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Çakar B, Bulut EÇ, Kahvecioglu O, Günay E, Ruzhanova-Gospodinova IS, Szara T. Bill shape variation in selected species in birds of prey. Anat Histol Embryol 2024; 53:e13085. [PMID: 38965917 DOI: 10.1111/ahe.13085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
At the top of many ecosystems, raptors, also known as birds of prey, hold major influence. They shape their surroundings through their powerful hunting skills and complex interactions with their environment. This study investigates the beak morphology of four prominent raptor species, Golden eagle (Aquila chrysaetos), Common buzzard (Buteo buteo), Peregrine falcon (Falco peregrinus) and Common kestrel (Falco tinnunculus), found in Türkiye. By employing geometric morphometric methods, we investigate shape variations in the beaks of these species to unravel the adaptive significance of their cranial structures. This analysis reveals distinct beak morphologies among the studied raptors, reflecting adaptations to their feeding habits, hunting techniques and ecological niches. The results from Principal component analysis and Canonical variate analysis demonstrate significant differences in beak morphology between the Falconiformes and Accipitriformes clades, as well as among all three groups. The overall mean beak shapes of Golden Eagles are quite similar to Common Buzzards, with both species having longer beaks. In contrast, Falcons exhibit a distinctly different beak morphology, characterized by wider and shorter beaks. Changes in beak shape can lead to changes depending on the skull. It is thought that skull shape variations among predator families may have an impact on beak shape. These findings highlight the importance of integrating morphometric analyses with ecological insights to enhance our understanding of the evolutionary processes shaping raptor beak morphology.
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Affiliation(s)
- Buket Çakar
- Institute of Graduate Studies, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Eren Çağatay Bulut
- Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Oya Kahvecioglu
- Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ebuderda Günay
- Department of Wild Animal Diseases and Ecology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | | | - Tomasz Szara
- Department of Morphological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
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2
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Cheng Y, Lei F. Avian lower beak is always overlooked: its coordinate role in shaping species-specific beak should not be underestimated. Integr Zool 2024; 19:339-342. [PMID: 37794566 DOI: 10.1111/1749-4877.12769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Affiliation(s)
- Yalin Cheng
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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3
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Struthers S, Andersson B, Schmutz M, Matika O, McCormack HA, Wilson PW, Dunn IC, Sandilands V, Schoenebeck JJ. An analysis of the maxillary beak shape variation between 2 pure layer lines and its relationship to the underlying premaxillary bone, feather cover, and mortality. Poult Sci 2023; 102:102854. [PMID: 37354620 PMCID: PMC10404746 DOI: 10.1016/j.psj.2023.102854] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023] Open
Abstract
Beak shape varies considerably within and between intact-beak laying hens, and aspects of beak shape appear to be heritable. As an alternative to beak treatment (an effective method of reducing damage from severe feather pecking (SFP)), this variation could be used to genetically select hens whose beak shapes are less apt to cause damage. To be able to select certain phenotypes, the beak shape variation that exists within laying hen flocks must first be characterized. The objectives of this study were to 1) describe the maxillary beak shape variation in 2 pure White Leghorn layer lines with intact beaks using geometric morphometrics to analyze images, and 2) examine the beak shape's relationship to the premaxillary bone, feather cover, and mortality. A lateral head image was taken of each hen (n = 710), and 20 landmarks were placed along each image's dorsal and ventral margins of the maxillary beak. Landmark coordinates were standardized by Procrustes superimposition, and the covariation was analyzed by principal components analysis and multivariate regression. Feather cover was scored at 3 ages and mortality was monitored throughout the production cycle. Three principal components (PCs) explained 83% of the maxillary beak shape variation and the first PC partially separated the 2 lines. Maxillary beak shapes ranged from long and narrow with pointed tips to short and wide with more curved tips. Moderate correlations were found between the maxillary beak and premaxillary bone shape (rs = 0.44) and size (rs = 0.52). Line A hens had better feather cover than Line B at all ages. Line A hens also had less total and cannibalism-related mortality than Line B (10.7 and 0.4% vs. 16.7 and 2.4%, respectively). Beak shape may be one factor contributing to the observed differences in feather cover and mortality. The results suggest that distinct maxillary beak phenotypes within each line could be selected to help reduce SFP damage and improve bird welfare.
