1
|
Coleman JL, Wyffels JT, Penfold LM, Richardson D, Maddox JD. Development of genetic markers for reproductive management of toucans. Zoo Biol 2023; 42:825-833. [PMID: 37338091 DOI: 10.1002/zoo.21792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 04/26/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.
Collapse
Affiliation(s)
- Jeffrey L Coleman
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Jennifer T Wyffels
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, Delaware, USA
- Ripley's Aquariums, Orlando, Florida, USA
| | - Linda M Penfold
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
| | | | - J Dylan Maddox
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, USA
| |
Collapse
|
2
|
Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01451-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSpecies are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
Collapse
|
3
|
Hsiao C, Lin HH, Kang SR, Hung CY, Sun PY, Yu CC, Toh KL, Yu PJ, Ju YT. Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer. PLoS One 2022; 17:e0265311. [PMID: 35363791 PMCID: PMC8975116 DOI: 10.1371/journal.pone.0265311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.
Collapse
Affiliation(s)
- Chen Hsiao
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hung Lin
- Kaohsiung Animal Propagation Station, Pingdong, Taiwan
| | | | - Chien-Yi Hung
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Sun
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Cheng Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kok-Lin Toh
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Pei-Ju Yu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
4
|
Krietsch J, Cragnolini M, Kuhn S, Lanctot RB, Saalfeld ST, Valcu M, Kempenaers B. Extrapair paternity in a sequentially polyandrous shorebird: limited evidence for the sperm storage hypothesis. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2021.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
5
|
Dawson Pell FSE, Senar JC, Franks DW, Hatchwell BJ. Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus. Mol Ecol 2021; 30:1531-1544. [PMID: 33502033 DOI: 10.1111/mec.15818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/01/2022]
Abstract
The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, Myiopsitta monachus, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are often aggregated within nesting trees. We determined patterns of relatedness within compound nests, within nesting trees and between trees. Spatial autocorrelation analyses of pairwise genetic relatedness revealed fine-scale genetic structure with relatives of both sexes spatially clustered within, but not beyond, nesting trees. In addition, males were more related to males sharing their compound nests than to other males occupying the same nesting tree. By contrast, males and females within compound nests were not significantly more closely related than elsewhere in the same tree, and we found no evidence for inbreeding. Adults showed high breeding site fidelity between years despite considerable disturbance of nest sites. Natal dispersal was female-biased, but dispersal distances were relatively short with some natal philopatry observed in both sexes. Sibling coalitions, typically of males, were observed amongst both philopatric and dispersing birds. Our results show significant clustering of kin within compound nests and nesting trees resulting from limited and coordinated natal dispersal, with subsequent breeding site fidelity. The resulting genetic structure has implications for social behaviour in this unusual parrot species.
Collapse
Affiliation(s)
| | | | - Daniel W Franks
- Department of Biology and Department of Computer Science, The University of York, York, UK
| | - Ben J Hatchwell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| |
Collapse
|
6
|
Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper ( Epinephelus tukula). BIOLOGY 2021; 10:biology10010036. [PMID: 33430356 PMCID: PMC7825770 DOI: 10.3390/biology10010036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022]
Abstract
Simple Summary The potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits. Abstract The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
Collapse
|
7
|
Perrin A, Khimoun A, Faivre B, Ollivier A, de Pracontal N, Théron F, Loubon M, Leblond G, Duron O, Garnier S. Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species. Heredity (Edinb) 2021; 126:148-162. [PMID: 32934360 PMCID: PMC7853120 DOI: 10.1038/s41437-020-00366-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/30/2020] [Accepted: 08/30/2020] [Indexed: 01/11/2023] Open
Abstract
Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper Glyphorynchus spirurus. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.
Collapse
Affiliation(s)
- Antoine Perrin
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France.
| | - Aurélie Khimoun
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - Nyls de Pracontal
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Franck Théron
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Maxime Loubon
- Groupe d'Etude et de Protection des Oiseaux en Guyane, 431 route d'Attila Cabassou, 97354, Rémire-Montjoly, France
| | - Gilles Leblond
- SARL BIOS, Route de Davidon, Duzer, 97115, Sainte-Rose, France
| | - Olivier Duron
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS), Institut pour la Recherche et le Développement (IRD), Université de Montpellier (UM), Montpellier, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| |
Collapse
|
8
|
Xu R, Zheng X. Hemocytes transcriptomes reveal metabolism changes and detoxification mechanisms in response to ammonia stress in Octopus minor. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:1441-1452. [PMID: 32945976 DOI: 10.1007/s10646-020-02279-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
Ammonia is one of the major aquatic environmental pollutants that can bring detrimental effects to the growth and survival of aquatic organisms. However, the molecular mechanisms of ammonia toxicity and ammonia excretion in marine invertebrates especially mollusks are still poorly understood. Cephalopods are exclusively ammonotelic with high protein metabolism and ammonia excretion rate, making this taxonomic group an ideal specimen to explore the ammonia detoxification mechanism. In this study, comparative transcriptomes were employed to investigate the transcriptional changes of O. minor in responses to acute ammonia exposure. A total of 63,237 unigenes with an average length of 811 bp were discovered and 25,708 unigenes were successfully annotated. The transcription of 1845 genes were significantly changed after ammonia stress, including 315 up-regulated genes and 1530 down-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis based on differentially expressed genes (DEGs) revealed that 44 GO terms and 55 KEGG pathways were over-represented. Notably, a large number of genes involved in immune defense, citric acid (TCA) cycle, oxidative phosphorylation and amino acid metabolisms were significantly down-regulated, indicating the decelerated energy production and amino acid rate in response to acute ammonia stress. These results provide new insights into the potential molecular mechanism of ammonia detoxification on transcriptomic level and will facilitate further mechanism studies on mollusks.
Collapse
Affiliation(s)
- Ran Xu
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Yushan Road 5, 266003, Qingdao, China
- Key Laboratory of Mariculture, Ocean University of China, Yushan Road 5, 266003, Qingdao, China
| | - Xiaodong Zheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Yushan Road 5, 266003, Qingdao, China.
- Key Laboratory of Mariculture, Ocean University of China, Yushan Road 5, 266003, Qingdao, China.
| |
Collapse
|
9
|
Koshiishi Y, Uchiyama H, Murata-Okubo M, Tanaka K, Kameyama Y, Hirayama H, Wada K. Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae). Gene 2020; 769:145238. [PMID: 33068676 DOI: 10.1016/j.gene.2020.145238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/16/2020] [Accepted: 10/11/2020] [Indexed: 10/23/2022]
Abstract
The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC)n, (AT)n and (AG)n, were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed NA ranged from 2 to 12, with an average of 4.2. HE/HO ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.
Collapse
Affiliation(s)
- Yuichi Koshiishi
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Michiko Murata-Okubo
- Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuichi Kameyama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Hiroki Hirayama
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan
| | - Kenta Wada
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan.
| |
Collapse
|
10
|
Zhao X, Qiu Q, Li C, Fu D, Hu X, Gao S, Zhu Y, Mu H, Wang R, Yang H, Li B. Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers. PeerJ 2020; 8:e8939. [PMID: 32411512 PMCID: PMC7210807 DOI: 10.7717/peerj.8939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/18/2020] [Indexed: 11/20/2022] Open
Abstract
As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.
