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Hui TCY, Tang Q, Ng EYX, Chong JL, Slade EM, Rheindt FE. Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations. Animals (Basel) 2024; 14:426. [PMID: 38338069 PMCID: PMC10854910 DOI: 10.3390/ani14030426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah's spiny rat Maxomys rajah, Whitehead's spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species.
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Affiliation(s)
- Tabitha C. Y. Hui
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Qian Tang
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
| | - Elize Y. X. Ng
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
- Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Hobart, TAS 7005, Australia
| | - Ju Lian Chong
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Terengganu 21030, Terengganu, Malaysia;
| | - Eleanor M. Slade
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore 117558, Singapore; (Q.T.); (E.Y.X.N.); (F.E.R.)
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Magoro AM, Mtileni B, Hadebe K, Zwane A. Assessment of Genetic Diversity and Conservation in South African Indigenous Goat Ecotypes: A Review. Animals (Basel) 2022; 12:ani12233353. [PMID: 36496874 PMCID: PMC9735466 DOI: 10.3390/ani12233353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.
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Affiliation(s)
- Aletta Matshidiso Magoro
- Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
- Agricultural Research Council, Animal Production, Irene 0062, South Africa
- Correspondence:
| | - Bohani Mtileni
- Department of Animal Sciences, Tshwane University of Technology, Pretoria 0001, South Africa
| | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Onderstepoort 0110, South Africa
| | - Avhashoni Zwane
- Agricultural Research Council, Animal Production, Irene 0062, South Africa
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Liu G, Zhang BF, Chang J, Hu XL, Li C, Xu TT, Liu SQ, Hu DF. Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan. BMC Genomics 2022; 23:668. [PMID: 36138352 PMCID: PMC9503231 DOI: 10.1186/s12864-022-08896-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province. RESULTS SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05-0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%-0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10-3). CONCLUSIONS Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.
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Affiliation(s)
- Gang Liu
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing, 100091, China.
| | - Bao-Feng Zhang
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100085, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiao-Long Hu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330022, China
| | - Chao Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing, 100091, China
| | - Tin-Tao Xu
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shu-Qiang Liu
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100085, China
| | - De-Fu Hu
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100085, China.
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Van Rossum F, Hardy OJ. Guidelines for genetic monitoring of translocated plant populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13670. [PMID: 33236806 DOI: 10.1111/cobi.13670] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/05/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Abstract
Plant translocation is a useful tool for implementing assisted gene flow in recovery plans of critically endangered plant species. Although it helps to restore genetically viable populations, it is not devoid of genetic risks, such as poor adaptation of transplants and outbreeding depression in the hybrid progeny, which may have negative consequences in terms of demographic growth and plant fitness. Hence, a follow-up genetic monitoring should evaluate whether the translocated populations are genetically viable and self-sustaining in the short and long term. The causes of failure to adjust management responses also need to be identified. Molecular markers and fitness-related quantitative traits can be used to determine whether a plant translocation enhanced genetic diversity, increased fitness, and improved the probability of long-term survival. We devised guidelines and illustrated them with studies from the literature to help practitioners determine the appropriate genetic survey methods so that management practices can better integrate evolutionary processes. These guidelines include methods for sampling and for assessing changes in genetic diversity and differentiation, contemporary gene flow, mode of local recruitment, admixture level, the effects of genetic rescue, inbreeding or outbreeding depression and local adaptation on plant fitness, and long-term genetic changes.
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Affiliation(s)
- Fabienne Van Rossum
- Meise Botanic Garden, Nieuwelaan 38, Meise, 1860, Belgium
- Service général de l'Enseignement supérieur et de la Recherche scientifique, Fédération Wallonie-Bruxelles, rue A. Lavallée 1, Brussels, 1080, Belgium
| | - Olivier J Hardy
- Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, CP 160/12, Brussels, 1050, Belgium
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Heydenrych MJ, Saunders BJ, Bunce M, Jarman SN. Epigenetic Measurement of Key Vertebrate Population Biology Parameters. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.617376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The age, sex, and sexual maturity of individual animals are key parameters in assessing wild populations and informing conservation management strategies. These parameters represent the reproductive potential of a population and can indicate recovery rates or vulnerabilities. Natural populations of wild animals are difficult to study; logistically, economically, and due to the impacts of invasive biomonitoring. Genetic and epigenetic analyses offer a low impact, low cost, and information-rich alternative. As epigenetic mechanisms are intrinsically linked with both biological aging and reproductive processes, DNA methylation can be used as a suitable biomarker for population biology study. This review assesses published research utilizing DNA methylation analysis in relation to three key population parameters: age, sex, and sexual maturity. We review studies on wild vertebrates that investigate epigenetic age relationships, with successful age estimation assays designed for mammals, birds, and fish. For both determination of sex and identification of sexual maturity, very little has been explored regarding DNA methylation-based assays. Related research, however, confirms the links between DNA methylation and these processes. Future development of age estimation assays for underrepresented and key conservation taxa is suggested, as is the experimental development and design of DNA methylation-based assays for both sex and sexual maturity identification, further expanding the genomics toolkit for population biology studies.
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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Zhang S, Li C, Li Y, Chen Q, Hu D, Cheng Z, Wang X, Shan Y, Bai J, Liu G. Genetic Differentiation of Reintroduced Père David's Deer ( Elaphurus davidianus) Based on Population Genomics Analysis. Front Genet 2021; 12:705337. [PMID: 34557217 PMCID: PMC8452920 DOI: 10.3389/fgene.2021.705337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David's deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David's deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David's deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David's deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David's deer, and low levels of genome-wide genetic diversity were observed in Père David's deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David's deer, especially between the captive population in Beijing Père David's deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David's deer started to decline ~25.8ka, and the similar levels of three populations' LD reflected the genetic impacts of long-term population bottlenecks in the Père David's deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.
