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Pelegrin JS, Cantalapiedra JL, Gamboa S, Menéndez I, Hernández Fernández M. Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for the first time, the evolution of biome occupation in birds. We aimed to analyse patterns of adaptation to different climatic regimes and the determinant factors for colonization of emerging biomes by clades from different ancestral biomes. In this work, we reconstructed the biome occupation history of two clades of birds (Galliformes and Falconiformes) under an integrative perspective through a comprehensive review of ecological, phylogenetic, palaeontological and biogeographical evidence. Our findings for both groups are consistent with a scenario of phylogenetic biome conservatism and highlight the importance of changes in climate during the Miocene in the adaptation and evolution of climatic niches. In particular, our results indicate high biome conservatism associated with biomes situated in some of the extremes of the global climate gradient (evergreen tropical rainforest, steppe and tundra) for both bird taxa. Finally, the historical dynamics of tropical seasonal biomes, such as tropical deciduous woodlands and savannas, appear to have played a preponderant role during the diversification processes of these bird lineages.
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Affiliation(s)
- Jonathan S Pelegrin
- Grupo de Investigación en Ecología y Conservación de la Biodiversidad (EcoBio), Área de Biología y Programa de Maestría en Educación Ambiental y Desarrollo Sostenible, Facultades de Ciencias Básicas y Educación, Universidad Santiago de Cali , Colombia
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle , Colombia
| | - Juan L Cantalapiedra
- GloCEE – Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá , 28805, Alcalá de Henares (Madrid ), Spain
| | - Sara Gamboa
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Iris Menéndez
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
| | - Manuel Hernández Fernández
- Departamento de Estratigrafía, Geodinámica y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid , C/ José Antonio Novais 2, 28040, Madrid , Spain
- Departamento de Cambio Medio Ambiental, Instituto de Geociencias (UCM, CSIC) , C/ José Antonio Novais 2, 28040, Madrid , Spain
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2
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Callender-Crowe LM, Sansom RS. Osteological characters of birds and reptiles are more congruent with molecular phylogenies than soft characters are. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Despite increased use of genomic data in phylogenetics, morphological information remains vital for resolving evolutionary relationships, particularly for fossil taxa. The properties and models of evolution of molecular sequence data are well characterized and mature, relative to those of morphological data. Furthermore, heterogeneity, integration and relative homoplasy of empirical morphological data could prove problematic for phylogenetic reconstruction. Here we compare osteological and non-osteological characters of 28 morphological datasets of extant saurians in terms of their homoplasy relative to molecular trees. Analysis of individual avian datasets finds osteological characters to be significantly more consistent with molecular data than soft characters are. Significant differences between morphological partitions were also observed in the age at which characters resolved on molecular trees. Osteological character changes occur relatively earlier in deep branches, whilst soft-tissue character transitions are more recent in shallow branches. The combined results demonstrate differences in evolutionary dynamics between morphological partitions. This may reflect evolutionary constraints acting on osteological characters, compared with the relative lability of soft characters. Furthermore, it provides some support to phylogenetic interpretations of fossil data, including dinosaurs, which are predominately osteological. Recent advances in amphibian and mammal phylogenetics may make these patterns possible to test for all tetrapods.
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Affiliation(s)
- Leah M Callender-Crowe
- The University of Manchester, Department of Earth and Environmental Sciences, Manchester, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Robert S Sansom
- The University of Manchester, Department of Earth and Environmental Sciences, Manchester, UK
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3
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Lawal RA, Hanotte O. Domestic chicken diversity: Origin, distribution, and adaptation. Anim Genet 2021; 52:385-394. [PMID: 34060099 DOI: 10.1111/age.13091] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.
