Conservation implications of significant population differentiation in an endangered estuarine seahorse

Mkare, Thomas K.; Vuuren, Bettine Jansen van; Teske, Peter R.

doi:10.1007/s10531-017-1300-5

Cited by 18 publications

(20 citation statements)

References 96 publications

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“…Finding independent markers confirming mitochondrial divergence may be difficult for recently diverged species, especially in non-model organisms with scarce to non-existing available genomic data. The most intuitive and popular approach for cryptic species delimitation consists of finding independent markers displaying reciprocal monophyly that are congruently associated within individuals (in linkage disequilibrium) (De Queiroz, 2007;Mkare et al, 2017). However, confirming absence of gene flow should not rely on finding reciprocal monophyly in independent markers (Zhang et al, 2011) for the following reasons: (i) Recently diverged species, especially when their reproductive isolation is conferred by a single locus or few loci, rarely display reciprocally monophyletic markers, as most loci are either monomorphic or display shared polymorphism among species (i.e.…”

Section: Introductionmentioning

confidence: 99%

Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata)

Weber

Stöhr

Chenuil

2019

Molecular Phylogenetics and Evolution

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Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenomenon. The brittle star cryptic species complex Ophioderma longicauda encompasses six mitochondrial lineages, including broadcast spawners and internal brooders, yet the actual species boundaries are unknown. Here, we combined three methods to delimit species in the Ophioderma longicauda complex and to infer its divergence history: (i) unsupervised species discovery based on multilocus genotypes; (ii) divergence time estimation using the multi-species coalescent; (iii) divergence scenario testing (including gene flow) using Approximate Bayesian Computation (ABC) methods. 30 sequence markers (transcriptome-based, mitochondrial or non-coding) for 89 O. longicauda and outgroup individuals were used. First, multivariate analyses revealed six genetic clusters, which globally corresponded to the mitochondrial lineages, yet with many exceptions, suggesting ancient hybridization events and challenging traditional mitochondrial barcoding approaches. Second, multi-species coalescent-based analyses confirmed the occurrence of six species and provided divergence time estimates, but the sole use of this method failed to accurately delimit species, highlighting the power of multilocus genotype clustering to delimit recently diverged species. Finally, Approximate Bayesian Computation showed that the most likely scenario involves hybridization between brooders and broadcasters. Our study shows that despite strong incomplete lineage sorting and past hybridization, accurate species delimitation in Ophioderma was possible using a combination of complementary methods. We propose that these methods, especially multilocus genotype clustering, may be useful to resolve other complex speciation histories.

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Section: Introductionmentioning

confidence: 99%

Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata)

Weber

Stöhr

Chenuil

2019

Molecular Phylogenetics and Evolution

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“…Genetic variation is necessary for natural stock of fish for the evolution purpose and to ensure their availability for the future generation (Xia et al, 2014, Xia et al, 2015). The decrease in genetic diversity in wild stock of freshwater fish species may influence on the adjustment of the fish into their changing environment (Arif and Khan, 2009, Mkare et al, 2017). The evolutionary variations are caused due to spontaneous mutation, migration, and genetic drift in the freshwater fish (Zhao et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity in tilapia populations in a freshwater reservoir assayed by randomly amplified polymorphic DNA markers

Mahboob

Al‐Ghanim

Al‐Misned

et al. 2019

Saudi Journal of Biological Sciences

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Genetic variation in fish stocks decreasing due to water pollution in the freshwater rivers, streams and canals. The objective of this study was to determine the genetic diversity and polymorphism in Oreochromis niloticus collected from the Wadi Hanefah Riyadh, Saudi Arabia by using RAPD-PCR. Total thirty fish specimens were harvested from each of four pre-determined locations of the reservoir which were designated as H1, H2, H3, and H4. Five random decamer primers were used to assess the diversity in the stock of O. niloticus. In this fish stock 48 bands were polymorphic and 12 were monomorphic. The maximum polymorphism (100%) was recorded in the fish samples procured from H4, followed by 88.75, 87.33 and 76.12% of the tilapia collected from H3, H2, and H4, respectively. Nei’s genetic distance value was ranged as 0.0005 to 0.1006. Maximum and minimum genetic distance was recorded as 0.1006 and 0.005 in tilapia harvested from H1 and H2 locations. Average heterozygosity was ranged from 0.3009 to 0.3744. This information about the genetic polymorphism of O. niloticus may be used by the concerned authorities to evolve strategies to conserve the diversity of tilapia in the country.

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“…The prevalence of bands differed greatly among the fish samples from different locations and use of primers. The maximum number of bands (14) was found in the fish collected from WH4 produced by primer OPF-03 and the lowest number of bands (9) in C. carpio was collected from WH1 by primer OPF-01.…”

Section: Rapd Analysismentioning

confidence: 97%

Genetic Diversity in Common Carp Stocks from a Natural Reservoir Assayed by Randomly Amplified Polymorphic DNA Markers

Mahboob

Al‐Ghanim

Al-Mulhim

2018

Preprint

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Background:The common carp (Cyprinus carpio) is a freshwater fish that is cultured throughout the world. C. carpio belongs to the family Cyprinidae, the largest family among freshwater teleosts, accounting for 10 % of total fish production. Specifically, the common carp is cultured in more than 100 countries in worldwide and accounts for over 3 million metric tons of total annual freshwater fish production. The population of common carp (C. carpio) is declining in freshwater reservoirs because of various human activities, such as overfishing, pollution, hybridization with domestic carp, and loss of breeding grounds because of habitat degradation. Results:In total, 30 specimens were collected from each of four different locations (WH1, WH2, WH3 and WH4) in the reservoir. Five random decamer primers were used to assay polymorphisms within and between the population of C. carpio. A total of 60 bands were produced by these primers, out of which 50 bands were polymorphic and 10 bands were monomorphic. The mean highest polymorphism (100 %) was observed in the specimen collected from WHS4 stock, followed by 89.05, 87.62 and 76.66 % of the fish collection from WH3, WH2, and WH4, respectively. Nei's genetic distance values ranged from 0.0006 to 0.1005. Highest and lowest genetic distance were 0.1005 and 0.006 in fish collected from WH1 and WH2, respectively. Average value of heterozygosity ranged from 0.3008 to 0.3748.A C. carpio UPGMA dendrogram was constructed to observe fish phylogeny. Phylogenetic clusters by RAPD indicated that fish stock of WH2, WH3, and WH4 were closely related to each other. Conclusion:It was concluded that RAPD analysis can be successfully used as a marker to generate information regarding the percent homology within stock of common carp, which may be used to trace the progeny to the parents and is helpful for the improvement of breeding programs.

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Conservation implications of significant population differentiation in an endangered estuarine seahorse

Cited by 18 publications

References 96 publications

Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata)

Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata)

Genetic diversity in tilapia populations in a freshwater reservoir assayed by randomly amplified polymorphic DNA markers

Genetic Diversity in Common Carp Stocks from a Natural Reservoir Assayed by Randomly Amplified Polymorphic DNA Markers

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