Distribution and habitat use of a cryptic small cetacean, the Burmeister's porpoise, monitored from a small-scale fishery platform

This is the final version. Available from Frontiers Media via the DOI in this record. There is widespread evidence that small-scale fisheries (SSF) bycatch threatens many populations of small cetaceans, yet conservation efforts are often limited by a lack of basic knowledge regarding their abundance, distribution, and habitat use. Here, we used passive acoustic monitoring from an SSF platform-of-opportunity to better characterize the distribution and habitat use of small cetaceans in northern Peru, focussing on the little-known Burmeister's porpoise Phocoena spinipinnis. From 2009 to 2012, acoustic click detectors (C-PODs) were attached to fishing nets for the duration of 116 fishing sets (30 fishing trips). Dolphins (unspecified delphinids) and porpoises were recorded around 71 and 22% of fishing sets, respectively. The probability of occurrence and buzzing behavior (a proxy for foraging), and time spent, were linked to both static and dynamic environmental variables to examine the drivers of habitat use. Dolphin activity was spread evenly throughout the fishing area and was not linked to any habitat variables. In contrast, porpoises were detected in neritic waters, and habitat models performed well, identifying preferences for shallow (< 200 m depth) and cooler (17-18°C) waters, close (< 50 km) to shore. The high bycatch rate of small cetaceans in Peruvian SSF gave us the unique opportunity to investigate the link between bycatch and cetacean activity around vessels. We found a positive relationship between the likelihood of a bycatch event and acoustic presence for both dolphins and porpoises, however as we did not know the timing of entanglement, we could not link vocalization rates to mortality events. Nonetheless, as small cetaceans (particularly dolphins) frequently encounter fishing boats, the likelihood of entanglements may be reduced through effective efforts to alert animals to the presence of the net, either acoustically (using acoustic alarms) or visually. This study demonstrates that passive acoustic monitoring from a fisheries platform can provide insights into the distribution and habitat use of small cetaceans at relatively low cost, and is likely to be suitable in regions with low monitoring effort and high fishing pressure.Natural Environment Research CouncilEuropean UnionDarwin Initiativ

Escaping the oligotrophic gyre? The year-round movements, foraging behaviour and habitat preferences of Murphy’s petrels

The South Pacific Gyre is the world’s largest expanse of oligotrophic ocean and supports communities of endemic gadfly petrels Pterodroma spp, yet little is known about their foraging ecology in this nutrient-poor environment. We tracked Murphy’s petrels Pterodroma ultima with geolocators from Henderson Island, Pitcairn Islands, for two consecutive years (2011 - 2013). During pre-laying exodus, petrels travelled south and southwest of the colony, with males travelling further than females to more productive waters. During incubation, birds foraged at the southern and eastern edges of the Gyre, with some travelling over 4,800 km from the colony, the greatest recorded foraging range of any breeding seabird. During non-breeding, the petrels migrated to the Subarctic Gyre in the North Pacific to forage in cool, mesotrophic waters. Habitat models revealed that birds do not have clear preferences for oceanographic (such as fronts or eddies) or topographic features (seamounts), generally favouring deep and unproductive waters. Analyses of activity patterns indicated Murphy’s petrels are amongst the most active of all seabirds, particularly during incubation when they spent c.95% of their time at sea in flight. The birds did not appear to forage during darkness, but flight activity peaked at dawn, particularly during non-breeding, suggesting they feed on mesopelagic prey that are diel vertical migrants. At-sea protection for such a wide-ranging species would require management at huge spatial scales, and hence in the short term, the principal focus for conservation should be on eliminating the immediate threat from invasive mammals at breeding sites.T.A.C. was supported by a studentship funded as part of the Natural Environment Research Council (NERC) Standard Grant NE/J021083/1. This study represents a contribution to the Ecosystems component of the British Antarctic Survey Polar Science for Planet Earth Programme, funded by NERC

Consistency in migration strategies and habitat preferences of brown skuas over two winters, a decade apart

