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Molecular Evolution of Mammalian Genes with Epistatic Interactions in Fertilization

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-07-25
Abstract: 

Background

Genes that encode proteins associated with sperm competition, fertilization, and sexual conflicts of interest are often among the most rapidly evolving parts of animal genomes. One family of sperm-expressed genes (Zp3r, C4bpa) in the mammalian gene cluster called the regulator of complement activation (RCA) encodes proteins that bind eggs and mediate reproductive success, and are therefore expected to show high relative rates of nonsynonymous nucleotide substitution in response to sexual selection in comparison to other genes not involved in gamete binding at fertilization. We tested that working hypothesis by using phylogenetic models of codon evolution to identify episodes of diversifying positive selection. We used a comparative approach to quantify the evidence for episodic diversifying selection acting on RCA genes with known functions in fertilization (and sensitivity to sexual selection), and contrast them with other RCA genes in the same gene family that function in innate immunity (and are not sensitive to sexual selection).

Results

We expected but did not find evidence for more episodes of positive selection on Zp3r in Glires (the rodents and lagomorphs) or on C4BPA in Primates, in comparison to other paralogous RCA genes in the same taxon, or in comparison to the same orthologous RCA gene in the other taxon. That result was not unique to RCA genes: we also found little evidence for more episodes of diversifying selection on genes that encode selective sperm-binding molecules in the egg coat or zona pellucida (Zp2, Zp3) in comparison to members of the same gene family that encode structural elements of the egg coat (Zp1, Zp4). Similarly, we found little evidence for episodic diversifying selection acting on two other recently discovered genes (Juno, Izumo1) that encode essential molecules for sperm–egg fusion.

Conclusions

These negative results help to illustrate the importance of a comparative context for this type of codon model analysis. The results may also point to other phylogenetic contexts in which the effects of selection acting on these fertilization proteins might be more readily discovered and documented in mammals and other taxa.

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Article
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Ecological Lifestyles and the Scaling Of Shark Gill Surface Area

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-12-01
Abstract: 

Fish gill surface area varies across species and with respect to ecological lifestyles. The majority of previous studies only qualitatively describe gill surface area in relation to ecology and focus primarily on teleosts. Here, we quantitatively examined the relationship of gill surface area with respect to specific ecological lifestyle traits in elasmobranchs, which offer an independent evalu- ation of observed patterns in teleosts. As gill surface area increases ontogenetically with body mass, examination of how gill surface area varies with ecological lifestyle traits must be assessed in the context of its allometry (scaling). Thus, we examined how the relationship of gill surface area and body mass across 11 shark species from the literature and one species for which we made measurements, the Gray Smoothhound, Mustelus californicus, varied with three ecological lifestyle traits: activity level, habitat, and maximum body size. Relative gill surface area (gill surface area at a specified body mass; here we used 5,000g, termed the ‘standardized intercept’) ranged from 4,724.98 to 35,694.39 cm2 (mean and standard error: 17,796.65  2,948.61 cm2) and varied across species and the ecological lifestyle traits examined. Specifically, larger-bodied, active, oceanic species had greater relative gill surface area than smaller-bodied, less active, coastal species. In contrast, the rate at which gill surface area scaled with body mass (slope) was generally consistent across species (0.85  0.02) and did not differ statistically with activity level, habitat, or maximum body size. Our results suggest that ecology may influence relative gill surface area, rather than the rate at which gill surface area scales with body mass. Future com- parisons of gill surface area and ecological lifestyle traits using the quantitative techniques applied in this study can provide further insight into patterns dictating the relationship between gill surface area, metabolism, and ecological lifestyle traits.