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Affiliation(s)
- Shumiao Zhang
- Beijing Milu Ecological Research Center, Beijing, China
| | - Chao Li
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yiping Li
- Beijing Milu Ecological Research Center, Beijing, China
| | - Qi Chen
- Beijing Milu Ecological Research Center, Beijing, China
| | - Defu Hu
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhibin Cheng
- Beijing Milu Ecological Research Center, Beijing, China
| | - Xiao Wang
- Beijing Milu Ecological Research Center, Beijing, China
| | - Yunfang Shan
- Beijing Milu Ecological Research Center, Beijing, China
| | - Jiade Bai
- Beijing Milu Ecological Research Center, Beijing, China
| | - Gang Liu
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
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8
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Dalapicolla J, Alves R, Jaffé R, Vasconcelos S, Pires ES, Nunes GL, Pereira JBDS, Guimarães JTF, Dias MC, Fernandes TN, Scherer D, dos Santos FMG, Castilho A, Santos MP, Calderón EN, Martins RL, da Fonseca RN, Esteves FDA, Caldeira CF, Oliveira G. Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon. Ecol Evol 2021; 11:10119-10132. [PMID: 34367563 PMCID: PMC8328431 DOI: 10.1002/ece3.7812] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
The quillwort Isoëtes cangae is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N e) are expected for narrow endemic species (NES). Conservation biology studies centered in a single species show some limitations, but they are still useful considering the limited time and resources available for protection of species at risk of extinction. Here, we evaluated the genetic diversity, population structure, N e, and minimum viable population (MVP) of I. cangae to provide information for effective conservation programs. Our analyses were based on 55 individuals collected from the Amendoim Lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and N e in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that I. cangae is not under risk of inbreeding depression. Our findings imply that I. cangae contains enough genetic diversity to ensure evolutionary potential and that all individuals should be treated as one demographic unit. These results provide essential information to optimize ex situ conservation efforts and genetic diversity monitoring, which are currently applied to guide I. cangae conservation plans.
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Affiliation(s)
| | | | - Rodolfo Jaffé
- Instituto Tecnológico ValeBelémBrazil
- ExponentBellevueWAUSA
| | | | | | | | | | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Daniela Scherer
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | | | - Alexandre Castilho
- VALE S/AGerência de Estudos AmbientaisLicenciamento e EspeleologiaNova LimaBrazil
| | - Mirella Pupo Santos
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Emiliano Nicolas Calderón
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Lemes Martins
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
| | - Rodrigo Nunes da Fonseca
- Instituto de Biodiversidade e Sustentabilidade NUPEMUniversidade Federal do Rio de JaneiroMacaéBrazil
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9
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Genomic Approaches for Conservation Management in Australia under Climate Change. Life (Basel) 2021; 11:life11070653. [PMID: 34357024 PMCID: PMC8304512 DOI: 10.3390/life11070653] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
Conservation genetics has informed threatened species management for several decades. With the advent of advanced DNA sequencing technologies in recent years, it is now possible to monitor and manage threatened populations with even greater precision. Climate change presents a number of threats and challenges, but new genomics data and analytical approaches provide opportunities to identify critical evolutionary processes of relevance to genetic management under climate change. Here, we discuss the applications of such approaches for threatened species management in Australia in the context of climate change, identifying methods of facilitating viability and resilience in the face of extreme environmental stress. Using genomic approaches, conservation management practices such as translocation, targeted gene flow, and gene-editing can now be performed with the express intention of facilitating adaptation to current and projected climate change scenarios in vulnerable species, thus reducing extinction risk and ensuring the protection of our unique biodiversity for future generations. We discuss the current barriers to implementing conservation genomic projects and the efforts being made to overcome them, including communication between researchers and managers to improve the relevance and applicability of genomic studies. We present novel approaches for facilitating adaptive capacity and accelerating natural selection in species to encourage resilience in the face of climate change.
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10
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Abstract
Genetic diversity is a critical resource for species’ survival during times of environmental change. Conserving and sustainably managing genetic diversity requires understanding the distribution and amount of genetic diversity (in situ and ex situ) across multiple species. This paper focuses on three emblematic and IUCN Red List threatened oaks (Quercus, Fagaceae), a highly speciose tree genus that contains numerous rare species and poses challenges for ex situ conservation. We compare the genetic diversity of three rare oak species—Quercus georgiana, Q. oglethorpensis, and Q. boyntonii—to common oaks; investigate the correlation of range size, population size, and the abiotic environment with genetic diversity within and among populations in situ; and test how well genetic diversity preserved in botanic gardens correlates with geographic range size. Our main findings are: (1) these three rare species generally have lower genetic diversity than more abundant oaks; (2) in some cases, small population size and geographic range correlate with genetic diversity and differentiation; and (3) genetic diversity currently protected in botanic gardens is inadequately predicted by geographic range size and number of samples preserved, suggesting non-random sampling of populations for conservation collections. Our results highlight that most populations of these three rare oaks have managed to avoid severe genetic erosion, but their small size will likely necessitate genetic management going forward.
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11
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Mandal S, Singh A, Sah P, Singh RK, Kumar R, Lal KK, Mohindra V. Genetic and morphological assessment of a vulnerable large catfish, Silonia silondia (Hamilton, 1822), in natural populations from India. JOURNAL OF FISH BIOLOGY 2021; 98:430-444. [PMID: 33044745 DOI: 10.1111/jfb.14587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Silonia silondia is a commercially important fish distributed in Asian countries, which is under threat due to overexploitation. This study focuses on the morphological analysis and genetic variation of S. silondia individuals, through truss network and sequencing of two mitochondrial regions, respectively, from six wild populations of the Ganga and Mahanadi river systems in India. A total of 38 haplotypes was observed by analysing combined mitochondrial genes (cytochrome b + ATPase 6/8) in 247 individuals of S. silondia collected from six populations. Average haplotype and nucleotide diversities were 0.8508 and 0.00231, respectively. Genetic structure analysis showed the predominant cause of genetic variation to be within populations. The two clades were observed among the haplotypes and time of divergence from their most probable ancestor was estimated to be around 0.3949 mya. Analysis of combined mitochondrial genes in six populations of S. silondia resulted into three management units or genetic stocks. The truss network analysis was carried out by interconnecting 12 landmarks from digital images of specimens to identify phenotypic stocks. Sixty-five truss morphometric variables were analysed for geometric shape variation which revealed morphological divergence in River Son specimens. The present study presents molecular markers and genetic diversity data which can be critical input for conservation and management of differentiated populations and future monitoring of the genetic bottleneck. The morphological shape analysis clearly shows that variation in the insertion of adipose fin is an important parameter influencing the morphological discrimination.