Collapse
Affiliation(s)
- Xiao Zhao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Qiguan Qiu
- Changsha Ecological Zoo, Changsha, China
| | - Chang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Dongke Fu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Forensics, BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xuesong Hu
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Shengjie Gao
- Forensic Genomics International (FGI), BGI-Shenzhen, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yugang Zhu
- Changsha Sanzhen Tiger Park, Changsha, China
| | - Haofang Mu
- Center of Forensic Sciences, BGI, Beijing, China
| | - Runping Wang
- BGI Shaanxi Xixian new area Institute of Forensic Science, Xi'an, China
| | - Huanming Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, China
| |
Collapse
|
11
|
Roh HJ, Kim SC, Cho CY, Lee J, Jeon D, Kim DK, Kim KW, Afrin F, Ko YG, Lee JH, Batsaikhan S, Susanti T, Hegay S, Kongvongxay S, Gorkhali NA, Thi LAN, Thao TTT, Manikku L. Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1896-1904. [PMID: 32299162 PMCID: PMC7649407 DOI: 10.5713/ajas.19.0958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
Objective Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies. Methods We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers. Results In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (Hexp, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (Hobs) was highest in LCH (0.690±0.039), whereas WLG showed the lowest Hexp (0.372±0.055), Hobs (0.384±0.019), and PIC (0.325±0.049). Nei’s DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92). Conclusion This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.
Collapse
Affiliation(s)
- Hee-Jong Roh
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Chang-Yeon Cho
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jinwook Lee
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dayeon Jeon
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Dong-Kyo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Kwan-Woo Kim
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Fahmida Afrin
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Yeoung-Gyu Ko
- Animal Genetic Resources Center, National Institute of Animal Science, RDA, Hamyang 50000, Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea
| | - Solongo Batsaikhan
- Production and technology, National Centre for Livestock Genebank, Ulaanbaatar, 210349, Mongolia
| | - Triana Susanti
- Indonesia Research Institute for Animal Production, Bogor, 16720, Indonesia
| | - Sergey Hegay
- Institute of Biochemistry & Physiology, National Academy of Science of Kyrgyzstan, Bishkek, 720071, Kyrgyzstan
| | - Siton Kongvongxay
- Livestock Research Centre, Vientiane, 7170, Lao People's Democratic Republic
| | - Neena Amatya Gorkhali
- Animal Breeding Division, Nepal Agricultural Research Council, Kathmandu, 44600, Nepal
| | - Lan Anh Nguyen Thi
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Trinh Thi Thu Thao
- Department of Animal Breeding and Genetics, Institute of Animal Sciences for Southern Vietnam, Binh Duong 75000, Vietnam
| | - Lakmalie Manikku
- Department of Animal Production and Health, Veterinary Research Institute, Colombo, 20400, Sri Lanka
| |
Collapse
|
12
|
Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J, Yao N. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS One 2020; 15:e0225084. [PMID: 32240167 PMCID: PMC7117670 DOI: 10.1371/journal.pone.0225084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/08/2020] [Indexed: 11/19/2022] Open
Abstract
Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
Collapse
Affiliation(s)
- Richard Habimana
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Tobias Otieno Okeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Kiplangat Ngeno
- Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya
| | - Sylvere Mboumba
- Faculty of Agronomy and Biotechnologies, Masuku University of Science and Techniques, Franceville, Gabon
| | - Pauline Assami
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
| | - Anique Ahou Gbotto
- Laboratoire de genomique Fonctionnelle et Amélioration Génétique Université Nangui Abrogoua, Abidjan, Cote d'Ivoire
| | - Christian Tiambo Keambou
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
- Faculty of Agriculture and Veterinary medicine, University of Buea, Buea, Cameroon
| | - Kizito Nishimwe
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Janvier Mahoro
- Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda
| | - Nasser Yao
- Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya
| |
Collapse
|
13
|
Banjanac T, Đurović S, Jelić M, Dragićević M, Mišić D, Skorić M, Nestorović Živković J, Šiler B. Phenotypic and Genetic Variation of an Interspecific Centaurium Hybrid ( Gentianaceae) and Its Parental Species. PLANTS 2019; 8:plants8070224. [PMID: 31337143 PMCID: PMC6681202 DOI: 10.3390/plants8070224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 11/16/2022]
Abstract
Interspecific hybridization is one of the major actuators of evolutionary changes in plants. As the result of allopolyploid hybridization, offspring may gain different ploidy levels in comparison to parental species, which can provide them instant reproductive isolation. Two tetraploid sister species, Centaurium erythraea and C. littorale, readily cross-fertilize, resulting in hybrids of various ploidy. In northern Serbia, two stable populations of a hexaploid taxon C. pannonicum have been documented. It has been proposed previously that this taxon emerged after an interspecific hybridization event between two tetraploid sister-species: C. erythraea and C. littorale subsp. compressum. The existing populations of the hybridogenic taxon, as well as neighboring populations of the two parental taxa were here characterized by both morphometrics and molecular markers (EST-SSR and trnL-F). Three leaf and two flower characteristics were found to be informative in delimitation of the parental taxa and in their discernment from hybrid individuals, the latter having intermediate values. Eight microsatellite markers were found to have good ability to distinguish studied taxa, placing C. pannonicum in closer relationship with C. erythraea. Conversely, trnL-F plastid marker nominated C. littorale subsp. compressum to be the donor of the C. pannonicum plastid DNA. Reproductive isolation of the hexaploid hybrid individuals from the parental species should be examined as the next logical step in describing the new species.
Collapse
Affiliation(s)
- Tijana Banjanac
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia.
| | - Sanja Đurović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Milan Dragićević
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Danijela Mišić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Marijana Skorić
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Jasmina Nestorović Živković
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| | - Branislav Šiler
- Institute for Biological Research "Siniša Stanković", University of Belgrade, Bulevar despota Stefana 142, 11060 Belgrade, Serbia
| |
Collapse
|
14
|
Wang Q, Li J, Guo H. Transcriptome analysis and discovery of genes involved in immune pathways in Solen strictus (Gould, 1861) under Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2019; 88:237-243. [PMID: 30790660 DOI: 10.1016/j.fsi.2019.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/10/2019] [Accepted: 01/20/2019] [Indexed: 06/09/2023]
Abstract
The Solen strictus (Gould, 1861) has been recognized as an important marine economic bivalve in Eastern and Southeast Asia. To gain a better understanding of the S. strictus immune system and its related genes in response to bacterial infections, we performed a comparative gene transcription analysis from S. strictus with Vibrio anguillarum through RNA-Seq technology, meanwhile the differentially expressed genes (DEGs) were investigated. After assembly, a total of 195,774 transcripts with an average length of 996 bp were obtained. Total 153,038 unigenes were annotated in the nr, Swiss-Prot, KEGG, COG, KOG, GO and Pfam databases, and 56,597 unigenes (36.98%) were annotated in at least one database. After bacterial challenge, there were 1588 significant differentially expressed genes (DEGs) between the challenged and control groups, including 999 up-regulated and 589 down-regulated genes. All the DEGs were classified into three gene ontology categories, and allocated to 225 KEGG pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways, such as Toll-like receptor signaling, RIG-I-like receptor signaling and NOD-like receptor signaling pathway. In addition, 56,079 potential simple sequence repeats (SSRs) and 1,031,521 candidate single nucleotide polymorphisms (SNPs) were detected and identified in the S. strictus transcriptome. Results of the present study will provide valuable theoretical resources for future genetic and genomic research on S. strictus. The research results will be helpful for improving the efficiency and quality of artificial breeding, establishing genetic linkage map, and enhancing health management for this species.
