The integration and application of genomic information in mangrove conservation

Wee, Alison K. S.; Mori, Gustavo Maruyama; Lira, Catarina Fonseca; Núñez‐Farfán, Juan; Takayama, Kōji; Faulks, Leanne K.; Shi, Suhua; Tsuda, Yoshiaki; Suyama, Yoshihisa; Yamamoto, Takashi; Iwasaki, Takaya; Nagano, Yukio; Wang, Zhengzhen; Watanabe, Shin; Kajita, Tadashi

doi:10.1111/cobi.13140

Cited by 29 publications

(18 citation statements)

References 13 publications

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“…Mangroves are a globally distributed group of salt tolerant trees and shrubs that are confined to brackish intertidal zones, estuaries, lagoons and backwaters throughout the tropics and subtropics (Thatoi et al 2013 ). Straddling the interface between marine and terrestrial ecosystems, they provide important buffers that dissipate wave energy, stabilising coastlines and protecting against coastal erosion and natural hazards such as hurricanes and tsunamis (Williams 2005 ; Wee et al 2019 ). Mangroves provide critical ecological habitats that host high levels of biodiversity and act as a nursery for many juvenile coral reef species (Abu El-Regal and Ibrahim 2014 ; Mehvar et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

et al. 2020

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Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.

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Section: Introductionmentioning

confidence: 99%

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

et al. 2020

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“…Recent advances in genomic tools are drastically changing biology, including ecological studies (Allendorf, Hohenlohe, & Luikart, 2010;Rudman et al, 2018). These technologies enable the collection of considerable genotype information even from nonmodel species with no prior genomic information, and results can be used for the establishment of conservation and management policies (Narum, Buerkle, Davey, Miller, & Hohenlohe, 2013;Wee et al, 2018). For example, a family of genotyping-by-sequencing (GBS) tools, such as RADseq, does not require any prior genomic information for the experimental organisms, and thus are widely used for ecological, evolutionary and conservation genomics (Andrews, Good, Miller, Luikart, & Hohenlohe, 2016).…”

Section: Introductionmentioning

confidence: 99%

Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes

Hosoya

Hirase

Kikuchi

et al. 2019

Molecular Ecology Resources

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While various technologies for high‐throughput genotyping have been developed for ecological studies, simple methods tolerant to low‐quality DNA samples are still limited. In this study, we tested the availability of a random PCR‐based genotyping‐by‐sequencing technology, genotyping by random amplicon sequencing, direct (GRAS‐Di). We focused on population genetic analysis of estuarine mangrove fishes, including two resident species, the Amboina cardinalfish (Fibramia amboinensis, Bleeker, 1853) and the Duncker's river garfish (Zenarchopterus dunckeri, Mohr, 1926), and a marine migrant, the blacktail snapper (Lutjanus fulvus, Forster, 1801). Collections were from the Ryukyu Islands, southern Japan. PCR amplicons derived from ~130 individuals were pooled and sequenced in a single lane on a HiSeq2500 platform, and an average of three million reads was obtained per individual. Consensus contigs were assembled for each species and used for genotyping of single nucleotide polymorphisms by mapping trimmed reads onto the contigs. After quality filtering steps, 4,000–9,000 putative single nucleotide polymorphisms were detected for each species. Although DNA fragmentation can diminish genotyping performance when analysed on next‐generation sequencing technology, the effect was small. Genetic differentiation and a clear pattern of isolation‐by‐distance was observed in F. amboinensis and Z. dunckeri by means of principal component analysis, FST and the admixture analysis. By contrast, L. fulvus comprised a genetically homogeneous population with directional recent gene flow. These genetic differentiation patterns reflect patterns of estuary use through life history. These results showed the power of GRAS‐Di for fine‐grained genetic analysis using field samples, including mangrove fishes.

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“…This framework is much more cost effective than protocols used in previous research and should enable the inclusion of more samples and collection sites in future research. These multiplex panels should also facilitate further genetic studies to address multiple pressing conservation questions, such as generating baseline genetic data from areas that have not been studied [i.e., much of Central America, Pacific South America, Caribbean islands, and West Africa (although considerable work has been done in R. racemosa; Ngeve et al 2016)], better defining management units to prioritize conservation measures (Wee et al 2019), and monitoring genetic effects of restoration projects (Granado et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Multiplex microsatellite PCR panels for the neotropical red mangrove, Rhizophora mangle: combining efforts towards a cost-effective and modifiable tool to better inform conservation and management

Kennedy

Craig

Jara-Cavieres

et al. 2020

Conservation Genet Resour

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Better-informed mangrove conservation and management practices are needed as the ecosystem services provided by these intertidal forests continue to be threatened by increasing anthropogenic pressures and climate change. Multiple layers of knowledge are required to achieve this goal, including insights into population genetics of mangrove species. Understanding the importance of population-genetic insights to conservation, multiple research groups have developed microsatellite loci for the widespread, neotropical red mangrove, Rhizophora mangle. However, although a wealth of genetic markers exist, empirical research is limited in the number of these loci employed. Here, we designed two multiplex PCR panels that combine seven novel loci developed for this work and eight previously-developed loci from three research groups to generate 15-locus genotypes, more than twice the average number of loci used in previous research, in only two PCR. We demonstrated utility in R. mangle from four sites across ~ 2500 km near this species' northern latitudinal limits, and that these multiplex panels were better able to delineate populations than data subsets with numbers of loci comparable to previous research. We focus our discussion on how this tool is a more-informative, efficient (both in terms of time and resources), and easily-modifiable alternative to address many pressing conservation and management issues, such as the generation of baseline genetic data for areas not yet studied, better defining management units, and monitoring genetic effects of restoration projects. We also provide a quick protocol that outlines each step in this procedure to facilitate the use of this tool by others.

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The integration and application of genomic information in mangrove conservation

Abstract: Article impact statement: Genomic information can help prevent species loss, facilitate reserve design and maximize adaptive potential of natural mangrove populations.

Cited by 29 publications

References 13 publications

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula

Random PCR‐based genotyping by sequencing technology GRAS‐Di (genotyping by random amplicon sequencing, direct) reveals genetic structure of mangrove fishes

Multiplex microsatellite PCR panels for the neotropical red mangrove, Rhizophora mangle: combining efforts towards a cost-effective and modifiable tool to better inform conservation and management

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