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Affiliation(s)
- R A Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - O Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.,LiveGene, International Livestock Research Institute (ILRI), P.O. 5689, Addis Ababa, Ethiopia
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4
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Hüppi E, Werneburg I, Sánchez-Villagra MR. Evolution and development of the bird chondrocranium. Front Zool 2021; 18:21. [PMID: 33926502 PMCID: PMC8082637 DOI: 10.1186/s12983-021-00406-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/08/2021] [Indexed: 01/29/2023] Open
Abstract
Background Birds exhibit an enormous diversity in adult skull shape (disparity), while their embryonic chondrocrania are considered to be conserved across species. However, there may be chondrocranial features that are diagnostic for bird clades or for Aves as a whole. We synthesized and analyzed information on the sequence of chondrification of 23 elements in ten bird species and five outgroups. Moreover, we critically considered the developmental morphology of the chondrocrania of 21 bird species and examined whether the diversity in adult skull shape is reflected in the development of the embryonic skull, and whether there are group-specific developmental patterns. Results We found that chondrocranial morphology is largely uniform in its major features, with some variation in the presence or absence of fenestrae and other parts. In kiwis (Apteryx), the unique morphology of the bony skull in the orbito-nasal region is reflected in its chondrocranial anatomy. Finally, differences in morphology and chondrification sequence may distinguish between different Palaeognathae and Neognathae and between the Galloanserae and Neoaves. The sequence of chondrification is largely conserved in birds, but with some variation in most regions. The peri- and prechordal areas in the base of the chondrocranium are largely conserved. In contrast to the outgroups, chondrification in birds starts in the acrochordal cartilage and the basicranial fenestra is formed secondarily. Further differences concern the orbital region, including early chondrification of the pila antotica and the late formation of the planum supraseptale. Conclusion Synthesizing information on chondrocranial development confronts terminological issues and a lack of comparable methods used (e.g., different staining; whole-mounts versus histology). These issues were taken into consideration when assessing differences across species. The summary of works on avian chondrocranial development, covered more than a century, and a comparison of the chondrification sequence among birds could be conducted. Future studies could test the hypothesis that chondrocranial disparity in Aves, in terms of the shape and proportion of individual elements, could be as large as adult skull disparity, despite conserved developmental patterns and the richness of forms in other (dermal) portions of the skull. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-021-00406-z.
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Affiliation(s)
- Evelyn Hüppi
- Universität Zürich, Paläontologisches Institut und Museum, Karl-Schmid-Straße 4, 8006, Zürich, Switzerland.
| | - Ingmar Werneburg
- Senckenberg Center for Human Evolution and Palaeoenvironment (HEP) an der Eberhard Karls Universität, Sigwartstraße 10, 72076, Tübingen, Germany.,Fachbereich Geowissenschaften der Eberhard-Karls-Universität Tübingen, Hölderlinstraße 12, 72074, Tübingen, Germany
| | - Marcelo R Sánchez-Villagra
- Universität Zürich, Paläontologisches Institut und Museum, Karl-Schmid-Straße 4, 8006, Zürich, Switzerland
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5
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Kimball RT, Hosner PA, Braun EL. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. Mol Phylogenet Evol 2021; 158:107091. [PMID: 33545275 DOI: 10.1016/j.ympev.2021.107091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
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Affiliation(s)
- Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32607, USA.
| | - Peter A Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA; Natural History Museum of Denmark and Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
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6
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Lawal RA, Martin SH, Vanmechelen K, Vereijken A, Silva P, Al-Atiyat RM, Aljumaah RS, Mwacharo JM, Wu DD, Zhang YP, Hocking PM, Smith J, Wragg D, Hanotte O. The wild species genome ancestry of domestic chickens. BMC Biol 2020; 18:13. [PMID: 32050971 PMCID: PMC7014787 DOI: 10.1186/s12915-020-0738-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/08/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. RESULTS In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. CONCLUSIONS Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.
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Affiliation(s)
- Raman Akinyanju Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Present Address: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Simon H Martin
- Present Address: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Koen Vanmechelen
- Open University of Diversity - Mouth Foundation, Hasselt, Belgium
| | - Addie Vereijken
- Technology and Service B.V., Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Pradeepa Silva
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Raed Mahmoud Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
| | | | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Dong-Dong Wu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ya-Ping Zhang
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.
- LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia.
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7
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Episodic positive diversifying selection on key immune system genes in major avian lineages. Genetica 2019; 147:337-350. [PMID: 31782071 DOI: 10.1007/s10709-019-00081-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/19/2019] [Indexed: 01/08/2023]
Abstract
The major histocompatibility complex (MHC) of the adaptive immune system and the toll-like receptor (TLR) family of the innate immune system are involved in the detection of foreign invaders, and thus are subject to parasite-driven molecular evolution. Herein, we tested for macroevolutionary signatures of selection in these gene families within and among all three major clades of birds (Paleognathae, Galloanserae, and Neoaves). We characterized evolutionary relationships of representative immune genes (Mhc1 and Tlr2b) and a control gene (ubiquitin, Ubb), using a relatively large and phylogenetically diverse set of species with complete coding sequences (34 orthologous loci for Mhc1, 29 for Tlr2b, and 37 for Ubb). Episodic positive diversifying selection was found in the gene-wide phylogenies of the two immune genes, as well as at specific sites within each gene (8.5% of codon sites in Mhc1 and 2.7% in Tlr2b), but not in the control gene (Ubb). We found 20% of lineages under episodic diversifying selection in Mhc1 versus 9.1% in Tlr2b. For Mhc1, selection was relaxed in the Galloanserae and intensified in the Neoaves relative to the other clades, but no differences were detected among clades in the Tlr2b gene. In summary, we provide evidence of episodic positive diversifying selection in key immune genes and demonstrate differential strengths of selection within Class Aves, with the adaptive gene showing an increased divergence and evolutionary rate over the innate gene, contributing to the growing understanding of vertebrate immune gene evolution.
