1
|
Qian W, Liu Y, Miao K, Chang Q, Hu C. Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes. Curr Genomics 2023; 24:263-272. [PMID: 38169623 PMCID: PMC10758130 DOI: 10.2174/0113892029273517231017051819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/19/2023] [Accepted: 10/02/2023] [Indexed: 01/05/2024] Open
Abstract
Background The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy. Methods In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection. Results Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family. Conclusion This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.
Collapse
Affiliation(s)
- Weiya Qian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yizheng Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Keer Miao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, China
| |
Collapse
|
2
|
Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
Collapse
Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
| |
Collapse
|
3
|
Galbraith JD, Kortschak RD, Suh A, Adelson DL. Genome Stability Is in the Eye of the Beholder: CR1 Retrotransposon Activity Varies Significantly across Avian Diversity. Genome Biol Evol 2021; 13:6433158. [PMID: 34894225 PMCID: PMC8665684 DOI: 10.1093/gbe/evab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/20/2022] Open
Abstract
Since the sequencing of the zebra finch genome it has become clear that avian genomes, while largely stable in terms of chromosome number and gene synteny, are more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element (TE) content have been noted across the avian tree. TEs are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through nonallelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, chicken repeat 1 (CR1) retrotransposons, either focusing on their expansion within single orders, or comparing passerines with nonpasserines. Here, we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and within orders. We describe high levels of TE expansion in genera which have speciated in the last 10 Myr including kiwis, geese, and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals and indicate that genome evolution in amniotes relies on universal TE-driven processes.
Collapse
Affiliation(s)
- James D Galbraith
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Sweden
| | - David L Adelson
- School of Biological Sciences, The University of Adelaide, South Australia, Australia
| |
Collapse
|
4
|
Zhang S, Zheng X, Zhou C, Yang K, Wu Y. The complete mitochondrial genome of Lesser Sand-Plover Charadrius mongolus atrifrons and its phylogenetic position. Mitochondrial DNA B Resour 2021; 6:2880-2881. [PMID: 34532576 PMCID: PMC8439239 DOI: 10.1080/23802359.2021.1972482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Lesser Sand-Plover (Charadrius mongolus atrifrons) is a small shorebird in Charadriiformes. Here we assembled the complete mitochondrial genome of C. m. atrifrons (Aves: Charadriiformes) which is 16,919 bp in length and consisting of 13 protein-coding (PCGs), 2 ribosomal RNA, 22 transfer RNA and 1 control region. The overall A + T content of was 55.5%. The Maximum Likelihood (ML) tree based on the 12 concatenated mitochondrial protein-coding genes (except ND6 gene) placed C. m. atrifrons in a clade with C. alexandrines but separate from C. vociferus.
Collapse
Affiliation(s)
- Shangmingyu Zhang
- Key Laboratory of Bio‐resources and Eco‐environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaofeng Zheng
- Key Laboratory of Bio‐resources and Eco‐environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuang Zhou
- Key Laboratory of Bio‐resources and Eco‐environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kunlin Yang
- Wildlife Resources Survey and Conservation Station of Sichuan Province, Chengdu, China
| | - Yongjie Wu
- Key Laboratory of Bio‐resources and Eco‐environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
5
|
Henrique EP, Oliveira MA, Paulo DC, Pereira PDC, Dias C, Siqueira LS, Lima CM, Miranda DDA, Rego PS, Araripe J, Melo MAD, Diniz DG, Morais Magalhães NG, Sherry DF, Picanço Diniz CW, Diniz CG. Contrasting migratory journeys and changes in hippocampal astrocyte morphology in shorebirds. Eur J Neurosci 2020; 54:5687-5704. [DOI: 10.1111/ejn.14781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/26/2020] [Accepted: 05/07/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Ediely Pereira Henrique
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - Marcus Augusto Oliveira
- Laboratório de Investigações em Neurodegeneração e Infecção no Hospital Universitário João de Barros Barreto Instituto de Ciências Biológicas Universidade Federal do Pará Belém Pará Brazil
| | - Dario Carvalho Paulo
- Laboratório de Investigações em Neurodegeneração e Infecção no Hospital Universitário João de Barros Barreto Instituto de Ciências Biológicas Universidade Federal do Pará Belém Pará Brazil
| | - Patrick Douglas Corrêa Pereira
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - Cleyssian Dias
- Curso de Pós‐Graduação em Zoologia Museu Paraense Emílio Goeldi Universidade Federal do Pará Belém Pará Brazil
| | - Lucas Silva Siqueira
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - Camila Mendes Lima
