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Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications. Animals (Basel) 2022; 13:ani13010096. [PMID: 36611705 PMCID: PMC9817927 DOI: 10.3390/ani13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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3
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The HLA A03 Supertype and Several Pan Species Major Histocompatibility Complex Class I A Allotypes Share a Preference for Binding Positively Charged Residues in the F Pocket: Implications for Controlling Retroviral Infections. J Virol 2020; 94:JVI.01960-19. [PMID: 32075930 DOI: 10.1128/jvi.01960-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
The major histocompatibility complex (MHC) class I region of humans, chimpanzees (Pan troglodytes), and bonobos (Pan paniscus) is highly similar, and orthologues of HLA-A, -B, and -C are present in both Pan species. Based on functional characteristics, the different HLA-A allotypes are classified into different supertypes. One of them, the HLA A03 supertype, is widely distributed among different human populations. All contemporary known chimpanzee and bonobo MHC class I A allotypes cluster genetically into one of the six HLA-A families, the HLA-A1/A3/A11/A30 family. We report here that the peptide-binding motif of the Patr-A*05:01 allotype, which is commonly present in a cohort of western African chimpanzees, has a strong preference for binding peptides with basic amino acids at the carboxyl terminus. This phenomenon is shared with the family members of the HLA A03 supertype. Based on the chemical similarities in the peptide-binding pocket, we inferred that the preference for binding peptides with basic amino acids at the carboxyl terminus is widely present among the human, chimpanzee, and bonobo MHC-A allotypes. Subsequent in silico peptide-binding predictions illustrated that these allotypes have the capacity to target conserved parts of the proteome of human immunodeficiency virus type 1 (HIV-1) and the simian immunodeficiency virus SIVcpz.IMPORTANCE Most experimentally infected chimpanzees seem to control an HIV-1 infection and are therefore considered to be relatively resistant to developing AIDS. Contemporary free-ranging chimpanzees may carry SIVcpz, and there is evidence for AIDS-like symptoms in these free-ranging animals, whereas SIV infections in bonobos appear to be absent. In humans, the natural control of an HIV-1 infection is strongly associated with the presence of particular HLA class I allotypes. The ancestor of the contemporary living chimpanzees and bonobos survived a selective sweep targeting the MHC class I repertoire. We have put forward a hypothesis that this may have been caused by an ancestral retroviral infection similar to SIVcpz. Characterization of the relevant MHC allotypes may contribute to understanding the shaping of their immune repertoire. The abundant presence of MHC-A allotypes that prefer peptides with basic amino acids at the C termini suggests that these molecules may contribute to the control of retroviral infections in humans, chimpanzees, and bonobos.
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Cao JJ, Wang Y, Huang YR, Li WH. Mitochondrial genomes of the stoneflies Mesonemourametafiligera and Mesonemouratritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea. Zookeys 2019; 835:43-63. [PMID: 31043849 PMCID: PMC6477857 DOI: 10.3897/zookeys.835.32470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/21/2019] [Indexed: 11/12/2022] Open
Abstract
In this study, two new mitochondrial genomes (mitogenomes) of Mesonemourametafiligera and Mesonemouratritaenia from the family Nemouridae (Insecta: Plecoptera) were sequenced. The Mesonemourametafiligera mitogenome was a 15,739 bp circular DNA molecule, which was smaller than that of M.tritaenia (15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNASer(AGN) which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.