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Rando JC, Alcover JA, Pieper H, Olson SL, Hernández CN, López-Jurado LF. Unforeseen diversity of quails (Galliformes: Phasianidae: Coturnix) in oceanic islands provided by the fossil record of Macaronesia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The original bird fauna of most oceanic islands has been affected by recent extinction processes associated with human arrival and its subsequent impacts. In the volcanic Macaronesian archipelagos (Azores, Madeira, Selvagens, Canary Islands and Cape Verde), in the North Atlantic, the Late Quaternary fossil record indicates that there was formerly a higher avian diversity, including a high number of now extinct endemic species. This assemblage of extinct birds includes endemic insular quails (Galliformes: Phasianidae). In this study, we describe three newly discovered extinct species of quails, two of which inhabited the archipelago of Madeira (Coturnix lignorum sp. nov. from Madeira Island and Coturnix alabrevis sp. nov. from Porto Santo Island) and one from Cape Verde (Coturnix centensis sp. nov.). The fossil record also indicates the presence of additional species of extinct endemic quails on other Macaronesian islands. These birds plus the extinct Canary Island quail (Coturnix gomerae) indicate a high former endemic diversity of this genus in Macaronesia, a feature unique among oceanic archipelagos. Anatomical traits show that the new taxa were flightless ground dwellers, making them vulnerable to human interference, with their extinction being linked to human arrival and subsequent habitat alterations and the introduction of invasive species.
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Affiliation(s)
- Juan C Rando
- Universidad de La Laguna (ULL), Departamento de Biología Animal, Edafología y Geología, Santa Cruz de Tenerife, Canary Islands, Spain
| | - Josep A Alcover
- Departament de Biodiversitat i Conservació, Institut Mediterrani d'Estudis Avançats, Cr Miquel Marquès 21, Esporles, Mallorca, Balearic Islands, Spain
| | | | - Storrs L Olson
- Division of Birds, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C Nayra Hernández
- Asociación de Estudios Paleontológicos de Canarias (PALEOCANARIAS), Laboratorio de Paleontogía, Facultad Ciencias del Mar, ULPGC, Las Palmas de Gran Canaria, Spain
| | - L Felipe López-Jurado
- Departamento de Biología, Facultad de Ciencias del Mar, ULPGC, Las Palmas de Gran Canaria, Spain
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van Raamsdonk LWD, Prins TW, Meijer N, Scholtens IMJ, Bremer MGEG, de Jong J. Bridging legal requirements and analytical methods: a review of monitoring opportunities of animal proteins in feed. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2019; 36:46-73. [PMID: 30608892 DOI: 10.1080/19440049.2018.1543956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Availability and safety of food ranks among the basic requirements for human beings. The importance of the food producing sector, inclusive of feed manufacturing, demands a high level of regulation and control. This paper will present and discuss the relationships in the triangle of legislation, the background of hazards with a biological nature, and opportunities for monitoring methods, most notable for prion-based diseases as primary issue. The European Union legislation for prevention of prion-based diseases since 2000 is presented and discussed. The definitions and circumscriptions of groups of species will be analysed in the view biological classification and evolutionary relationships. The state of the art of monitoring methods is presented and discussed. Methods based on visual markers (microscopy), DNA-based methods (PCR), protein-based methods (ELISA, mass spectroscopy, proteomics), near infrared oriented methods and combinations thereof are being evaluated. It is argued that the use in legislation of non-homogeneous groups of species in a biological sense will hamper the optimal design of monitoring methods. Proper definitions are considered to act as bridges between legal demands and suitable analytical methods for effective monitoring. Definitions including specified groups of species instead of single species are more effective for monitoring in a range of cases. Besides the desire of precise circumscription of animal groups targeted by legislation, processed products need well defined definitions as well. Most notable examples are blood versus blood products, and hydrolysis of several types of material. The WISE principle for harmonising the design of legislation and of analytical methods is discussed. This principle includes the elements Witful (reasonable legal principles), Indicative (clear limits between prohibition and authorisation), Societal demands (public health, environment, economy), and Enforceable (presence of suited monitoring methods) in order to promote a balanced effort for reaching the desired level of safety in the food production chain.