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Affiliation(s)
- Sangeeta Mandal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Achal Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Priyanka Sah
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Rajeev K Singh
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Raj Kumar
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Kuldeep K Lal
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
| | - Vindhya Mohindra
- ICAR-National Bureau of Fish Genetic Resources (NBFGR), Lucknow, India
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12
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Rius M, Turon X. Phylogeography and the Description of Geographic Patterns in Invasion Genomics. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.595711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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13
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Cros E, Chattopadhyay B, Garg KM, Ng NSR, Tomassi S, Benedick S, Edwards DP, Rheindt FE. Quaternary land bridges have not been universal conduits of gene flow. Mol Ecol 2020; 29:2692-2706. [PMID: 32542783 DOI: 10.1111/mec.15509] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of more than 100 individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in nondispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.
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Affiliation(s)
- Emilie Cros
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Nathaniel S R Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Suzanne Tomassi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Suzan Benedick
- Sustainable Agriculture School, Universiti Malaysia Sabah, Sabah, Malaysia
| | - David P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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14
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Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X, Huang J, Zhang X, Sun H, Wang H. Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization. iScience 2020; 23:101124. [PMID: 32428861 PMCID: PMC7232092 DOI: 10.1016/j.isci.2020.101124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/20/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.
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Affiliation(s)
- Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | | | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA; School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
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15
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Cros E, Ng EYX, Oh RRY, Tang Q, Benedick S, Edwards DP, Tomassi S, Irestedt M, Ericson PGP, Rheindt FE. Fine-scale barriers to connectivity across a fragmented South-East Asian landscape in six songbird species. Evol Appl 2020; 13:1026-1036. [PMID: 32431750 PMCID: PMC7232758 DOI: 10.1111/eva.12918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/10/2019] [Accepted: 12/08/2019] [Indexed: 12/28/2022] Open
Abstract
Habitat fragmentation is a major extinction driver. Despite dramatically increasing fragmentation across the globe, its specific impacts on population connectivity across species with differing life histories remain difficult to characterize, let alone quantify. Here, we investigate patterns of population connectivity in six songbird species from Singapore, a highly fragmented tropical rainforest island. Using massive panels of genome-wide single nucleotide polymorphisms across dozens of samples per species, we examined population genetic diversity, inbreeding, gene flow and connectivity among species along a spectrum of ecological specificities. We found a higher resilience to habitat fragmentation in edge-tolerant and forest-canopy species as compared to forest-dependent understorey insectivores. The latter exhibited levels of genetic diversity up to three times lower in Singapore than in populations from contiguous forest elsewhere. Using dense genomic and geographic sampling, we identified individual barriers such as reservoirs that effectively minimize gene flow in sensitive understorey birds, revealing that terrestrial forest species may exhibit levels of sensitivity to fragmentation far greater than previously expected. This study provides a blueprint for conservation genomics at small scales with a view to identifying preferred locations for habitat corridors, flagging candidate populations for restocking with translocated individuals and improving the design of future reserves.
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Affiliation(s)
- Emilie Cros
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Elize Y. X. Ng
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Rachel R. Y. Oh
- Centre for Urban Greenery and EcologyNational Parks BoardSingaporeSingapore
- School of Biological SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Qian Tang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Suzan Benedick
- Sustainable Agriculture SchoolUniversiti Malaysia SabahSabahMalaysia
| | - David P. Edwards
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Suzanne Tomassi
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Martin Irestedt
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Per G. P. Ericson
- Department of ZoologySwedish Museum of Natural HistoryStockholmSweden
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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16
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Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SA, Sung YY, Van de Peer Y, Sorgeloos P, Danish-Daniel M. Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review. Evol Bioinform Online 2019; 15:1176934319892284. [PMID: 31839703 PMCID: PMC6896124 DOI: 10.1177/1176934319892284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.
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Affiliation(s)
- Min Pau Tan
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Li Lian Wong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Siti Aisyah Razali
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Nor Afiqah-Aleng
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Yves Van de Peer
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Patrick Sorgeloos
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Laboratory of Aquaculture & Artemia Reference Center, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Muhd Danish-Daniel
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia.,Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
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17
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Li YL, Xue DX, Zhang BD, Liu JX. Population Genomic Signatures of Genetic Structure and Environmental Selection in the Catadromous Roughskin Sculpin Trachidermus fasciatus. Genome Biol Evol 2019; 11:1751-1764. [PMID: 31173074 PMCID: PMC6601870 DOI: 10.1093/gbe/evz118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Understanding the patterns of genetic diversity and adaptation across species' range is crucial to assess its long-term persistence and determine appropriate conservation measures. The impacts of human activities on the genetic diversity and genetic adaptation to heterogeneous environments remain poorly understood in the marine realm. The roughskin sculpin (Trachidermus fasciatus) is a small catadromous fish, and has been listed as a second-class state protected aquatic animal since 1988 in China. To elucidate the underlying mechanism of population genetic structuring and genetic adaptations to local environments, RAD tags were sequenced for 202 individuals in nine populations across the range of T. fasciatus in China. The pairwise FST values over 9,271 filtered SNPs were significant except that between Dongying and Weifang. All the genetic clustering analysis revealed significant population structure with high support for eight distinct genetic clusters. Both the minor allele frequency spectra and Ne estimations suggested extremely small Ne in some populations (e.g., Qinhuangdao, Rongcheng, Wendeng, and Qingdao), which might result from recent population bottleneck. The strong genetic structure can be partly attributed to genetic drift and habitat fragmentation, likely due to the anthropogenic activities. Annotations of candidate adaptive loci suggested that genes involved in metabolism, development, and osmoregulation were critical for adaptation to spatially heterogenous environment of local populations. In the context of anthropogenic activities and environmental change, results of the present population genomic work provided important contributions to the understanding of genetic differentiation and adaptation to changing environments.
