Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico

Hammerman, Nicholas M.; Rivera‐Vicéns, Ramón E.; Galaska, Matthew P.; Weil, Ernesto; Appledoorn, R.S.; Alfaro, Mónica; Schizas, Nikolaos V.

doi:10.1007/s00338-017-1646-x

Cited by 25 publications

(23 citation statements)

References 46 publications

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“…In addition, reduced mortality at depth is necessary but not sufficient for the realisation of a deep reef refuge [5]. There is a requirement of reproductive connectivity, not yet assessed on Utila, but found elsewhere [42]. We stress the distinction between refuge from general disturbance, and refugium specifically referring to climate related effects [43].…”

Section: Limitations-mentioning

confidence: 89%

Experimental evidence for reduced mortality of Agaricia lamarcki on a mesophotic reef

Laverick

Rogers

2018

Marine Environmental Research

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Mesophotic Coral Ecosystems (MCEs) may act as a refuge for impacted shallow reefs as some of the stressors affecting tropical reefs attenuate with depth. A less impacted population at depth could provide recruits to recolonise shallow reefs. Recently, disturbance has been reported on several mesophotic reefs including storm damage, biological invasions, and coral bleaching; calling into question the extent of deep reef refuges. We report on a reciprocal transplant experiment between shallow and mesophotic reefs in the Caribbean, which occurred during a period of coral bleaching. 102 fragments of Agaricia lamarcki were collected down a continuous depth gradient at two sites to a maximum depth of 60m. Fragments were transplanted to either a shallow or mesophotic station at a third site, with controls. This allowed the disaggregation of the effect of the disturbance experienced during the observation period, and any potential acclimation resulting from the historical location of a fragment. Mortality and bleaching were quantitatively assessed. We found the relocation depth of a coral fragment had the strongest effect on both survival and the degree of bleaching recorded. The site a fragment was collected from, and the original collection depth, failed to explain mortality or bleaching with statistical significance. This experiment provides support for the assumption that mesophotic corals may be protected in comparison to shallow reefs, in spite of the potential effects of differing susceptibilities to stress.

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Section: Limitations-mentioning

confidence: 89%

Experimental evidence for reduced mortality of Agaricia lamarcki on a mesophotic reef

Laverick

Rogers

2018

Marine Environmental Research

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“…RAD-sequencing approaches, including double-digest RAD-seq and its variants [5, 20, 46, 53, 54], have allowed a cost-effective discovery of thousands of genetic markers in both model and non-model organisms [22, 63], proving to be a transformative research tool in population genetics ([7, 12, 26]), phylogeography and phylogenetics [3, 25, 29, 60], marker development [52], linkage mapping studies [6], species differentiation [49] and detecting selection [65]. However, despite the widespread use of this approach to genome-wide marker discovery, only few studies have used RAD-seq in mammals [18, 32, 35, 48, 64].…”

