Analyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate ...relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system. This has the undesirable outcome of making choice of relatedness estimator limited by operating system preference, rather than being based on scientific rationale. Here, we present a new R package, called related, that can calculate relatedness based on seven estimators, can account for genotyping errors, missing data and inbreeding, and can estimate 95% confidence intervals. Moreover, simulation functions are provided that allow for easy comparison of the performance of different estimators and for analyses of how much resolution to expect from a given data set. Because this package works in R, it is platform independent. Combined, this functionality should allow for more appropriate analyses and interpretation of pairwise relatedness and will also allow for the integration of relatedness data into larger R workflows.
Limited scope for latitudinal extension of reef corals Muir, Paul R.; Wallace, Carden C.; Done, Terence ...
Science (American Association for the Advancement of Science),
06/2015, Letnik:
348, Številka:
6239
Journal Article
Recenzirano
An analysis of present-day global depth distributions of reef-building corals and underlying environmental drivers contradicts a commonly held belief that ocean warming will promote tropical coral ...expansion into temperate latitudes. Using a global data set of a major group of reef corals, we found that corals were confined to shallower depths at higher latitudes (up to 0.6 meters of predicted shallowing per additional degree of latitude). Latitudinal attenuation of the most important driver of this phenomenon—the dose of photosynthetically available radiation over winter—would severely constrain latitudinal coral range extension in response to ocean warming. Latitudinal gradients in species richness for the group also suggest that higher winter irradiance at depth in low latitudes allowed a deep-water fauna that was not viable at higher latitudes.
The susceptibility of reef-building corals to climatic anomalies is well documented and a cause of great concern for the future of coral reefs. Reef corals are normally considered to tolerate only a ...narrow range of climatic conditions with only a small number of species considered heat-tolerant. Occasionally however, corals can be seen thriving in unusually harsh reef settings and these are cause for some optimism about the future of coral reefs. Here we document for the first time a diverse assemblage of 225 species of hard corals occurring in the intertidal zone of the Bonaparte Archipelago, north western Australia. We compare the environmental conditions at our study site (tidal regime, SST and level of turbidity) with those experienced at four other more typical tropical reef locations with similar levels of diversity. Physical extremes in the Bonaparte Archipelago include tidal oscillations of up to 8 m, long subaerial exposure times (>3.5 hrs), prolonged exposure to high SST and fluctuating turbidity levels. We conclude the timing of low tide in the coolest parts of the day ameliorates the severity of subaerial exposure, and the combination of strong currents and a naturally high sediment regime helps to offset light and heat stress. The low level of anthropogenic impact and proximity to the Indo-west Pacific centre of diversity are likely to further promote resistance and resilience in this community. This assemblage provides an indication of what corals may have existed in other nearshore locations in the past prior to widespread coastal development, eutrophication, coral predator and disease outbreaks and coral bleaching events. Our results call for a re-evaluation of what conditions are optimal for coral survival, and the Bonaparte intertidal community presents an ideal model system for exploring how species resilience is conferred in the absence of confounding factors such as pollution.
Mesophotic coral ecosystems in the Indo-Pacific remain relatively unexplored, particularly at lower mesophotic depths (≥60 m), despite their potentially large spatial extent. Here, we used a remotely ...operated vehicle to conduct a qualitative assessment of the zooxanthellate coral community at lower mesophotic depths (60-125 m) at 10 different locations in the Great Barrier Reef Marine Park and the Coral Sea Commonwealth Marine Reserve. Lower mesophotic coral communities were present at all 10 locations, with zooxanthellate scleractinian corals extending down to ~100 metres on walls and ~125 m on steep slopes. Lower mesophotic coral communities were most diverse in the 60-80 m zone, while at depths of ≥100 m the coral community consisted almost exclusively of the genus Leptoseris. Collections of coral specimens (n = 213) between 60 and 125 m depth confirmed the presence of at least 29 different species belonging to 18 genera, including several potential new species and geographic/depth range extensions. Overall, this study highlights that lower mesophotic coral ecosystems are likely to be ubiquitous features on the outer reefs of the Great Barrier Reef and atolls of the Coral Sea, and harbour a generic and species richness of corals that is much higher than thus far reported. Further research efforts are urgently required to better understand and manage these ecosystems as part of the Great Barrier Reef Marine Park and Coral Sea Commonwealth Marine Reserve.
Coral reefs are increasingly threatened by thermal bleaching and tropical storm events associated with rising sea surface temperatures. Deeper habitats offer some protection from these impacts and ...may safeguard reef-coral biodiversity, but their faunas are largely undescribed for the Indo-Pacific. Here, we show high species richness of scleractinian corals in mesophotic habitats (30-125 m) for the northern Great Barrier Reef region that greatly exceeds previous records for mesophotic habitats globally. Overall, 45% of shallow-reef species (less than or equal to 30 m), 78% of genera, and all families extended below 30 m depth, with 13% of species, 41% of genera, and 78% of families extending below 45 m. Maximum depth of occurrence showed a weak relationship to phylogeny, but a strong correlation with maximum latitudinal extent. Species recorded in the mesophotic had a significantly greater than expected probability of also occurring in shaded microhabitats and at higher latitudes, consistent with light as a common limiting factor. The findings suggest an important role for deeper habitats, particularly depths 30-45 m, in preserving evolutionary lineages of Indo-Pacific corals. Deeper reef areas are clearly more diverse than previously acknowledged and therefore deserve full consideration in our efforts to protect the world's coral reef biodiversity.