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Affiliation(s)
- Jin-Jun Cao
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Ying Wang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China.,Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Yao-Rui Huang
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
| | - Wei-Hai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China Henan Institute of Science and Technology Xinxiang China
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Khanal L, Chalise MK, Wan T, Jiang X. Riverine barrier effects on population genetic structure of the Hanuman langur (Semnopithecus entellus) in the Nepal Himalaya. BMC Evol Biol 2018; 18:159. [PMID: 30382913 PMCID: PMC6211570 DOI: 10.1186/s12862-018-1280-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 10/24/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Past climatological events and contemporary geophysical barriers shape the distribution, population genetic structure, and evolutionary history of many organisms. The Himalayan region, frequently referred to as the third pole of the Earth, has experienced large-scale climatic oscillations in the past and bears unique geographic, topographic, and climatic areas. The influences of the Pleistocene climatic fluctuations and present-day geographical barriers such as rivers in shaping the demographic history and population genetic structure of organisms in the Nepal Himalaya have not yet been documented. Hence, we examined the effects of late-Quaternary glacial-interglacial cycles and riverine barriers on the genetic composition of Hanuman langurs (Semnopithecus entellus), a colobine primate with a wide range of altitudinal distribution across the Nepalese Himalaya, using the mitochondrial DNA control region (CR, 1090 bp) and cytochrome B (CYTB, 1140 bp) sequences combined with paleodistribution modeling. RESULTS DNA sequences were successfully retrieved from 67 non-invasively collected fecal samples belonging to 18 wild Hanuman langur troops covering the entire distribution range of the species in Nepal. We identified 37 haplotypes from the concatenated CR + CYTB (2230 bp) sequences, with haplotype and nucleotide diversities of 0.958 ± 0.015 and 0.0237 ± 0.0008, respectively. The troops were clustered into six major clades corresponding to their river-isolated spatial distribution, with the significantly high genetic variation among these clades confirming the barrier effects of the snow-fed Himalayan rivers on genetic structuring. Analysis of demographic history projected a decrease in population size with the onset of the last glacial maximum (LGM); and, in accordance with the molecular analyses, paleodistribution modeling revealed a range shift in its suitable habitat downward/southward during the LGM. The complex genetic structure among the populations of central Nepal, and the stable optimal habitat through the last interglacial period to the present suggest that the central mid-hills of Nepal served as glacial refugia for the Hanuman langur. CONCLUSIONS Hanuman langurs of the Nepal Himalaya region exhibit high genetic diversity, with their population genetic structure is strongly shaped by riverine barrier effects beyond isolation by distance; hence, this species demands detailed future phylogenetic study.
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Affiliation(s)
- Laxman Khanal
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650223 China
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Mukesh Kumar Chalise
- Central Department of Zoology, Institute of Science and Technology, Tribhuvan University, Kathmandu, 44613 Nepal
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 Yunnan China
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
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Yang H, Li T, Dang K, Bu W. Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera). BMC Genomics 2018; 19:264. [PMID: 29669515 PMCID: PMC5907366 DOI: 10.1186/s12864-018-4650-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 04/08/2018] [Indexed: 01/24/2023] Open
Abstract
Background Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Results Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably, the value of Ka/Ks ratios of all PCGs is less than 1, indicating that these genes are likely evolving under purifying selection. Conclusions Our results demonstrate that mt-genomes have sites with strong phylogenetic signals for the inference of higher-level phylogeny of Cimicomorpha. Consequently, bioinformatic approaches to removing sites with weak phylogenetic signals in mt-genome without relying on an a priori tree topology would greatly improve this field. Electronic supplementary material The online version of this article (10.1186/s12864-018-4650-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huanhuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Teng Li
- Institute of Zoology and Developmental Biology, College of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou, 730000, China.
| | - Kai Dang
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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Meza-Lázaro RN, Poteaux C, Bayona-Vásquez NJ, Branstetter MG, Zaldívar-Riverón A. Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae). Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:1203-1214. [PMID: 29385929 DOI: 10.1080/24701394.2018.1431228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts. Heteroplasmy due to hybrid paternal leakage is not supported by phylogenetic analyses. Our results reveal the presence of a fast-evolving secondary mitochondrial lineage of uncertain origin in the E. ruidum complex.
