Publications by authors named "Luca Mirimin"

7 Publications

  • Page 1 of 1

Quantifying dispersal between marine protected areas by a highly mobile species, the bottlenose dolphin, .

Ecol Evol 2018 Sep 23;8(18):9241-9258. Epub 2018 Aug 23.

School of Biological, Earth and Environmental Sciences University College Cork Cork Ireland.

The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin . We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity.
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http://dx.doi.org/10.1002/ece3.4343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194238PMC
September 2018

Gene expression analysis of Atlantic salmon gills reveals mucin 5 and interleukin 4/13 as key molecules during amoebic gill disease.

Sci Rep 2018 09 12;8(1):13689. Epub 2018 Sep 12.

Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, 12595, Spain.

Amoebic gill disease (AGD) is one of the main diseases affecting Atlantic salmon (Salmo salar L.) mariculture. Hallmarks of AGD are hyperplasia of the lamellar epithelium and increased production of gill mucus. This study investigated the expression of genes involved in mucus secretion, cell cycle regulation, immunity and oxidative stress in gills using a targeted 21-gene PCR array. Gill samples were obtained from experimental and natural Neoparamoeba perurans infections, and sampling points included progressive infection stages and post-freshwater treatment. Up-regulation of genes related to mucin secretion and cell proliferation, and down-regulation of pro-inflammatory and pro-apoptotic genes were associated with AGD severity, while partial restoration of the gill homeostasis was detected post-treatment. Mucins and Th2 cytokines accoun ted for most of the variability observed between groups highlighting their key role in AGD. Two mucins (muc5, muc18) showed differential regulation upon disease. Substantial up-regulation of the secreted muc5 was detected in clinical AGD, and the membrane bound muc18 showed an opposite pattern. Th2 cytokines, il4/13a and il4/13b2, were significantly up-regulated from 2 days post-infection onwards, and changes were lesion-specific. Despite the differences between experimental and natural infections, both yielded comparable results that underline the importance of the studied genes in the respiratory organs of fish, and during AGD progression.
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http://dx.doi.org/10.1038/s41598-018-32019-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135806PMC
September 2018

Historical gene flow constraints in a northeastern Atlantic fish: phylogeography of the ballan wrasse across its distribution range.

R Soc Open Sci 2017 Feb 15;4(2):160773. Epub 2017 Feb 15.

MARE-Marine and Environmental Sciences Centre , ISPA Instituto Universitário , Rua Jardim do Tabaco 34, 1149-041 Lisboa , Portugal.

The distribution and demographic patterns of marine organisms in the north Atlantic were largely shaped by climatic changes during the Pleistocene, when recurrent glacial maxima forced them to move south or to survive in northern peri-glacial refugia. These patterns were also influenced by biological and ecological factors intrinsic to each species, namely their dispersion ability. The ballan wrasse (), the largest labrid fish along Europe's continental margins, is a target for fisheries and aquaculture industry. The phylogeographic pattern, population structure, potential glacial refugia and recolonization routes for this species were assessed across its full distribution range, using mitochondrial and nuclear markers. The existence of a marked population structure can reflect both recolonization from three distinct glacial refugia and current and past oceanographic circulation patterns. Although isolated in present times, shared haplotypes between continental and Azores populations and historical exchange of migrants in both directions point to a common origin of . This situation is likely to be maintained and/or accentuated by current circulation patterns in the north Atlantic, and may lead to incipient speciation in the already distinct Azorean population. Future monitoring of this species is crucial to evaluate how this species is coping with current environmental changes.
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http://dx.doi.org/10.1098/rsos.160773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367310PMC
February 2017

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding.

R Soc Open Sci 2016 Jan 20;3(1):150565. Epub 2016 Jan 20.

Area 52 Research Group, University College Dublin, Belfield, Dublin, Republic of Ireland; Earth Institute, University College Dublin, Belfield, Dublin, Republic of Ireland.

This study examines the potential of next-generation sequencing based 'genotyping-by-sequencing' (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
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http://dx.doi.org/10.1098/rsos.150565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736940PMC
January 2016

Genetic and Morphological Characterization of Freshwater Shrimps (Caridina africana Kingsley, 1882) Reveals the Presence of Alien Shrimps in the Cape Floristic Region, South Africa.

