Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.

The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci

Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia.

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1-oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2-oceanic and inhabited (high human impact); and cluster 3-lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an 'opportunistic' scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities

fish_transects_2012_13_14

Fish transects in the Atoll of Ulithi, Yap State, Federated states of Micronesi

benthic composition summary data

Benthic surveys of reefs in the Atoll of Ulithi, Yap State, Micronesi

Data from: Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an ‘opportunistic’ scleractinian coral (Montipora sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities

Fish biomass, abundance and size on Ulithi Atoll.

<p>Fish trophic categories (Piscivores, Carnivores, Corallivores, Planktivores, and Herbivores) are compared among site groups (cluster 1: uninhabited, oceanic; cluster 2: inhabited, oceanic; cluster 3: inhabited & uninhabited, lagoonal) for biomass (a-e), numerical abundance (g-k) and average length (TL, m-q). The stacked bar plots (f & l) show the mean values from sites within each of the 3 clusters, and the dot chart (r) compares the mean TL for fishes from trophic categories found within sites from the 3 clusters. The box-and-whisker plots show the median value (dark horizontal bar); the box length is the interquartile range, the upper whisker marks the smaller of the maximum value and quartile 3+1.5 interquartile range (IQR), and the lower whisker marks the larger of the smallest value and quartile 1–1.5 IQR. Outliers are not shown. Plots produced using the R package <i>graphics</i>, version 3.3.1.</p

Environmental effects and fish community structure.

<p>PERMANOVA results from the model <i>fish ~ exposure + distance + population</i>, stratified by year and terms added sequentially (first to last). Df = degree(s) of freedom, SS = Sums of Squares, MS = Mean Squares, F = F statistic obtained from the model, R² = coefficient of determination, and p = probability of the obtained (model) F exceeding the predicted F statistic by chance.</p

Benthic cover (% cover) compared across sites from cluster 1 (uninhabited, oceanic), cluster 2 (inhabited, oceanic), and cluster 3 (inhabited & uninhabited, lagoonal) (a-f).

<p>The relative abundance of hard coral morphotypes is shown for the 3 site clusters in e1-e3. Note that the opportunistic <i>Montipora</i> sp. is considered separately from all other stony corals for both cover and morphotype. The box-and-whisker plots show the median value (dark horizontal bar); the box length is the interquartile range, the upper whisker marks the smaller of the maximum value and quartile 3+1.5 interquartile range (IQR), and the lower whisker marks the larger of the smallest value and quartile 1–1.5 IQR. Outliers are not shown. Plots produced using the R package <i>graphics</i>, version 3.3.1.</p

Environmental effects and benthic cover composition.

<p>PERMANOVA results from the model <i>benthic ~ exposure + distance * population</i>, stratified by year and terms added sequentially (first to last). Df = degree(s) of freedom, SS = Sums of Squares, MS = Mean Squares, F = F statistic obtained from the model, R² = coefficient of determination, and p = probability of the obtained (model) F exceeding the predicted F statistic by chance.</p

Atoll-scale patterns in coral reef community structure: Human signatures on Ulithi Atoll, Micronesia

<div><p>The dynamic relationship between reefs and the people who utilize them at a subsistence level is poorly understood. This paper characterizes atoll-scale patterns in shallow coral reef habitat and fish community structure, and correlates these with environmental characteristics and anthropogenic factors, critical to conservation efforts for the reefs and the people who depend on them. Hierarchical clustering analyses by site for benthic composition and fish community resulted in the same 3 major clusters: cluster 1–oceanic (close proximity to deep water) and uninhabited (low human impact); cluster 2–oceanic and inhabited (high human impact); and cluster 3–lagoonal (facing the inside of the lagoon) and inhabited (highest human impact). Distance from village, reef exposure to deep water and human population size had the greatest effect in predicting the fish and benthic community structure. Our study demonstrates a strong association between benthic and fish community structure and human use across the Ulithi Atoll (Yap State, Federated States of Micronesia) and confirms a pattern observed by local people that an ‘opportunistic’ scleractinian coral (<i>Montipora</i> sp.) is associated with more highly impacted reefs. Our findings suggest that small human populations (subsistence fishing) can nevertheless have considerable ecological impacts on reefs due, in part, to changes in fishing practices rather than overfishing per se, as well as larger global trends. Findings from this work can assist in building local capacity to manage reef resources across an atoll-wide scale, and illustrates the importance of anthropogenic impact even in small communities.</p></div