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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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2
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Bai G, Yuan Q, Guo Q, Duan Y. Identification and phylogenetic analysis in Pterorhinuschinensis (Aves, Passeriformes, Leiothrichidae) based on complete mitogenome. Zookeys 2023; 1172:15-30. [PMID: 38312436 PMCID: PMC10838554 DOI: 10.3897/zookeys.1172.107098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/05/2023] [Indexed: 02/06/2024] Open
Abstract
The Black-throated Laughingthrush (Pterorhinuschinensis) is a bird belonging to the order Passeriformes and the family Leiothrichidae, and is found in Cambodia, China, Laos, Myanmar, Thailand and Vietnam. Pterorhinuschinensis was once classified as belonging to the genus Garrulax. However, recent research has reclassified it in the genus Pterorhinus. In this study, we sequenced and characterized the complete mitogenome of P.chinensis. The complete mitochondrial genome of P.chinensis is 17,827 bp in length. It consists of 13 PCGs, 22 tRNAs, two rRNAs, and two control regions. All genes are coded on the H-strand, except for one PCG (nad6) and eight tRNAs. All PCGs are initiated with ATG and stopped by five types of stop codons. Our comparative analyses show irregular gene rearrangement between trnT and trnP genes with another similar control region emerging between trnE and trnF genes compared with the ancestral mitochondrial gene order, called "duplicate CR gene order". The phylogenetic position of P.chinensis and phylogenetic relationships among members of Leiothrichidae are assessed based on complete mitogenomes. Phylogenetic relationships based on Bayesian inference and maximum likelihood methods showed that Garrulax and (Pterorhinus + Ianthocincla) formed a clade. Leiothrix and Liocichla also formed a clade. Our study provides support for the transfer of P.chinensis from Garrulax to Pterorhinus. Our results provide mitochondrial genome data to further understand the mitochondrial genome characteristics and taxonomic status of Leiothrichidae.
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Affiliation(s)
- Guirong Bai
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Qingmiao Yuan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Qiang Guo
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Yubao Duan
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
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Westbury MV, Lorenzen ED. Iteratively mapping ancient
DNA
to reconstruct highly divergent mitochondrial genomes: An evaluation of software, parameters and bait reference. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Verry AJF, Lubbe P, Mitchell KJ, Rawlence NJ. Thirty years of ancient DNA and the faunal biogeography of Aotearoa New Zealand: lessons and future directions. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2093227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Alexander J. F. Verry
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
- Centre for Anthropobiology and Genomics of Toulouse, Faculté de Médecine Purpan, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Pascale Lubbe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kieren J. Mitchell
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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5
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Almeida FC, Porzecanski AL, Cracraft JL, Bertelli S. The evolution of tinamous (Palaeognathae: Tinamidae) in light of molecular and combined analyses. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The Neotropical tinamous are of particular interest in our efforts to understand the evolution of modern birds. They inhabit both forested and open environments and, although volant, have limited flight capabilities. Numerous studies have recognized the monophyly of tinamous and their relationships either as sister to the flightless ratites (ostriches, emus and their relatives) or within the ratites themselves. Despite the numerous bird phylogenies published recently, modern investigations of relationships within the tinamous themselves have been limited. Here, we present the first detailed phylogenetic analysis and divergence-date estimation including a significant number of tinamou species, both extant and fossil. The monophyly of most currently recognized polytypic genera is recovered with high support, with the exception of the paraphyletic Nothura and Nothoprocta. The traditional subdivision between those tinamous inhabiting open areas (Nothurinae) and forest environments (Tinaminae) is also confirmed. A temporal calibration of the resultant phylogeny estimates that the basal divergence of crown Tinamidae took place between 31 and 40 Mya.
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Affiliation(s)
- Francisca C Almeida
- Instituto de Ecología, Genética y Evolución (IEGEBA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/ Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana L Porzecanski
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Joel L Cracraft
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
| | - Sara Bertelli
- American Museum of Natural History, 200 Central Park West, New York, NY, 10024-5102, USA
- Fundación Miguel Lillo (FML), Miguel Lillo 251, 4000 San Miguel de Tucumán, Argentina
- Unidad Ejecutora Lillo (UEL) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), San Miguel de Tucumán, Tucumán, Argentina
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Undin M, Lockhart PJ, Hills SFK, Castro I. Genetic Rescue and the Plight of Ponui Hybrids. FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2020.622191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long-term sustainable and resilient populations is a key goal of conservation. How to best achieve this is controversial. There are, for instance, polarized views concerning the fitness and conservation value of hybrid populations founded through multi-origin translocations. A classic example concerns Apteryx (kiwi) in New Zealand. The A. mantelli of Ponui Island constitute a hybrid population where the birds are highly successful in their island habitat. A key dilemma for managers is understanding the reason for this success. Are the hybrid birds of Ponui Island of “no future conservation value” as recently asserted, or do they represent an outstanding example of genetic rescue and an important resource for future translocations? There has been a paradigm shift in scientific thinking concerning hybrids, but the ecological significance of admixed genomes remains difficult to assess. This limits what we can currently predict in conservation science. New understanding from genome science challenges the sufficiency of population genetic models to inform decision making and suggests instead that the contrasting outcomes of hybridization, “outbreeding depression” and “heterosis,” require understanding additional factors that modulate gene and protein expression and how these factors are influenced by the environment. We discuss these findings and the investigations that might help us to better understand the birds of Ponui, inform conservation management of kiwi and provide insight relevant for the future survival of Apteryx.