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10
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Lee CY, Hsieh PH, Chiang LM, Chattopadhyay A, Li KY, Lee YF, Lu TP, Lai LC, Lin EC, Lee H, Ding ST, Tsai MH, Chen CY, Chuang EY. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. Gigascience 2018; 7:4990948. [PMID: 29722814 PMCID: PMC5941149 DOI: 10.1093/gigascience/giy044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/13/2018] [Indexed: 01/10/2023] Open
Abstract
Background The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. Results We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. Conclusions This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.
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Affiliation(s)
- Chien-Yueh Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Ping-Han Hsieh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Mei Chiang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Kuan-Yi Li
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Fang Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei 10051, Taiwan
| | - En-Chung Lin
- Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsinyu Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Shih-Torng Ding
- Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Center for Systems Biology, National Taiwan University, Taipei 10672, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Chinese Medical Science, China Medical University, Taichung 40402, Taiwan
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11
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Mounce R, Murray-Rust P, Wills M. A machine-compiled microbial supertree from figure-mining thousands of papers. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e13589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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12
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Wang N, Hosner PA, Liang B, Braun EL, Kimball RT. Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data. Mol Phylogenet Evol 2017; 109:217-225. [DOI: 10.1016/j.ympev.2017.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 12/24/2016] [Accepted: 01/07/2017] [Indexed: 12/09/2022]
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13
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Calvo Carrasco D, Sabater González M. Reproductive Disorders in Commonly Kept Fowl. Vet Clin North Am Exot Anim Pract 2017; 20:509-538. [PMID: 28169183 DOI: 10.1016/j.cvex.2016.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Backyard poultry and other commonly kept fowl species are often kept for their ability to lay eggs. Reproductive disease is common in fowl species. Despite being classified as food-producing species, they can be considered valuable pets, and the demand for adequate veterinary care is constantly increasing. The clinician should be familiar with the different abnormalities and the potential treatment options. Fowl species have been traditionally an anatomic, physiologic, and experimental model for avian medicine; however, information about treatment options is often limited and extrapolated from other species.
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Affiliation(s)
- Daniel Calvo Carrasco
- Great Western Exotics, Vets-Now Referrals, Unit 10 Berkshire House, County Business Park, Shrivenham Road, Swindon SN1 2NR, UK.
| | - Mikel Sabater González
- Avian, Reptile and Exotic Pet Hospital, University of Sydney, 415 Werombi Road, Brownlow Hil, New South Wales 2570, Australia
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14
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Lüpold S, Manier MK, Puniamoorthy N, Schoff C, Starmer WT, Luepold SHB, Belote JM, Pitnick S. How sexual selection can drive the evolution of costly sperm ornamentation. Nature 2016; 533:535-8. [PMID: 27225128 DOI: 10.1038/nature18005] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/13/2016] [Indexed: 01/17/2023]
Abstract
Post-copulatory sexual selection (PSS), fuelled by female promiscuity, is credited with the rapid evolution of sperm quality traits across diverse taxa. Yet, our understanding of the adaptive significance of sperm ornaments and the cryptic female preferences driving their evolution is extremely limited. Here we review the evolutionary allometry of exaggerated sexual traits (for example, antlers, horns, tail feathers, mandibles and dewlaps), show that the giant sperm of some Drosophila species are possibly the most extreme ornaments in all of nature and demonstrate how their existence challenges theories explaining the intensity of sexual selection, mating-system evolution and the fundamental nature of sex differences. We also combine quantitative genetic analyses of interacting sex-specific traits in D. melanogaster with comparative analyses of the condition dependence of male and female reproductive potential across species with varying ornament size to reveal complex dynamics that may underlie sperm-length evolution. Our results suggest that producing few gigantic sperm evolved by (1) Fisherian runaway selection mediated by genetic correlations between sperm length, the female preference for long sperm and female mating frequency, and (2) longer sperm increasing the indirect benefits to females. Our results also suggest that the developmental integration of sperm quality and quantity renders post-copulatory sexual selection on ejaculates unlikely to treat male-male competition and female choice as discrete processes.