Document type: 
Article

Near Disappearance of the Angelshark Squatina Squatina Over Half A Century of Observations

Peer reviewed: 
Yes, item is peer reviewed.
Abstract: 

Marine extinctions are particularly difficult to detect and almost all have been discovered after the fact. Retrospective analyses are essential to avoid concluding no-extinction when one has occurred. We reconstruct the Angelshark population trajectory in a former hotspot (Wales), using interviews and opportunistic records. After correcting for observation effort and recall bias, we estimate a 70% (1.5% yr-1) decline in abundance over 46 years. While formerly widespread, Angelshark distribution contracted to a central core of Cardigan Bay. Angelshark declined almost unnoticed in one of the best-monitored and most intensively managed seas in the world. Bycatch may be minimised by limiting netting on shingle reefs in Cardigan Bay. We provide the first quantitative time series to reveal the timing and trajectory of decline of Angelshark in the coastal waters of Wales and uncover historical centres of abundance and remnant populations that provide the first opportunity for the focus of conservation. 

Document type: 
Article

Landscape Structure and Species Interactions Drive the Distribution of Salmon Carcasses in Coastal Watersheds

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-06-07
Abstract: 

The disproportionate effects of some species can drive ecosystem processes and shape communities. This study investigates how distributions of spawning Pacific salmon within streams, salmon consumers, and the surrounding landscape mediate the distribution of salmon carcasses to riparian forests and estuaries. This work demonstrates how carcass transfer can vary spatially, within and among watersheds, through differences in pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon distributions within 16 streams on the central coast of British Columbia over a five-year period. Spawning pink salmon concentrated in the lower reaches of all streams, whereas chum salmon shifted from lower to upper stream reaches as the area of spawning habitat increased. Salmon carcasses transferred to riparian areas by gray wolves (Canis lupus) were concentrated in estuaries and lower stream reaches, particularly shallow reaches of larger streams surrounded by large meadow expanses. Black and grizzly bears (Ursus americanus and U. arctos) transferred higher numbers and proportions of salmon carcasses to riparian areas compared to wolves, transferred more carcasses in areas of higher spawning density, and tended to focus more on chum salmon. Riparian subsides were increasingly driven by bear-chum salmon associations in upper stream reaches. In addition, lower proportions of salmon carcasses were exported into estuaries when densities of spawning salmon were lower and spawning reaches of streams were longer. This study demonstrates how salmon subsidies vary between and within watersheds as a result of species associations and landscape traits, and provides a nuanced species-specific and spatially explicit understanding of salmon-subsidy dynamics.

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Article
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Moving Beyond Silos in Cumulative Effects Assessment

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-06-11
Abstract: 

Many of the world's ecosystems are experiencing a suite of changes from anthropogenic activities; the multiple stressors from those activities result in cumulative impacts. Understanding how these activities translate into ecological consequences is exceedingly challenging because of the inherent complexity within natural systems and the variability in how stressors act and how species respond. While there have been substantial advancements within the field of cumulative effects assessment to address these issues and improve our understanding of the consequences of our actions, many challenges remain. Here, we detail advances and remaining challenges, and propose five priorities for addressing these challenges in the near future. In particular, we suggest prioritizing risk-based approaches that account for uncertainty in our understanding and establishing an underlying theory for when we expect particular impacts to occur. We also propose the need for a defined subdiscipline focused on cumulative effects, to help reduce the silos of research that are often disconnected, and to work toward a common set of definitions, methods and the consistent use of open data.

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Article
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Marine Protected Areas Enhance Coral Reef Functioning By Promoting Fish Biodiversity

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-03-01
Abstract: 

Preserving biodiversity and ecosystem function in the Anthropocene is one of humanity's greatest challenges. Ecosystem‐based management and area closures are considered an effective way to maintain ecological processes, especially in marine systems. Although there is strong evidence that such measures positively affect community structure, their impact on the rate of key ecological processes remains unclear. Here, we provide evidence that marine protected areas enhance herbivory rates on coral reefs via direct and indirect pathways. Using meta‐analysis and a path‐analytical framework, we demonstrate that, on average, protected areas increase the species richness of herbivorous fishes, which, in turn, enhances browsing rates on macroalgae. However, in all three regions studied (the Atlantic, Indian, and Pacific Ocean), a small subset of the herbivore assemblage accounted for the majority of browsing. Our results therefore indicate that ecosystem functioning on coral reefs may respond positively to both area closures and the protection of key species.