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Affiliation(s)
- Rubi N Meza-Lázaro
- a Colección Nacional de Insectos, Instituto de Biología , Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria , CdMx, México , México
| | - Chantal Poteaux
- b Laboratoire d'Ethologie Expérimentale et Comparée E.A. 4443 (LEEC), Université Paris 13, Sorbonne Paris Cité , Villetaneuse , France
| | | | - Michael G Branstetter
- d USDA-ARS Pollinating Insects Research Unit, Utah State University , Logan , UT , USA
| | - Alejandro Zaldívar-Riverón
- a Colección Nacional de Insectos, Instituto de Biología , Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria , CdMx, México , México
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8
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Schroeder L, von Cramon-Taubadel N. The evolution of hominoid cranial diversity: A quantitative genetic approach. Evolution 2017; 71:2634-2649. [DOI: 10.1111/evo.13361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/03/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Lauren Schroeder
- Department of Anthropology; University of Toronto Mississauga; Mississauga ON L5L 1C6 Canada
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
- Human Evolution Research Institute; University of Cape Town; Rondebosch 7701 South Africa
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
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de Groot NG, Heijmans CMC, Helsen P, Otting N, Pereboom Z, Stevens JMG, Bontrop RE. Limited MHC class I intron 2 repertoire variation in bonobos. Immunogenetics 2017. [PMID: 28623393 DOI: 10.1007/s00251-017-1010-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2-3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1.5 to 2 million years ago. To investigate whether the signature of this selective sweep is also detectable in bonobos, the MHC class I gene repertoire of two bonobo panels comprising in total 29 animals was investigated by Sanger sequencing. We identified 14 Papa-A, 20 Papa-B and 11 Papa-C alleles, of which eight, five and eight alleles, respectively, have not been reported previously. Within this pool of MHC class I variation, we recovered only 2 Papa-A, 3 Papa-B and 6 Papa-C intron 2 sequences. As compared to humans, bonobos appear to have an even more diminished MHC class I intron 2 lineage repertoire than common chimpanzees. This supports the notion that the selective sweep may have predated the speciation of common chimpanzees and bonobos. The further reduction of the MHC class I intron 2 lineage repertoire observed in bonobos as compared to the common chimpanzee may be explained by a founding effect or other subsequent selective processes.
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Affiliation(s)
- Natasja G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.
| | - Corrine M C Heijmans
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Nel Otting
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Zjef Pereboom
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jeroen M G Stevens
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ronald E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
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Takemoto H, Kawamoto Y, Higuchi S, Makinose E, Hart JA, Hart TB, Sakamaki T, Tokuyama N, Reinartz GE, Guislain P, Dupain J, Cobden AK, Mulavwa MN, Yangozene K, Darroze S, Devos C, Furuichi T. The mitochondrial ancestor of bonobos and the origin of their major haplogroups. PLoS One 2017; 12:e0174851. [PMID: 28467422 PMCID: PMC5414932 DOI: 10.1371/journal.pone.0174851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/16/2017] [Indexed: 11/28/2022] Open
Abstract
We report here where the most recent common ancestor (MRCA) of bonobos (Pan paniscus) ranged and how they dispersed throughout their current habitat. Mitochondrial DNA (mtDNA) molecular dating to analyze the time to MRCA (TMRCA) and the major mtDNA haplogroups of wild bonobos were performed using new estimations of divergence time of bonobos from other Pan species to investigate the dispersal routes of bonobos over the forest area of the Congo River’s left bank. The TMRCA of bonobos was estimated to be 0.64 or 0.95 million years ago (Ma). Six major haplogroups had very old origins of 0.38 Ma or older. The reconstruction of the ancestral area revealed the mitochondrial ancestor of the bonobo populations ranged in the eastern area of the current bonobos’ habitat. The haplogroups may have been formed from either the riparian forests along the Congo River or the center of the southern Congo Basin. Fragmentation of the forest refugia during the cooler periods may have greatly affected the formation of the genetic structure of bonobo populations.