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Affiliation(s)
- S Struthers
- Department of Agriculture, Horticulture, and Engineering Science, Scotland's Rural College, Midlothian EH25 9RG, United Kingdom; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.
| | - B Andersson
- Lohmann Breeders GmbH, Cuxhaven DE 27472, Germany
| | - M Schmutz
- Lohmann Breeders GmbH, Cuxhaven DE 27472, Germany
| | - O Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - H A McCormack
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - P W Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - I C Dunn
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - V Sandilands
- Department of Agriculture, Horticulture, and Engineering Science, Scotland's Rural College, Midlothian EH25 9RG, United Kingdom
| | - J J Schoenebeck
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
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Diversification of the shell shape and size in Baikal Candonidae ostracods inferred from molecular phylogeny. Sci Rep 2023; 13:2950. [PMID: 36806355 PMCID: PMC9941104 DOI: 10.1038/s41598-023-30003-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Ostracod shells are used extensively in paleontology, but we know little about their evolution, especially in ancient lakes. Lake Baikal (LB) is the world's most important stronghold of Candonidae diversity. These crustaceans radiated here rapidly (12-5 Ma) and with an unprecedented morphological diversity. We reconstruct their molecular phylogeny with 46 species and two markers (18S and 16S rRNA), and use it to estimate the evolution of the shell shape and size with landmark-based geometric morphometrics (LBGM). High posterior probabilities support four major clades, which differ in node depth and morphospace clustering. After removing a significant allometry, the first three principal components (PCs) describe about 88% of total variability, suggesting a strong integration. Reconstructed ancestral shapes are similar for all four clades, indicating that diversification happened after colonization. Major evolutionary changes occurred from trapezoidal to elongated shapes. Sister species are separated in morphospace, by centroid size, or both, as well as by vertical and horizontal distributions in LB. Ostracod shell is a strongly integrated structure that exhibits high evolvability, with some extreme shapes, although mostly along the first PC. This is the first study that combines molecular phylogeny and LBGM for ostracods and for any LB group.
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Boer EF, Maclary ET, Shapiro MD. Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons. Evol Dev 2021; 23:477-495. [PMID: 34914861 PMCID: PMC9119316 DOI: 10.1111/ede.12395] [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: 03/20/2021] [Revised: 10/28/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
Deciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak shape, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.
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Affiliation(s)
- Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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6
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Cheng Y, Miller MJ, Zhang D, Xiong Y, Hao Y, Jia C, Cai T, Li SH, Johansson US, Liu Y, Chang Y, Song G, Qu Y, Lei F. Parallel genomic responses to historical climate change and high elevation in East Asian songbirds. Proc Natl Acad Sci U S A 2021; 118:e2023918118. [PMID: 34873033 PMCID: PMC8685689 DOI: 10.1073/pnas.2023918118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2021] [Indexed: 12/01/2022] Open
Abstract
Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Matthew J Miller
- Reneco International Wildlife Consultants, LLC, Abu Dhabi, UAE
- University of Alaska Museum, University of Alaska Fairbanks, AK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianlong Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shou-Hsien Li
- Department of Life Sciences, National Taiwan Normal University, Taipei, 116, Taiwan, China
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongbin Chang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China
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7
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Macpherson MP, Jahn AE, Mason NA. Morphology of migration: associations between wing shape, bill morphology and migration in kingbirds (Tyrannus). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviours also interact with diet, such that migratory animals tend to be dietary generalists, whereas sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations that selection favours improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.