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Article
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Assessing the Effect of Seasonal Agriculture on the Condition and Winter Survival of a Migratory Songbird in Mexico

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-03-20
Abstract: 

 

Migratory birds can spend 8 months of the year on their wintering grounds and the conversion of natural habitats to agriculture in Latin America has been implicated in population declines of several Neotropical migrants. Despite this, few studies have directly assessed the value of agricultural habitat for wintering migrants. We compared the condition and survival of Yellow Warblers (Setophaga petechia) occupying natural (riparian forest, scrub‐mangrove) and agricultural habitat (annually cropped sorghum, corn, and chili‐peppers separated by hedgerow) in western Mexico. We assessed condition with five metrics (daily and seasonal changes in size‐adjusted body mass, leukocyte profiles, rectrix regrowth rate, rectrix quality, and dates of departure on spring migration). We used Cormack–Jolly–Seber models fitted to mark‐resighting data collected over 4 years (2012–2015) to estimate January–May monthly survival rates. We found that birds occupying agricultural habitat and riparian forest had higher monthly apparent survival between January and May than birds in scrub‐mangrove. Birds in agricultural habitat also grew higher quality feathers (i.e., rectrices with a higher barbule density) than those in natural habitat. In contrast, birds in agricultural habitat were lighter than those in riparian habitat. We found no detectable effect of winter habitat use on daily or season changes in size‐adjusted mass and H/L ratios, although the effect of winter habitat use on departure rates differed for males and females. Our results demonstrate that agricultural habitat may provide suitable winter habitat for a long‐distance migrant and suggest that feather quality can be an indicator of winter habitat quality.

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The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-12-03
Abstract: 

The composition, abundance, and diversity of midgut bacteria in mosquitoes can influence pathogen transmission. We used 16S rRNA microbiome profiling to survey midgut microbial diversity in pooled samples of laboratory colonized dengue-refractory, Cali-MIB, and dengue-susceptible, Cali-S Aedes aegypti (Linnaeus). The 16S rRNA sequences from the sugar-fed midguts of adult females clustered to 63 amplicon sequence variants (ASVs), primarily from Proteobacteria, Firmicutes, Flavobacteria, and Actinobacteria. An average of five ASVs dominated the midguts, and most ASVs were present in both Cali-MIB and Cali-S midguts. No differences in abundance were noted at any phylogenetic level (Phylum, Class, Order, Family, Genus) by analysis of composition of microbiome (w = 0). No community diversity metrics were significantly different between refractory and susceptible mosquitoes. These data suggest that phenotypic differences in the susceptibility to dengue virus between Cali-MIB and Cali-S are not likely due to major differences in midgut bacterial communities.

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Article
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Haematological Traits Co-Vary With Migratory Status, Altitude and Energy Expenditure: A Phylogenetic, Comparative

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-04-23
Abstract: 

Aerobic capacity is assumed to be a main predictor of workload ability and haematocrit (Hct) and haemoglobin (Hb) have been suggested as key determinants of aerobic performance. Intraspecific studies have reported increases in Hct and Hb in response to increased workload. Furthermore, Hct and Hb vary markedly among individuals and throughout the annual cycle in free-living birds and it has been suggested that this variation reflects adaptive modulation of these traits to meet seasonal changes in energy demands. We used a comparative dataset of haematological traits, measures of metabolic rate (57 species), and life-history traits (160 species) to test several hypotheses for adaptive variation in haematology in relation to migration and altitude. We then extended these general ideas to test relationships between Hct and basal metabolic rate, daily energy expenditure and activity energy expenditure, using the 57 species that we have metabolic rate information for. We found that at the interspecific level, full migrants have higher Hct and Hb than partial migrants and non-migrants, and that altitude is positively correlated with Hb but not Hct. Hct is positively associated with activity energy expenditure (energy spent specifically on costly activities), suggesting that haematological traits could be adaptively modulated based on life-history traits and that Hct is a potential physiological mediator of energetic constraint.

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