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Affiliation(s)
- Hiroyuki Takemoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail: (HT); (TF)
| | - Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Shoko Higuchi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Emiko Makinose
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - John A. Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | - Térese B. Hart
- Lukuru Foundation, Projet Tshuapa-Lomami-Lualaba (TL2), Kinshasa, Democratic Republic of Congo
| | | | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Gay E. Reinartz
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Patrick Guislain
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Jef Dupain
- African Wildlife Foundation, Nairobi, Kenya
| | - Amy K. Cobden
- Department of Anthropology, Emory University, Atlanta, Georgia, United States of America
| | - Mbangi N. Mulavwa
- Research Center for Ecology and Forestry, Ministry of high Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Kumugo Yangozene
- Research Center for Ecology and Forestry, Ministry of high Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Serge Darroze
- Consultant Biodiversity, Sustainable Use of Natural Resources, Protected Areas Management and Adaptation to Climate Change, Bangkok, Thailand
| | - Céline Devos
- Department of Behavioral Biology, University of Liège, Liège, Belgium
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail: (HT); (TF)
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11
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Lobon I, Tucci S, de Manuel M, Ghirotto S, Benazzo A, Prado-Martinez J, Lorente-Galdos B, Nam K, Dabad M, Hernandez-Rodriguez J, Comas D, Navarro A, Schierup MH, Andres AM, Barbujani G, Hvilsom C, Marques-Bonet T. Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions. Genome Biol Evol 2016; 8:2020-30. [PMID: 27345955 PMCID: PMC4943195 DOI: 10.1093/gbe/evw124] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 01/02/2023] Open
Abstract
The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81-1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41-0.78] with further internal separations at 0.32 Mya [0.22-0.43] and 0.16 Mya [0.17-0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.
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Affiliation(s)
- Irene Lobon
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Serena Tucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marc de Manuel
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | | | - Kiwoong Nam
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Mikkel H Schierup
- Bioinformatics Research Center, C.F. Møllers Alle, Aarhus University, Denmark
| | - Aida M Andres
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Tomas Marques-Bonet
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, Barcelona, Spain CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
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12
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Takemoto H, Kawamoto Y, Furuichi T. How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations. Evol Anthropol 2016; 24:170-84. [PMID: 26478139 DOI: 10.1002/evan.21456] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
While investigating the genetic structure in wild bonobos,(1) we realized that the widely accepted scenario positing that the Pleistocene appearance of the Congo River separated the common ancestor of chimpanzees (Pan troglodytes) and bonobos (P. paniscus) into two species is not supported by recent geographical knowledge about the formation of the Congo River. We explored the origin of bonobos using a broader biogeographical perspective by examining local faunas in the central African region. The submarine Congo River sediments and paleotopography of central Africa show that the Congo River has functioned as a geographical barrier for the last 34 million years. This evidence allows us to hypothesize that when the river was first formed, the ancestor of bonobos did not inhabit the current range of the species on the left bank of the Congo River but that, during rare times when the Congo River discharge decreased during the Pleistocene, one or more founder populations of ancestral Pan paniscus crossed the river to its left bank. The proposed scenario for formation of the Congo River and the corridor hypothesis for an ancestral bonobo population is key to understanding the distribution of great apes and their evolution.
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13
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Clay Z, Furuichi T, de Waal FB. Obstacles and catalysts to peaceful coexistence in chimpanzees and bonobos. BEHAVIOUR 2016. [DOI: 10.1163/1568539x-00003335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
As our closest living relatives, comparisons of the social lives and behavioural ecologies of chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) provide relevant insights into the evolutionary constraints of peaceful coexistence in Hominid societies. In this review, we compare and contrast findings from the two Pan species in order to examine some of the obstacles and catalysts for peaceful behaviour in our ape relatives. Through comparing the social structures, behavioural mechanisms and ecological drivers for peaceful behaviours in Pan, we develop hypotheses regarding the evolutionary constraints of peaceful co-existence in hominid societies.