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Affiliation(s)
- Maggie P Macpherson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
- Louisiana State University Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Alex E Jahn
- Departamento de Biodiversidade, Universidade Estadual Paulista, Av. 24a No. 1515, Rio Claro, Brazil
- Environmental Resilience Institute, Indiana University, 717 E 8th St., Bloomington, IN, USA
| | - Nicholas A Mason
- Louisiana State University Museum of Natural Sciences, Louisiana State University, Baton Rouge, LA, USA
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Determining the variation in premaxillary and dentary bone morphology that may underlie beak shape between two pure layer lines. Poult Sci 2021; 100:101500. [PMID: 34700097 PMCID: PMC8554249 DOI: 10.1016/j.psj.2021.101500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Beak treatment is an effective method of reducing the damage inflicted by severe feather pecking (SFP) but there is significant pressure to eliminate these treatments and rely solely on alternative strategies. Substantial variation in beak shape exists within non-beak treated layer flocks and beak shape appears to be heritable. There is the potential to use this pre-existing variation and genetically select for hens whose beak shapes are less apt to cause damage during SFP. To do this, we must first understand the range of phenotypes that exist for both the external beak shape and the bones that provide its structure. The objective of this study was to determine the variation in premaxillary (within the top beak) and dentary (within the bottom beak) bone morphology that exists in 2 non-beak treated pure White Leghorn layer lines using geometric morphometrics to analyze radiographs. Lateral head radiographs were taken of 825 hens and the premaxillary and dentary bones were landmarked. Landmark coordinates were standardized by Procrustes superimposition and the covariation was analyzed by principal components analysis and multivariate regression using Geomorph (an R package). Three principal components (PCs) explained 85% of total premaxillary bone shape variation and showed that the shape ranged from long and narrow with pointed bone tips to short and wide with more curved tips. Two PCs explained 81% of total dentary bone shape variation. PC1 described the dentary bone length and width and PC2 explained the angle between the bone tip and its articular process. For both bones, shape was significantly associated with bone size and differed significantly between the two lines. Bone size accounted for 42% of the total shape variation for both bones. Together, the results showed a range of phenotypic variation in premaxillary and dentary bone shape, which in turn may influence beak shape. These bone phenotypes will guide further quantitative genetic and behavioral analyses that will help identify which beaks shapes cause the least damage when birds engage in SFP.
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She H, Jiang Z, Song G, Ericson PGP, Luo X, Shao S, Lei F, Qu Y. Quantifying adaptive divergence of the snowfinches in a common landscape. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Huishang She
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science University of Chinese Academy of Sciences Beijing China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per G. P. Ericson
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Xu Luo
- Faculty of Biodiversity and Conservation Southwest Forestry University Kunming China
| | - Shimiao Shao
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
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10
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Cheng Y, Miller MJ, Zhang D, Song G, Jia C, Qu Y, Lei F. Comparative Genomics Reveals Evolution of a Beak Morphology Locus in a High-Altitude Songbird. Mol Biol Evol 2020; 37:2983-2988. [PMID: 32592485 DOI: 10.1093/molbev/msaa157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Ground Tit (Pseudopodoces humilis) has lived on the Qinghai-Tibet Plateau for ∼5.7 My and has the highest altitudinal distribution among all parids. This species has evolved an elongated beak in response to long-term selection imposed by ground-foraging and cavity-nesting habits, yet the genetic basis for beak elongation remains unknown. Here, we perform genome-wide analyses across 14 parid species and identify 25 highly divergent genomic regions that are significantly associated with beak length, finding seven candidate genes involved in bone morphogenesis and remolding. Neutrality tests indicate that a model allowing for a selective sweep in the highly conserved COL27A1 gene best explains variation in beak length. We also identify two nonsynonymous fixed mutations in the collagen domain that are predicted to be functionally deleterious yet may have facilitated beak elongation. Our study provides evidence of adaptive alleles in COL27A1 with major effects on beak elongation of Ps. humilis.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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11
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Ma W, Brusatte SL, Lü J, Sakamoto M. The skull evolution of oviraptorosaurian dinosaurs: the role of niche partitioning in diversification. J Evol Biol 2019; 33:178-188. [PMID: 31622509 DOI: 10.1111/jeb.13557] [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] [Received: 06/19/2019] [Revised: 09/28/2019] [Accepted: 10/04/2019] [Indexed: 11/30/2022]
Abstract
Oviraptorosaurs are bird-like theropod dinosaurs that thrived in the final pre-extinction ecosystems during the latest Cretaceous, and the beaked, toothless skulls of derived species are regarded as some of the most peculiar among dinosaurs. Their aberrant morphologies are hypothesized to have been caused by rapid evolution triggered by an ecological/biological driver, but little is known about how their skull shapes and functional abilities diversified. Here, we use quantitative techniques to study oviraptorosaur skull form and mandibular function. We demonstrate that the snout is particularly variable, that mandibular form and upper/lower beak form are significantly correlated with phylogeny, and that there is a strong and significant correlation between mandibular function and mandible/lower beak shape, suggesting a form-function association. The form-function relationship and phylogenetic signals, along with a moderate allometric signal in lower beak form, indicate that similar mechanisms governed beak shape in oviraptorosaurs and extant birds. The two derived oviraptorosaur clades, oviraptorids and caenagnathids, are significantly separated in morphospace and functional space, indicating that they partitioned niches. Oviraptorids coexisting in the same ecosystem are also widely spread in morphological and functional space, suggesting that they finely partitioned feeding niches, whereas caenagnathids exhibit extreme disparity in beak size. The diversity of skull form and function was likely key to the diversification and evolutionary success of oviraptorosaurs in the latest Cretaceous.