Section: Discussionmentioning

confidence: 99%

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

Cerezo

Kučka

Zub

et al. 2019

Preprint

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Background: Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.Results: Here we present results from the whole-genome, high-density genotyping using double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average sequence divergence, based on 21377 common loci, of 1.51% and an evolutionary rate of 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average genome-wide population structure, with largest pairwise F ST < 0.086. Conclusion:Our study demonstrates the feasibility of genome-wide, high-density genotyping in Apodemus and provides the first insights into the population genomics of one of the species. 1 2 Background 3 Mice of the genus Apodemus (Kaup, 1829) (Rodentia: Muridae) are one the most 4 common mammals in the Palaearctic region [43]. The genus comprises of three 5 subgenera (Sylvaemus, Apodemus and Karstomys) [43], however the systematic 6 classification of the 20 species belonging to the genus [16] is not fully settled [36]. 7 In the Western Palearctic, the yellow-necked mice A. flavicollis (Melchior, 1934) 8 and the woodmice A. sylvaticus (Linnaeus, 1758) are widespread, sympatric and 9 occasionally syntopic species. They are often difficult to distinguish morphologically 10 in their southern range [30], but in the Central and Northern Europe both are 11 easily recognisable by the yellow collar around the neck of A. flavicollis, absent in 12 A. sylvaticus. 13 Their prevalence in Western Palearctic and common status in Western and Central 14 Europe made them one of the model organisms to study post-glacial movement of context, as one of the vectors of Borellia-carrying ticks Ixodes ricinus, who often feed 17 on Apodemus [13, 61], tick-borne encephalitis virus [47] and hantaviruses [33, 50] 18 and have been used as markers for environmental quality [40, 66]. Lastly, they 19 have extra-autosomal chromosomes, called B chromosomes, with varied distribution 20 among the populations [59] but unknown role, although it has been suggested they 21are involved in cellular metabolism [34, 39]. 22Previous studies on Apodemus typically employed a small number of microsatellite 23 [62] and mtDNA markers [24, 42, 44, 45], which are insufficient to learn about the 24 species' population structure and admixture patterns in detail,...

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“…In areas where there is a substantial degree of community overlap between shallow reefs and MCEs, species may persist locally on MCEs despite extirpation in the shallows [16,17]. If these deep populations are reproductively active [18] then shallow reefs may be able to recover through vertical connectivity [10,19].…”

Section: Introductionmentioning

confidence: 99%

To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic review

Laverick

Piango²,

Andradi-Brown

et al. 2018

Environ Evid

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Background: Globally, shallow-water coral reef biodiversity is at risk from a variety of threats, some of which may attenuate with depth. Mesophotic coral ecosystems (MCEs), occurring from 30 to 40 m and deeper in tropical locations, have been subject to a surge of research this century. Though a number of valuable narrative reviews exist, a systematic quantitative synthesis of published MCE studies is lacking. We conducted a systematic review to collate mesophotic research, including studies from the twentieth century to the present. We highlight current biases in research effort, regarding locations and subject matter, and suggest where more attention may be particularly valuable. Following a notable number of studies considering the potential for mesophotic reefs to act as refuges, it is important to know how comprehensive these sources of recruits and organisms capable of moving to shallow water reefs may be. Methods: We search seven sources of bibliographic data with two search strings, as well as personal libraries. Articles were included if they contained species presence data from both shallower and deeper than 30 m depth on tropical coral reefs. Studies were critically appraised based on the number of species identified and balanced sampling effort with depth. Maximum and minimum depths per species were extracted from each study, along with study region and taxon. We quantified the degree of community overlap between shallow tropical reefs (< 30 m) and reefs surveyed at the same locations below 30 m. Proportions of shallow species, across all studied taxa, observed deeper than 30 m were used to generate log odds ratios and passed to a mixed-effects model. Study location and taxon were included as effect modifiers. Funnel plots, regression tests, fail safe numbers, and analysis of a high validity subgroup contributed to sensitivity analyses and tests of bias. Results: Across all studies synthesised we found two-thirds of shallow species were present on mesophotic reefs. Further analysis by taxon and broad locations show that this pattern is influenced geographically and taxonomically. Community overlap was estimated as low as 26% and as high as 97% for some cases. Conclusions: There is clear support for the hypothesis that protecting mesophotic reefs will also help to conserve shallow water species. At the same time, it is important to note that this study does not address mesophotic-specialist communities, or the ecological forces which would permit refuge dynamics. As we limit our analysis to species only present above 30 m it is also possible diversity found exclusively deeper than 30 m warrants protection in its own right. Further research into relatively ignored taxa and geographic regions will help improve the design of protected areas in future.

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Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico

Cited by 25 publications

References 46 publications

Experimental evidence for reduced mortality of Agaricia lamarcki on a mesophotic reef

Experimental evidence for reduced mortality of Agaricia lamarcki on a mesophotic reef

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

To what extent do mesophotic coral ecosystems and shallow reefs share species of conservation interest? A systematic review

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