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Urantówka AD, Kroczak A, Mackiewicz P. New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves. BMC Genomics 2020; 21:874. [PMID: 33287726 PMCID: PMC7720580 DOI: 10.1186/s12864-020-07284-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans. RESULTS Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication. CONCLUSIONS The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.
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Affiliation(s)
- Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
| | - Aleksandra Kroczak
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, 7 Kozuchowska Street, 51-631 Wroclaw, Poland
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, 14a Fryderyka Joliot-Curie Street, 50-383 Wrocław, Poland
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Sun G, Zhao C, Xia T, Wei Q, Yang X, Feng S, Sha W, Zhang H. Sequence and organisation of the mitochondrial genome of Japanese Grosbeak ( Eophona personata), and the phylogenetic relationships of Fringillidae. Zookeys 2020; 995:67-80. [PMID: 33281468 PMCID: PMC7688617 DOI: 10.3897/zookeys.995.34432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 10/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial DNA is a useful molecular marker for phylogenetic and evolutionary analysis. In the current study, we determined the complete mitochondrial genome of Eophona personata, the Japanese Grosbeak, and the phylogenetic relationships of E. personata and 16 other species of the family Fringillidae based on the sequences of 12 mitochondrial protein-coding genes. The mitochondrial genome of E. personata consists of 16,771 base pairs, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one control region. Analysis of the base composition revealed an A+T bias, a positive AT skew and a negative GC skew. The mitochondrial gene order and arrangement in E. personata was similar to the typical avian mitochondrial gene arrangement. Phylogenetic analysis of 17 species of Fringillidae, based on Bayesian inference and Maximum Likelihood (ML) estimation, showed that the genera Coccothraustes and Hesperiphona are closely related to the genus Eophona, and further showed a sister-group relationship of E. personata and E. migratoria.
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Affiliation(s)
- Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Tian Xia
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Shi Feng
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Weilai Sha
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong province, ChinaQufu Normal UniversityQufuChina
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9
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Expanding the eggshell colour gamut: uroerythrin and bilirubin from tinamou (Tinamidae) eggshells. Sci Rep 2020; 10:11264. [PMID: 32647200 PMCID: PMC7347609 DOI: 10.1038/s41598-020-68070-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/01/2020] [Indexed: 11/10/2022] Open
Abstract
To date, only two pigments have been identified in avian eggshells: rusty-brown protoporphyrin IX and blue-green biliverdin IXα. Most avian eggshell colours can be produced by a mixture of these two tetrapyrrolic pigments. However, tinamou (Tinamidae) eggshells display colours not easily rationalised by combination of these two pigments alone, suggesting the presence of other pigments. Here, through extraction, derivatization, spectroscopy, chromatography, and mass spectrometry, we identify two novel eggshell pigments: yellow–brown tetrapyrrolic bilirubin from the guacamole-green eggshells of Eudromia elegans, and red–orange tripyrrolic uroerythrin from the purplish-brown eggshells of Nothura maculosa. Both pigments are known porphyrin catabolites and are found in the eggshells in conjunction with biliverdin IXα. A colour mixing model using the new pigments and biliverdin reproduces the respective eggshell colours. These discoveries expand our understanding of how eggshell colour diversity is achieved. We suggest that the ability of these pigments to photo-degrade may have an adaptive value for the tinamous.
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10
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Pan T, Miao JS, Zhang HB, Yan P, Lee PS, Jiang XY, Ouyang JH, Deng YP, Zhang BW, Wu XB. Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa074] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract
Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.
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Affiliation(s)
- Tao Pan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Shun Miao
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hua-Bin Zhang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Peng Yan
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Ping-Shin Lee
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Xin-Yue Jiang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Jia-Hui Ouyang
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - You-Peng Deng
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Bao-Wei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xiao-Bing Wu
- Anhui Province Key Laboratory for Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
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De Cahsan B, Westbury MV. Complete mitochondrial genomes offer insights into the evolutionary relationships and comparative genetic diversity of New Zealand’s iconic kiwi (Apteryx spp.). NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1766520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Binia De Cahsan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael V. Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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12
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Sun CH, Liu HY, Lu CH. Five new mitogenomes of Phylloscopus (Passeriformes, Phylloscopidae): Sequence, structure, and phylogenetic analyses. Int J Biol Macromol 2020; 146:638-647. [DOI: 10.1016/j.ijbiomac.2019.12.253] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/09/2019] [Accepted: 12/28/2019] [Indexed: 11/30/2022]
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13
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McCulloch GA, Waters JM. Phylogenetic divergence of island biotas: Molecular dates, extinction, and "relict" lineages. Mol Ecol 2019; 28:4354-4362. [PMID: 31544990 DOI: 10.1111/mec.15229] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 01/08/2023]
Abstract
Island formation is a key driver of biological evolution, and several studies have used geological ages of islands to calibrate rates of DNA change. However, many islands are home to "relict" lineages whose divergence apparently pre-dates island age. The geologically dynamic New Zealand (NZ) archipelago sits upon the ancient, largely submerged continent Zealandia, and the origin and age of its distinctive biota have long been contentious. While some researchers have interpreted NZ's biota as equivalent to that of a post-Oligocene island, a recent review of genetic studies identified a sizeable proportion of pre-Oligocene "relict" lineages, concluding that much of the biota survived an incomplete drowning event. Here, we assemble comparable genetic divergence data sets for two recently formed South Pacific archipelagos (Lord Howe; Chatham Islands) and demonstrate similarly substantial proportions of relict lineages. Similar to the NZ biota, our island reviews provide surprisingly little evidence for major genetic divergence "pulses" associated with island emergence. The dominance of Quaternary divergence estimates in all three biotas may highlight the importance of rapid biological turnover and new arrivals in response to recent climatic and/or geological disturbance and change. We provide a schematic model to help account for discrepancies between expected versus observed divergence-date distributions for island biotas, incorporating the effects of both molecular dating error and lineage extinction. We conclude that oceanic islands can represent both evolutionary "cradles" and "museums" and that the presence of apparently archaic island lineages does not preclude dispersal origins.