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Affiliation(s)
- Waisum Ma
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen L Brusatte
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Junchang Lü
- Institute of Geology, Chinese Academy of Geological Sciences, Beijing, China
| | - Manabu Sakamoto
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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12
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Tao Q, Tamura K, U. Battistuzzi F, Kumar S. A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies. Mol Biol Evol 2019; 36:811-824. [PMID: 30689923 PMCID: PMC6804408 DOI: 10.1093/molbev/msz014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.
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Affiliation(s)
- Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | | | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
- Department of Biology, Temple University, Philadelphia, PA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding author: E-mail:
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13
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Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives. Proc Natl Acad Sci U S A 2019; 116:11851-11856. [PMID: 31127049 DOI: 10.1073/pnas.1819657116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
High-altitude environments present strong stresses for living organisms, which have driven striking phenotypic and genetic adaptations. While previous studies have revealed multiple genetic adaptations in high-altitude species, how evolutionary history (i.e., phylogenetic background) contributes to similarity in genetic adaptations to high-altitude environments is largely unknown, in particular in a group of birds. We explored this in 3 high-altitude passerine birds from the Qinghai-Tibet Plateau and their low-altitude relatives in lowland eastern China. We generated transcriptomic data for 5 tissues across these species and compared sequence changes and expression shifts between high- and low-altitude pairs. Sequence comparison revealed that similarity in all 3 high-altitude species was high for genes under positive selection (218 genes) but low in amino acid substitutions (only 4 genes sharing identical amino acid substitutions). Expression profiles for all genes identified a tissue-specific expression pattern (i.e., all species clustered by tissue). By contrast, an altitude-related pattern was observed in genes differentially expressed between all 3 species pairs and genes associated with altitude, suggesting that the high-altitude environment may drive similar expression shifts in the 3 high-altitude species. Gene expression level, gene connectivity, and the interactions of these 2 factors with altitude were correlated with evolutionary rates. Our results provide evidence for how gene sequence changes and expression shifts work in a concerted way in a group of high-altitude birds, leading to similar evolution routes in response to high-altitude environmental stresses.
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14
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Alves VM, Hernández MIM. Local extinctions may be evidenced by the holes of the morphometric hypervolume in dung beetle communities. AUSTRAL ECOL 2019. [DOI: 10.1111/aec.12752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Victor Michelon Alves
- Programa de Pós Graduação em Ecologia; Departamento de Ecologia e Zoologia; Universidade Federal de Santa Catarina; Florianópolis Santa Catarina 88040-900 Brazil
| | - Malva Isabel Medina Hernández
- Programa de Pós Graduação em Ecologia; Departamento de Ecologia e Zoologia; Universidade Federal de Santa Catarina; Florianópolis Santa Catarina 88040-900 Brazil
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15
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Heim W, Eccard JA, Bairlein F. Migration phenology determines niche use of East Asian buntings (Emberizidae) during stopover. Curr Zool 2018; 64:681-692. [PMID: 30538727 PMCID: PMC6280105 DOI: 10.1093/cz/zoy016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/25/2018] [Indexed: 12/03/2022] Open
Abstract
Stopover niche utilization of birds during migration has not gained much attention so far, since the majority of the studies focuses on breeding or wintering areas. However, stopover sites are crucial for migratory birds. They are often used by a multitude of species, which could lead to increased competition. In this work, we investigated niche use of 8 migratory and closely related Emberiza bunting species at a stopover site in Far East Russia, situated on the poorly studied East Asian flyway. We used bird ringing data to evaluate morphological similarity as well as niche overlap on the trophic, spatial, and temporal dimension. Bill morphology was used as a proxy for their trophic niche. We were able to prove that a majority of the species occupies well-defined stopover niches on at least one of the dimensions. Niche breadth and niche overlap differ between spring and autumn season with higher overlap found during spring. Morphological differences are mostly related to overall size and wing pointedness. The temporal dimension is most important for segregation among the studied species. Furthermore, all species seem to exhibit a rather strict and consistent phenological pattern. Their occurrence at the study site is highly correlated with their geographic origin and the length of their migration route. We assume that buntings are able to use available resources opportunistically during stopover, while trying to follow a precise schedule in order to avoid competition and to ensure individual fitness.