Collapse
Affiliation(s)
- Qiang Wang
- Department of Animal Nutrition and Aquaculture, Shandong Vocational Animal Science and Veterinary College, 88 Shengli East Street, Weifang 261061, China
| | - Jing Li
- College of Economics and Management in Shanghai Ocean University, Shanghai 201306, China
| | - Hongmei Guo
- Department of Animal Nutrition and Aquaculture, Shandong Vocational Animal Science and Veterinary College, 88 Shengli East Street, Weifang 261061, China.
| |
Collapse
|
15
|
Rampant introgressive hybridization in Pogoniulus tinkerbirds (Piciformes: Lybiidae) despite millions of years of divergence. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
16
|
Li F, Liu X, Wu S, Luo Q, Yu B. Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance. PeerJ 2019; 7:e6483. [PMID: 30809456 PMCID: PMC6385681 DOI: 10.7717/peerj.6483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/19/2019] [Indexed: 01/06/2023] Open
Abstract
Glycine max cultivars Lee68, Nannong 1138-2, and Nannong 8831 were used as the female parents, and hybrid lines (F5) 4,111, 4,076 (N23674 × BB52), 3,060 (Lee68 × N23227), and 185 (Jackson × BB52) that selected for salt tolerance generation by generation from the cross combination of G. max and G. soja were used as the male parents, 11 (A-K) backcrosses or three-way crosses were designed and 213 single hybrids were harvested. The optimized soybean simple sequence repeat (SSR)-polymerase chain reaction (PCR) system was used to analyze the SSR polymorphism of above parental lines and get the parental co-dominant SSR markers for hybrid identification, and in which 30 true hybrids were gained. The true hybrids (G1, G3, G9, G12, G13, G16) of G cross combination were chosen as the representative for the salt tolerance test, and the results showed that, as exposed to salt stress, the seedlings of G9 line displayed higher salt tolerant coefficient, relative growth rate, and dry matter accumulation, when compared with their female parent Nannong 1138-2, and even performed equally strong salt tolerance as the male parent 3,060. It provides a feasible method of the combination of molecular SSR markers and simple physiological parameters to identify the true hybrids of G. max and G. soja, and to innovate the salt-tolerant soybean germplasms.
Collapse
Affiliation(s)
- Fayuan Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xun Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Shengyan Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Qingyun Luo
- College of Horticulture Sciences, Nanjing Agricultural University, Nanjing, China
| | - Bingjun Yu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
17
|
Xiang XW, Xiao JX, Zhou YF, Zheng B, Wen ZS. Liver transcriptome analysis of the Sparus macrocephlus in response to Vibrio parahaemolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2019; 84:825-833. [PMID: 30248404 DOI: 10.1016/j.fsi.2018.09.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/16/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
The black seabream (Sparus macrocephlus) is an economically pivotal aquaculture species cultured in China and Southeast Asian countries. To understand the molecular immune mechanisms underlying the response to Vibrio parahaemolyticus, a comparative gene transcription analysis were performed with utilized fresh livers of V. parahaemolyticus-immunized Sparus macrocephlus with a control group through RNA-Seq technology. A total of 256663 contigs were obtained after excluded the low-quality sequences and assembly. The average length of contigs collected from this research is 1066.93 bp. Furthermore, blast analysis indicates 30747 contigs were annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was employed to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. A total of 14470 genes were discovered in 303 KEGG pathways. RSEM and EdgeR were introduced to estimate 3841 genes significantly different expressed (False Discovery Rate<0.001) which includes 4072 up-regulated genes and 3771 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes were conducted to reveal the major immune-related pathways which refer to the toll-like receptor, complement, coagulation cascades, and chemokine signaling pathways. In addition, 92175 potential simple sequence repeats (SSRs) and 121912 candidate single nucleotide polymorphisms (SNPs) were detected and identified sequencely in the Sparus macrocephlus liver transcriptome. This research characterized a gene expression pattern for normal and the V. parahaemolyticus -immunized Sparus macrocephlus for the first time and not only sheds new light on the molecular mechanisms underlying the host-V. parahaemolyticus interaction but contribute to facilitate future studies on Sparus macrocephlus gene expression and functional genomics.
Collapse
Affiliation(s)
- Xing-Wei Xiang
- College of Food Science and Pharmacy, Zhejiang Ocean University, Haida Road 1, New Town, Zhoushan, Zhejiang Province, 316000, China; Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China
| | - Jin-Xing Xiao
- Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China
| | - Yu-Fang Zhou
- Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China.
| | - Bin Zheng
- College of Food Science and Pharmacy, Zhejiang Ocean University, Haida Road 1, New Town, Zhoushan, Zhejiang Province, 316000, China; Zhejiang Marine Development Research Institute, Tiyu Road 10, New Town, Zhoushan, Zhejiang Province, 316000, China.
| | - Zheng-Shun Wen
- College of Food Science and Pharmacy, Zhejiang Ocean University, Haida Road 1, New Town, Zhoushan, Zhejiang Province, 316000, China.
| |
Collapse
|
18
|
O'Brien DM, Keogh JS, Silla AJ, Byrne PG. The unexpected genetic mating system of the red‐backed toadlet (
Pseudophryne coriacea
): A species with prolonged terrestrial breeding and cryptic reproductive behaviour. Mol Ecol 2018; 27:3001-3015. [DOI: 10.1111/mec.14737] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/26/2018] [Accepted: 05/18/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel M. O'Brien
- Centre for Sustainable Ecosystem Solutions School of Earth, Atmospheric and Life Sciences University of Wollongong Wollongong NSW Australia
| | - J. Scott Keogh
- Ecology and Evolution Research School of Biology The Australian National University Canberra ACT Australia
| | - Aimee J. Silla
- Centre for Sustainable Ecosystem Solutions School of Earth, Atmospheric and Life Sciences University of Wollongong Wollongong NSW Australia
| | - Phillip G. Byrne
- Centre for Sustainable Ecosystem Solutions School of Earth, Atmospheric and Life Sciences University of Wollongong Wollongong NSW Australia
| |
Collapse
|
19
|
Haworth ES, Cunningham MJ, Calf Tjorve KM. Population diversity and relatedness in Sugarbirds (Promeropidae: Promerops spp.). PeerJ 2018; 6:e5000. [PMID: 29915704 PMCID: PMC6004301 DOI: 10.7717/peerj.5000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Sugarbirds are a family of two socially-monogamous passerine species endemic to southern Africa. Cape and Gurney’s Sugarbird (Promerops cafer and P. gurneyi) differ in abundance, dispersion across their range and in the degree of sexual dimorphism in tail length, factors that affect breeding systems and potentially genetic diversity. According to recent data, P. gurneyi are in decline and revision of the species’ IUCN conservation status to a threatened category may be warranted. It is therefore necessary to understand genetic diversity and risk of inbreeding in this species. We used six polymorphic microsatellite markers and one mitochondrial gene (ND2) to compare genetic diversity in P. cafer from Helderberg Nature Reserve and P. gurneyi from Golden Gate Highlands National Park, sites at the core of each species distribution. We describe novel universal avian primers which amplify the entire ND2 coding sequence across a broad range of bird orders. We observed high mitochondrial and microsatellite diversity in both sugarbird populations, with no detectable inbreeding and large effective population sizes.
