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Wolf M, Zapf K, Gupta DK, Hiller M, Árnason Ú, Janke A. The genome of the pygmy right whale illuminates the evolution of rorquals. BMC Biol 2023; 21:79. [PMID: 37041515 PMCID: PMC10091562 DOI: 10.1186/s12915-023-01579-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Baleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales. RESULTS Here, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance. CONCLUSIONS Our results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Konstantin Zapf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
| | - Deepak Kumar Gupta
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
| | - Michael Hiller
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-Von-Laue-Str. 9, Frankfurt Am Main, Germany
| | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Neurosurgery, Skane University Hospital in Lund, Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt Am Main, Germany
- Institute for Ecology, Evolution and Diversity, Goethe University, Max-Von-Laue-Strasse. 9, Frankfurt Am Main, Germany
- LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt Am Main, Germany
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Phylogenetic relationships in southern African Bryde’s whales inferred from mitochondrial DNA: further support for subspecies delineation between the two allopatric populations. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1105-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kulemzina AI, Proskuryakova AA, Beklemisheva VR, Lemskaya NA, Perelman PL, Graphodatsky AS. Comparative Chromosome Map and Heterochromatin Features of the Gray Whale Karyotype (Cetacea). Cytogenet Genome Res 2016; 148:25-34. [PMID: 27088853 DOI: 10.1159/000445459] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2016] [Indexed: 11/19/2022] Open
Abstract
Cetacean karyotypes possess exceptionally stable diploid numbers and highly conserved chromosomes. To date, only toothed whales (Odontoceti) have been analyzed by comparative chromosome painting. Here, we studied the karyotype of a representative of baleen whales, the gray whale (Eschrichtius robustus, Mysticeti), by Zoo-FISH with dromedary camel and human chromosome-specific probes. We confirmed a high degree of karyotype conservation and found an identical order of syntenic segments in both branches of cetaceans. Yet, whale chromosomes harbor variable heterochromatic regions constituting up to a third of the genome due to the presence of several types of repeats. To investigate the cause of this variability, several classes of repeated DNA sequences were mapped onto chromosomes of whale species from both Mysticeti and Odontoceti. We uncovered extensive intrapopulation variability in the size of heterochromatic blocks present in homologous chromosomes among 3 individuals of the gray whale by 2-step differential chromosome staining. We show that some of the heteromorphisms observed in the gray whale karyotype are due to distinct amplification of a complex of common cetacean repeat and heavy satellite repeat on homologous autosomes. Furthermore, we demonstrate localization of the telomeric repeat in the heterochromatin of both gray and pilot whale (Globicephala melas, Odontoceti). Heterochromatic blocks in the pilot whale represent a composite of telomeric and common repeats, while heavy satellite repeat is lacking in the toothed whale consistent with previous studies.
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Xiong Y, Brandley MC, Xu S, Zhou K, Yang G. Seven new dolphin mitochondrial genomes and a time-calibrated phylogeny of whales. BMC Evol Biol 2009; 9:20. [PMID: 19166626 PMCID: PMC2656474 DOI: 10.1186/1471-2148-9-20] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Accepted: 01/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The phylogeny of Cetacea (whales) is not fully resolved with substantial support. The ambiguous and conflicting results of multiple phylogenetic studies may be the result of the use of too little data, phylogenetic methods that do not adequately capture the complex nature of DNA evolution, or both. In addition, there is also evidence that the generic taxonomy of Delphinidae (dolphins) underestimates its diversity. To remedy these problems, we sequenced the complete mitochondrial genomes of seven dolphins and analyzed these data with partitioned Bayesian analyses. Moreover, we incorporate a newly-developed "relaxed" molecular clock to model heterogenous rates of evolution among cetacean lineages. RESULTS The "deep" phylogenetic relationships are well supported including the monophyly of Cetacea and Odontoceti. However, there is ambiguity in the phylogenetic affinities of two of the river dolphin clades Platanistidae (Indian River dolphins) and Lipotidae (Yangtze River dolphins). The phylogenetic analyses support a sister relationship between Delphinidae and Monodontidae + Phocoenidae. Additionally, there is statistically significant support for the paraphyly of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins). CONCLUSION Our phylogenetic analysis of complete mitochondrial genomes using recently developed models of rate autocorrelation resolved the phylogenetic relationships of the major Cetacean lineages with a high degree of confidence. Our results indicate that a rapid radiation of lineages explains the lack of support the placement of Platanistidae and Lipotidae. Moreover, our estimation of molecular divergence dates indicates that these radiations occurred in the Middle to Late Oligocene and Middle Miocene, respectively. Furthermore, by collecting and analyzing seven new mitochondrial genomes, we provide strong evidence that the delphinid genera Tursiops and Stenella are not monophyletic, and the current taxonomy masks potentially interesting patterns of morphological, physiological, behavioral, and ecological evolution.