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Affiliation(s)
- Wieland Heim
- Institute of Landscape Ecology, Münster University, Heisenbergstraße 2, Münster, Germany
| | - Jana A Eccard
- Animal Ecology, Institute of Biology and Biochemistry, Universität Potsdam, Maulbeerallee 1, Potsdam, Germany
| | - Franz Bairlein
- Institute of Avian Research “Vogelwarte Helgoland”, An der Vogelwarte 21, Wilhelmshaven, Germany
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16
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Runemark A, Fernández LP, Eroukhmanoff F, Sætre GP. Genomic Contingencies and the Potential for Local Adaptation in a Hybrid Species. Am Nat 2018; 192:10-22. [DOI: 10.1086/697563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Norman JA, Christidis L, Schodde R. Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0364-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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18
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Cheng Y, Gao B, Wang H, Han N, Shao S, Wu S, Song G, Zhang YE, Zhu X, Lu X, Qu Y, Lei F. Evolution of beak morphology in the Ground Tit revealed by comparative transcriptomics. Front Zool 2017; 14:58. [PMID: 29299037 PMCID: PMC5740785 DOI: 10.1186/s12983-017-0245-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Beak morphology exhibits considerable adaptive plasticity in birds, which results in highly varied or specialized forms in response to variations in ecology and life history. As the only parid species endemic to the Qinghai-Tibet Plateau, the Ground Tit (Parus humilis) has evolved a distinctly long and curved beak from other parids. An integration of morphometrics, phylogenetics, transcriptomics and embryology allows us to address the evolutionary and developmental mechanisms of the adaptive beak structure observed in the Ground Tit. Results A morphometric approach quantified that the Ground Tit has a comparatively longer and more decurved upper beaks than other parids. We estimated that the ancestor of the Ground Tit likely had a short straight upper beak similar to most current recognized parid species using an ancestral state reconstruction. This morphological specialization is considered an adaptation to its ground-oriented behavior on the high plateau. To identify genetic mechanisms behind this adaptive change, a comparative transcriptomic analysis was applied between the Ground Tit and its closely related species, the Great Tit (Parus major). We detected that 623 genes were significantly differentially expressed in embryonic upper beaks between the two species, 17 of which were functionally annotated to correlate with bone development and morphogenesis, although genes related to bone development were not found to undergo accelerated evolution in the Ground Tit. RT-qPCR validation confirmed differential expression of five out of eight genes that were selected from the 17 genes. Subsequent functional assays in chicken embryos demonstrated that two of these genes, FGF13 and ITGB3, may affect beak morphology by modulating levels of osteoblasts and osteoclasts. Conclusions Our results provide preliminary evidence that development of the long decurved beak of the Ground Tit is likely regulated by transcriptional activities of multiple genes coordinating osteoblasts and osteoclasts. The integration of multiple approaches employed here sheds light on ecological and genetic mechanisms in the evolution of avian morphology.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bin Gao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haitao Wang
- School of Life Sciences, Northeast Normal University, Changchun, 130024 China
| | - Naijian Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Shimiao Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shaoyuan Wu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xin Lu
- Department of Ecology, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, 430072 China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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Dalton HA, Wood BJ, Widowski TM, Guerin MT, Torrey S. An analysis of beak shape variation in two ages of domestic turkeys (Meleagris gallopavo) using landmark-based geometric morphometrics. PLoS One 2017; 12:e0185159. [PMID: 28934330 PMCID: PMC5608350 DOI: 10.1371/journal.pone.0185159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 09/07/2017] [Indexed: 12/31/2022] Open
Abstract