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Affiliation(s)
- Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Dong-Xiu Xue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Bai-Dong Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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18
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Hamabata T, Kinoshita G, Kurita K, Cao PL, Ito M, Murata J, Komaki Y, Isagi Y, Makino T. Endangered island endemic plants have vulnerable genomes. Commun Biol 2019; 2:244. [PMID: 31263788 PMCID: PMC6597543 DOI: 10.1038/s42003-019-0490-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/03/2019] [Indexed: 11/29/2022] Open
Abstract
Loss of genetic diversity is known to decrease the fitness of species and is a critical factor that increases extinction risk. However, there is little evidence for higher vulnerability and extinction risk in endangered species based on genomic differences between endangered and non-endangered species. This is true even in the case of functional loci, which are more likely to relate to the fitness of species than neutral loci. Here, we compared the genome-wide genetic diversity, proportion of duplicated genes (PD), and accumulation of deleterious variations of endangered island endemic (EIE) plants from four genera with those of their non-endangered (NE) widespread congeners. We focused on exhaustive sequences of expressed genes obtained by RNA sequencing. Most EIE species exhibited significantly lower genetic diversity and PD than NE species. Additionally, all endangered species accumulated deleterious variations. Our findings provide new insights into the genomic traits of EIE species.
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Affiliation(s)
- Tomoko Hamabata
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
| | - Gohta Kinoshita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Kazuki Kurita
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Ping-Lin Cao
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902 Japan
| | - Jin Murata
- Koishikawa Botanical Garden, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 112-0001 Japan
| | - Yoshiteru Komaki
- Koishikawa Botanical Garden, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 112-0001 Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502 Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8578 Japan
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19
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Amish SJ, Ali O, Peacock M, Miller M, Robinson M, Smith S, Luikart G, Neville H. Assessing thermal adaptation using family‐based association and
F
ST
outlier tests in a threatened trout species. Mol Ecol 2019; 28:2573-2593. [DOI: 10.1111/mec.15100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Stephen J. Amish
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
| | - Omar Ali
- Department of Animal Science University of California Davis California
| | - Mary Peacock
- Department of Biology University of Nevada Reno Nevada
| | - Michael Miller
- Department of Animal Science University of California Davis California
| | | | - Seth Smith
- Flathead Biological Station University of Montana Polson Montana
| | - Gordon Luikart
- Conservation Genomics Group, Division of Biological Sciences University of Montana Missoula Montana
- Flathead Biological Station University of Montana Polson Montana
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20
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Phair NL, Toonen RJ, Knapp I, von der Heyden S. Shared genomic outliers across two divergent population clusters of a highly threatened seagrass. PeerJ 2019; 7:e6806. [PMID: 31106053 PMCID: PMC6497040 DOI: 10.7717/peerj.6806] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/18/2019] [Indexed: 12/15/2022] Open
Abstract
The seagrass, Zostera capensis, occurs across a broad stretch of coastline and wide environmental gradients in estuaries and sheltered bays in southern and eastern Africa. Throughout its distribution, habitats are highly threatened and poorly protected, increasing the urgency of assessing the genomic variability of this keystone species. A pooled genomic approach was employed to obtain SNP data and examine neutral genomic variation and to identify potential outlier loci to assess differentiation across 12 populations across the ∼9,600 km distribution of Z. capensis. Results indicate high clonality and low genomic diversity within meadows, which combined with poor protection throughout its range, increases the vulnerability of this seagrass to further declines or local extinction. Shared variation at outlier loci potentially indicates local adaptation to temperature and precipitation gradients, with Isolation-by-Environment significantly contributing towards shaping spatial variation in Z. capensis. Our results indicate the presence of two population clusters, broadly corresponding to populations on the west and east coasts, with the two lineages shaped only by frequency differences of outlier loci. Notably, ensemble modelling of suitable seagrass habitat provides evidence that the clusters are linked to historical climate refugia around the Last Glacial Maxi-mum. Our work suggests a complex evolutionary history of Z. capensis in southern and eastern Africa that will require more effective protection in order to safeguard this important ecosystem engineer into the future.
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Affiliation(s)
- Nikki Leanne Phair
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert John Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Ingrid Knapp
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, Hawai’i, United States of America
| | - Sophie von der Heyden
- Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
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21
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Leitwein M, Gagnaire PA, Desmarais E, Berrebi P, Guinand B. Genomic consequences of a recent three-way admixture in supplemented wild brown trout populations revealed by local ancestry tracts. Mol Ecol 2018; 27:3466-3483. [PMID: 30054960 DOI: 10.1111/mec.14816] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022]
Abstract
Understanding the evolutionary consequences of human-mediated introductions of domesticated strains into the wild and their subsequent admixture with natural populations is of major concern in conservation biology. However, the genomic impacts of stocking from distinct sources (locally derived vs. divergent) on the genetic integrity of wild populations remain poorly understood. We designed an approach based on estimating local ancestry along individual chromosomes to provide a detailed picture of genomic admixture in supplemented populations. We used this approach to document admixture consequences in the brown trout Salmo trutta, for which decades of stocking practices have profoundly impacted the genetic make-up of wild populations. In southern France, small local Mediterranean populations have been subject to successive introductions of domestic strains derived from the Atlantic and Mediterranean lineages. To address the impact of stocking, we evaluate the extent of admixture from both domestic strains within populations, using 75,684 mapped SNPs obtained from double-digested restriction site-associated DNA sequencing. Then, the chromosomal ancestry profiles of admixed individuals reveal a wider diversity of hybrid and introgressed genotypes than estimated using classical methods for inferring ancestry and hybrid pedigrees. In addition, the length distribution of introgressed tracts retained different timings of introgression between the two domestic strains. We finally reveal opposite consequences of admixture on the level of polymorphism of the recipient populations between domestic strains. Our study illustrates the potential of using the information contained in the genomic mosaic of ancestry tracts in combination with classical methods based on allele frequencies for analysing multiple-way admixture with population genomic data.