Collapse
Affiliation(s)
- Evan S Haworth
- Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | - Michael J Cunningham
- Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria, South Africa
| | | |
Collapse
|
20
|
Transcriptome Analysis of Epithelioma Papulosum Cyprini Cells Infected by Reovirus Isolated from Allogynogenetic Silver Crucian Carp. Viruses 2018; 10:v10030135. [PMID: 29562634 PMCID: PMC5869528 DOI: 10.3390/v10030135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/07/2018] [Accepted: 03/16/2018] [Indexed: 11/17/2022] Open
Abstract
The present study aimed to identify differentially expressed genes (DEGs) and major signal transduction pathways that were related to the immune response of epithelioma papulosum cyprinid (EPC) cells to reoviruses isolated from allogynogenetic silver crucian carp. The study also lays a theoretical foundation for the pathogenesis and immunity of the reovirus, which is helpful to the breeding of cyprinids fish. Reovirus infected and uninfected EPC cells were analyzed by using a new-generation high-throughput sequencing technology. DEGs were identified, annotated, and classified, and the signal pathways involved in the response to reovirus infection were identified by using bioinformatics tool. The data were assembled into 92,101 contigs with an average length of 835.24 bp and an N50 value of 1432 nt. Differential expression analysis of all the genes identified 3316 DEGs at a false discovery rate (FDR) of <0.01 and a fold-change of ≥3, of which 1691 were upregulated genes, 1625 were downregulated, and about 305 were immune-related genes. Gene Ontology (GO) enrichment analysis resulted in the annotation of 3941 GO terms, including 2719 biological processes (37,810 unigenes), 376 cell components (7943 unigenes), and 846 molecular functions (11,750 unigenes). KEGG metabolic pathway analysis matched the DEGs from pre-and post-infection EPC cells to 193 pathways, of which 35 were immune-related, including the Toll-like receptor, cytokine-cytokine receptor interaction, and the JAK-STAT signaling pathways.
Collapse
|
21
|
Phenotypic divergence despite low genetic differentiation in house sparrow populations. Sci Rep 2018; 8:394. [PMID: 29321524 PMCID: PMC5762629 DOI: 10.1038/s41598-017-18718-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/17/2017] [Indexed: 11/09/2022] Open
Abstract
Studying patterns of phenotypic variation among populations can shed light on the drivers of evolutionary processes. The house sparrow (Passer domesticus) is one of the world's most ubiquitous bird species, as well as a successful invader. We investigated phenotypic variation in house sparrow populations across a climatic gradient and in relation to a possible scenario of an invasion. We measured variation in morphological, coloration, and behavioral traits (exploratory behavior and neophobia) and compared it to the neutral genetic variation. We found that sparrows were larger and darker in northern latitudes, in accordance with Bergmann's and Gloger's biogeographic rules. Morphology and behavior mostly differed between the southernmost populations and the other regions, supporting the possibility of an invasion. Genetic differentiation was low and diversity levels were similar across populations, indicating high gene flow. Nevertheless, the southernmost and northern populations differed genetically to some extent. Furthermore, genetic differentiation (F ST) was lower in comparison to phenotypic variation (P ST), indicating that the phenotypic variation is shaped by directional selection or by phenotypic plasticity. This study expands our knowledge on evolutionary mechanisms and biological invasions.
Collapse
|
22
|
Liu Y, Xin ZZ, Zhang DZ, Wang ZF, Zhu XY, Tang BP, Jiang SH, Zhang HB, Zhou CL, Chai XY, Liu QN. Transcriptome analysis of yellow catfish (Pelteobagrus fulvidraco) liver challenged with polyriboinosinic polyribocytidylic acid (poly I:C). FISH & SHELLFISH IMMUNOLOGY 2017; 68:395-403. [PMID: 28732769 DOI: 10.1016/j.fsi.2017.07.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/06/2017] [Accepted: 07/16/2017] [Indexed: 06/07/2023]
Abstract
Yellow catfish (Pelteobagrus fulvidraco) is one of the most important economic freshwater species in China. However, infection by bacterial pathogenic diseases has caused high mortality and great economic loss in aquaculture. It is necessary for disease control to know more about the P. fulvidraco immune system and its related genes in response to bacterial or viral infections. In this study, the transcriptomic profiles of liver from P. fulvidraco stimulated by polyriboinosinic polyribocytidylic acid (poly I:C) was analyzed using high-throughput sequencing method. After assembly and annotation, total 67,447 unigenes were acquired, with an average length of 1091 bp. Under the infection of poly I:C, 522 differentially expressed genes (DEGs) were identified, including 307 up-regulated genes and 215 down-regulated genes. To further investigate the immune-related DEGs, Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were performed. The result of GO enrichment indicated gene response to external stimulus, regulation of response to stimulus, cellular response to stimulus, immune response and immune system progress. Significant KEGG enrichment analysis identified major immune related pathways. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis revealed that 13 immune response genes were identified to be up-regulated after 12 h of poly I:C stimulation compared to controls. Taken together, the results of our study are beneficial for better understanding of the immune system and defense mechanisms of yellow catfish in response to poly I:C infection.
Collapse
Affiliation(s)
- Yu Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Zheng-Fei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Xiao-Yu Zhu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
| | - Sen-Hao Jiang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China
| | - Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224051, PR China.
| |
Collapse
|
23
|
Ren Y, Xue J, Yang H, Pan B, Bu W. Transcriptome analysis of Ruditapes philippinarum hepatopancreas provides insights into immune signaling pathways under Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2017; 64:14-23. [PMID: 28267631 DOI: 10.1016/j.fsi.2017.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/24/2017] [Accepted: 03/02/2017] [Indexed: 05/27/2023]
Abstract
The Manila clam, Ruditapes philippinarum, is one of the most economically important aquatic clams that are harvested on a large scale by the mariculture industry in China. However, increasing reports of bacterial pathogenic diseases have had a negative effect on the aquaculture industry of R. philippinarum. In the present study, the two transcriptome libraries of untreated (termed H) and challenged Vibrio anguillarum (termed HV) hepatopancreas were constructed and sequenced from Manila clam using an Illumina-based paired-end sequencing platform. In total, 75,302,886 and 66,578,976 high-quality clean reads were assembled from 101,080,746 and 99,673,538 raw data points from the two transcriptome libraries described above, respectively. Furthermore, 156,116 unigenes were generated from 210,685 transcripts, with an N50 length of 1125 bp, and from the annotated SwissProt, NR, NT, KO, GO, KOG and KEGG databases. Moreover, a total of 4071 differentially expressed unigenes (HV vs H) were detected, including 903 up-regulated and 3168 down-regulated genes. Among these differentially expressed unigenes, 226 unigenes were annotated using KEGG annotation in 16 immune-related signaling pathways, including Toll-like receptor, NF-kappa B, MAPK, NOD-like receptor, RIG-I-like receptor, and the TNF and chemokine signaling pathways. Finally, 20,341 simple sequence repeats (SSRs) and 214,430 potential single nucleotide polymorphisms (SNPs) were detected from the H and HV transcriptome libraries. In conclusion, these studies identified many candidate immune-related genes and signaling pathways and conducted a comparative analysis of the differentially expressed unigenes from Manila clam hepatopancreas in response to V. anguillarum stimulation. These data laid the foundation for studying the innate immune systems and defense mechanisms in R. philippinarum.