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Affiliation(s)
- Stefan Lüpold
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mollie K Manier
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA.,Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington DC 20052, USA
| | - Nalini Puniamoorthy
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA.,Department of Biological Sciences, National University of Singapore, 14 Science Drive, SG 117543, Singapore
| | - Christopher Schoff
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA
| | - William T Starmer
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA
| | - Shannon H Buckley Luepold
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA
| | - John M Belote
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, 107 College Place, Syracuse, New York 13244-1270, USA
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15
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Sabater González M, Calvo Carrasco D. Emergencies and Critical Care of Commonly Kept Fowl. Vet Clin North Am Exot Anim Pract 2016; 19:543-65. [PMID: 26948266 PMCID: PMC7110600 DOI: 10.1016/j.cvex.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Fowl are birds belonging to one of the 2 biological orders, the game fowl or land fowl (Galliformes) and the waterfowl (Anseriformes). Studies of anatomic and molecular similarities suggest these two groups are close evolutionary relatives. Multiple fowl species have a long history of domestication. Fowl are considered food-producing animals in most countries and clinicians should follow legislation regarding reportable diseases and antibiotic use, even if they are pets. This article reviews aspects of emergency care for most commonly kept fowl, including triage, patient assessment, diagnostic procedures, supportive care, short-term hospitalization, and common emergency presentations.
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Affiliation(s)
| | - Daniel Calvo Carrasco
- Great Western Exotics, Vets-Now Referrals, Unit 10 Berkshire House, County Business Park, Shrivenham Road, Swindon SN1 NR, UK
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16
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Vinkler M, Bainová H, Bryja J. Protein evolution of Toll-like receptors 4, 5 and 7 within Galloanserae birds. Genet Sel Evol 2014; 46:72. [PMID: 25387947 PMCID: PMC4228102 DOI: 10.1186/s12711-014-0072-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/10/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Toll-like receptors (TLR) are essential activators of the innate part of the vertebrate immune system. In this study, we analysed the interspecific variability of three TLR (bacterial-sensing TLR4 and TLR5 and viral-sensing TLR7) within the Galloanserae bird clade, investigated their phylogeny, assessed their structural conservation and estimated site-specific selection pressures. RESULTS Physiochemical properties varied according to the TLR analysed, mainly with regards to the surface electrostatic potential distribution. The predicted ligand-binding features (mainly in TLR4 and TLR5) differed between the avian proteins and their fish and mammalian counterparts, but also varied within the Galloanserae birds. We identified 20 positively selected sites in the three TLR, among which several are topologically close to ligand-binding sites reported for mammalian and fish TLR. We described 26, 28 and 25 evolutionarily non-conservative sites in TLR4, TLR5 and TLR7, respectively. Thirteen of these sites in TLR4, and ten in TLR5 were located in functionally relevant regions. The variability appears to be functionally more conserved for viral-sensing TLR7 than for the bacterial-sensing TLR. Amino-acid positions 268, 270, 343, 383, 444 and 471 in TLR4 and 180, 183, 209, 216, 264, 342 and 379 in TLR5 are key candidates for further functional research. CONCLUSIONS Host-pathogen co-evolution has a major effect on the features of host immune receptors. Our results suggest that avian and mammalian TLR may be differentially adapted to pathogen-derived ligand recognition. We have detected signatures of positive selection even within the Galloanserae lineage. To our knowledge, this is the first study to depict evolutionary pressures on Galloanserae TLR and to estimate the validity of current knowledge on TLR function (based on mammalian and chicken models) for non-model species of this clade.
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Affiliation(s)
- Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University in Prague, Praha, Czech Republic.
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Brennan PLR, Adkins-Regan E. Endocrine regulation and sexual differentiation of avian copulatory sexually selected characters. Neurosci Biobehav Rev 2014; 46 Pt 4:557-66. [PMID: 25179524 DOI: 10.1016/j.neubiorev.2014.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 07/18/2014] [Accepted: 08/21/2014] [Indexed: 01/12/2023]
Abstract
Reproductive specializations in birds have provided intriguing model systems to better understand the role of endocrine mechanisms that regulate phenotype expression and the action of sexual selection. A comparative approach can elucidate how endocrine systems associated with control of sexual differentiation, sexual maturation, and reproductive physiology and behavior have diversified. Here we compare the copulatory sexually selected traits of two members of the galloanseriform superfamily: quail and ducks. Japanese quail have a non-intromittent penis, and they have evolved a unique foam gland that is known to be involved in post-copulatory sexual selection. In contrast, ducks have maintained a large intromittent penis that has evolved via copulatory male-male competition and has been elaborated in a sexually antagonistic race due to sexual conflict with females over mating. These adaptations function in concert with sex-specific and, in part, species-specific behaviors. Although the approaches to study these traits have been different, exploring the differences in neuroendocrine regulation of sexual behavior, development and seasonality of the foam gland and the penis side by side, allow us to suggest some areas where future research would be productive to better understand the evolution of novelty in sexually selected traits.