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Affiliation(s)
- Maeva Leitwein
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | | | - Erick Desmarais
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Bruno Guinand
- ISEM, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Département Biologie-Ecologie, Université de Montpellier, Montpellier Cedex 5, France
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22
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Christensen KA, Leong JS, Sakhrani D, Biagi CA, Minkley DR, Withler RE, Rondeau EB, Koop BF, Devlin RH. Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome. PLoS One 2018; 13:e0195461. [PMID: 29621340 PMCID: PMC5886536 DOI: 10.1371/journal.pone.0195461] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/22/2018] [Indexed: 11/18/2022] Open
Abstract
When unifying genomic resources among studies and comparing data between species, there is often no better resource than a genome sequence. Having a reference genome for the Chinook salmon (Oncorhynchus tshawytscha) will enable the extensive genomic resources available for Pacific salmon, Atlantic salmon, and rainbow trout to be leveraged when asking questions related to the Chinook salmon. The Chinook salmon's wide distribution, long cultural impact, evolutionary history, substantial hatchery production, and recent wild-population decline make it an important research species. In this study, we sequenced and assembled the genome of a Chilliwack River Hatchery female Chinook salmon (gynogenetic and homozygous at all loci). With a reference genome sequence, new questions can be asked about the nature of this species, and its role in a rapidly changing world.
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Affiliation(s)
- Kris A. Christensen
- Fisheries and Oceans Canada, West Vancouver, BC, Canada
- University of Victoria, Victoria, BC, Canada
| | | | | | | | | | - Ruth E. Withler
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Ben F. Koop
- University of Victoria, Victoria, BC, Canada
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23
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Aavik T, Helm A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor Ecol 2017. [DOI: 10.1111/rec.12634] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Tsipe Aavik
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences; University of Tartu, Lai 40; 51005, Tartu Estonia
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24
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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25
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Brown AP, Greenway R, Morgan S, Quackenbush CR, Giordani L, Arias-Rodriguez L, Tobler M, Kelley JL. Genome-scale data reveal that endemic Poecilia populations from small sulphidic springs display no evidence of inbreeding. Mol Ecol 2017; 26:4920-4934. [PMID: 28731545 DOI: 10.1111/mec.14249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/04/2017] [Accepted: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Populations with limited ranges can be highly vulnerable to changes in their environment and are, thus, of high conservation concern. Populations that experience human-induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes Poecilia sulphuraria (listed as critically endangered) and Poecilia thermalis, which are endemic to small hydrogen sulphide-rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of P. sulphuraria and one population of P. thermalis. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. The genetic data were also used to infer the demographic history of these populations to obtain estimates for effective population sizes and migration rates. Effective population sizes were large given the small habitats of these populations. Our results imply that these three endemic extremophile populations should each be considered separately for conservation purposes. Additionally, this study suggests that populations in naturally small habitats may have lower rates of inbreeding and higher genetic diversity than expected, and therefore may be better equipped to handle environmental perturbations than anticipated. We caution, however, that the inferred lack of inbreeding and the large effective population sizes could potentially be a result of colonization by genetically diverse ancestors.
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Affiliation(s)
- Anthony P Brown
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Samuel Morgan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, Tabasco, México
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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26
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Spatial conservation prioritization of biodiversity spanning the evolutionary continuum. Nat Ecol Evol 2017; 1:151. [PMID: 28812637 DOI: 10.1038/s41559-017-0151] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/22/2017] [Indexed: 11/09/2022]
Abstract
Accounting for evolutionary relationships between and within species is important for biodiversity conservation planning, but is rarely considered in practice. Here we introduce a novel framework to identify priority conservation areas accounting for phylogenetic and intraspecific diversity, integrating concepts from phylogeny, phylogeography, spatial statistics and spatial conservation prioritization. The framework allows planners to incorporate and combine different levels of evolutionary diversity and can be applied to any taxonomic group and to any region in the world. We illustrate our approach using amphibian and reptile species occurring in a biodiversity hotspot region, the Iberian Peninsula. We found that explicitly incorporating phylogenetic and intraspecific diversity in systematic conservation planning provides advantages in terms of maximizing overall biodiversity representation while enhancing its persistence and evolutionary potential. Our results emphasize the need to account for the evolutionary continuum in order to efficiently implement biodiversity conservation planning decisions.
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Landguth EL, Holden ZA, Mahalovich MF, Cushman SA. Using Landscape Genetics Simulations for Planting Blister Rust Resistant Whitebark Pine in the US Northern Rocky Mountains. Front Genet 2017; 8:9. [PMID: 28239390 PMCID: PMC5300977 DOI: 10.3389/fgene.2017.00009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 01/18/2017] [Indexed: 11/20/2022] Open
Abstract
Recent population declines to the high elevation western North America foundation species whitebark pine, have been driven by the synergistic effects of the invasive blister rust pathogen, mountain pine beetle (MPB), fire exclusion, and climate change. This has led to consideration for listing whitebark pine (WBP) as a threatened or endangered species under the Endangered Species Act, which has intensified interest in developing management strategies for maintaining and restoring the species. An important, but poorly studied, aspect of WBP restoration is the spatial variation in adaptive genetic variation and the potential of blister rust resistant strains to maintain viable populations in the future. Here, we present a simulation modeling framework to improve understanding of the long-term genetic consequences of the blister rust pathogen, the evolution of rust resistance, and scenarios of planting rust resistant genotypes of whitebark pine. We combine climate niche modeling and eco-evolutionary landscape genetics modeling to evaluate the effects of different scenarios of planting rust-resistant genotypes and impacts of wind field direction on patterns of gene flow. Planting scenarios showed different levels for local extirpation of WBP and increased population-wide blister rust resistance, suggesting that the spatial arrangement and choice of planting locations can greatly affect survival rates of whitebark pine. This study presents a preliminary, but potentially important, framework for facilitating the conservation of whitebark pine.