Collapse
Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Junli Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Huanhuan Yang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Baoping Pan
- Tianjin Key Laboratory of Animal and Plant Resistance, School of Life Sciences, Tianjin Normal University, Tianjin, 300387, PR China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| |
Collapse
|
24
|
Seo JH, Lee JH, Kong HS. Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1365-1371. [PMID: 28335091 PMCID: PMC5582319 DOI: 10.5713/ajas.16.0514] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/15/2016] [Accepted: 03/10/2017] [Indexed: 11/27/2022]
Abstract
Objective This study was conducted to investigate the basic information on genetic structure and characteristics of Korean Native chickens (NC) and foreign breeds through the analysis of the pure chicken populations and commercial chicken lines of the Hanhyup Company which are popular in the NC market, using the 20 microsatellite markers. Methods In this study, the genetic diversity and phylogenetic relationships of 445 NC from five different breeds (NC, Leghorn [LH], Cornish [CS], Rhode Island Red [RIR], and Hanhyup [HH] commercial line) were investigated by performing genotyping using 20 microsatellite markers. Results The highest genetic distance was observed between RIR and LH (18.9%), whereas the lowest genetic distance was observed between HH and NC (2.7%). In the principal coordinates analysis (PCoA) illustrated by the first component, LH was clearly separated from the other groups. The correspondence analysis showed close relationship among individuals belonging to the NC, CS, and HH lines. From the STRUCTURE program, the presence of 5 clusters was detected and it was found that the proportion of membership in the different clusters was almost comparable among the breeds with the exception of one breed (HH), although it was highest in LH (0.987) and lowest in CS (0.578). For the cluster 1 it was high in HH (0.582) and in CS (0.368), while for the cluster 4 it was relatively higher in HH (0.392) than other breeds. Conclusion Our study showed useful genetic diversity and phylogenetic relationship data that can be utilized for NC breeding and development by the commercial chicken industry to meet consumer demands.
Collapse
Affiliation(s)
- Joo Hee Seo
- Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.,Department of Genomic Informatics, Graduate School of Future Convergence Technology, Hankyong National University, Anseong 456-749, Korea
| | - Jun Heon Lee
- Department of Animal Science and Biotechnology, Chunam National University, Daejeon 305-764, Korea
| | - Hong Sik Kong
- Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea
| |
Collapse
|
25
|
Moura RF, Dawson DA, Nogueira DM. The use of microsatellite markers in Neotropical studies of wild birds: a literature review. AN ACAD BRAS CIENC 2017; 89:145-154. [PMID: 28177053 DOI: 10.1590/0001-3765201620160378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
Despite extensive habitat fragmentation, the Neotropical region possesses 30% of the world´s bird species. Microsatellites have remained one of the most popular genetic markers and have been used in ecological and conservation studies since the 1990's. We conducted a literature review comparing the number of papers published from January 1990 to July 2015 that used microsatellite markers for studies of wild birds in the Neotropical region, USA and some European countries. We assigned the articles to three categories of studies: population genetics, animal behavior/kinship analysis and the development of species-specific bird microsatellite markers. We also compared the studies in the Neotropics that used heterologous versus species-specific markers and provide a list of heterologous markers of utility in multiple birds. Despite the rich bird fauna in the Neotropics, the number of articles published represents only 5.6% of that published by the USA and selected European countries. Within the Neotropical region, Brazil possessed 60.5% of the total papers published, with the remaining 39.5% shared between five countries. We conclude that the lack of specialized laboratories and resources still represents a limit to microsatellite-based genetic studies of birds within the Neotropical region. To overcome these limitations, we suggest the use of heterologous microsatellite markers as a cost-effective and time-effective tool to assist ecological studies of wild birds.
Collapse
Affiliation(s)
- Renan F Moura
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465, Km 07, 23890-000 Seropédica, RJ, Brazil
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Denise M Nogueira
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465 Km 07, 23890-000 Seropédica, RJ, Brazil
| |
Collapse
|
26
|
Khimoun A, Ollivier A, Faivre B, Garnier S. Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs. Mol Ecol Resour 2017; 17:893-903. [PMID: 27978606 DOI: 10.1111/1755-0998.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/26/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022]
Abstract
Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
Collapse
Affiliation(s)
- Aurélie Khimoun
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| |
Collapse
|
27
|
Amavet PS, Rueda E, Vilardi J, Siroski P, Larriera A, Saidman BO. The broad-snouted caiman population recovery in Argentina. A case of genetics conservation. AMPHIBIA-REPTILIA 2017. [DOI: 10.1163/15685381-00003123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Caiman latirostriswild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure ofC. latirostrispopulations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.
Collapse
Affiliation(s)
- Patricia Susana Amavet
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL / MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
| | - Eva Carolina Rueda
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
| | - Juan César Vilardi
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Pab II, UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| | - Pablo Siroski
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL / MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
- Instituto de Ciencias Veterinarias del Litoral, ICiVet-UNL-CONICET, Kreder 2805, 3080 Esperanza, Argentina
| | - Alejandro Larriera
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL / MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
| | - Beatriz Ofelia Saidman
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Pab II, UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| |
Collapse
|
28
|
Grendelmeier A, Arlettaz R, Olano-Marin J, Pasinelli G. Experimentally provided conspecific cues boost bird territory density but not breeding performance. Behav Ecol 2016. [DOI: 10.1093/beheco/arw144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
29
|
Kaiser SA, Taylor SA, Chen N, Sillett TS, Bondra ER, Webster MS. A comparative assessment of
SNP
and microsatellite markers for assigning parentage in a socially monogamous bird. Mol Ecol Resour 2016; 17:183-193. [DOI: 10.1111/1755-0998.12589] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Sara A. Kaiser
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Scott A. Taylor
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology University of Colorado at Boulder 1900 Pleasant Street 334 UCB Boulder CO 80309 USA
| | - Nancy Chen
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - T. Scott Sillett
- Migratory Bird Center Center for Conservation Genomics Smithsonian Conservation Biology Institute National Zoological Park MRC 5503 Washington DC 20013 USA
| | - Eliana R. Bondra
- Department of Ecology and Evolutionary Biology Cornell University E145 Corson Hall 215 Tower Road Ithaca NY 14853 USA
| | - Michael S. Webster
- Macaulay Library Cornell Lab of Ornithology 159 Sapsucker Woods Rd Ithaca NY 14850 USA
| |
Collapse
|
30
|
Bi G, dos Remedios N, Dawson DA, Kingma SA, Schroeder J, Dugdale HL. A multiplex set for microsatellite typing and sexing of the European bee-eater (Merops apiaster). EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1012-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
31
|
Khimoun A, Eraud C, Ollivier A, Arnoux E, Rocheteau V, Bely M, Lefol E, Delpuech M, Carpentier ML, Leblond G, Levesque A, Charbonnel A, Faivre B, Garnier S. Habitat specialization predicts genetic response to fragmentation in tropical birds. Mol Ecol 2016; 25:3831-44. [PMID: 27314987 DOI: 10.1111/mec.13733] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 01/19/2023]
Abstract
Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.
