pterosaurs at the same time modern birds radiate. The penguin fossils comprise four naturally associated skeletons from the New Zealand Waipara Greensand, a Paleocene (early Tertiary) formation just above a well-known Cretaceous/Tertiary boundary site. The fossils, in a new genus (Waimanu), provide a lower estimate of 61-62 Ma for the divergence between penguins and other birds and thus establish a reliable calibration point for avian evolution. Combining fossil calibration points, DNA sequences, maximum likelihood, and Bayesian analysis, the penguin calibrations imply a radiation of modern (crown group) birds in the Late Cretaceous. This includes a conservative estimate that modern sea and shorebird lineages diverged at least by the Late Cretaceous about 74 +/- 3 Ma (Campanian). It is clear that modern birds from at least the latest Cretaceous lived at the same time as archaic birds including Hesperornis, Ichthyornis, and the diverse Enantiornithiformes. Pterosaurs, which also coexisted with early crown birds, show notable changes through the Late Cretaceous. There was a decrease in taxonomic diversity, and small- to medium-sized species disappeared well before the end of the Cretaceous. A simple reading of the fossil record might suggest competitive interactions with birds, but much more needs to be understood about pterosaur life histories. Additional fossils and molecular data are still required to help understand the role of biotic interactions in the evolution of Late Cretaceous birds and thus to test that the mechanisms of microevolution are sufficient to explain macroevolution.
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| 9. |
- Slack, Kerryn, et al.
(författare)
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Resolving the root of the avian mitogenomic tree by breaking up long branches
- 2007
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1095-9513 .- 1055-7903. ; 42:1, s. 1-13
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Tidskriftsartikel (refereegranskat)abstract
- Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes. Breaking these long branches leaves the root, as inferred by maximum likelihood and Bayesian phylogenetic analyses, between paleognaths and neognaths. This means that morphological, nuclear, and mitochondrial data are now in agreement on the position of the root of the avian tree and we can, move on to other questions. An overview is then given of the deepest divisions in the mitogenomic tree inferred from complete mitochondrial genomes. The strict monophyly of both the galloanseres and the passerines is strongly supported, leaving the deep six-way split within Neoaves as the next major question for which resolution is still lacking. Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution. (c) 2006 Elsevier Inc. All rights reserved.
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| 10. |
- Xu, Xiufeng, et al.
(författare)
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The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs
- 1996
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Ingår i: Journal of Molecular Evolution. - 0022-2844. ; 43:5, s. 438-446
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Tidskriftsartikel (refereegranskat)abstract
- The nucleotide sequence of the complete mitochondrial genome of the donkey, Equus asinus, was determined. The length of the molecule is 16,670 bp. The length, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of two types of repetitive motifs in the control region. The sequence of the repeats is (a) 5'-CACACCCA and (b) 5'-TGCGCGCA, respectively. The order of (a) and (b) can be expressed as {n[2(a)+(b)]+m(a)}. In 32 different clones analyzed the number of n and m ranged from 0 to 9 and 1 to 7. The two rRNA genes, the 13 peptide-coding genes, and the 22 tRNA genes of the donkey and the horse, Equus caballus, were compared in detail. Total nucleotide difference outside the control region was 6.9%. Nucleotide difference between peptide-coding genes ranged from 6.4% to 9.4% with a mean of 8.0%. In the inferred protein sequences of the 13 peptide-coding genes the amino acid difference was 0.2-8.8%, and the mean for the 13 concatenated amino acid sequences was 1.9%. In the 22 tRNA genes, the mean difference was 3.5%, and that in the two rRNA genes was 4.1%. The mtDNA differences between the donkey and the horse suggest that the evolutionary separation of the two species occurred approximate to 9 million years ago. Analyses of differences among the mtDNAs of three other species-pairs, harbor seal/grey seal, fin whale/blue whale, and Homo/common chimpanzee, showed that the relative evolutionary rate of individual peptide-coding genes varies among different species-pairs and modes of comparison. The findings show that the superimposition of sequence data of one lineage for resolving and dating evolutionary divergences of other lineages should be performed with caution unless based on comprehensive data.
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