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Affiliation(s)
- Erin L Landguth
- Division of Biological Sciences, University of Montana Missoula, MT, USA
| | | | - Mary F Mahalovich
- U.S. Department of Agriculture Forest Service, Northern, Rocky Mountain, Southwestern and Intermountain Regions Moscow, ID, USA
| | - Samuel A Cushman
- U.S. Department of Agriculture Forest Service, Rocky Mountain Research Station Flagstaff, AZ, USA
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Wang J, Xue DX, Zhang BD, Li YL, Liu BJ, Liu JX. Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus). PLoS One 2016; 11:e0157809. [PMID: 27336696 PMCID: PMC4919078 DOI: 10.1371/journal.pone.0157809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/06/2016] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dong-Xiu Xue
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bai-Dong Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Long Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing-Jian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xian Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons). Int J Genomics 2016; 2016:5613862. [PMID: 27069913 PMCID: PMC4812450 DOI: 10.1155/2016/5613862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/07/2016] [Indexed: 01/08/2023] Open
Abstract
The list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which often little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations of S. cebifrons exist, which originated from two different Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to other Sus species potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well.
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Yoshida K, Miyagi R, Mori S, Takahashi A, Makino T, Toyoda A, Fujiyama A, Kitano J. Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. Ecol Evol 2016; 6:2190-204. [PMID: 27069575 PMCID: PMC4782248 DOI: 10.1002/ece3.2047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/13/2023] Open
Abstract
Invasive species pose a major threat to biological diversity. Although introduced populations often experience population bottlenecks, some invasive species are thought to be originated from hybridization between multiple populations or species, which can contribute to the maintenance of high genetic diversity. Recent advances in genome sequencing enable us to trace the evolutionary history of invasive species even at whole‐genome level and may help to identify the history of past hybridization that may be overlooked by traditional marker‐based analysis. Here, we conducted whole‐genome sequencing of eight threespine stickleback (Gasterosteus aculeatus) individuals, four from a recently introduced crater lake population and four of the putative source population. We found that both populations have several small genomic regions with high genetic diversity, which resulted from introgression from a closely related species (Gasterosteus nipponicus). The sizes of the regions were too small to be detected with traditional marker‐based analysis or even some reduced‐representation sequencing methods. Further amplicon sequencing revealed linkage disequilibrium around an introgression site, which suggests the possibility of selective sweep at the introgression site. Thus, interspecies introgression might predate introduction and increase genetic variation in the source population. Whole‐genome sequencing of even a small number of individuals can therefore provide higher resolution inference of history of introduced populations.
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Affiliation(s)
- Kohta Yoshida
- Division of Ecological Genetics Department of Population Genetics National Institute of Genetics Mishima Shizuoka Japan
| | - Ryutaro Miyagi
- Evolutionary Genetics Laboratory Department of Biological Sciences Tokyo Metropolitan University Hachioji Tokyo Japan
| | - Seiichi Mori
- Biological Laboratory Gifu-keizai University Ogaki Gifu Japan
| | - Aya Takahashi
- Evolutionary Genetics Laboratory Department of Biological Sciences Tokyo Metropolitan University Hachioji Tokyo Japan
| | - Takashi Makino
- Division of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory Center for Information Biology National Institute of Genetics Mishima Shizuoka Japan
| | - Asao Fujiyama
- Division of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan; Department of Genetics SOKENDAI (The Graduate University for Advanced Studies) Mishima Shizuoka Japan
| | - Jun Kitano
- Division of Ecological Genetics Department of Population Genetics National Institute of Genetics Mishima Shizuoka Japan; Department of Genetics SOKENDAI (The Graduate University for Advanced Studies) Mishima Shizuoka Japan
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Haig SM, Miller MP, Bellinger R, Draheim HM, Mercer DM, Mullins TD. The conservation genetics juggling act: integrating genetics and ecology, science and policy. Evol Appl 2015; 9:181-95. [PMID: 27087847 PMCID: PMC4780381 DOI: 10.1111/eva.12337] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/27/2015] [Indexed: 01/08/2023] Open
Abstract
The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has ‘grown up’ with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de‐list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions.
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Affiliation(s)
- Susan M Haig
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Mark P Miller
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
| | - Renee Bellinger
- Department of Biology, Tropical Conservation Biology and Environmental Science University of Hawaii Hilo HI USA
| | - Hope M Draheim
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Laboratory Eagle ID USA
| | - Dacey M Mercer
- Hatfield Marine Science Center Oregon State University Newport OR USA
| | - Thomas D Mullins
- U.S. Geological Survey Forest and Rangeland Ecosystem Science Center Corvallis OR USA
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Olivieri I, Tonnabel J, Ronce O, Mignot A. Why evolution matters for species conservation: perspectives from three case studies of plant metapopulations. Evol Appl 2015; 9:196-211. [PMID: 27087848 PMCID: PMC4780382 DOI: 10.1111/eva.12336] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 09/30/2015] [Indexed: 01/16/2023] Open
Abstract
We advocate the advantage of an evolutionary approach to conservation biology that considers evolutionary history at various levels of biological organization. We review work on three separate plant taxa, spanning from one to multiple decades, illustrating extremes in metapopulation functioning. We show how the rare endemics Centaurea corymbosa (Clape Massif, France) and Brassica insularis in Corsica (France) may be caught in an evolutionary trap: disruption of metapopulation functioning due to lack of colonization of new sites may have counterselected traits such as dispersal ability or self‐compatibility, making these species particularly vulnerable to any disturbance. The third case study concerns the evolution of life history strategies in the highly diverse genus Leucadendron of the South African fynbos. There, fire disturbance and the recolonization phase after fires are so integral to the functioning of populations that recruitment of new individuals is conditioned by fire. We show how past adaptation to different fire regimes and climatic constraints make species with different life history syndromes more or less vulnerable to global changes. These different case studies suggest that management strategies should promote evolutionary potential and evolutionary processes to better protect extant biodiversity and biodiversification.
