1
|
Ray K, Basak SK, Giri CK, Kotal HN, Mandal A, Chatterjee K, Saha S, Biswas B, Mondal S, Das I, Ghosh A, Bhadury P, Joshi R. Ecological restoration at pilot-scale employing site-specific rationales for small-patch degraded mangroves in Indian Sundarbans. Sci Rep 2024; 14:12952. [PMID: 38839775 PMCID: PMC11153218 DOI: 10.1038/s41598-024-63281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
To date, degraded mangrove ecosystem restoration accomplished worldwide primarily aligns towards rehabilitation with monotypic plantations, while ecological restoration principles are rarely followed in these interventions. However, researchers admit that most of these initiatives' success rate is not appreciable often. An integrative framework of ecological restoration for degraded mangroves where site-specific observations could be scientifically rationalized, with co-located reference pristine mangroves as the target ecosystem to achieve is currently distinctively lacking. Through this experimental scale study, we studied the suitability of site-specific strategies to ecologically restore degraded mangrove patches vis-à-vis the conventional mono-species plantations in a highly vulnerable mangrove ecosystem in Indian Sundarbans. This comprehensive restoration framework was trialed in small discrete degraded mangrove patches spanning ~ 65 ha. Site-specific key restoration components applied are statistically validated through RDA analyses and Bayesian t-tests. 25 quantifiable metrics evaluate the restoration success of a ~ 3 ha degraded mangrove patch with Ridgeline distribution, Kolmogorov-Smirnov (K-S) tests, and Mahalanobis Distance (D2) measure to prove the site's near-equivalence to pristine reference in multiple ecosystem attributes. This restoration intervention irrevocably establishes the greater potential of this framework in the recovery of ecosystem functions and self-sustenance compared to that of predominant monoculture practices for vulnerable mangroves.
Collapse
Affiliation(s)
- Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India.
| | - Sandip Kumar Basak
- Sarat Centenary College, Dhaniakhali, Hooghly, West Bengal, 712302, India.
| | - Chayan Kumar Giri
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Hemendra Nath Kotal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Anup Mandal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Kiranmoy Chatterjee
- Department of Statistics, Bidhannagar College, Salt Lake City, Sector 1, Block EB, Kolkata, 700064, India
| | - Subhajit Saha
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Biswajit Biswas
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Sumana Mondal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Ipsita Das
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Berunanpukuria, Malikapur, Barasat, Kolkata, 700126, India
| | - Anwesha Ghosh
- Centre for Climate and Environmental Studies, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Punyasloke Bhadury
- Integrative Taxonomy and Microbial Ecology Research Group, Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal, 741246, India
| | - Rahul Joshi
- Zoological Survey of India (ZSI), Prani Vigyan Bhawan, Block M, New Alipore, Kolkata, 700053, India
| |
Collapse
|
2
|
White LC. Shallow sequencing can mislead when evaluating hybridization capture methods. CONSERV GENET RESOUR 2023. [DOI: 10.1007/s12686-023-01298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
3
|
Woudstra Y, Viruel J, Fritzsche M, Bleazard T, Mate R, Howard C, Rønsted N, Grace OM. A customised target capture sequencing tool for molecular identification of Aloe vera and relatives. Sci Rep 2021; 11:24347. [PMID: 34934068 PMCID: PMC8692607 DOI: 10.1038/s41598-021-03300-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.
Collapse
Affiliation(s)
- Yannick Woudstra
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK.
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark.
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK
| | - Martin Fritzsche
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Thomas Bleazard
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Ryan Mate
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Nina Rønsted
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, HI, 96741, USA
| | | |
Collapse
|
4
|
Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
Collapse
Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| |
Collapse
|
5
|
Sparrow BD, Foulkes JN, Wardle GM, Leitch EJ, Caddy-Retalic S, van Leeuwen SJ, Tokmakoff A, Thurgate NY, Guerin GR, Lowe AJ. A Vegetation and Soil Survey Method for Surveillance Monitoring of Rangeland Environments. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00157] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
6
|
Disentangling the evolutionary history of three related shrub species using genome-wide molecular markers. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01197-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
7
|
Stouthamer CM, Kelly S, Hunter MS. Enrichment of low-density symbiont DNA from minute insects. J Microbiol Methods 2018; 151:16-19. [DOI: 10.1016/j.mimet.2018.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023]
|
8
|
Puritz JB, Lotterhos KE. Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms. Mol Ecol Resour 2018; 18:1209-1222. [DOI: 10.1111/1755-0998.12905] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/30/2018] [Accepted: 05/08/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Jonathan B. Puritz
- Department of Marine and Environmental Sciences Northeastern Marine Science Center Nahant Massachusetts
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences Northeastern Marine Science Center Nahant Massachusetts
| |
Collapse
|
9
|
Baruch Z, Jones AR, Hill KE, McInerney FA, Blyth C, Caddy-Retalic S, Christmas MJ, Gellie NJC, Lowe AJ, Martin-Fores I, Nielson KE, Breed MF. Functional acclimation across microgeographic scales in Dodonaea viscosa. AOB PLANTS 2018; 10:ply029. [PMID: 29942458 PMCID: PMC6007226 DOI: 10.1093/aobpla/ply029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 05/09/2018] [Indexed: 05/11/2023]
Abstract
Intraspecific plant functional trait variation provides mechanistic insight into persistence and can infer population adaptive capacity. However, most studies explore intraspecific trait variation in systems where geographic and environmental distances co-vary. Such a design reduces the certainty of trait-environment associations, and it is imperative for studies that make trait-environment associations be conducted in systems where environmental distance varies independently of geographic distance. Here we explored trait variation in such a system, and aimed to: (i) quantify trait variation of parent and offspring generations, and associate this variation to parental environments; (ii) determine the traits which best explain population differences; (iii) compare parent and offspring trait-trait relationships. We characterized 15 plant functional traits in eight populations of a shrub with a maximum separation ca. 100 km. Populations differed markedly in aridity and elevation, and environmental distance varied independently of geographic distance. We measured traits in parent populations collected in the field, as well as their offspring reared in greenhouse conditions. Parent traits regularly associated with their environment. These associations were largely lost in the offspring generation, indicating considerable phenotypic plasticity. An ordination of parent traits showed clear structure with strong influence of leaf area, specific leaf area, stomatal traits, isotope δ13C and δ15N ratios, and Narea, whereas the offspring ordination was less structured. Parent trait-trait correlations were in line with expectations from the leaf economic spectrum. We show considerable trait plasticity in the woody shrub over microgeographic scales (<100 km), indicating it has the adaptive potential within a generation to functionally acclimate to a range of abiotic conditions. Since our study shrub is commonly used for restoration in southern Australia and local populations do not show strong genetic differentiation in functional traits, the potential risks of transferring seed across the broad environmental conditions are not likely to be a significant issue.