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14
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Caparroz R, Rocha AV, Cabanne GS, Tubaro P, Aleixo A, Lemmon EM, Lemmon AR. Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes. Mol Biol Rep 2018; 45:279-285. [PMID: 29455315 DOI: 10.1007/s11033-018-4160-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/06/2018] [Indexed: 11/27/2022]
Abstract
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.
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Affiliation(s)
- Renato Caparroz
- Departamento de Genética e Morfologia, Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal, CEP 70910-900, Brazil.
| | - Amanda V Rocha
- Departamento de Genética e Morfologia, Laboratório de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Asa Norte, Brasília, Distrito Federal, CEP 70910-900, Brazil
| | - Gustavo S Cabanne
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Ciudad de Buenos Aires, Argentina
| | - Pablo Tubaro
- División de Ornitología, Museo Argentino de Ciencias Naturales Bernardino Rivadavia, Ciudad de Buenos Aires, Argentina
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | - Emily M Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL, 32306-4295, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4102, USA
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15
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Faux C, Field DJ. Distinct developmental pathways underlie independent losses of flight in ratites. Biol Lett 2017; 13:rsbl.2017.0234. [PMID: 28679696 DOI: 10.1098/rsbl.2017.0234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/30/2017] [Indexed: 12/30/2022] Open
Abstract
Recent phylogenetic studies question the monophyly of ratites (large, flightless birds incorporating ostriches, rheas, kiwis, emus and cassowaries), suggesting their paraphyly with respect to flying tinamous (Tinamidae). Flightlessness and large body size have thus likely evolved repeatedly among ratites, and separately in ostriches (Struthio) and emus (Dromaius). Here, we test this hypothesis with data from wing developmental trajectories in ostriches, emus, tinamous and chickens. We find the rate of ostrich embryonic wing growth falls within the range of variation exhibited by flying taxa (tinamous and chickens), but that of emus is extremely slow. These results indicate flightlessness was acquired by different developmental mechanisms in the ancestors of ostriches (peramorphosis) and the emu-cassowary clade (paedomorphosis), and corroborate the hypothesis that flight loss has evolved repeatedly among ratites.
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Affiliation(s)
- Cynthia Faux
- Department of Integrated Physiology and Neurosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA .,Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA
| | - Daniel J Field
- Department of Geology and Geophysics, Yale University, 210 Whitney Avenue, New Haven, CT 06511, USA .,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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16
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Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. Complete mitochondrial genome sequences of the northern spotted owl ( Strix occidentalis caurina) and the barred owl ( Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 2017; 5:e3901. [PMID: 29038757 PMCID: PMC5639871 DOI: 10.7717/peerj.3901] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.
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Affiliation(s)
- Zachary R Hanna
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America.,Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - James B Henderson
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
| | - Anna B Sellas
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America.,Chan Zuckerberg Biohub, San Francisco, CA, United States of America
| | - Jérôme Fuchs
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,UMR 7205 Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, United States of America.,Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - John P Dumbacher
- Department of Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, United States of America.,Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA, United States of America
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17
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Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing. Nat Commun 2017; 8:132. [PMID: 28743862 PMCID: PMC5526984 DOI: 10.1038/s41467-017-00112-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/02/2017] [Indexed: 01/12/2023] Open
Abstract
The ratites are a distinctive clade of flightless birds, typified by the emu and ostrich that have acquired a range of unique anatomical characteristics since diverging from basal Aves at least 100 million years ago. The emu possesses a vestigial wing with a single digit and greatly reduced forelimb musculature. However, the embryological basis of wing reduction and other anatomical changes associated with loss of flight are unclear. Here we report a previously unknown co-option of the cardiac transcription factor Nkx2.5 to the forelimb in the emu embryo, but not in ostrich, or chicken and zebra finch, which have fully developed wings. Nkx2.5 is expressed in emu limb bud mesenchyme and maturing wing muscle, and mis-expression of Nkx2.5 throughout the limb bud in chick results in wing reductions. We propose that Nkx2.5 functions to inhibit early limb bud expansion and later muscle growth during development of the vestigial emu wing. The transcription factor Nkx2.5 is essential for heart development. Here, the authors identify a previously unknown expression domain for Nkx2.5 in the emu wing and explore its role in diminished wing bud development in the flightless emu, compared with three other birds that have functional wings.
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18
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Time to Spread Your Wings: A Review of the Avian Ancient DNA Field. Genes (Basel) 2017; 8:genes8070184. [PMID: 28718817 PMCID: PMC5541317 DOI: 10.3390/genes8070184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Ancient DNA (aDNA) has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation) is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP) material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.