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Affiliation(s)
- Zanna Clay
- aSchool of Psychology, University of Birmingham, Birmingham, UK
| | - Takeshi Furuichi
- bPrimate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Frans B.M. de Waal
- cLiving Links Center, Yerkes National Primate Research Center and Psychology Department, Emory University, Atlanta, GA, USA
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14
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Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC. The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Genome Biol Evol 2014; 6:886-96. [PMID: 24696399 PMCID: PMC4007550 DOI: 10.1093/gbe/evu059] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/21/2022] Open
Abstract
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
| | - Joana Vilela
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
| | - Miguel M. Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Spain
| | - Rute R. da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
| | - Pierre Boursot
- Institut des Sciences de l’Evolution, Université Montpellier 2, CNRS, IRD, France
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula
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15
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Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martínez I, Gracia A, de Castro JMB, Carbonell E, Pääbo S. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 2013; 505:403-6. [PMID: 24305051 DOI: 10.1038/nature12788] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/17/2013] [Indexed: 12/22/2022]
Abstract
Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene. One of these sites, the 'Sima de los Huesos' ('pit of bones'), has yielded the world's largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
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Affiliation(s)
- Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany [2] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Juan-Luis Arsuaga
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Departamento de Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Ignacio Martínez
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Área de Paleontología, Depto. de Geografía y Geología, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | - Ana Gracia
- 1] Centro de Investigación Sobre la Evolución y Comportamiento Humanos, Universidad Complutense de Madrid-Instituto de Salud Carlos III, 28029 Madrid, Spain [2] Área de Paleontología, Depto. de Geografía y Geología, Universidad de Alcalá, Alcalá de Henares, 28871 Madrid, Spain
| | | | - Eudald Carbonell
- 1] Institut Català de Paleoecologia Humana i Evolució Social, C/Marcel·lí Domingo s/n (Edifici W3), Campus Sescelades, 43007 Tarragona, Spain [2] Àrea de Prehistòria, Dept. d'Història i Història de l'Art, Univ. Rovira i Virgili, Fac. de Lletres, Av. Catalunya, 35, 43002 Tarragona, Spain
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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16
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Hvilsom C, Carlsen F, Heller R, Jaffré N, Siegismund HR. Contrasting demographic histories of the neighboring bonobo and chimpanzee. Primates 2013; 55:101-12. [DOI: 10.1007/s10329-013-0373-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/10/2013] [Indexed: 12/01/2022]
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17
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Kawamoto Y, Takemoto H, Higuchi S, Sakamaki T, Hart JA, Hart TB, Tokuyama N, Reinartz GE, Guislain P, Dupain J, Cobden AK, Mulavwa MN, Yangozene K, Darroze S, Devos C, Furuichi T. Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution. PLoS One 2013; 8:e59660. [PMID: 23544084 PMCID: PMC3609822 DOI: 10.1371/journal.pone.0059660] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/16/2013] [Indexed: 11/18/2022] Open
Abstract
Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.
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Affiliation(s)
- Yoshi Kawamoto
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - Shoko Higuchi
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | | | - John A. Hart
- Lukuru Wildlife Research Foundation, Kinshasa, Democratic Republic of Congo
| | - Terese B. Hart
- Lukuru Wildlife Research Foundation, Kinshasa, Democratic Republic of Congo
| | - Nahoko Tokuyama
- Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Gay E. Reinartz
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Patrick Guislain
- Bonobo and Congo Biodiversity Initiative, Zoological Society of Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Jef Dupain
- African Wildlife Foundation, Kinshasa, Democratic Republic of Congo
| | - Amy K. Cobden
- African Wildlife Foundation, Kinshasa, Democratic Republic of Congo
- Department of Anthropology, Emory University, Atlanta, Georgia, United States of America
| | - Mbangi N. Mulavwa
- Research Center for Ecology and Forestry, Ministry of High Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Kumugo Yangozene
