Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Phylogeography of the Common New Zealand Wrasse Species, Notolabrus Celidotus, and the Phylogenetics of the Pseudolabrine Tribe

<p>The New Zealand coastline and marine environment is a diverse place and presents plenty of dispersal obstacles to many of the organisms that live there. This thesis investigates the phylogeography of one of the most common fish species around the coast of New Zealand, the endemic wrasse Notolabrus celidotus, using the mitochondrial DNA control region and compares genetic variability to another common New Zealand wrasse, Notolabrus fucicola in a local setting. These species are part of a tribe of temperate fish, the pseudolabrines, which can be found throughout the South and North-West Pacific. The phylogeny of this tribe was also analysed using the mitochondrial 16S gene to investigate the relationships among the New Zealand pseudolabrines and to those species elsewhere. The results suggest that pseudolabrines from mainland New Zealand are closely related and are likely to have originated from southern Australia while species from the Kermadec Islands and other northern islands are more closely related to the species of eastern Australia. The Notolabrus and Pseudolabrus genera should be reviewed to remedy paraphyly of Pseudolabrus. Furthermore, N. celidotus shows no population structuring throughout its range and appears to be rapidly expanding. Genetic variability was similar for both N. celidotus and N. fucicola. The results suggest that the pseudolabrine tribe has made multiple migrations to New Zealand where Notolabrus celidotus was able to spread around the three main islands and, likely facilitated by a long planktonic larval duration, was able to maintain high gene flow among populations.</p>

Upwelling-level acidification and pH variability moderate effects of ocean acidification on brain gene expression in black surfperch (Embiotoca jacksoni), a temperate fish with no pelagic larval stage

Acidification-induced changes in cognitive function and behavior have recently been documented in tropical marine fishes, raising concerns about related shifts in species interactions. Here, we investigate whether similar patterns of broad neurological impacts are observed in a temperate Pacific fish that experiences regular and often large shifts in environmental pH due to upwelling events and other natural phenomena. In two manipulative laboratory experiments, we tested the effect of acidification, as well as pH variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni. We found that patterns of global gene expression in brain tissue differed significantly across pH level treatments. Additionally, differential gene expression analysis and gene set enrichment analysis identified significant differential expression of specific genes and gene sets both in comparisons of static pH level treatments as well as in static vs. variable pH treatment comparisons where mean pH was consistent. Enriched gene sets included those related to ion transport, signaling pathways, mRNA processing and splicing, and epigenetic regulation of gene expression, among others. Importantly, we found that pH variability decreased the number of differentially expressed genes detected between high and low pH treatments, and that the inter-individual variability in gene expression was significantly greater in variable pH treatments than static treatments of the same mean pH. By demonstrating a broad shift in brain gene expression, these results provide important confirmation of neurological impacts of acidification in a temperate fish species, which are likely to translate to shifts in behavior. This study also provides critical insight into the potential of natural environmental variability to mediate the impacts of ocean acidification.

Fish functional diversity as an indicator of resilience to industrial fishing in Patagonia Argentina

The relationship between fish functional diversity and fishing levels at which its baselines shift is important to identify the consequences of fishing in ecosystem functioning. For the first time, we implemented a trait-based approach in the Argentine Patagonian sea to identify the vulnerability and spatiotemporal changes in functional diversity of fish assemblages bycatch by a trawling fleet targeting the Argentine red shrimp Pleoticus muelleri (Spence Bate, 1888) between 2003 and 2014. We coupled seven fish trophic traits to a reconstructed fish assemblage for the study area and bycatch and evaluated changes in fish species richness and four complementary functional diversity metrics [functional richness, redundancy, dispersion, and community trait values] along with fishing intensity, temporal use, latitudinal location, and depth of fishing grounds. Resident fishes larger than 30 cm in TL, with depressed and fusiform bodies, intermediate to high trophic levels, and feeding in shallow benthic, benthodemersal, and benthopelagic areas were vulnerable to bycatch. Fish assemblages exhibited a low functional trait redundancy, likely related to species influxes in a biogeographic ecotone with tropicalisation signs. Significantly increases in fish trait richness and dispersion polewards and with depth suggested new functional roles in these grounds, matching trends in community body size, reproductive load, maximum depth, trophic level, and diet breadth. Finally, a temporal increase in fish species and functional trait removal in fishing grounds led to trait homogenisation since the first year of trawling. The identified tipping points in temperate fish functional trait diversity highlight trait-based approaches within ecosystem-based fisheries management.