Collapse
Affiliation(s)
- Aurélie Khimoun
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Cyril Eraud
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Anthony Ollivier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Emilie Arnoux
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Vincent Rocheteau
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Marine Bely
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Emilie Lefol
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Martin Delpuech
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Marie-Laure Carpentier
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Gilles Leblond
- SARL BIOS, 168 rue de Brindeau, 97190, Le Gosier, France
| | - Anthony Levesque
- Office National de la Chasse et de la Faune Sauvage, Cellule Technique des Antilles Françaises, Chemin de Boyer, Section Boisbert, 97129, Le Lamentin, France
| | - Anaïs Charbonnel
- Office National de la Chasse et de la Faune Sauvage, CNERA Avifaune Migratrice, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Bruno Faivre
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, CNRS/Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| |
Collapse
|
32
|
Krzemińska U, Wilson R, Song BK, Seneviratne S, Akhteruzzaman S, Gruszczyńska J, Świderek W, Huy TS, Austin CM, Rahman S. Genetic diversity of native and introduced populations of the invasive house crow (Corvus splendens) in Asia and Africa. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1130-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
33
|
Gerchen JF, Reichert SJ, Röhr JT, Dieterich C, Kloas W, Stöck M. A Single Transcriptome of a Green Toad (Bufo viridis) Yields Candidate Genes for Sex Determination and -Differentiation and Non-Anonymous Population Genetic Markers. PLoS One 2016; 11:e0156419. [PMID: 27232626 PMCID: PMC4883742 DOI: 10.1371/journal.pone.0156419] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/15/2016] [Indexed: 12/13/2022] Open
Abstract
Large genome size, including immense repetitive and non-coding fractions, still present challenges for capacity, bioinformatics and thus affordability of whole genome sequencing in most amphibians. Here, we test the performance of a single transcriptome to understand whether it can provide a cost-efficient resource for species with large unknown genomes. Using RNA from six different tissues from a single Palearctic green toad (Bufo viridis) specimen and Hiseq2000, we obtained 22,5 Mio reads and publish >100,000 unigene sequences. To evaluate efficacy and quality, we first use this data to identify green toad specific candidate genes, known from other vertebrates for their role in sex determination and differentiation. Of a list of 37 genes, the transcriptome yielded 32 (87%), many of which providing the first such data for this non-model anuran species. However, for many of these genes, only fragments could be retrieved. In order to allow also applications to population genetics, we further used the transcriptome for the targeted development of 21 non-anonymous microsatellites and tested them in genetic families and backcrosses. Eleven markers were specifically developed to be located on the B. viridis sex chromosomes; for eight markers we can indeed demonstrate sex-specific transmission in genetic families. Depending on phylogenetic distance, several markers, which are sex-linked in green toads, show high cross-amplification success across the anuran phylogeny, involving nine systematic anuran families. Our data support the view that single transcriptome sequencing (based on multiple tissues) provides a reliable genomic resource and cost-efficient method for non-model amphibian species with large genome size and, despite limitations, should be considered as long as genome sequencing remains unaffordable for most species.
Collapse
Affiliation(s)
- Jörn F Gerchen
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Samuel J Reichert
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Johannes T Röhr
- Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany.,Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Werner Kloas
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| |
Collapse
|
34
|
Khimoun A, Arnoux E, Martel G, Pot A, Eraud C, Condé B, Loubon M, Théron F, Covas R, Faivre B, Garnier S. Contrasted patterns of genetic differentiation across eight bird species in the Lesser Antilles. Genetica 2016; 144:125-38. [PMID: 26797853 DOI: 10.1007/s10709-016-9883-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/18/2016] [Indexed: 11/26/2022]
Abstract
Archipelagoes are considered as "natural laboratories" for studying processes that shape the distribution of diversity. The Lesser Antilles provide a favorable geographical context for divergence to occur. However, although morphological subspecies have been described across this archipelago in numerous avian species, the potential for the Lesser Antilles in driving intra-specific genetic divergence in highly mobile organisms such as birds remains understudied. Here, we assessed level of intra-specific genetic diversity and differentiation between three islands of the Lesser Antilles (Guadeloupe, Dominica and Martinique) using a multi-species approach on eight bird species. For each species, we built a set of microsatellite markers from cross-species amplifications. Significant patterns of inter-island and/or within-island genetic differentiation were detected in all species. However, levels of intra-specific genetic differentiation among the eight bird species were not always consistent with the boundaries of subspecies previously described in the sampled islands. These results suggest different histories of colonization/expansion and/or different species-specific ecological traits affecting gene flow, advocating for multi-species studies of historical and contemporary factors shaping the distribution of diversity on islands.
Collapse
Affiliation(s)
- Aurélie Khimoun
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France.
| | - Emilie Arnoux
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Guillaume Martel
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Alexandre Pot
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Cyril Eraud
- CNERA Avifaune migratrice, Office National de la Chasse et de la Faune Sauvage, Station biologique de Chizé, Carrefour de la Canauderie, 79360, Villiers en Bois, France
| | - Béatriz Condé
- Cellule Technique des Antilles Françaises, Office National de la Chasse et de la Faune Sauvage, 5 rue de la Dorade, 79229, Les Trois-Ilets, Martinique, France
| | - Maxime Loubon
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Franck Théron
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Rita Covas
- Research Centre in Biodiversity and Genetic Resources, CIBIO, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Bruno Faivre
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| | - Stéphane Garnier
- CNRS, Biogéosciences UMR6282, Univ. Bourgogne Franche-Comté, 21000, Dijon, France
| |
Collapse
|
35
|
Wang P, Wang J, Su YQ, Mao Y, Zhang JS, Wu CW, Ke QZ, Han KH, Zheng WQ, Xu ND. Transcriptome analysis of the Larimichthys crocea liver in response to Cryptocaryon irritans. FISH & SHELLFISH IMMUNOLOGY 2016; 48:1-11. [PMID: 26578248 DOI: 10.1016/j.fsi.2015.11.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 11/02/2015] [Accepted: 11/05/2015] [Indexed: 05/28/2023]
Abstract
The large yellow croaker (Larimichthys crocea) is an economically important marine fish cultured in China and East Asian countries and is facing a serious threat from Cryptocaryon irritans, which is a protozoan ectoparasite that infects most reared marine fish species. To understand the molecular immune mechanisms underlying the response to C. irritans, we first performed a comparative gene transcription analysis using livers from C. irritans-immunized L. croceas and from a control group through RNA-Seq technology. After the removal of low-quality sequences and assembly, 51360 contigs were obtained, with an average length of 1066.93 bp. Further, a blast analysis indicates that 30747 contigs can be annotated based on homology with matches in the NT, NR, gene, and string databases. A gene ontology analysis was used to classify 21598 genes according to three major functional categories: molecular function, cellular component, and biological process. Moreover, 14470 genes were found in 303 KEGG pathways. We used RSEM and EdgeR to determine that 3841 genes were significantly differentially expressed (FDR < 0.001), including 2129 up-regulated genes and 1712 down-regulated genes. A significant enrichment analysis of these differentially expressed genes and isogenes revealed major immune-related pathways, including the toll-like receptor, complement and coagulation cascades, and chemokine signaling pathways. In addition, 28748 potential simple sequence repeats (SSRs) were detected from 12776 transcripts, and 62992 candidate single nucleotide polymorphisms (SNPs) were identified in the L. croceas liver transcriptome. This study characterized a gene expression pattern for normal and C. irritans-immunized L. croceas for the first time and not only sheds new light on the molecular mechanisms underlying the host-C. irritans interaction but also facilitates future studies on L. croceas gene expression and functional genomics.