- Research Center for Ecology and Forestry, Ministry of High Education and Scientific Research, Mabali, Democratic Republic of Congo
| | - Serge Darroze
- World Wide Fund for Nature, Kinshasa, Democratic Republic of Congo
| | - Céline Devos
- World Wide Fund for Nature, Kinshasa, Democratic Republic of Congo
| | - Takeshi Furuichi
- Primate Research Institute, Kyoto University, Inuyama, Japan
- * E-mail:
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18
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Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S. Comparative population genomics of the ejaculate in humans and the great apes. Mol Biol Evol 2013; 30:964-76. [PMID: 23329688 DOI: 10.1093/molbev/mst005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The rapid molecular evolution of reproductive genes is nearly ubiquitous across animals, yet the selective forces and functional targets underlying this divergence remain poorly understood. Humans and closely related species of great apes show strongly divergent mating systems, providing a powerful system to investigate the influence of sperm competition on the evolution of reproductive genes. This is complemented by detailed information on male reproductive biology and unparalleled genomic resources in humans. Here, we have used custom microarrays to capture and sequence 285 genes encoding proteins present in the ejaculate as well as 101 randomly selected control genes in 21 gorillas, 20 chimpanzees, 20 bonobos, and 20 humans. In total, we have generated >25× average genomic coverage per individual for over 1 million target base pairs. Our analyses indicate high levels of evolutionary constraint across much of the ejaculate combined with more rapid evolution of genes involved in immune defense and proteolysis. We do not find evidence for appreciably more positive selection along the lineage leading to bonobos and chimpanzees, although this would be predicted given more intense sperm competition in these species. Rather, the extent of positive and negative selection depended more on the effective population sizes of the species. Thus, general patterns of male reproductive protein evolution among apes and humans depend strongly on gene function but not on inferred differences in the intensity of sperm competition among extant species.
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Affiliation(s)
- Jeffrey M Good
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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19
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Li H, Liu H, Song F, Shi A, Zhou X, Cai W. Comparative mitogenomic analysis of damsel bugs representing three tribes in the family Nabidae (Insecta: Hemiptera). PLoS One 2012; 7:e45925. [PMID: 23029320 PMCID: PMC3461043 DOI: 10.1371/journal.pone.0045925] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/23/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Nabidae, a family of predatory heteropterans, includes two subfamilies and five tribes. We previously reported the complete mitogenome of Alloeorhynchus bakeri, a representative of the tribe Prostemmatini in the subfamily Prostemmatinae. To gain a better understanding of architecture and evolution of mitogenome in Nabidae, mitogenomes of five species representing two tribes (Gorpini and Nabini) in the subfamily Nabinae were sequenced, and a comparative mitogenomic analysis of three nabid tribes in two subfamilies was carried out. METHODOLOGY/PRINCIPAL FINDINGS Nabid mitogenomes share a similar nucleotide composition and base bias, except for the control region, where differences are observed at the subfamily level. In addition, the pattern of codon usage is influenced by the GC content and consistent with the standard invertebrate mitochondrial genetic code and the preference for A+T-rich codons. The comparison among orthologous protein-coding genes shows that different genes have been subject to different rates of molecular evolution correlated with the GC content. The stems and anticodon loops of tRNAs are extremely conserved, and the nucleotide substitutions are largely restricted to TψC and DHU loops and extra arms, with insertion-deletion polymorphisms. Comparative analysis shows similar rates of substitution between the two rRNAs. Long non-coding regions are observed in most Gorpini and Nabini mtDNAs in-between trnI-trnQ and/or trnS2-nad1. The lone exception, Nabis apicalis, however, has lost three tRNAs. Overall, phylogenetic analysis using mitogenomic data is consistent with phylogenies constructed mainly form morphological traits. CONCLUSIONS/SIGNIFICANCE This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the family Nabidae. Nucleotide diversity and mitogenomic traits are phylogenetically informative at subfamily level. Furthermore, inclusion of a broader range of samples representing various taxonomic levels is critical for the understanding of mitogenomic evolution in damsel bugs.