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19
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Liu J, Ding QX, Gao LZ. The complete mitochondrial genome of North Island brown kiwi ( Apteryx mantelli). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 2:1-2. [PMID: 33490432 PMCID: PMC7800362 DOI: 10.1080/23802359.2016.1186511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Here, we report the complete mitochondrial genome sequence of North Island brown kiwi(Apteryx mantelli). The genome is found to be 16,694 bp in length and has a base composition of A (30.74%), G (13.46%), C (26.50%), and T (29.30%). Similar to other Apteryx species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22tRNA genes. The proportion of coding sequences with a total length of 11,431 bp is 68.47%, which encodes 3776 amino acids. All protein-coding genes started with Met, and ND2, COX2, and COX3 ended by TAA as a stop codon. The lengths of 12S ribosomal RNA and 16S ribosomal RNA are 973 bp and 1596 bp, respectively. The length of control region is 1112 bp, ranging from 15,583 bp to 16,694 bp. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of A. mantelli.
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Affiliation(s)
- Jia Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Qing-Xia Ding
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Li-Zhi Gao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China.,Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Science, Kunming, China
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20
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Anmarkrud JA, Lifjeld JT. Complete mitochondrial genomes of eleven extinct or possibly extinct bird species. Mol Ecol Resour 2016; 17:334-341. [DOI: 10.1111/1755-0998.12600] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 08/18/2016] [Accepted: 09/16/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Jarl A. Anmarkrud
- Natural History Museum University of Oslo PO Box 1172 Blindern Oslo 0318 Norway
| | - Jan T. Lifjeld
- Natural History Museum University of Oslo PO Box 1172 Blindern Oslo 0318 Norway
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21
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Wang CX, Xu HS, Li XF, Lu J, Hu XX, Liu X. The complete mitochondrial genome of the white-tailed tropicbird, Phaethon lepturus. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4259-4260. [PMID: 27207227 DOI: 10.3109/19401736.2015.1053076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The white-tailed tropicbird, Phaethon lepturus (Pelecaniformes, Phaethontidae) is a tropicbird, smallest of three closely related seabirds of the tropical oceans and smallest member of the order Pelecaniformes. Here, we first determined the complete mitochondrial genome of while-tailed tropicbird. The mitogenome (17,773 bp) was composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 putative control region. Most protein-coding genes started with a traditional ATG codon except for COX1, COX2, and ND3, which initiated with non-typical start codon GTG, GTG, and ATA instead, respectively, and terminated with the mitochondria stop codon (TAA/TCC/AGG/AGA). The mitogenome structural organization was identical to the same genus species Phaethon rubricauda. The overall AT content was 52.04%, which was higher than GC. To obtain the phylogenetic status of Phaethon lepturus, we constructed the species phylogenetic tree together with the 12 protein-coding genes of nine other closely species. We expected that the complete mitogenome of while-tailed tropicbird would contribute to address taxonomic issues and study the related evolution events.
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Affiliation(s)
- Chang-Xi Wang
- a College of Life Science, University of Chinese Academy of Sciences , Beijing , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Han-Shi Xu
- a College of Life Science, University of Chinese Academy of Sciences , Beijing , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Xiang-Feng Li
- a College of Life Science, University of Chinese Academy of Sciences , Beijing , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Jiang Lu
- a College of Life Science, University of Chinese Academy of Sciences , Beijing , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Xiao-Xiao Hu
- a College of Life Science, University of Chinese Academy of Sciences , Beijing , China and.,b BGI-Shenzhen , Shenzhen , China
| | - Xiao Liu
- b BGI-Shenzhen , Shenzhen , China
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22
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McCulloch GA, Wallis GP, Waters JM. A time-calibrated phylogeny of southern hemisphere stoneflies: Testing for Gondwanan origins. Mol Phylogenet Evol 2016; 96:150-160. [DOI: 10.1016/j.ympev.2015.10.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 10/06/2015] [Accepted: 10/25/2015] [Indexed: 10/22/2022]
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23
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Eliason CM, Shawkey MD, Clarke JA. Evolutionary shifts in the melanin-based color system of birds. Evolution 2016; 70:445-55. [PMID: 26767728 DOI: 10.1111/evo.12855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/18/2015] [Indexed: 11/30/2022]
Abstract
Melanin pigments contained in organelles (melanosomes) impart earthy colors to feathers. Such melanin-based colors are distributed across birds and thought to be the ancestral color-producing mechanism in birds. However, we have had limited data on melanin-based color and melanosome diversity in Palaeognathae, which includes the flighted tinamous and large-bodied, flightless ratites and is the sister taxon to all other extant birds. Here, we use scanning electron microscopy and spectrophotometry to assess melanosome morphology and quantify reflected color for 19 species within this clade. We find that brown colors in ratites are uniquely associated with elongated melanosomes nearly identical in shape to those associated with black colors. Melanosome and color diversity in large-bodied ratites is limited relative to other birds (including flightless penguins) and smaller bodied basal maniraptoran dinosaur outgroups of Aves, whereas tinamous show a wider range of melanosome forms similar to neognaths. The repeated occurrence of novel melanosome forms in the nonmonophyletic ratites suggests that melanin-based color tracks changes in body size, physiology, or other life history traits associated with flight loss, but not feather morphology. We further anticipate these findings will be useful for future color reconstructions in extinct species, as variation in melanosome shape may potentially be linked to a more nuanced palette of melanin-based colors.