J Hered 2015 Nov-Dec;106(6):711-8. Epub 2015 Aug 21.

From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels).

Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identified as Caridina africana Kingsley, 1882, whose main natural distribution is in the KwaZulu-Natal (KZN) Province, more than 1200 km from the point of new discovery. Subsequently, sequence data from natural populations occurring in seven rivers throughout KZN showed the presence of nuclear copies of the mtDNA COI gene (NUMTs) in 46 out of 140 individuals. Upon removal of sequences containing NUMTs, levels of genetic diversity were low in the alien population (possibly as a consequence of a bottleneck event), while varying levels of genetic diversity and differentiation were found in natural populations, indicating habitat heterogeneity, fragmentation and restricted gene flow between rivers. Following the present study, the alien shrimp has survived the Western Cape's winter and dispersed into a nearby tributary of the Eerste River System, hence posing an additional potential threat to endangered endemics. Understanding the biology of this alien species will aid detection and eradication procedures.
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http://dx.doi.org/10.1093/jhered/esv063DOI Listing
April 2016

Multiplexing with three-primer PCR for rapid and economical microsatellite validation.

Hereditas 2014 Jun;151(2-3):43-54

Carna Research Station, Ryan Institute, National University of Ireland, Galway, Carna, Connemara, Co. Galway, Ireland; Area 52 Research Group, School of Biology & Environment Science, University College Dublin, Belfield, Dublin, Ireland.

The next generation sequencing revolution has enabled rapid discovery of genetic markers, however, development of fully functioning new markers still requires a long and costly process of marker validation. This study reports a rapid and economical approach for the validation and deployment of polymorphic microsatellite markers obtained from a 454 pyrosequencing library of Atlantic cod, Gadus morhua, Linnaeus 1758. Primers were designed from raw reads to amplify specific amplicon size ranges, allowing effective PCR multiplexing. Multiplexing was combined with a three-primer PCR approach using four universal tails to label amplicons with separate fluorochromes. A total of 192 primer pairs were tested, resulting in 73 polymorphic markers. Of these, 55 loci were combined in six multiplex panels each containing between six and eleven markers. Variability of the loci was assessed on G. morhua from the Celtic Sea (n = 46) and the Scotian Shelf (n = 46), two locations that have shown genetic differentiation in previous studies. Multilocus F(ST) between the two samples was estimated at 0.067 (P = 0.001). After three loci potentially under selection were excluded, the global F(ST) was estimated at 0.043 (P = 0.001). Our technique combines three-primer and multiplex PCR techniques, allowing simultaneous screening and validation of relatively large numbers of microsatellite loci.
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http://dx.doi.org/10.1111/hrd2.00044DOI Listing
June 2014

Insights into genetic diversity, parentage, and group composition of Atlantic white-sided dolphins (Lagenorhynchus acutus) off the west of Ireland based on nuclear and mitochondrial genetic markers.

J Hered 2011 Jan-Feb;102(1):79-87. Epub 2010 Nov 8.

Department of Zoology, Ecology and Plant Sciences, University College Cork, North Mall, Distillery Fields, Cork, Ireland.

The analysis of stranding events and the application of molecular markers can be powerful tools to study cryptic biological aspects of delphinid species that occur mainly in open ocean habitat. In the present study, we investigated nuclear and mitochondrial genetic variability of Atlantic white-sided dolphins that stranded from 1990 to 2006 (n = 42) along the west coast of Ireland, using 8 microsatellite loci and 599 bp of the mitochondrial DNA control region. Results from both classes of markers are concordant with the hypothesis of a large random-mating population of white-sided dolphins along the west coast of Ireland. In addition, the analyses of 2 live mass stranding events (19 and 5 individuals, respectively) revealed that dolphins within each group were mainly unrelated to each other, suggesting dispersal of both sexes from the natal group (i.e., no natal phylopatry). Parentage analyses allowed the identification of mother-offspring pairs but ruled out all adult males as possible fathers. In combination with data on age of individuals, these results confirmed previous knowledge on life-history parameters, with sexually mature females ranging between 11 and 15 years of age and an interbirth interval of at least 2 years. The present study provides novel information on population and group composition of Atlantic white-sided dolphins along the west coast of Ireland, where population and social structure of the species are still poorly understood.
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http://dx.doi.org/10.1093/jhered/esq106DOI Listing
April 2011