Temperate fish detection and classification: a deep learning based approach

A wide range of applications in marine ecology extensively uses underwater cameras. Still, to efficiently process the vast amount of data generated, we need to develop tools that can automatically detect and recognize species captured on film. Classifying fish species from videos and images in natural environments can be challenging because of noise and variation in illumination and the surrounding habitat. In this paper, we propose a two-step deep learning approach for the detection and classification of temperate fishes without pre-filtering. The first step is to detect each single fish in an image, independent of species and sex. For this purpose, we employ the You Only Look Once (YOLO) object detection technique. In the second step, we adopt a Convolutional Neural Network (CNN) with the Squeeze-and-Excitation (SE) architecture for classifying each fish in the image without pre-filtering. We apply transfer learning to overcome the limited training samples of temperate fishes and to improve the accuracy of the classification. This is done by training the object detection model with ImageNet and the fish classifier via a public dataset (Fish4Knowledge), whereupon both the object detection and classifier are updated with temperate fishes of interest. The weights obtained from pre-training are applied to post-training as a priori. Our solution achieves the state-of-the-art accuracy of 99.27% using the pre-training model. The accuracies using the post-training model are also high; 83.68% and 87.74% with and without image augmentation, respectively. This strongly indicates that the solution is viable with a more extensive dataset.

No detrimental effects of desalination waste on temperate fish assemblages

Water resources are becoming increasingly scarce due to population growth and global changes in weather patterns. Desalination plants that extract freshwater from brackish or seawater are already being used worldwide, with many new plants being developed and built. The waste product from the extraction processes has an elevated salt concentration and can potentially cause substantial impacts to local marine flora and fauna. The present study assesses the impact of saline waste from a 100 GL/year desalination plant on southern Australian temperate fish assemblages, using baited remote underwater video. The study compared four reference sites to the impact site (desalination outfall) and found no evidence that the saline waste was having a detrimental effect on fish assemblages in proximity to the outfall, with species diversity and abundance comparable to those observed at reference sites. However, species diversity and abundance varied across geographical location, protection from fishing pressure, and reef type. Our study is one of the few assessing the ecological impacts of saline waste discharged from a large desalination plant and shows no decrease in fish diversity or abundance, which is the response typically associated with the negative impacts of anthropogenic activities on fish assemblages.

Elevated temperature, but not decreased pH, impairs reproduction in a temperate fish

Fish reproductive success is linked to the ability of couples to mate and produce clutches that successfully hatch. Environmental stressors like high temperature and low pH can jeopardize this energetically costly process. In this study, exposure to high temperature and low pH was tested on a marine temperate species, Gobiusculus flavescens, to evaluate effects on reproductive performance. Breeding pairs were assigned to different temperatures (+ 0 °C, + 3 °C relative to in situ temperature) and pH levels (8.0, 7.6), in a cross-factorial design for a 3-month period. Reproduction activity, success, and paternal investment were measured throughout the exposure period. Results show reproduction is impaired by elevated temperature, while low pH had little impact. Breeding pairs under high temperature had 3% to 10% hatching success, up to 30% less eggs and eggs up to 20% smaller. Although paternal investment was not affected by tested parameters, males of breeding pairs exposed to elevated temperature had smaller gonadosomatic indexes, which might indicate a lack of investment in the reproductive process. Overall, results show that elevated temperature, expected more frequently in the near future, as a consequence of global warming, may impair key processes like reproduction in temperate fish, with potential consequences for fitness and population replenishment.