- Laboratório de Investigações em Neurodegeneração e Infecção no Hospital Universitário João de Barros Barreto Instituto de Ciências Biológicas Universidade Federal do Pará Belém Pará Brazil
| | - Diego de Almeida Miranda
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - Péricles Sena Rego
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Pará Brazil
| | - Juliana Araripe
- Instituto de Estudos Costeiros Universidade Federal do Pará Bragança Pará Brazil
| | - Mauro André Damasceno Melo
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - Daniel Guerreiro Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção no Hospital Universitário João de Barros Barreto Instituto de Ciências Biológicas Universidade Federal do Pará Belém Pará Brazil
- Instituto Evandro Chagas Laboratório de Miscroscopia Eletrônica Belém Pará Brazil
| | - Nara Gyzely Morais Magalhães
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| | - David Francis Sherry
- Department of Psychology Advanced Facility for Avian Research University of Western Ontario London ON Canada
| | - Cristovam Wanderley Picanço Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção no Hospital Universitário João de Barros Barreto Instituto de Ciências Biológicas Universidade Federal do Pará Belém Pará Brazil
| | - Cristovam Guerreiro Diniz
- Laboratório de Biologia Molecular e Neuroecologia Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança Bragança Pará Brazil
| |
Collapse
|
6
|
Rexer-Huber K, Veale AJ, Catry P, Cherel Y, Dutoit L, Foster Y, McEwan JC, Parker GC, Phillips RA, Ryan PG, Stanworth AJ, van Stijn T, Thompson DR, Waters J, Robertson BC. Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel. Mol Ecol 2019; 28:4552-4572. [PMID: 31541577 DOI: 10.1111/mec.15248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023]
Abstract
The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.
Collapse
Affiliation(s)
- Kalinka Rexer-Huber
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Parker Conservation, Dunedin, New Zealand
| | - Andrew J Veale
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Paulo Catry
- MARE - Marine and Environmental Sciences Centre, ISPA - Instituto Universitário, Lisboa, Portugal
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch, Mosgiel, New Zealand
| | | | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa
| | | | | | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Jonathan Waters
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
7
|
Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC. Virome heterogeneity and connectivity in waterfowl and shorebird communities. THE ISME JOURNAL 2019; 13:2603-2616. [PMID: 31239538 PMCID: PMC6775988 DOI: 10.1038/s41396-019-0458-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 05/27/2019] [Indexed: 11/09/2022]
Abstract
Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
Collapse
Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
| |
Collapse
|
8
|
Wallis GP, Jorge F. Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia. Mol Ecol 2018; 27:4368-4396. [DOI: 10.1111/mec.14875] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
| |
Collapse
|
9
|
Dos Remedios N, Lee PLM, Burke T, Székely T, Küpper C. North or south? Phylogenetic and biogeographic origins of a globally distributed avian clade. Mol Phylogenet Evol 2015; 89:151-9. [PMID: 25916188 DOI: 10.1016/j.ympev.2015.04.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 11/16/2022]
Abstract
Establishing phylogenetic relationships within a clade can help to infer ancestral origins and indicate how widespread species reached their current biogeographic distributions. The small plovers, genus Charadrius, are cosmopolitan shorebirds, distributed across all continents except Antarctica. Here we present a global, species-level molecular phylogeny of this group based on four nuclear (ADH5, FIB7, MYO2 and RAG1) and two mitochondrial (COI and ND3) genes, and use the phylogeny to examine the biogeographic origin of the genus. A Bayesian multispecies coalescent approach identified two major clades (CRD I and CRD II) within the genus. Clade CRD I contains three species (Thinornis novaeseelandiae, Thinornis rubricollis and Eudromias morinellus), and CRD II one species (Anarhynchus frontalis), that were previously placed outside the Charadrius genus. In contrast to earlier work, ancestral area analyses using parsimony and Bayesian methods supported an origin of the Charadrius plovers in the Northern hemisphere. We propose that major radiations in this group were associated with shifts in the range of these ancestral plover species, leading to colonisation of the Southern hemisphere.
Collapse
Affiliation(s)
- Natalie Dos Remedios
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK; NERC-Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Patricia L M Lee
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Warrnambool, Victoria 3280, Australia; Department of Biosciences, College of Science, Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Terry Burke
- NERC-Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Tamás Székely
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Clemens Küpper
- NERC-Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| |
Collapse
|