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Affiliation(s)
- Chad M Eliason
- Department of Geological Sciences and Integrated Bioscience, University of Texas at Austin, Austin, Texas, 78712.
| | - Matthew D Shawkey
- Department of Biology and Integrated Bioscience, University of Akron, Akron, Ohio, 44325.,Current address: University of Ghent, Department of Biology, Terrestrial Ecology Unit, Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Julia A Clarke
- Department of Geological Sciences and Integrated Bioscience, University of Texas at Austin, Austin, Texas, 78712
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24
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Claramunt S, Cracraft J. A new time tree reveals Earth history's imprint on the evolution of modern birds. SCIENCE ADVANCES 2015; 1:e1501005. [PMID: 26824065 PMCID: PMC4730849 DOI: 10.1126/sciadv.1501005] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/02/2015] [Indexed: 05/21/2023]
Abstract
Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.
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25
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Berger BA, Kriebel R, Spalink D, Sytsma KJ. Divergence times, historical biogeography, and shifts in speciation rates of Myrtales. Mol Phylogenet Evol 2015; 95:116-36. [PMID: 26585030 DOI: 10.1016/j.ympev.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 09/03/2015] [Accepted: 10/04/2015] [Indexed: 01/22/2023]
Abstract
We examine the eudicot order Myrtales, a clade with strong Gondwanan representation for most of its families. Although previous phylogenetic studies greatly improved our understanding of intergeneric and interspecific relationships within the order, our understanding of inter-familial relationships still remains unresolved; hence, we also lack a robust time-calibrated chronogram to address hypotheses (e.g., biogeography and diversification rates) that have implicit time assumptions. Six loci (rbcL, ndhF, matK, matR, 18S, and 26S) were amplified and sequenced for 102 taxa across Myrtales for phylogenetic reconstruction and ten fossil priors were utilized to produce a chronogram in BEAST. Combretaceae is identified as the sister clade to all remaining families with moderate support, and within the latter clade, two strongly supported groups are seen: (1) Onagraceae+Lythraceae, and (2) Melastomataceae+the Crypteroniaceae, Alzateaceae, Penaeaceae clade along with Myrtaceae+Vochysiaceae. Divergence time estimates suggest Myrtales diverged from Geraniales ∼124Mya during the Aptian of the Early Cretaceous. The crown date for Myrtales is estimated at ∼116Mya (Albian-Aptian). BioGeoBEARS showed significant improvement in the likelihood score when the "jump dispersal" parameter was added. South America and/or Africa are implicated as important ancestral areas in all deeper nodes. BAMM analyses indicate that the best configuration included three significant shifts in diversification rates within Myrtales: near the crown of Melastomataceae (∼67-64Mya), along the stem of subfamily Myrtoideae (Myrtaceae; ∼75Mya), and along the stem of tribe Combreteae (Combretaceae; ∼50-45Mya). Issues with conducting diversification analyses more generally are examined in the context of scale, taxon sampling, and larger sets of phylogenetic trees.
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Affiliation(s)
- Brent A Berger
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY 11432, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Daniel Spalink
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Dr., Madison, WI 53706, USA
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26
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An M, Zhang Z, Li X, Yang S. The complete mitochondrial genome of the White-throated Tinamou, Tinamus guttatus (Tinamiformes, Tinamidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015. [PMID: 26195216 DOI: 10.3109/19401736.2015.1053073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The White-throated Tinamou, Tinamus guttatus (Tinamiformes, Tinamidae) is a species of the family Tinamidae. Herein, we firstly reported the complete mitochondrial genome of White-throated Tinamou. The length of mitogenome was 16 750 bp, and composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 putative misc-feature region. Most protein-coding genes started with a traditional ATG codon, but specially, COX1 and COX2 initiated with an infrequent start codon GTG instead, ND3 and ND5 initiated with ATA instead. Protein-coding genes terminated with the mitochondria stop codon (TAA/TAG/AGG/AGA) or a single base(A/T). The mitogenome structural organization was identical to the closely related species Tinamus major. The GC content was 42.66%. To verify the accuracy and utility of new determined mitogenome sequences, we constructed the species phylogenetic tree with the 12 protein-coding genes of Tinamus guttatus together with nine other closely species. We expected that using the full mitogenome to address taxonomic issues and study the related evolution events.
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Affiliation(s)
- Mei An
- a BGI Education Center, University of Chinese Academy of Sciences , Shenzhen , China .,b BGI-Shenzhen , Shenzhen , China , and
| | - Zhi Zhang
- a BGI Education Center, University of Chinese Academy of Sciences , Shenzhen , China .,b BGI-Shenzhen , Shenzhen , China , and
| | - Xiangfeng Li
- b BGI-Shenzhen , Shenzhen , China , and.,c College of Life Science, University of Chinese Academy of Sciences , Beijing , China
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27
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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28
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Graf DL, Jones H, Geneva AJ, Pfeiffer JM, Klunzinger MW. Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa. Mol Phylogenet Evol 2015; 85:1-9. [PMID: 25659337 DOI: 10.1016/j.ympev.2015.01.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 01/22/2015] [Accepted: 01/28/2015] [Indexed: 10/24/2022]
Abstract
The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent.