At-sea movements and activity patterns of brown skuas Stercorarius antarcticus lonnbergi from South Georgia were analysed in 2 winters, a decade apart, to examine the degree of consistency in migration strategies and habitat preferences during the non-breeding and pre-laying exodus periods. Oceanographic habitat preferences of tracked skuas were determined using a robust model accounting for availability. At the population level, brown skuas were broadly consistent in their choice of wintering areas and habitat preferences, although the distribution extended farther east in 2012 than in 2002. Skuas preferred areas associated with static oceanography (bathymetric features) both during the non-breeding and pre-laying periods, which may explain the consistency between years in habitat use. There was no significant effect of year on departure dates from South Georgia, but birds returned earlier to the colony in 2002. Migration schedules varied according to breeding status, with failed birds departing earlier than birds that bred successfully. Although failed birds travelled farther from the colony, there was little variation in dates of return. In general the timing of movements was similar between sexes, but females were more likely than males to engage in a pre-laying exodus. Brown skuas spent a much higher proportion of time sitting on the water than other seabirds during both the non-breeding and pre-laying exodus periods, and the number of flight bouts per day was surprisingly low. The selection of static features by brown skuas may indicate that skuas may have less flexibility to track environmental changes than species that use dynamic cues

Proximate drivers of spatial segregation in non-breeding albatrosses

Many animals partition resources to avoid competition, and in colonially-breeding species this often leads to divergent space or habitat use. During the non-breeding season, foraging constraints are relaxed, yet the patterns and drivers of segregation both between and within populations are poorly understood. We modelled habitat preference to examine how extrinsic (habitat availability and intra-specific competition) and intrinsic factors (population, sex and breeding outcome) influence the distributions of non-breeding grey-headed albatrosses $\textit{Thalassarche}$ chrysostoma tracked from two major populations, South Georgia (Atlantic Ocean) and the Prince Edward Islands (Indian Ocean). Spatial segregation was greater than expected, reflecting distinct seasonal differences in habitat selection and accessibility, and avoidance of intra-specific competition with local breeders. Previously failed birds segregated spatially from successful birds during summer, when they used less productive waters, suggesting a link between breeding outcome and subsequent habitat selection. In contrast, we found weak evidence of sexual segregation, which did not reflect a difference in habitat use. Our results indicate that the large-scale spatial structuring of albatross distributions results from interactions between extrinsic and intrinsic factors, with important implications for population dynamics. As habitat preferences differed substantially between colonies, populations should be considered independently when identifying critical areas for protection.TAC was supported by a studentship funded as part of Natural Environment Research Council (NERC) Standard Grant NE/J021083/1. This study represents a contribution to the Ecosystems component of the British Antarctic Survey Polar Science for Planet Earth Programme, funded by NERC

Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case

Background:In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.Results:Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.Conclusions:Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution

Cdk2 Is Required for p53-Independent G2/M Checkpoint Control

The activation of phase-specific cyclin-dependent kinases (Cdks) is associated with ordered cell cycle transitions. Among the mammalian Cdks, only Cdk1 is essential for somatic cell proliferation. Cdk1 can apparently substitute for Cdk2, Cdk4, and Cdk6, which are individually dispensable in mice. It is unclear if all functions of non-essential Cdks are fully redundant with Cdk1. Using a genetic approach, we show that Cdk2, the S-phase Cdk, uniquely controls the G2/M checkpoint that prevents cells with damaged DNA from initiating mitosis. CDK2-nullizygous human cells exposed to ionizing radiation failed to exclude Cdk1 from the nucleus and exhibited a marked defect in G2/M arrest that was unmasked by the disruption of P53. The DNA replication licensing protein Cdc6, which is normally stabilized by Cdk2, was physically associated with the checkpoint regulator ATR and was required for efficient ATR-Chk1-Cdc25A signaling. These findings demonstrate that Cdk2 maintains a balance of S-phase regulatory proteins and thereby coordinates subsequent p53-independent G2/M checkpoint activation