Aim
We investigate how susceptibility to mass bleaching varies between closely related coral species, and the validity of applying these susceptibility data (at the appropriate taxonomic level) ...across geographical regions. We also conduct a preliminary analysis of factors likely to affect geographical variability and examine which data are required for adequate assessment of the risk to species and regional populations from repeated mass bleaching events.
Location
Twenty‐two sites in the central Great Barrier Reef, Australia (GBR) and 30 sites in the central Maldives Archipelago (MA).
Time period
2002 for the GBR and 2016 for the MA.
Major taxa studied
Corals (order Scleractinia).
Methods
After marine heat‐wave conditions, timed in situ surveys recorded bleaching responses of 7,368 coral colonies exposed to similar levels of temperature stress at a similar depth of occurrence and with similar subsequent mortality. In each region, a separate phylogenetic mixed model was used to estimate deep‐time phylogenetic‐, contemporary‐ (indicative of recent adaptation/acclimatization) and local‐scale effects. The results were compared between regions in relative terms as a hierarchy of species susceptibilities.
Results
Susceptibility varied widely between regions: 27 of 106 species analysed were in the same quartile for relative susceptibility in both regions. Closely related species varied widely in their individual susceptibilities. Phylogenetic effects were moderate in both regions, but greater contemporary effects in the MA suggested recent evolution and acclimatization, consistent with a stronger history of recent bleaching events.
Main conclusions
The high regional and intrageneric variation in susceptibility to bleaching described here suggests that there might be important differences in the extent to which these Indian and Pacific Ocean coral populations are exhibiting responses to deep‐time evolutionary changes, on the one hand, versus recent adaptation, on the other. We reveal a concerning lack of regional‐scale data identifying species most at risk from this, the greatest current threat to coral reefs.
Composite ewes (244 single, 258 twin and 255 triplet born) lambed first either as a one or two-year-old. One-year-old lambing resulted in lighter ewes at both 2nd and 3rd mating. Twin and triplet ...born ewes were lighter than single born ewes throughout their life. Ewe losses due to lambing as a one-year-old meant fewer ewes left to lamb in later years. This meant that after the two-year-old lambing the ewes that first lambed as a two-year-old weaned more lambs per original ewe than ewes that had lambed previously. This difference got smaller over time and the extra lambing meant the ewes that first lambed as a hogget produced more weaned lambs in total (6.7 vs. 5.9 lambs, P < 0.05). Lifetime weaning weight per original ewe did not differ with ewe birth rank groups but the triplet and twin born ewes were smaller than single born ewes. Thus, mating ewes to lamb as a hogget produced an advantage in the amount of lamb weaning weight produced over a ewe's lifetime but other than frame size, there was no effect of the ewes own birth rank on lamb production.
Two of Australia's most iconic ecosystems have recently sustained heavy damage related to climatic changes: the extensive eucalypt forests from catastrophic bushfires and the Great Barrier Reef from ...mass coral bleaching. Despite obvious differences, eucalypt trees and reef corals share some similarities in biology and ecology, particularly in relation to climate change impacts and adaptation. Both groups are the focus of an increasing research effort to characterize and respond to climate changes and here we examine how sharing research experiences can benefit both fields. Four key areas of research are considered: (a) modeling current distributions, (b) assessing impacts of climate change on future distributions, (c) using human‐assisted migration to improve survival, and (d) applying genetic enhancement to improve the species’ survival. Examples of each research area are used to examine potential crossovers, limitations of the methods, and future requirements. We conclude that eucalypt and coral researchers, and indeed researchers for many other endangered taxa, can gain much by comparing experiences and methods, despite the apparent differences in their respective taxa.
This article is categorized under:
Assessing Impacts of Climate Change > Observed Impacts of Climate Change
Eucalypt and coral scientists, as well as other researchers studying species distributions under climate change, can gain much by comparing experiences and methods.
Pseudogenes are ideal markers of genome remodelling. In turn, the mouse is an ideal platform for studying them, particularly with the recent availability of strain-sequencing and transcriptional ...data. Here, combining both manual curation and automatic pipelines, we present a genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains (available via the mouse.pseudogene.org resource). We also annotate 165 unitary pseudogenes in mouse, and 303, in human. The overall pseudogene repertoire in mouse is similar to that in human in terms of size, biotype distribution, and family composition (e.g. with GAPDH and ribosomal proteins being the largest families). Notable differences arise in the pseudogene age distribution, with multiple retro-transpositional bursts in mouse evolutionary history and only one in human. Furthermore, in each strain about a fifth of all pseudogenes are unique, reflecting strain-specific evolution. Finally, we find that ~15% of the mouse pseudogenes are transcribed, and that highly transcribed parent genes tend to give rise to many processed pseudogenes.
Post-translational phosphorylation is essential to human cellular processes, but the transient, heterogeneous nature of this modification complicates its study in native systems. We developed an ...approach to interrogate phosphorylation and its role in protein-protein interactions on a proteome-wide scale. We genetically encoded phosphoserine in recoded E. coli and generated a peptide-based heterologous representation of the human serine phosphoproteome. We designed a single-plasmid library encoding >100,000 human phosphopeptides and confirmed the site-specific incorporation of phosphoserine in >36,000 of these peptides. We then integrated our phosphopeptide library into an approach known as Hi-P to enable proteome-level screens for serine-phosphorylation-dependent human protein interactions. Using Hi-P, we found hundreds of known and potentially new phosphoserine-dependent interactors with 14-3-3 proteins and WW domains. These phosphosites retained important binding characteristics of the native human phosphoproteome, as determined by motif analysis and pull-downs using full-length phosphoproteins. This technology can be used to interrogate user-defined phosphoproteomes in any organism, tissue, or disease of interest.
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