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Affiliation(s)
- Isabelle Olivieri
- Institut des Sciences de l'Evolution Université Montpellier CNRS IRD EPHE CC65 Place Eugène Bataillon, 34095, Montpellier cedex 5 France
| | - Jeanne Tonnabel
- Institut des Sciences de l'Evolution Université Montpellier CNRS IRD EPHE CC65 Place Eugène Bataillon, 34095, Montpellier cedex 5 France; Department of Ecology and Evolution Le Biophore UNIL-SORGE University of Lausanne Lausanne Switzerland
| | - Ophélie Ronce
- Institut des Sciences de l'Evolution Université Montpellier CNRS IRD EPHE CC65 Place Eugène Bataillon, 34095, Montpellier cedex 5 France
| | - Agnès Mignot
- Institut des Sciences de l'Evolution Université Montpellier CNRS IRD EPHE CC65 Place Eugène Bataillon, 34095, Montpellier cedex 5 France
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Lal MM, Southgate PC, Jerry DR, Zenger KR. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. Mar Genomics 2015; 25:57-68. [PMID: 26545807 DOI: 10.1016/j.margen.2015.10.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 01/01/2023]
Abstract
Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fst outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fst=0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (NeLD=6.1), compared to wild populations (NeLD>192.5). Fst outlier detection revealed 42-62 highly differentiated SNPs (p<0.02), while case-control association discovered up to 152 SNPs (p<0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.
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Affiliation(s)
- Monal M Lal
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Paul C Southgate
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture (CSTFA), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia; College of Marine and Environmental Sciences (CMES), James Cook University, Townsville Campus, Townsville, QLD 4811, Australia.
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Genome-wide SNP loci reveal novel insights into koala (Phascolarctos cinereus) population variability across its range. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0784-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Miller JM, Poissant J, Malenfant RM, Hogg JT, Coltman DW. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep. Ecol Evol 2015; 5:3401-12. [PMID: 26380673 PMCID: PMC4569035 DOI: 10.1002/ece3.1612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D', and χ ('2). We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - Jocelyn Poissant
- Centre for Ecology and Conservation, University of Exeter Penryn Campus, UK
| | - René M Malenfant
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - John T Hogg
- Montana Conservation Science Institute 5200 Upper Miller Creek Road, Missoula, Montana, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
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Reynolds MH, Pearce JM, Lavretsky P, Seixas PP, Courtot KN. Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions. ENDANGER SPECIES RES 2015. [DOI: 10.3354/esr00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Miller JM, Moore SS, Stothard P, Liao X, Coltman DW. Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics 2015; 16:397. [PMID: 25990117 PMCID: PMC4438629 DOI: 10.1186/s12864-015-1618-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023] Open
Abstract
Background Whole genome sequences (WGS) have proliferated as sequencing technology continues to improve and costs decline. While many WGS of model or domestic organisms have been produced, a growing number of non-model species are also being sequenced. In the absence of a reference, construction of a genome sequence necessitates de novo assembly which may be beyond the ability of many labs due to the large volumes of raw sequence data and extensive bioinformatics required. In contrast, the presence of a reference WGS allows for alignment which is more tractable than assembly. Recent work has highlighted that the reference need not come from the same species, potentially enabling a wide array of species WGS to be constructed using cross-species alignment. Here we report on the creation a draft WGS from a single bighorn sheep (Ovis canadensis) using alignment to the closely related domestic sheep (Ovis aries). Results Two sequencing libraries on SOLiD platforms yielded over 865 million reads, and combined alignment to the domestic sheep reference resulted in a nearly complete sequence (95% coverage of the reference) at an average of 12x read depth (104 SD). From this we discovered over 15 million variants and annotated them relative to the domestic sheep reference. We then conducted an enrichment analysis of those SNPs showing fixed differences between the reference and sequenced individual and found significant differences in a number of gene ontology (GO) terms, including those associated with reproduction, muscle properties, and bone deposition. Conclusion Our results demonstrate that cross-species alignment enables the creation of novel WGS for non-model organisms. The bighorn sheep WGS will provide a resource for future resequencing studies or comparative genomics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1618-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, QLD, Australia. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Xiaoping Liao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - David W Coltman
- Department of Biological Science, University of Alberta, Edmonton, Alberta, Canada.
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Williams AV, Boykin LM, Howell KA, Nevill PG, Small I. The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene. PLoS One 2015; 10:e0125768. [PMID: 25955637 PMCID: PMC4425659 DOI: 10.1371/journal.pone.0125768] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 03/26/2015] [Indexed: 11/25/2022] Open
Abstract
Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex.
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Affiliation(s)
- Anna V. Williams
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, Kings Park, Western Australia, Australia
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Laura M. Boykin
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Katharine A. Howell
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Paul G. Nevill
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, Fraser Avenue, Kings Park, Western Australia, Australia
- School of Plant Biology, The University of Western Australia, Crawley, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia
- Centre of Excellence in Computational Systems Biology, The University of Western Australia, Crawley, Western Australia, Australia
- * E-mail:
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40
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Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM. Impacts of degraded
DNA
on restriction enzyme associated
DNA
sequencing (
RADS
eq). Mol Ecol Resour 2015; 15:1304-15. [DOI: 10.1111/1755-0998.12404] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Carly F. Graham
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Travis C. Glenn
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Andrew G. McArthur
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Douglas R. Boreham
- Medical Sciences Northern Ontario School of Medicine Greater Sudbury Ontario P0M Canada
| | - Troy Kieran
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Stacey Lance
- Savannah River Ecology Laboratory University of Georgia Athens GA 30602 USA
| | - Richard G. Manzon
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Jessica A. Martino
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Todd Pierson
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Sean M. Rogers
- Department of Biological Sciences University of Calgary Calgary Alberta T2N 1N4 Canada
| | - Joanna Y. Wilson
- Department of Biology McMaster University Hamilton Ontario L8S 4M1 Canada
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41
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Shafer AB, Wolf JB, Alves PC, Bergström L, Bruford MW, Brännström I, Colling G, Dalén L, De Meester L, Ekblom R, Fawcett KD, Fior S, Hajibabaei M, Hill JA, Hoezel AR, Höglund J, Jensen EL, Krause J, Kristensen TN, Krützen M, McKay JK, Norman AJ, Ogden R, Österling EM, Ouborg NJ, Piccolo J, Popović D, Primmer CR, Reed FA, Roumet M, Salmona J, Schenekar T, Schwartz MK, Segelbacher G, Senn H, Thaulow J, Valtonen M, Veale A, Vergeer P, Vijay N, Vilà C, Weissensteiner M, Wennerström L, Wheat CW, Zieliński P. Genomics and the challenging translation into conservation practice. Trends Ecol Evol 2015; 30:78-87. [DOI: 10.1016/j.tree.2014.11.009] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 10/24/2022]