Collapse
Affiliation(s)
- Panpan Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jun Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yong-Quan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yong Mao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
| | | | - Chang-Wen Wu
- Zhejiang Ocean University, Zhoushan, 316022, China
| | - Qiao-Zhen Ke
- Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China
| | - Kun-Huang Han
- Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China
| | | | - Nen-di Xu
- Ningde Fufa Fisheries Co., LTD, Ningde, 352002, China
| |
Collapse
|
36
|
Tuler AC, Carrijo TT, Nóia LR, Ferreira A, Peixoto AL, da Silva Ferreira MF. SSR markers: a tool for species identification in Psidium (Myrtaceae). Mol Biol Rep 2015; 42:1501-13. [DOI: 10.1007/s11033-015-3927-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 10/15/2015] [Indexed: 11/28/2022]
|
37
|
Paquet M, Doutrelant C, Hatchwell BJ, Spottiswoode CN, Covas R. Antagonistic effect of helpers on breeding male and female survival in a cooperatively breeding bird. J Anim Ecol 2015; 84:1354-62. [PMID: 25850564 PMCID: PMC4557059 DOI: 10.1111/1365-2656.12377] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/31/2015] [Indexed: 11/28/2022]
Abstract
1. Cooperatively breeding species are typically long lived and hence, according to theory, are expected to maximize their lifetime reproductive success through maximizing survival. Under these circumstances, the presence of helpers could be used to lighten the effort of current reproduction for parents to achieve higher survival. 2. In addition, individuals of different sexes and ages may follow different strategies, but whether male and female breeders and individuals of different ages benefit differently from the presence of helpers has often been overlooked. Moreover, only one study that investigated the relationship between parental survival and the presence of helpers used capture-mark-recapture analyses (CMR). These methods are important since they allow us to account for the non-detection of individuals that are alive in the population but not detected, and thus, the effects on survival and recapture probability to be disentangled. 3. Here, we used multi-event CMR methods to investigate whether the number of helpers was associated with an increase in survival probability for male and female breeders of different ages in the sociable weaver Philetairus socius. In this species, both sexes reduce their feeding rate in the presence of helpers. We therefore predicted that the presence of helpers should increase the breeders' survival in both sexes, especially early in life when individuals potentially have more future breeding opportunities. In addition, sociable weaver females reduce their investment in eggs in the presence of helpers, so we predicted a stronger effect of helpers on female than male survival. 4. As expected we found that females had a higher survival probability when breeding with more helpers. Unexpectedly, however, male survival probability decreased with increasing number of helpers. This antagonistic effect diminished as the breeders grew older. 5. These results illustrate the complexity of fitness costs and benefits underlying cooperative behaviours and how these may vary with the individuals' sex and age. They also highlight the need for further studies on the sex-specific effects of helpers on survival.
Collapse
Affiliation(s)
- Matthieu Paquet
- CEFE-CNRS1919 Route de Mende, 34293, Montpellier, France
- Percy FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape TownCape Town, South Africa
| | | | - Ben J Hatchwell
- Department of Animal and Plant Sciences, University of SheffieldWestern Bank, Sheffield, UK
| | - Claire N Spottiswoode
- Percy FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape TownCape Town, South Africa
- Department of Zoology, University of CambridgeDowning Street, Cambridge, CB2 3EJ, UK
| | - Rita Covas
- Percy FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape TownCape Town, South Africa
- CIBIO, Research Centre in Biodiversity and Genetic ResourcesCampus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
- Biology Department, Science Faculty, University of PortoPorto, Portugal
| |
Collapse
|
38
|
Restrepo A, Páez VP, Vásquez A, Daza JM. Rapid microsatellite marker development in the endangered neotropical freshwater turtle Podocnemis lewyana (Testudines: Podocnemididae) using 454 sequencing. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
39
|
Amavet PS, Rueda EC, Siroski PA, Larriera A, Saidman BO. Isolation and characterization of new microsatellite markers for application in population genetic studies of Caiman latirostris and related species. AMPHIBIA-REPTILIA 2015. [DOI: 10.1163/15685381-00002987] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Wild populations ofCaiman latirostrisare subject to sustainable use programs in Argentina, becoming a species with important impact in the regional economy, based in their skin and meat. Genetic studies are fundamental to acquire information on important parameters for conservation and management, which may be obtained from analysis of molecular markers. Some microsatellites have been previously isolated in this species, but due to some difficulties in using them, we obtained new ones using Next Generation Sequencing approach. This study reports eight new microsatellites forC. latirostrisand tests their utility in a related species,Caiman yacare, with successful application in population genetics and mating systems studies. In addition, we shared data about a novel and fast bioinformatics tool to find microsatellites and to design their corresponding primers.
Collapse
Affiliation(s)
- Patricia Susana Amavet
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, Ciudad Universitaria, 3000 Santa Fe, Argentina
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
| | - Eva Carolina Rueda
- Laboratorio de Genética, Departamento de Ciencias Naturales, Facultad de Humanidades y Ciencias, UNL, Ciudad Universitaria, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
| | - Pablo Ariel Siroski
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
- Instituto de Ciencias Veterinarias del Litoral (ICiVet-UNL-CONICET), Kreder 2805, S3080HOF Esperanza, Argentina
| | - Alejandro Larriera
- Proyecto Yacaré – Laboratorio de Zoología Aplicada: Anexo Vertebrados (FHUC – UNL/MASPyMA), A. del Valle 8700, 3000 Santa Fe, Argentina
| | - Beatriz Ofelia Saidman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Rivadavia 1917, C1033AAJ Buenos Aires, Argentina
- Departamento Ecología, Genética y Evolución, IEGEBA, CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
| |
Collapse
|
40
|
Schlick-Steiner BC, Arthofer W, Moder K, Steiner FM. Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution. Ecol Evol 2014; 5:24-35. [PMID: 25628861 PMCID: PMC4298431 DOI: 10.1002/ece3.1330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/27/2014] [Accepted: 10/30/2014] [Indexed: 01/18/2023] Open
Abstract
Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search.
Collapse
Affiliation(s)
- Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| | - Karl Moder
- Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Peter Jordan-Str. 82, 1180, Vienna, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck Technikerstr. 25, 6020, Innsbruck, Austria
| |
Collapse
|
41
|
Fourcade Y, Keišs O, Richardson DS, Secondi J. Continental-scale patterns of pathogen prevalence: a case study on the corncrake. Evol Appl 2014; 7:1043-55. [PMID: 25553066 PMCID: PMC4231594 DOI: 10.1111/eva.12192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/03/2014] [Indexed: 11/28/2022] Open
Abstract
Pathogen infections can represent a substantial threat to wild populations, especially those already limited in size. To determine how much variation in the pathogens observed among fragmented populations is caused by ecological factors, one needs to examine systems where host genetic diversity is consistent among the populations, thus controlling for any potentially confounding genetic effects. Here, we report geographic variation in haemosporidian infection among European populations of corncrake. This species now occurs in fragmented populations, but there is little genetic structure and equally high levels of genetic diversity among these populations. We observed a longitudinal gradient of prevalence from western to Eastern Europe negatively correlated with national agricultural yield, but positively correlated with corncrake census population sizes when only the most widespread lineage is considered. This likely reveals a possible impact of local agriculture intensity, which reduced host population densities in Western Europe and, potentially, insect vector abundance, thus reducing the transmission of pathogens. We conclude that in the corncrake system, where metapopulation dynamics resulted in variations in local census population sizes, but not in the genetic impoverishment of these populations, anthropogenic activity has led to a reduction in host populations and pathogen prevalence.
Collapse
Affiliation(s)
- Yoan Fourcade
- Université d'Angers, GECCOAngers, France
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East AngliaNorwich, UK
| | - Oskars Keišs
- Laboratory of Ornithology, Institute of Biology, University of LatviaSalaspils, Latvia
| | - David S Richardson
- Centre for Ecology, Evolution and Conservation, School of Biological Sciences, University of East AngliaNorwich, UK
| | | |
Collapse
|
42
|
Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 2014; 4:4399-428. [PMID: 25540699 PMCID: PMC4267876 DOI: 10.1002/ece3.1305] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022] Open
Abstract
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
Collapse
Affiliation(s)
- Alexander I Putman
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| |
Collapse
|
43
|
Butler IA, Siletti K, Oxley PR, Kronauer DJC. Conserved microsatellites in ants enable population genetic and colony pedigree studies across a wide range of species. PLoS One 2014; 9:e107334. [PMID: 25244681 PMCID: PMC4170976 DOI: 10.1371/journal.pone.0107334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/15/2014] [Indexed: 01/05/2023] Open
Abstract
Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.