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Affiliation(s)
- Daniel L Graf
- Biology Department, University of Wisconsin-Stevens Point, Stevens Point, WI 54481, USA.
| | - Hugh Jones
- Department of Anatomy & Histology, University of Sydney, Sydney, NSW 2006, Australia
| | | | - John M Pfeiffer
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Michael W Klunzinger
- School of Veterinary & Life Sciences, Murdoch University, Perth, WA 6230, Australia
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29
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Eocene diversification of crown group rails (Aves: Gruiformes: Rallidae). PLoS One 2014; 9:e109635. [PMID: 25291147 PMCID: PMC4188725 DOI: 10.1371/journal.pone.0109635] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/05/2014] [Indexed: 12/29/2022] Open
Abstract
Central to our understanding of the timing of bird evolution is debate about an apparent conflict between fossil and molecular data. A deep age for higher level taxa within Neoaves is evident from molecular analyses but much remains to be learned about the age of diversification in modern bird families and their evolutionary ecology. In order to better understand the timing and pattern of diversification within the family Rallidae we used a relaxed molecular clock, fossil calibrations, and complete mitochondrial genomes from a range of rallid species analysed in a Bayesian framework. The estimated time of origin of Rallidae is Eocene, about 40.5 Mya, with evidence of intrafamiliar diversification from the Late Eocene to the Miocene. This timing is older than previously suggested for crown group Rallidae, but fossil calibrations, extent of taxon sampling and substantial sequence data give it credence. We note that fossils of Eocene age tentatively assigned to Rallidae are consistent with our findings. Compared to available studies of other bird lineages, the rail clade is old and supports an inference of deep ancestry of ground-dwelling habits among Neoaves.
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Keith Barker F. Mitogenomic data resolve basal relationships among passeriform and passeridan birds. Mol Phylogenet Evol 2014; 79:313-24. [DOI: 10.1016/j.ympev.2014.06.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 05/31/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022]
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Zhou X, Lin Q, Fang W, Chen X. The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements. BMC Genomics 2014; 15:573. [PMID: 25001581 PMCID: PMC4111848 DOI: 10.1186/1471-2164-15-573] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 07/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds. RESULTS The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea. CONCLUSIONS The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.
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Affiliation(s)
- Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coast and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102 People’s Republic of China
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Mitchell KJ, Llamas B, Soubrier J, Rawlence NJ, Worthy TH, Wood J, Lee MSY, Cooper A. Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution. Science 2014; 344:898-900. [PMID: 24855267 DOI: 10.1126/science.1251981] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence toward gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche after the extinction of the dinosaurs.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Nicolas J Rawlence
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Trevor H Worthy
- School of Biological Sciences, Flinders University, South Australia 5001, Australia
| | - Jamie Wood
- Landcare Research, Post Office Box 40, Lincoln 7640, New Zealand
| | - Michael S Y Lee
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia. South Australian Museum, North Terrace, South Australia 5000, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia.
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Baker AJ, Haddrath O, McPherson JD, Cloutier A. Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites. Mol Biol Evol 2014; 31:1686-96. [PMID: 24825849 DOI: 10.1093/molbev/msu153] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
One of the most startling discoveries in avian molecular phylogenetics is that the volant tinamous are embedded in the flightless ratites, but this topology remains controversial because recent morphological phylogenies place tinamous as the closest relative of a monophyletic ratite clade. Here, we integrate new phylogenomic sequences from 1,448 nuclear DNA loci totaling almost 1 million bp from the extinct little bush moa, Chilean tinamou, and emu with available sequences from ostrich, elegant crested tinamou, four neognaths, and the green anole. Phylogenetic analysis using standard homogeneous models and heterogeneous models robust to common topological artifacts recovered compelling support for ratite paraphyly with the little bush moa closest to tinamous within ratites. Ratite paraphyly was further corroborated by eight independent CR1 retroposon insertions. Analysis of morphological characters reinterpreted on a 27-gene paleognath topology indicates that many characters are convergent in the ratites, probably as the result of adaptation to a cursorial life style.
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Affiliation(s)
- Allan J Baker
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, CanadaDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | | | - Alison Cloutier
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Paijmans JL, Gilbert MTP, Hofreiter M. Mitogenomic analyses from ancient DNA. Mol Phylogenet Evol 2013; 69:404-16. [DOI: 10.1016/j.ympev.2012.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 05/27/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
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Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae). Mol Phylogenet Evol 2013; 69:728-39. [PMID: 23850499 DOI: 10.1016/j.ympev.2013.07.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/19/2013] [Accepted: 07/03/2013] [Indexed: 12/11/2022]
Abstract
Leaf-nosed bats (Phyllostomidae) are one of the most studied groups within the order Chiroptera mainly because of their outstanding species richness and diversity in morphological and ecological traits. Rapid diversification and multiple homoplasies have made the phylogeny of the family difficult to solve using morphological characters. Molecular data have contributed to shed light on the evolutionary history of phyllostomid bats, yet several relationships remain unresolved at the intra-familial level. Complete mitochondrial genomes have proven useful to deal with this kind of situation in other groups of mammals by providing access to a large number of molecular characters. At present, there are only two mitogenomes available for phyllostomid bats hinting at the need for further exploration of the mitogenomic approach in this group. We used both standard Sanger sequencing of PCR products and next-generation sequencing (NGS) of shotgun genomic DNA to obtain new complete mitochondrial genomes from 10 species of phyllostomid bats, including representatives of major subfamilies, plus one outgroup belonging to the closely-related mormoopids. We then evaluated the contribution of mitogenomics to the resolution of the phylogeny of leaf-nosed bats and compared the results to those based on mitochondrial genes and the RAG2 and VWF nuclear makers. Our results demonstrate the advantages of the Illumina NGS approach to efficiently obtain mitogenomes of phyllostomid bats. The phylogenetic signal provided by entire mitogenomes is highly comparable to the one of a concatenation of individual mitochondrial and nuclear markers, and allows increasing both resolution and statistical support for several clades. This enhanced phylogenetic signal is the result of combining markers with heterogeneous evolutionary rates representing a large number of nucleotide sites. Our results illustrate the potential of the NGS mitogenomic approach for resolving the evolutionary history of phyllostomid bats based on a denser species sampling.