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42
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Mergeay J, Santamaria L. Evolution and Biodiversity: the evolutionary basis of biodiversity and its potential for adaptation to global change. Evol Appl 2015; 5:103-6. [PMID: 25568033 PMCID: PMC3353341 DOI: 10.1111/j.1752-4571.2011.00232.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Joachim Mergeay
- Research Institute for Nature and Forest Geraardsbergen, Belgium e-mail:
| | - Luis Santamaria
- Laboratory of Spatial Ecology, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB) Balearic Islands, Spain e-mail:
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43
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Santamaría L, Méndez PF. Evolution in biodiversity policy - current gaps and future needs. Evol Appl 2015; 5:202-18. [PMID: 25568042 PMCID: PMC3353340 DOI: 10.1111/j.1752-4571.2011.00229.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/17/2011] [Indexed: 12/25/2022] Open
Abstract
The intensity and speed of human alterations to the planet's ecosystems are yielding our static, ahistorical view of biodiversity obsolete. Human actions frequently trigger fast evolutionary responses, affect extant genetic variation and result in the establishment of new communities and co-evolutionary networks for which we lack past analogues. Contemporary evolution interplays with ecological changes to determine the response of organisms and ecosystems to anthropogenic pressures. Examples on wild species include responses to harvest (e.g. fisheries, hunting, angling), habitat loss and fragmentation (e.g. genetic effects of isolation), biotic exchange (e.g. evolutionary responses to control measures), climate change (e.g. local adaptation and its interplay with dispersal processes) and the responses of endangered species to conservation measures. A review of international and EU biodiversity policies showed numerous opportunities for the integration of evolutionary knowledge, with the realistic prospect of improving their efficacy. Such opportunities should be extended to other sectoral policies of direct relevance for biodiversity – notably nature conservation, fisheries, agriculture, water resources, spatial planning and climate change. These avenues for improvement are, however, challenged by the low level of enforcement of biodiversity policies, linked to the nonbinding nature of most biodiversity-policy documents, and the decreasing representation of biodiversity in EU's research policy.
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Affiliation(s)
- Luis Santamaría
- Laboratory of Spatial Ecology, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB) Esporles, Balearic Islands, Spain
| | - Pablo F Méndez
- Laboratory of Spatial Ecology, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB) Esporles, Balearic Islands, Spain
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44
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Queirós J, Godinho R, Lopes S, Gortazar C, de la Fuente J, Alves PC. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications. Mol Ecol Resour 2014; 15:747-60. [PMID: 25403329 DOI: 10.1111/1755-0998.12349] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/27/2022]
Abstract
Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.
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Affiliation(s)
- J Queirós
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - R Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - S Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - C Gortazar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - J de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - P C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
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45
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Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
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46
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Rius M, Turon X, Bernardi G, Volckaert FAM, Viard F. Marine invasion genetics: from spatio-temporal patterns to evolutionary outcomes. Biol Invasions 2014. [DOI: 10.1007/s10530-014-0792-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Wright DJ, Spurgin LG, Collar NJ, Komdeur J, Burke T, Richardson DS. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler. Mol Ecol 2014; 23:2165-77. [PMID: 24689851 PMCID: PMC4237152 DOI: 10.1111/mec.12740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/10/2023]
Abstract
Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.
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Affiliation(s)
- David J Wright
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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48
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Miller JM, Coltman DW. Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta-analysis. Mol Ecol 2014; 23:1899-909. [DOI: 10.1111/mec.12707] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Joshua M. Miller
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
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49
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Larson WA, Seeb LW, Everett MV, Waples RK, Templin WD, Seeb JE. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 2014; 7:355-69. [PMID: 24665338 PMCID: PMC3962296 DOI: 10.1111/eva.12128] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/02/2013] [Indexed: 12/14/2022] Open
Abstract
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Meredith V Everett
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - William D Templin
- Gene Conservation Laboratory, Alaska Department of Fish and Game Anchorage, AK, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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50
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Hughes GM, Gang L, Murphy WJ, Higgins DG, Teeling EC. Using Illumina next generation sequencing technologies to sequence multigene families in de novo species. Mol Ecol Resour 2013; 13:510-21. [PMID: 23480365 DOI: 10.1111/1755-0998.12087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 01/27/2013] [Accepted: 01/29/2013] [Indexed: 11/27/2022]
Abstract
The advent of Next Generation Sequencing Technology (NGST) has revolutionized molecular biology research, allowing for rapid gene/genome sequencing from a multitude of diverse species. As high throughput sequencing becomes more accessible, more efficient workflows must be developed to deal with the amounts of data produced and better assemble the genomes of de novo lineages. We combine traditional laboratory methods with Illumina NGST to amplify and sequence the largest mammalian multigene family, the Olfactory Receptor gene family, for species with and without a reference genome. We develop novel assembly methods to annotate and filter these data, which can be utilized for any gene family or any species. We find no significant difference between the ratio of genes within their respective gene families of our data compared with available genomic data. Using simulated data we explore the limitations of short-read sequence data and our assembly in recovering this gene family. We highlight the benefits and shortcomings of these methods. Compared with data generated from traditional polymerase chain reaction, cloning and Sanger sequencing methodologies, sequence data generated using our pipeline increases yield and sequencing efficiency without reducing the number of unique genes amplified. A cloning step is not required, therefore shortening data generation time. The novel downstream methodologies and workflows described provide a tool to be utilized by many fields of biology, to access and analyze the vast quantities of data generated. By combining laboratory and in silico methods, we provide a means of extracting genomic information for multigene families without complete genome sequencing.
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Affiliation(s)
- Graham M Hughes
- UCD School of Biological and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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