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Affiliation(s)
- Ye Xiong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Matthew C Brandley
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
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Sasaki T, Nikaido M, Hamilton H, Goto M, Kato H, Kanda N, Pastene L, Cao Y, Fordyce R, Hasegawa M, Okada N. Mitochondrial phylogenetics and evolution of mysticete whales. Syst Biol 2005; 54:77-90. [PMID: 15805012 DOI: 10.1080/10635150590905939] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The phylogenetic relationships among baleen whales (Order: Cetacea) remain uncertain despite extensive research in cetacean molecular phylogenetics and a potential morphological sample size of over 2 million animals harvested. Questions remain regarding the number of species and the monophyly of genera, as well as higher order relationships. Here, we approach mysticete phylogeny with complete mitochondrial genome sequence analysis. We determined complete mtDNA sequences of 10 extant Mysticeti species, inferred their phylogenetic relationships, and estimated node divergence times. The mtDNA sequence analysis concurs with previous molecular studies in the ordering of the principal branches, with Balaenidae (right whales) as sister to all other mysticetes base, followed by Neobalaenidae (pygmy right whale), Eschrichtiidae (gray whale), and finally Balaenopteridae (rorquals + humpback whale). The mtDNA analysis further suggests that four lineages exist within the clade of Eschrichtiidae + Balaenopteridae, including a sister relationship between the humpback and fin whales, and a monophyletic group formed by the blue, sei, and Bryde's whales, each of which represents a newly recognized phylogenetic relationship in Mysticeti. We also estimated the divergence times of all extant mysticete species, accounting for evolutionary rate heterogeneity among lineages. When the mtDNA divergence estimates are compared with the mysticete fossil record, several lineages have molecular divergence estimates strikingly older than indicated by paleontological data. We suggest this discrepancy reflects both a large amount of ancestral polymorphism and long generation times of ancestral baleen whale populations.
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Affiliation(s)
- Takeshi Sasaki
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku Yokohama, Kanagawa 226-8501, Japan
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Arnason U, Gullberg A, Janke A. Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene 2004; 333:27-34. [PMID: 15177677 DOI: 10.1016/j.gene.2004.02.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Revised: 06/30/2003] [Accepted: 02/05/2004] [Indexed: 11/21/2022]
Abstract
The evolution of the order Cetacea (whales, dolphins, porpoises) has, for a long time, attracted the attention of evolutionary biologists. Here we examine cetacean phylogenetic relationships on the basis of analyses of complete mitochondrial genomes that represent all extant cetacean families. The results suggest that the ancestors of recent cetaceans had an explosive evolutionary radiation 30-35 million years before present. During this period, extant cetaceans divided into the two primary groups, Mysticeti (baleen whales) and Odontoceti (toothed whales). Soon after this basal split, the Odontoceti diverged into the four extant lineages, sperm whales, beaked whales, Indian river dolphins and delphinoids (iniid river dolphins, narwhals/belugas, porpoises and true dolphins). The current data set has allowed test of two recent morphological hypotheses on cetacean origin. One of these hypotheses posits that Artiodactyla and Cetacea originated from the extinct group Mesonychia, and the other that Mesonychia/Cetacea constitutes a sister group to Artiodactyla. The current results are inconsistent with both these hypotheses. The findings suggest that the claimed morphological similarities between Mesonychia and Cetacea are the result of evolutionary convergence rather than common ancestry.
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Affiliation(s)
- Ulfur Arnason
- Division of Evolutionary Molecular Systematics, Department of Cell and Organism Biology, University of Lund, S-223 62 Lund, Sweden.
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Crovella S, Montagnon D, Rumpler Y. Highly repeated DNA sequences and systematics of malagasy primates. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf02437512] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Plohl M, Ugarković D. Characterization of two abundant satellite DNAs from the mealworm Tenebrio obscurus. J Mol Evol 1994; 39:489-95. [PMID: 7807538 DOI: 10.1007/bf00173418] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.
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Affiliation(s)
- M Plohl
- Department of Molecular Genetics, Ruder Bosković Institute, Zagreb, Croatia
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Scherthan H, Cremer T, Arnason U, Weier HU, Lima-de-Faria A, Frönicke L. Comparative chromosome painting discloses homologous segments in distantly related mammals. Nat Genet 1994; 6:342-7. [PMID: 8054973 DOI: 10.1038/ng0494-342] [Citation(s) in RCA: 167] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Comparative chromosome painting, termed ZOO-FISH, using DNA libraries from flow sorted human chromosomes 1, 16, 17 and X, and mouse chromosome 11 discloses the presence of syntenic groups in distantly related mammalian orders ranging from primates (Homo sapiens), rodents (Mus musculus), even-toed ungulates (Muntiacus muntjak vaginalis and Muntiacus reevesi) and whales (Balaenoptera physalus). These mammalian orders have evolved separately for 55-80 million years (Myr). We conclude that ZOO-FISH can be used to generate comparative chromosome maps of a large number of mammalian species.