Collapse
Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Alice R Jones
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Kathryn E Hill
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Francesca A McInerney
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stefan Caddy-Retalic
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Matthew J Christmas
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Andrew J Lowe
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Irene Martin-Fores
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- National Museum of Natural Sciences, Spanish National Research Council, Madrid, Spain
| | - Kristine E Nielson
- Sprigg Geobiology Centre and School of Physical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, Adelaide, SA, Australia
- Corresponding author’s e-mail address:
| |
Collapse
|
10
|
Caddy-Retalic S, Andersen AN, Aspinwall MJ, Breed MF, Byrne M, Christmas MJ, Dong N, Evans BJ, Fordham DA, Guerin GR, Hoffmann AA, Hughes AC, van Leeuwen SJ, McInerney FA, Prober SM, Rossetto M, Rymer PD, Steane DA, Wardle GM, Lowe AJ. Bioclimatic transect networks: Powerful observatories of ecological change. Ecol Evol 2017; 7:4607-4619. [PMID: 28690791 PMCID: PMC5496522 DOI: 10.1002/ece3.2995] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 03/21/2017] [Indexed: 01/02/2023] Open
Abstract
Transects that traverse substantial climate gradients are important tools for climate change research and allow questions on the extent to which phenotypic variation associates with climate, the link between climate and species distributions, and variation in sensitivity to climate change among biomes to be addressed. However, the potential limitations of individual transect studies have recently been highlighted. Here, we argue that replicating and networking transects, along with the introduction of experimental treatments, addresses these concerns. Transect networks provide cost‐effective and robust insights into ecological and evolutionary adaptation and improve forecasting of ecosystem change. We draw on the experience and research facilitated by the Australian Transect Network to demonstrate our case, with examples, to clarify how population‐ and community‐level studies can be integrated with observations from multiple transects, manipulative experiments, genomics, and ecological modeling to gain novel insights into how species and systems respond to climate change. This integration can provide a spatiotemporal understanding of past and future climate‐induced changes, which will inform effective management actions for promoting biodiversity resilience.
Collapse
Affiliation(s)
- Stefan Caddy-Retalic
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Alan N Andersen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Charles Darwin University Darwin NT Australia
| | - Michael J Aspinwall
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Martin F Breed
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Margaret Byrne
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Matthew J Christmas
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ning Dong
- Department of Biological Sciences Macquarie University North Ryde NSW Australia.,Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Bradley J Evans
- Ecosystem Modelling and Scaling Infrastructure Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School Life and Environmental Sciences University of Sydney Sydney NSW Australia
| | - Damien A Fordham
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Greg R Guerin
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| | - Ary A Hoffmann
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of BioSciences, Bio 21 InstituteThe University of Melbourne Parkville VIC Australia
| | - Alice C Hughes
- Centre for Integrative Conservation Xishuangbanna Tropical Botanic Garden Chinese Academy of Sciences Menglun, Mengla County Yunnan China
| | - Stephen J van Leeuwen
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Science and Conservation Division Western Australian Department of Parks and Wildlife Kensington WA Australia
| | - Francesca A McInerney
- Sprigg Geobiology Centre and School of Physical Sciences University of Adelaide Adelaide SA Australia
| | - Suzanne M Prober
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia
| | - Maurizio Rossetto
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,National Herbarium of NSW Royal Botanic Gardens and Domain Trust Sydney NSW Australia
| | - Paul D Rymer
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,Hawkesbury Institute for the Environment Western Sydney University Parramatta NSW Australia
| | - Dorothy A Steane
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,CSIRO Land and Water Wembley WA Australia.,School of Biological Sciences University of Tasmania Private Bag 55 Hobart Tasmania 7001 Australia.,Faculty of Science, Health, Education and Engineering University of the Sunshine Coast Maroochydore QLD Australia
| | - Glenda M Wardle
- School Life and Environmental Sciences University of Sydney Sydney NSW Australia.,Long Term Ecological Research Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia
| | - Andrew J Lowe
- Australian Transect Network Terrestrial Ecosystem Research Network (TERN) Adelaide SA Australia.,School of Biological Sciences and Environment InstituteUniversity of Adelaide Adelaide SA Australia
| |
Collapse
|