The objective of this study was to assess beak shape variation in domestic turkeys (Meleagris gallopavo) and determine the effects of age, sex, and beak size on beak shape variation using geometric morphometrics. Dorsal and right lateral images were taken of 2442 turkeys at 6 and 18.5 weeks of age. Landmarks were digitized in tpsDig in three analyses of the dorsal upper mandible, lateral upper mandible, and lateral lower mandible shape of each turkey at both ages. The coordinate data were then subjected to a principal components analysis (PCA), multivariate regression, and a canonical variates analysis (CVA) with a Procrustes ANOVA in MorphoJ. For the dorsal images, three principal components (PCs) showed beak shape variation ranged from long, narrow, and pointed to short, wide, and blunt upper mandibles at both ages (6 weeks: 95.36%, 18.5 weeks: 92.21%). Three PCs showed the lateral upper mandible shape variation ranged from long, wide beaks with long, curved beak tips to short, narrow beaks with short, pointed beak tips at both ages (6 weeks: 94.91%, 18.5 weeks: 94.33%). Three PCs also explained 97.80% (6 weeks) and 97.11% (18.5 weeks) of the lateral lower mandible shape variation ranging from wide and round to narrow and thin lower mandibles with superior/inferior beak tip shifts. Beak size accounted for varying proportions of the beak shape variation (0.96-54.76%; P < 0.0001) in the three analyses of each age group. For all the analyses, the CVA showed sexual dimorphism in beak shape (P < 0.0001) with female upper mandibles appearing wider and blunter dorsally with long, curved beak tips laterally. Whereas male turkey upper mandibles had a narrow, pointed dorsal appearance and short, pointed beak tips laterally. Future applications of beak shape variability could have a genetic and welfare value by incorporating beak shape variation to select for specific turkey beak phenotypes as an alternative to beak treatment.
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Affiliation(s)
- Hillary A. Dalton
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Benjamin J. Wood
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Hybrid Turkeys, Kitchener, Ontario, Canada
| | - Tina M. Widowski
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, Guelph, Ontario, Canada
| | - Michele T. Guerin
- Department of Population Medicine, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie Torrey
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, Guelph, Ontario, Canada
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20
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Outomuro D, Johansson F. A potential pitfall in studies of biological shape: Does size matter? J Anim Ecol 2017; 86:1447-1457. [PMID: 28699246 DOI: 10.1111/1365-2656.12732] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 01/26/2023]
Abstract
The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.
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Affiliation(s)
- David Outomuro
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Frank Johansson
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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21
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Improved sampling at the subspecies level solves a taxonomic dilemma - A case study of two enigmatic Chinese tit species (Aves, Passeriformes, Paridae, Poecile). Mol Phylogenet Evol 2016; 107:538-550. [PMID: 27965081 DOI: 10.1016/j.ympev.2016.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/25/2016] [Accepted: 12/09/2016] [Indexed: 11/24/2022]
Abstract
A recent full species-level phylogeny of tits, titmice and chickadees (Paridae) has placed the Chinese endemic black-bibbed tit (Poecile hypermelaenus) as the sister to the Palearctic willow tit (P. montanus). Because this sister-group relationship is in striking disagreement with the traditional affiliation of P. hypermelaenus close to the marsh tit (P. palustris) we tested this phylogenetic hypothesis in a multi-locus analysis with an extended taxon sampling including sixteen subspecies of willow tits and marsh tits. As a taxonomic reference we included type specimens in our analysis. The molecular genetic study was complemented with an analysis of biometric data obtained from museum specimens. Our phylogenetic reconstructions, including a comparison of all GenBank data available for our target species, clearly show that the genetic lineage previously identified as P. hypermelaenus actually refers to P. weigoldicus because sequences were identical to that of a syntype of this taxon. The close relationship of P. weigoldicus and P. montanus - despite large genetic distances between the two taxa - is in accordance with current taxonomy and systematics. In disagreement with the previous phylogenetic hypothesis but in accordance with most taxonomic authorities, all our P. hypermelaenus specimens fell in the sister clade of all western and eastern Palearctic P. palustris. Though shared haplotypes among the Chinese populations of the two latter species might indicate mitochondrial introgression in this part of the breeding range, further research is needed here due to the limitations of our own sampling.
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