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Affiliation(s)
- H Scherthan
- Institute of Human Genetics and Anthropology, Heidelberg, Germany
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10
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Arnason U, Gullberg A. Relationship of baleen whales established by cytochrome b gene sequence comparison. Nature 1994; 367:726-8. [PMID: 8107866 DOI: 10.1038/367726a0] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A recent revision of whale phylogeny suggested that the sperm whale was more closely related to rorquals than to other toothed whales. This made the suborder Odontoceti (toothed whales) paraphyletic, and implied that the latest common ancestor of rorquals and sperm whales may have lived only 10-13 million years ago. This is at variance with palaeontological evidence for the greater antiquity for both mysticetes (baleen whales) and sperm whales, so the Mysticeti, as well as the Odontoceti, must also be paraphyletic if the dates implied in ref. 1 were correct. Here we present a more comprehensive phylogenetic analysis that demonstrates the monophyly of mysticetes and identifies no particular affinity between the sperm whales and rorquals.
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Affiliation(s)
- U Arnason
- Department of Genetics, University of Lund, Sweden
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11
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Crovella S, Masters JC, Rumpler Y. Highly repeated DNA sequences as phylogenetic markers among the galaginae. Am J Primatol 1994; 32:177-185. [DOI: 10.1002/ajp.1350320304] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/1993] [Revised: 09/15/1993] [Indexed: 11/06/2022]
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Adegoke JA, Arnason U, Widegren B. Sequence organization and evolution, in all extant whalebone whales, of a DNA satellite with terminal chromosome localization. Chromosoma 1993; 102:382-8. [PMID: 8365348 DOI: 10.1007/bf00360402] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A heavy (GC rich) DNA satellite with terminal chromosomal localization is characteristic for all mysticete (whalebone whale) genomes. Sequences of 58 repeats of the satellite were compared in all ten extant mysticete species. In three families comprising eight species, the typical repeat length was 422 (421) bp. In two species, the northern right whale and the bowhead, of family Balaenidae (right whales) the repeats were much longer, typically ca. 900 and ca. 1200 bp. In all species the repeats were composed of a unique portion of constant length (212/211 bp), and a subrepeat portion, the length of which was variable. The evolutionary rigidity of the unique portion of the repeat is contrasted by the pronounced length variability of the subrepeat portion. The subrepeat portion consists essentially of 6 bp motifs, such that length differences are usually in multiples of 6 bp. The motif TTAGGG constituted 35%-50% of the subrepeats. Comparison between the unique portion of the 58 sequenced repeats revealed that the repeats divided into two primary groups, one comprising the two balaenids, the other including the eight remaining species. The mean difference between the two groups averaged 8.4%. In this sequence comparison the repeats of the pygmy right whale constituted a group that was separated from repeats of the other species. In all other cases repeats were intermingled to some extent between species. Comparison of individual repeats suggests that the unique portion evolves in concert, at a slow rate. A neighbor-joining comparison between the consensuses of all species suggests that the unique portion of the repeats evolves at a somewhat different rate in different lineages.
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Affiliation(s)
- J A Adegoke
- Department of Genetics, University of Lund, Wallenberg Laboratory, Sweden
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Grétarsdóttir S, Arnason U. Evolution of the common cetacean highly repetitive DNA component and the systematic position of Orcaella brevirostris. J Mol Evol 1992; 34:201-8. [PMID: 1588595 DOI: 10.1007/bf00162969] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The common cetacean highly repetitive DNA component was analyzed with respect to its evolution and value for establishing phylogenetic relationships. The repeat length of the component, which is tandemly organized, is approximately 1750 bp in all cetaceans except the delphinids, in which the repeat length is approximately 1580 bp. The evolution of the component was studied after sequencing the component in different odontocetes representing the Delphinidae (delphinids), Monodontidae (narwhals), and Ziphiidae (beaked whales). The evolution of this component is very slow, and comparisons showed that sequence divergence among species corresponds closely to their generally accepted phylogenetic relationships and that the component evolves in a concerted manner. The phylogenetic information obtained in this study identified the Irrawaddy dolphin (Orcaella brevirostris) as a delphinid and did not support a close relationship of this species with the Monodontidae.
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Affiliation(s)
- S Grétarsdóttir
- Department of Molecular Genetics, University of Lund, Sweden
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Arnason U, Spilliaert R, Pálsdóttir A, Arnason A. Molecular identification of hybrids between the two largest whale species, the blue whale (Balaenoptera musculus) and the fin whale (B. physalus). Hereditas 1991; 115:183-9. [PMID: 1687408 DOI: 10.1111/j.1601-5223.1991.tb03554.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Three anomalous balaenopterid whales, one pregnant female and two sterile males, were investigated by applying molecular approaches in order to establish their identity. The analysis showed that the whales were species hybrids between the blue and the fin whales. The female and one of the males had a blue whale mother and a fin whale father. The other male had a fin whale mother and a blue whale father. The difference between the mitochondrial cytochrome b gene of the two species suggests that they separated greater than or equal to 3.5 million years ago. The sequences of the mitochondrial control region of the blue and the fin whales differ by 7%. The difference in the mtDNA control region between three blue whale mtDNA haplotypes was less than or equal to 1%, about one tenth of the difference between the two species.
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Affiliation(s)
- U Arnason
- Department of Genetics--Molecular Genetics, Wallenberg Laboratory, University of Lund, Sweden
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