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du Plessis L, Soley JT. A novel transient structure with phylogenetic implications found in ratite spermatids. BMC Evol Biol 2013; 13:104. [PMID: 23705947 PMCID: PMC3689617 DOI: 10.1186/1471-2148-13-104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 05/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A novel transient structure was observed in the spermatids of three ratite species using transmission electron microscopy. RESULTS The structure first appeared at the circular manchette stage of sperm development, was most prominent during the longitudinal manchette phase and disappeared abruptly prior to spermiation. It was composed of regularly-spaced finger-like projections which were closely associated with the outer nuclear membrane, giving the nucleus a cogwheel-like appearance. The projections were approximately 30 nm long and 14 nm wide. Although a similar structure has been described in certain lizard and crocodile species, this is the first report of a similar structure in the developing spermatids of birds. CONCLUSIONS The potential value of non-traditional characters, such as spermiogenesis and sperm ultrastructure, as phylogenetic markers has recently been advocated. The morphologically unique structure found in ratite spermatids provides additional evidence of a possible phylogenetic link between the reptiles and birds. It also endorses the basal positioning of the ratites as a monophyletic group within the avian phylogenetic tree.
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Olson VA, Turvey ST. The evolution of sexual dimorphism in New Zealand giant moa (Dinornis) and other ratites. Proc Biol Sci 2013; 280:20130401. [PMID: 23576789 DOI: 10.1098/rspb.2013.0401] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The extinct giant moa Dinornis is one of the most remarkable known examples of reversed sexual size dimorphism (RSD), with males weighing 34-85 kg, but females weighing up to 240 kg. However, there has been little consideration of the evolutionary mechanism that produced this level of dimorphism, and most living palaeognaths also exhibit varying levels of RSD. Using male and female body mass data for extant ratites and tinamous and four extinct moa genera, and tests of phylogenetic dependence (λ) of body size evolution among these species, we investigated whether Dinornis was truly unusual with respect to RSD relative to other palaeognaths, which sex was under greater pressure to change in size over evolutionary time, and which candidate hypotheses explaining the presence and variability of RSD in the genus are most plausible. We demonstrate that the extreme level of RSD exhibited by Dinornis represents a straightforward consequence of positive allometric scaling of body size. However, Dinornis females have undergone more evolutionary change than males, and larger females from high-productivity environments are associated with greater differentiation, possibly driven by intraspecific competition and female-biased selection for increased offspring investment.
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Affiliation(s)
- Valérie A Olson
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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38
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Flightlessness affects cranial morphology in birds. ZOOLOGY 2013; 116:75-84. [DOI: 10.1016/j.zool.2012.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 06/28/2012] [Accepted: 09/06/2012] [Indexed: 11/20/2022]
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39
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Nabholz B, Uwimana N, Lartillot N. Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds. Genome Biol Evol 2013; 5:1273-90. [PMID: 23711670 PMCID: PMC3730341 DOI: 10.1093/gbe/evt083] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2013] [Indexed: 12/22/2022] Open
Abstract
The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.
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Affiliation(s)
- Benoit Nabholz
- Institut des Sciences de l’Evolution, UMR 5554 CNRS, Universite Montpellier II, France
| | - Nicole Uwimana
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Québec, Canada
| | - Nicolas Lartillot
- Département de Biochimie, Centre Robert Cedergren, Université de Montréal, Québec, Canada
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, UMR 5506, CNRS-Université de Montpellier 2, France
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40
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Holt BG, Lessard JP, Borregaard MK, Fritz SA, Araújo MB, Dimitrov D, Fabre PH, Graham CH, Graves GR, Jønsson KA, Nogués-Bravo D, Wang Z, Whittaker RJ, Fjeldså J, Rahbek C. An Update of Wallace’s Zoogeographic Regions of the World. Science 2012; 339:74-8. [PMID: 23258408 DOI: 10.1126/science.1228282] [Citation(s) in RCA: 516] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.
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Affiliation(s)
- Ben G Holt
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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41
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Ledger JM, Malecki I, Groth DM. Characterisation of tetra-nucleotide microsatellite loci in the ostrich (Struthio camelus). Br Poult Sci 2012; 53:460-4. [PMID: 23130580 DOI: 10.1080/00071668.2012.715280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. Eleven polymorphic tetra-nucleotide microsatellite loci were identified in the ostrich (Struthio camelus) using a selective enrichment protocol. 2. The average number of alleles observed was 6·6 with an average heterozygosity of 0·4. 3. The population was found to be in Hardy-Weinberg equilibrium and two of the loci had a greater than 95% probability of having null alleles. 4. These microsatellite loci will add to the existing pool of markers available for the ostrich and help to facilitate analysis of population structure and pedigree determination.
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Affiliation(s)
- J M Ledger
- School of Animal Biology, University of Western Australia, Hackett Drive, Crawley, Western Australia 6009.