Collapse
Affiliation(s)
- Ian A. Butler
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Kimberly Siletti
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Peter R. Oxley
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Daniel J. C. Kronauer
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| |
Collapse
|
44
|
Martín-Gálvez D, Molina-Morales M, Dawson DA, Parejo D, Martínez JG, Avilés JM. Characterization of 28 microsatellite loci in the European roller Coracias garrulus (Coracidae, AVES). EUR J WILDLIFE RES 2014. [DOI: 10.1007/s10344-014-0851-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
45
|
Spurgin LG, Illera JC, Jorgensen TH, Dawson DA, Richardson DS. Genetic and phenotypic divergence in an island bird: isolation by distance, by colonization or by adaptation? Mol Ecol 2014; 23:1028-39. [PMID: 24447303 DOI: 10.1111/mec.12672] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/30/2013] [Accepted: 01/08/2014] [Indexed: 02/02/2023]
Abstract
Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure exist across archipelagos and that these are consistent with a pattern of isolation by colonization, but not with isolation by distance or adaptation. Finally, we show that substantial morphological divergence also exists and that this is strongly concordant with patterns of genetic structure and bottleneck history, but not with environmental differences or geographic distance. Overall, our data suggest that founder effects are responsible for both genetic and phenotypic changes across archipelagos. Our findings provide a rare example of how founder effects can persist over evolutionary timescales and suggest that they may play an important role in the early stages of speciation.
Collapse
Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; Behavioural Ecology and Self-organization, Centre for Ecological and Evolutionary Studies, University of Groningen, 9700 CC, Groningen, The Netherlands; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | | | |
Collapse
|
46
|
Ekblom R, Wennekes P, Horsburgh GJ, Burke T. Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. Mol Ecol Resour 2014; 14:636-46. [PMID: 24345231 DOI: 10.1111/1755-0998.12213] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15,250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.
Collapse
Affiliation(s)
- Robert Ekblom
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, Uppsala, SE-75236, Sweden; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | | |
Collapse
|
47
|
Dufresnes C, Brelsford A, Béziers P, Perrin N. Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs. Mol Ecol Resour 2014; 14:716-25. [PMID: 24345298 DOI: 10.1111/1755-0998.12215] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 12/03/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
A simple way to quickly optimize microsatellites in nonmodel organisms is to reuse loci available in closely related taxa; however, this approach can be limited by the stochastic and low cross-amplification success experienced in some groups (e.g. amphibians). An efficient alternative is to develop loci from transcriptome sequences. Transcriptomic microsatellites have been found to vary in their levels of cross-species amplification and variability, but this has to date never been tested in amphibians. Here, we compare the patterns of cross-amplification and levels of polymorphism of 18 published anonymous microsatellites isolated from genomic DNA vs. 17 loci derived from a transcriptome, across nine species of tree frogs (Hyla arborea and Hyla cinerea group). We established a clear negative relationship between divergence time and amplification success, which was much steeper for anonymous than transcriptomic markers, with half-lives (time at which 50% of the markers still amplify) of 1.1 and 37 My, respectively. Transcriptomic markers are significantly less polymorphic than anonymous loci, but remain variable across diverged taxa. We conclude that the exploitation of amphibian transcriptomes for developing microsatellites seems an optimal approach for multispecies surveys (e.g. analyses of hybrid zones, comparative linkage mapping), whereas anonymous microsatellites may be more informative for fine-scale analyses of intraspecific variation. Moreover, our results confirm the pattern that microsatellite cross-amplification is greatly variable among amphibians and should be assessed independently within target lineages. Finally, we provide a bank of microsatellites for Palaearctic tree frogs (so far only available for H. arborea), which will be useful for conservation and evolutionary studies in this radiation.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, Lausanne , 1015, Switzerland
| | | | | | | |
Collapse
|
48
|
Clayton DF, London SE. Advancing avian behavioral neuroendocrinology through genomics. Front Neuroendocrinol 2014; 35:58-71. [PMID: 24113222 DOI: 10.1016/j.yfrne.2013.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/14/2022]
Abstract
Genome technologies are transforming all areas of biology, including the study of hormones, brain and behavior. Annotated reference genome assemblies are rapidly being produced for many avian species. Here we briefly review the basic concepts and tools used in genomics. We then consider how these are informing the study of avian behavioral neuroendocrinology, focusing in particular on lessons from the study of songbirds. We discuss the impact of having a complete "parts list" for an organism; the transformational potential of studying large sets of genes at once instead one gene at a time; the growing recognition that environmental and behavioral signals trigger massive shifts in gene expression in the brain; and the prospects for using comparative genomics to uncover the genetic roots of behavioral variation. Throughout, we identify promising new directions for bolstering the application of genomic information to further advance the study of avian brain and behavior.
Collapse
Affiliation(s)
- David F Clayton
- Biological & Experimental Psychology Division, School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, Committee on Neurobiology, University of Chicago, 940 E 57th Street, Chicago, IL, USA.
| |
Collapse
|
49
|
Huang D, Zhang Y, Jin M, Li H, Song Z, Wang Y, Chen J. Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae). Mol Ecol Resour 2013; 14:569-77. [PMID: 24286608 DOI: 10.1111/1755-0998.12197] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 10/28/2013] [Accepted: 10/28/2013] [Indexed: 11/29/2022]
Abstract
Recent studies utilizing transcriptome sequences generated by next-generation sequencing (NGS) technologies have demonstrated the ability to rapidly detect and characterize thousands of gene-based microsatellites from different plants. However, these simple sequence repeats (SSRs) were seldom used directly to test interspecific transferability in the populations of closely related species. Aspidistra Ker-Gawl. is a monocot genus with high species richness and diversity in flower structure, but its fresh floral materials are not easy to obtain. Until now, little is known about genetic background in the species of Aspidistra, quite apart from the fearful reduction of their natural habitats. In this study, the floral transcriptome of Aspidistra saxicola was obtained using NGS. Based on these data, a total of 5527 SSRs were identified in the unigenes. Among these SSRs, the proportions of di- and tri-nucleotide repeats were quite close (49.6% verse 46.8%), and the most tri-nucleotide repeats were AGG/CCT followed by AAG/CTT and AGC/GCT in A. saxicola, showing distinct differences with other angiosperm species. To assess genetic diversity in the species of Aspidistra, 48 SSR loci were tested in four available populations of A. elatior. The results revealed that more than a third of the loci were polymorphic. The majority of these primers could be amplified in 24 species representing the main clades of Aspidistra. The primer subsets from transcriptome data proved highly useful for detecting polymorphisms in the related species, supporting the finding that NGS is an efficient approach to molecular marker development at both intra- and interspecies levels, especially in endangered nonmodel species.
Collapse
Affiliation(s)
- Danni Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, China
| | | | | | | | | | | | | |
Collapse
|
50
|
Preston SAJ, Briskie JV, Burke T, Hatchwell BJ. Genetic analysis reveals diverse kin-directed routes to helping in the riflemanAcanthisitta chloris. Mol Ecol 2013; 22:5027-39. [DOI: 10.1111/mec.12448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/07/2013] [Accepted: 07/11/2013] [Indexed: 01/10/2023]
Affiliation(s)
| | - James V. Briskie
- Department of Zoology; University of Canterbury; Private Bag 4800 Christchurch New Zealand
| | - Terry Burke
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Ben J. Hatchwell
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| |
Collapse
|