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Affiliation(s)
- Patricia L R Brennan
- Organismic and Evolutionary Biology Graduate Program and Departments of Psychology and of Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA.
| | - Elizabeth Adkins-Regan
- Departments of Psychology and of Neurobiology and Behavior, Cornell University, Ithaca, NY 14850, USA
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18
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Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii). Gene 2014; 539:21-9. [DOI: 10.1016/j.gene.2014.01.067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/26/2014] [Accepted: 01/29/2014] [Indexed: 01/20/2023]
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Omeire D, Abdin S, Brooks DM, Miranda HC. Complete mitochondrial genome of Germain's Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae). MITOCHONDRIAL DNA 2014; 26:319-20. [PMID: 24460165 DOI: 10.3109/19401736.2013.830292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Germain's Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae) is classified as Near Threatened on the IUCN Red List. The complete mitochondrial genome of P. germaini is 16,699 bp, consisting of 13 protein-coding genes, 2 rRNA, 22 tRNA genes and 1 control region. All of the 13 protein-coding genes have ATG as start codon. Eight of the 13 protein-coding genes have TAA as stop codon.
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Affiliation(s)
- Destiny Omeire
- Department of Biology, Texas Southern University , TX , USA and
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20
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Zhou TC, Sha T, Irwin DM, Zhang YP. Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae. MITOCHONDRIAL DNA 2014; 26:912-3. [PMID: 24409883 DOI: 10.3109/19401736.2013.863287] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Pavo cristatus, known as the Indian peafowl, is endemic to India and Sri Lanka and has been domesticated for its ornamental and food value. However, its phylogenetic status is still debated. Here, to clarify the phylogenetic status of P. cristatus within Phasianidae, we analyzed its mitochondrial genome (mtDNA). The complete mitochondrial DNA (mtDNA) genome was determined using 34 pairs of primers. Our data show that the mtDNA genome of P. cristatus is 16,686 bp in length. Molecular phylogenetic analyses of P. cristatus was performed along with 22 complete mtDNA genomes belonging to other species in Phasianidae using Bayesian and maximum likelihood methods, where Aythya americana and Anas platyrhynchos were used as outgroups. Our results show that P. critatus has its closest genetic affinity with Pavo muticus and belongs to clade that contains Gallus, Bambusicola and Francolinus.
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Affiliation(s)
- Tai-Cheng Zhou
- a Laboratory for Conservation and Utilization of Bio-resources , Yunnan University , Kunming , China .,b State Key Laboratory of Genetic Resources and Evolution , Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China , and
| | - Tao Sha
- a Laboratory for Conservation and Utilization of Bio-resources , Yunnan University , Kunming , China
| | - David M Irwin
- b State Key Laboratory of Genetic Resources and Evolution , Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China , and.,c Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Ya-Ping Zhang
- a Laboratory for Conservation and Utilization of Bio-resources , Yunnan University , Kunming , China .,b State Key Laboratory of Genetic Resources and Evolution , Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming , China , and
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21
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Gluckman TL. Pathways to elaboration of sexual dimorphism in bird plumage patterns. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Thanh-Lan Gluckman
- Department of Zoology; University of Melbourne; Parkville Victoria 3010 Australia
- Department of Zoology; University of Cambridge; Cambridge CB2 3EJ UK
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22
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Rodrigues BS, de Assis MDFL, O'Brien PCM, Ferguson-Smith MA, de Oliveira EHC. Chromosomal studies onCoscoroba coscoroba(Aves: Anseriformes) reinforce theCoscoroba-Cereopsisclade. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benilson S. Rodrigues
- Programa de Pós Graduação em Genética e Biologia Molecular; ICB; Universidade Federal do Pará, Campus Universitário do Guamá; 66075-110 Belém-PA, Brazil
| | - Maria De Fatima L. de Assis
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua-PA, Brazil
| | - Patricia C. M. O'Brien
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
| | - Edivaldo H. C. de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética; SAMAM; Instituto Evandro Chagas; BR 316 KM 7 s/n Levilândia 67020-000 Ananindeua-PA, Brazil
- Cambridge Resource Centre for Comparative Genomics; Department of Veterinary Medicine; University of Cambridge; Madingley Road Cambridge CB3 0ES UK
- Faculdade de Ciências Naturais; ICEN; Universidade Federal do Pará, Campus Universitário do Guamá; 66075-110 Belém-PA, Brazil
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23
