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Abstract Limited dispersal of individuals between generations results in isolation by distance, in which individuals further apart in space tend to be less related. Classic models of isolation by distance assume that dispersal distances are drawn from a thin-tailed distribution and predict that the proportion of the genome that is identical by descent between a pair of individuals should decrease exponentially with the spatial separation between them. However, in many natural populations, individuals occasionally disperse over very long distances. In this work, we use mathematical analysis and coalescent simulations to study the effect of long-range (power-law) dispersal on patterns of isolation by distance. We find that it leads to power-law decay of identity-by-descent at large distances with the same exponent as dispersal. We also find that broad power-law dispersal produces another, shallow power-law decay of identity-by-descent at short distances. These results suggest that the distribution of long-range dispersal events could be estimated from sequencing large population samples taken from a wide range of spatial scales. 

Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N 2-methylguanosine, N 2, N 2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N 2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context. 

Climate change is radically altering coral reef ecosystems, mainly through increasingly frequent and severe bleaching events. Yet, some reefs have exhibited higher thermal tolerance after bleaching severely the first time. To understand changes in thermal tolerance in the eastern tropical Pacific (ETP), we compiled four decades of temperature, coral cover, coral bleaching, and mortality data, including three mass bleaching events during the 1982 to 1983, 1997 to 1998 and 2015 to 2016 El Niño heatwaves. Higher heat resistance in later bleaching events was detected in the dominant framework-building genus, Pocillopora, while other coral taxa exhibited similar susceptibility across events. Genetic analyses of Pocillopora spp . colonies and their algal symbionts (2014 to 2016) revealed that one of two Pocillopora lineages present in the region ( Pocillopora “ type 1”) increased its association with thermotolerant algal symbionts ( Durusdinium glynnii ) during the 2015 to 2016 heat stress event. This lineage experienced lower bleaching and mortality compared with Pocillopora “type 3”, which did not acquire D. glynnii . Under projected thermal stress, ETP reefs may be able to preserve high coral cover through the 2060s or later, mainly composed of Pocillopora colonies that associate with D. glynnii . However, although the low-diversity, high-cover reefs of the ETP could illustrate a potential functional state for some future reefs, this state may only be temporary unless global greenhouse gas emissions and resultant global warming are curtailed. 

Abstract Thermal stress is expected to compromise the persistence of tropical corals throughout their biogeographic ranges, making many reefs inhospitable to corals by the end of the century. We integrated models of local predictions of thermal stress throughout the coming century, coral larval dispersal, and the persistence of a coral’s metapopulation(s) in the Caribbean to investigate broad trends in metapopulation fragmentation and decline. As coral reef patches become inhospitable throughout the next century, the metapopulation of Orbicella annularis is predicted to fragment, with sub-networks centered around highly connected patches and thermal refuges. Some of these are predicted to include the reefs of Colombia, Panama, Honduras, Guatemala, Belize, Southern and Northern Cuba, Haiti, and the Bahamas. Unknown coral population demographic parameters, such as lifetime egg production and stock-recruitment rates, limit the model’s predictions; however, a sensitivity analysis demonstrates that broadscale patterns of fragmentation and metapopulation collapse before the end of the century are consistent across a range of potential parameterizations. Despite dire predictions, the model highlights the potential value in protecting and restoring coral populations at strategic locations that are highly connected and/or influential to persistence. Coordinated conservation activities that support local resilience at low coral cover have the potential to stave off metapopulation collapse for decades, buying valuable time. Thermal refuges are linchpins of metapopulation persistence during moderate thermal stress, and targeted conservation or restoration that supports connectivity between these refuges by enhancing local population growth or sexual propagation may be critically important to species conservation on coral reefs. 

Stony coral tissue loss disease (SCTLD), one of the most pervasive and virulent coral diseases on record, affects over 22 species of reef-building coral and is decimating reefs throughout the Caribbean. To understand how different coral species and their algal symbionts (family Symbiodiniaceae) respond to this disease, we examine the gene expression profiles of colonies of five species of coral from a SCTLD transmission experiment. The included species vary in their purported susceptibilities to SCTLD, and we use this to inform gene expression analyses of both the coral animal and their Symbiodiniaceae. We identify orthologous coral genes exhibiting lineage-specific differences in expression that correlate to disease susceptibility, as well as genes that are differentially expressed in all coral species in response to SCTLD infection. We find that SCTLD infection induces increased expression ofrab7, an established marker of in situ degradation of dysfunctional Symbiodiniaceae, in all coral species accompanied by genus-level shifts in Symbiodiniaceae photosystem and metabolism gene expression. Overall, our results indicate that SCTLD infection induces symbiophagy across coral species and that the severity of disease is influenced by Symbiodiniaceae identity.