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Ha HJ, Alley M, Howe L, Castro I, Gartrell B. Avipoxvirus infections in brown kiwi (Apteryx mantelli). N Z Vet J 2012; 61:49-52. [PMID: 22984886 DOI: 10.1080/00480169.2012.700629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
CASE HISTORY Nodular lesions were found on the skin of two immature brown kiwi (Apteryx mantelli) less than 6 months of age living freely on Ponui Island off the North Island of New Zealand. The lesions were observed during routine external examination undertaken as a part of the management of other research projects, one in 2006 and the other in 2011. Apart from the skin lesions, both birds showed no signs of illness and the lesions resolved spontaneously over a 2-month period. PATHOLOGICAL FINDINGS The first case showed several 3-mm diameter firm, brown nodules located on the skin below the hock of both legs. The second case had a single multinodular mass that measured 7×20 mm, on the base of the bill. A portion of the mass and scab samples were collected for diagnosis. Histological examination of the nodules revealed severe ballooning degeneration of keratinocytes and epithelial hyperplasia. Round eosinophilic structures resembling avipoxvirus (APV) intracytoplasmic inclusion bodies (Bollinger bodies) were observed in the layers of keratinocytes. In deeper layers of the epidermis, there was evidence of secondary bacterial growth and inflammation. DIAGNOSIS DNA was extracted from tissue samples and subjected to PCR analysis. Avipoxvirus 4b core protein gene was detected in both samples by PCR. Bootstrap analysis of APV 4b core protein gene revealed that APV isolates from two kiwi comprised two different subclades. One isolate displayed 100% sequence homology to subclade B1, and the other presented 100% sequence homology to subclade A3. CLINICAL RELEVANCE This study confirmed that kiwi are susceptible to APV infection and that at least two different strains of APV are present in the population examined. Since there is no information on the origin, virulence, or prevalence of APV in kiwi, a seroprevalence study would be useful to elucidate the degree of exposure and immune response to the disease. This would allow a more informed approach to risk management of the disease in wild and captive populations.
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Affiliation(s)
- H J Ha
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
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43
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Haddrath O, Baker AJ. Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds. Proc Biol Sci 2012; 279:4617-25. [PMID: 22977150 DOI: 10.1098/rspb.2012.1630] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122-138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous-Paleogene extinction event.
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Affiliation(s)
- Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada.
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44
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Smith JV, Braun EL, Kimball RT. Ratite nonmonophyly: independent evidence from 40 novel Loci. Syst Biol 2012; 62:35-49. [PMID: 22831877 DOI: 10.1093/sysbio/sys067] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Large-scale multilocus studies have become common in molecular phylogenetics, but the best way to interpret these studies when their results strongly conflict with prior information about phylogeny remains unclear. An example of such a conflict is provided by the ratites (the large flightless birds of southern land masses, including ostriches, emus, and rheas). Ratite monophyly is strongly supported by both morphological data and many earlier molecular studies and is used as a textbook example of vicariance biogeography. However, recent studies have indicated that ratites are not monophyletic; instead, the volant tinamous nest inside the ratites rather than forming their sister group within the avian superorder Palaeognathae. Large-scale studies can exhibit biases that reflect a number of factors, including limitations in the fit of the evolutionary models used for analyses and problems with sequence alignment, so the unexpected conclusion that ratites are not monophyletic needs to be rigorously evaluated. A rigorous approach to testing novel hypotheses generated by large-scale studies is to collect independent evidence (i.e., excluding the loci and/or traits used to generate the hypotheses). We used 40 nuclear loci not used in previous studies that investigated the relationship among ratites and tinamous. Our results strongly support the recent molecular studies, revealing that the deepest branch within Palaeognathae separates the ostrich from other members of the clade, rather than the traditional hypothesis that separates the tinamous from the ratites. To ensure these results reflected evolutionary history, we examined potential biases in types of loci used, heterotachy, alignment biases, and discordance between gene trees and the species tree. All analyses consistently supported nonmonophyly of the ratites and no confounding biases were identified. This confirmation that ratites are not monophyletic using independent evidence will hopefully stimulate further comparative research on paleognath development and genetics that might reveal the basis of the morphological convergence in these large, flightless birds.
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Affiliation(s)
- Jordan V Smith
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
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45
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Huynen L, Millar CD, Lambert DM. Resurrecting ancient animal genomes: the extinct moa and more. Bioessays 2012; 34:661-9. [PMID: 22674514 DOI: 10.1002/bies.201200040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
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46
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Worthy TH, Scofield RP. Twenty-first century advances in knowledge of the biology of moa (Aves: Dinornithiformes): a new morphological analysis and moa diagnoses revised. NEW ZEALAND JOURNAL OF ZOOLOGY 2012. [DOI: 10.1080/03014223.2012.665060] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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Schirtzinger EE, Tavares ES, Gonzales LA, Eberhard JR, Miyaki CY, Sanchez JJ, Hernandez A, Müeller H, Graves GR, Fleischer RC, Wright TF. Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes. Mol Phylogenet Evol 2012; 64:342-56. [PMID: 22543055 DOI: 10.1016/j.ympev.2012.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 04/08/2012] [Accepted: 04/10/2012] [Indexed: 01/06/2023]
Abstract
Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.
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Affiliation(s)
- Erin E Schirtzinger
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA.
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Bon C, Berthonaud V, Maksud F, Labadie K, Poulain J, Artiguenave F, Wincker P, Aury JM, Elalouf JM. Coprolites as a source of information on the genome and diet of the cave hyena. Proc Biol Sci 2012; 279:2825-30. [PMID: 22456883 DOI: 10.1098/rspb.2012.0358] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.
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Affiliation(s)
- Céline Bon
- iBiTec-S/SBiGeM, CEA Saclay, 91191 Gif-sur-Yvette cedex, France
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