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Cunningham SJ, Corfield JR, Iwaniuk AN, Castro I, Alley MR, Birkhead TR, Parsons S. The anatomy of the bill tip of kiwi and associated somatosensory regions of the brain: comparisons with shorebirds. PLoS One 2013; 8:e80036. [PMID: 24244601 PMCID: PMC3828210 DOI: 10.1371/journal.pone.0080036] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/27/2013] [Indexed: 11/18/2022] Open
Abstract
Three families of probe-foraging birds, Scolopacidae (sandpipers and snipes), Apterygidae (kiwi), and Threskiornithidae (ibises, including spoonbills) have independently evolved long, narrow bills containing clusters of vibration-sensitive mechanoreceptors (Herbst corpuscles) within pits in the bill-tip. These 'bill-tip organs' allow birds to detect buried or submerged prey via substrate-borne vibrations and/or interstitial pressure gradients. Shorebirds, kiwi and ibises are only distantly related, with the phylogenetic divide between kiwi and the other two taxa being particularly deep. We compared the bill-tip structure and associated somatosensory regions in the brains of kiwi and shorebirds to understand the degree of convergence of these systems between the two taxa. For comparison, we also included data from other taxa including waterfowl (Anatidae) and parrots (Psittaculidae and Cacatuidae), non-apterygid ratites, and other probe-foraging and non probe-foraging birds including non-scolopacid shorebirds (Charadriidae, Haematopodidae, Recurvirostridae and Sternidae). We show that the bill-tip organ structure was broadly similar between the Apterygidae and Scolopacidae, however some inter-specific variation was found in the number, shape and orientation of sensory pits between the two groups. Kiwi, scolopacid shorebirds, waterfowl and parrots all shared hypertrophy or near-hypertrophy of the principal sensory trigeminal nucleus. Hypertrophy of the nucleus basorostralis, however, occurred only in waterfowl, kiwi, three of the scolopacid species examined and a species of oystercatcher (Charadriiformes: Haematopodidae). Hypertrophy of the principal sensory trigeminal nucleus in kiwi, Scolopacidae, and other tactile specialists appears to have co-evolved alongside bill-tip specializations, whereas hypertrophy of nucleus basorostralis may be influenced to a greater extent by other sensory inputs. We suggest that similarities between kiwi and scolopacid bill-tip organs and associated somatosensory brain regions are likely a result of similar ecological selective pressures, with inter-specific variations reflecting finer-scale niche differentiation.
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Affiliation(s)
- Susan J. Cunningham
- Percy FitzPatrick Institute, DST/NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa
- Institute of Natural Resources, Massey University, Palmerston North, New Zealand
| | - Jeremy R. Corfield
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Andrew N. Iwaniuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Isabel Castro
- Institute of Natural Resources, Massey University, Palmerston North, New Zealand
| | - Maurice R. Alley
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Tim R. Birkhead
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Stuart Parsons
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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Abstract
In this study, based on phylogenetic diversity (PD), I develop a conservation strategy for Galliformes species around the world. A cladogram of 197 Galliformes species derived from a previous study was used for calculating PD metrics. Branch length is an important aspect of the phylogenetic information a tree can convey, but 2 traditionally-used metrics, the number of phylogenetic groups to which a taxon belongs (I) and the proportion that each taxon contributes to the total diversity of the group (W), are fully node-based and do not take branch length into account. Therefore, to measure PD more appropriately, I combined a branch-related metric, pendant edge (P), in addition to I and W. A final combined rank for Galliformes species was obtained by summing the ranks of the 3 metrics. My results showed that the 5% top priority species for conserving evolutionary potential were Galloperdix lunulata, Haematortyx sanguiniceps, Margaroperdix madagarensis, Syrmaticus soemmerringii, Coturnix pectoralis, Polyplectron napoleonis, Alectoris melanocephala, Xenoperdix udzungwensis, Afropavo congensis and Syrmaticus reevesii. The current species priority ranking based on pylogenetic diversity and the official International Union for Conservation of Nature (IUCN) ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN (critical endangered, endangered, vulnerable, near threatened and least concern). This indicated the feasibility of introducing the PD index into the network of IUCN regional Red List assessment. The 5% top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China, Indonesia, Mexico, India, Colombia, Australia, Brazil, Angola, Congo and Japan (in descending order). China, Indonesia, Mexico, Brazil, India and Colombia are consistently selected among the 4 top priority sets of richness, rarity, endemicity and PD. This result indicated that the priority result from PD is highly congruent with conventional measures. Along with other conventional ecological attributes, the alternative conservation scenario based on PD is reasonable and can be adopted in systematic conservation planning.