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Affiliation(s)
- Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Haiyu Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Aimin Shi
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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20
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Yarham JW, McFarland R, Taylor RW, Elson JL. A proposed consensus panel of organisms for determining evolutionary conservation of mt-tRNA point mutations. Mitochondrion 2012; 12:533-8. [PMID: 22781547 PMCID: PMC3510436 DOI: 10.1016/j.mito.2012.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/19/2012] [Accepted: 06/28/2012] [Indexed: 11/23/2022]
Abstract
Assigning pathogenicity to mt-tRNA variants requires multiple strands of evidence. Evolutionary conservation is often considered mandatory, but lack of a standard panel of organisms to assess conservation complicates comparison between reports and undermines the value of conservation-based evidence. We demonstrate that intra-species MTT sequence variation is sufficiently low for sequence data from a single organism to adequately represent a species. On this basis, we propose a standardised panel of organisms for conservation assessment and describe integration of this conservation panel into a pathogenicity scoring system designed to assess mt-tRNA variation associated with mitochondrial disease.
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Affiliation(s)
- John W Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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21
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Pacheu-Grau D, Gómez-Durán A, López-Gallardo E, Pinós T, Andreu AL, López-Pérez MJ, Montoya J, Ruiz-Pesini E. 'Progress' renders detrimental an ancient mitochondrial DNA genetic variant. Hum Mol Genet 2011; 20:4224-31. [PMID: 21828074 DOI: 10.1093/hmg/ddr350] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A human mitochondrial DNA (mtDNA) transition, m.1555A>G, in the 12S rRNA gene causes non-syndromic hearing loss. However, this pathological mutation is the wild-type allele in orangutan mtDNA. Here we rule out different genetic factors as the reason for its fixation in orangutans and show that aminoglycosides negatively affect the oxidative phosphorylation function by decreasing the synthesis of mtDNA-encoded proteins and the amount and activity of respiratory complex IV. These drugs also diminish the growth rate of orangutan cells. The m.1555G nucleotide is also the wild-type allele in other mammal species and they might be at risk of suffering a mitochondrial disorder if treated with aminoglycosides. Therefore, pharmacogenomic approaches should be used to confirm this possibility. These observations are important for human health. Due to the fact that old age and high frequency are criteria widely used in mitochondrial medicine to rule out a genetic change as being a pathological mutation, our results prevent against simplistic genetic approaches that do not consider the potential effect of environmental conditions. Hence, these results suggest that some ancient and highly frequent human population polymorphisms, such as those defining mtDNA haplogroups, in mitochondrial rRNA genes can be deleterious in association with new environmental conditions. Therefore, as the discovery of ribosomal antibiotics has allowed to fight infectious diseases and this breakthrough can be considered an important scientific advance or 'progress', our results suggest that 'progress' can also have a negative counterpart and render detrimental many of these mtDNA genotypes.
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Affiliation(s)
- David Pacheu-Grau
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
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22
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Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm. PLoS One 2011; 6:e17729. [PMID: 21445268 PMCID: PMC3060828 DOI: 10.1371/journal.pone.0017729] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/12/2011] [Indexed: 11/19/2022] Open
Abstract
Background Complete mitochondrial (mt) genome sequencing is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. For long template sequencing, i.e., like the entire mtDNA, it is essential to design primers for Polymerase Chain Reaction (PCR) amplicons which are partly overlapping each other. The presented chromosome walking strategy provides the overlapping design to solve the problem for unreliable sequencing data at the 5′ end and provides the effective sequencing. However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA. Methodology/Principal Findings The purpose of this study is to develop an integrated primer design algorithm for entire mt genome in general, and for the common primer sets for closely-related species in particular. We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. Using a heuristic algorithm particle swarm optimization (PSO), all the designed primers were computationally validated to fit the common primer design constraints, such as the melting temperature, primer length and GC content, PCR product length, secondary structure, specificity, and terminal limitation. The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology. Finally, primer sets were designed within the overlapping region. The primer sets for the entire mtDNA sequences were successfully demonstrated in the example of two closely-related fish species. The pseudo code for the primer design algorithm is provided. Conclusions/Significance In conclusion, it can be said that our proposed sliding window-based PSO algorithm provides the necessary primer sets for the entire mt genome amplification and sequencing.
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