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Affiliation(s)
- Youhua Chen
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada. ,
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25
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Promerová M, Králová T, Bryjová A, Albrecht T, Bryja J. MHC class IIB exon 2 polymorphism in the Grey partridge (Perdix perdix) is shaped by selection, recombination and gene conversion. PLoS One 2013; 8:e69135. [PMID: 23935938 PMCID: PMC3720538 DOI: 10.1371/journal.pone.0069135] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022] Open
Abstract
Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.
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Affiliation(s)
- Marta Promerová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tereza Králová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Tomáš Albrecht
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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26
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Wang N, Kimball RT, Braun EL, Liang B, Zhang Z. Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS One 2013; 8:e64312. [PMID: 23741315 PMCID: PMC3669371 DOI: 10.1371/journal.pone.0064312] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 04/11/2013] [Indexed: 12/16/2022] Open
Abstract
Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups ("pheasants" and "partridges") is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.
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Affiliation(s)
- Ning Wang
- Key Laboratory for Biodiversity Sciences and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Key Laboratory for Tropical Plant and Animal Ecology of Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Bin Liang
- Key Laboratory for Tropical Plant and Animal Ecology of Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Zhengwang Zhang
- Key Laboratory for Biodiversity Sciences and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
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27
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Klingenberg CP, Marugán-Lobón J. Evolutionary Covariation in Geometric Morphometric Data: Analyzing Integration, Modularity, and Allometry in a Phylogenetic Context. Syst Biol 2013; 62:591-610. [DOI: 10.1093/sysbio/syt025] [Citation(s) in RCA: 267] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Christian Peter Klingenberg
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK; and 2Unidad de Paleontología, Departamento de Biología, C/Darwin 2, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jesús Marugán-Lobón
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK; and 2Unidad de Paleontología, Departamento de Biología, C/Darwin 2, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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28
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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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Kimball RT, Mary CMS, Braun EL. A macroevolutionary perspective on multiple sexual traits in the phasianidae (galliformes). INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:423938. [PMID: 21716735 PMCID: PMC3119463 DOI: 10.4061/2011/423938] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 02/26/2011] [Indexed: 11/20/2022]
Abstract
Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them. Even with this limitation, when the predictions of these alternative models were compared with the heterogeneous patterns of evolution of dimorphism in phasianids, it is clear that many different selective processes have been involved in the evolution of sexual signals in this group.
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Affiliation(s)
- Rebecca T. Kimball
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
| | - Colette M. St. Mary
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
| | - Edward L. Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611, USA
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Andres K, Kapkowska E. Applicability of anatid and galliform microsatellite markers to the genetic diversity studies of domestic geese (Anser anser domesticus) through the genotyping of the endangered zatorska breed. BMC Res Notes 2011; 4:65. [PMID: 21410974 PMCID: PMC3069940 DOI: 10.1186/1756-0500-4-65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 03/16/2011] [Indexed: 11/10/2022] Open
Abstract
Background The lack of a sufficient number of molecular markers seriously limits the cognition of genetic relationships within and between populations of many species. Likewise, the genetic diversity of domestic goose (Anser anser domesticus), with a great number of breeds throughout the world, remains poorly understood at the molecular level. Findings Thirty-five goose, seventeen duck and eight chicken microsatellite primer pairs were screened for their utility in the cross-species amplification on DNA from 96 individuals of Zatorska breed of domestic geese. Twenty-seven of 42 amplifying primer pairs revealed length-polymorphic products, but three of them were difficult to score. Fifteen primer pairs amplifying the same length product across all individuals. One polymorphic microsatellite locus was assigned by genotyping of known sex individuals to the Z-chromosome. Conclusions We present a set of 24 polymorphic microsatellite markers useful for population genetic studies of the domestic goose. Another 15 markers were classified as monomorphic, but they might also be suitable for the assessment of genetic diversity in geese.
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Affiliation(s)
- Krzysztof Andres
- Department of Poultry and Fur Animal Breeding and Animal Hygiene, Agricultural University of Krakow, Mickiewicza 24/28, 30-059 Kraków, Poland.
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Eo SH, Doyle JM, DeWoody JA. Genetic diversity in birds is associated with body mass and habitat type. J Zool (1987) 2010. [DOI: 10.1111/j.1469-7998.2010.00773.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Klug S, Kriwet J. Timing of deep-sea adaptation in dogfish sharks: insights from a supertree of extinct and extant taxa. ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00427.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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