Genetic Level Investigations Into the Species Diversity, Biogeography and Trophic Traits of Antarctic Polychaetes
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Genetic level investigations into the species diversity, biogeography and trophic traits of Antarctic Polychaetes A thesis submitted for the degree of Doctor of Philosophy Madeleine Julie Brasier University of Liverpool School of Environmental Science December 2017 Supervised by: Dr Rachel Jeffreys Dr Adrian Glover Examined by: Dr Henry Ruhl Dr Leonie Robinson Professor George Wolff Professor A. Lousie Allcock Declaration This thesis is an account of my research undertaken within the Life Science Department, Natural History Museum, London, UK, and the School of Environmental Sciences, Liverpool, UK, between December 2013 and December 2017. Unless acknowledged the material presented in this thesis is, to the best of my knowledge, original and has not been previously submitted. Madeleine Brasier December 2017 i Abstract The diversity and biogeography of the Antarctic benthos has been shaped by its unique history through glacial cycles, the influence of circumpolar current regimes and seasonal food inputs. There is currently a large international research effort to define levels of species diversity, biogeography, functional traits and their sensitivity to changing environmental conditions. These data are vital in setting ecological baselines to monitor the effects of climate change and manage the impacts of human activities in the Southern Ocean. The findings from genetic level analyses into species diversity, biogeography and the trophic traits of two groups of benthic Antarctic polychaetes, an abundant taxa within macrofaunal communities are presented here. The first group contained free-living polychaetes collected from the Scotia, Amundsen and Weddell Seas, whilst the second group consisted of symbiotic polynoids taken from coral host species in the South Orkney Islands Southern Shelf Marine Protected Area. The application of DNA barcoding to a subset of 15 morphologically identified polychaete species (morphospecies) from the free-living polychaetes, uncovered 10 additional cryptic species (these individuals are morphologically identical but genetically distinct) and 10 previously overlooked morphospecies. These findings suggest that the levels of Antarctic benthic diversity may be largely underestimated. The difficulty in determining true ‘species’ from genetic analysis for which there are no genetic cut offs or rules is discussed, as well as the causes of misidentification of soft bodied species within large sample sets. The distribution of cryptic species are often more restricted that that of their original morphospecies. This is potentially related to geographic or reproductive isolation of populations during the speciation process. In this study, the cryptic species previously considered to be circum-Antarctic remained widespread. This demonstrates the importance of considering dispersal mechanisms, including developmental mode and larval biology and subsequently transport via cicrum-Antarctic currents. The determination of trophic traits using both bulk and compound specific stable isotope analysis, revealed high levels of variability within and between species with the same categorical trophic traits. These data suggest a high degree of omnivory coupled with variation at the base of the food web i.e. in d15N of phytoplankton/phytodetritus. The use of genetic and ii biochemical analyses to describe the symbiotic relationship between polynoid symbionts and their host corals identified polymorphisms with significantly different trophic signatures. The relevance and significance of the findings are discussed with regard to environmental change in the Southern Ocean and the future of Antarctic marine management and scientific research. Antarctica represents one of the most rapidly changing and vulnerable ecosystems on our planet. Any means to mitigate the effects of climate change or to sustainably manage Antarctic marine resources requires international and multidisciplinary research collaborations. Future research should focus on understanding the interacting and changing relationships between the biological, chemical, physical and geological environments. iii I have lots of heroes: anyone and everyone who does whatever they can to leave the natural world better than they found it. - Sylvia Earle Acknowledgments My love of marine ecosystems evolved from many happy days face first in a rock pool in Cornwall whilst visiting my grandparents. I hope they’d both be proud of this thesis and all the adventures my PhD brought with it. My interest in Antarctic biology came apparent during my undergraduate studies at the University of Southampton. I would like to thank Professor Paul Tyler for introducing me to the wonders of deep-sea life and all Antarctic science had to offer. My passion for polychaetes was perhaps an unexpected one. Shortly after graduating I was welcomed into Dr Adrian Glover’s lab at the Natural History Museum, London. I soon realised there was a lot of polychaete related fun to be had. I feel very lucky to have been a part of Adrian’s research group and am grateful for all friendships and fieldwork opportunities that came with it. My PhD maintained connections with the Natural History Museum but the University of Liverpool soon became my new home. Whilst in Liverpool, my supervisor Dr Rachel Jeffreys became not only a great source of support and guidance through this PhD but also my ‘academic mum’. Thank you Rachel for your kindness through the rough times and the laughs along the way. Thanks are also due to Professor George Wolff for keeping me on the straight and narrow to get this thesis finished. I would also like to thank Lenka Neal and Dr’s Helen Wiklund and Anu Petal for their incredible patience with me in the lab and help in the collection of taxonomic, genetic and isotope data, and, Drs Henry Ruhl and James Harle for their collaborative work in the publication of my second chapter. Over the last four years my fellow PhD students and postdocs helped me in many ways from PhD and academic advice, proof reading, post conference travelling, endless tea breaks, hugs, shared ranting and encouragement. To name a few; Maggie Georgiva, Olivia Hicks, Hannah Whitby, Alice Trevail, Nealy Carr, Callum Preece, James Pobert, Arthur Gourian, Hannah iv Griffiths, Robyn Tuerena, Clare Davis and Peter Davis - I am most thankful for your friendship and support. During my PhD I had the opportunity to work with British Antarctic Survey in the Southern Ocean on the State of the Antarctic Ecosystem project. Thanks are due to Dr’s Huw Griffiths and Susie Grant for this opportunity and the 3 month internship in Cambridge following the expedition. Whilst there I was able to collaborate further with both Dr’s Katrin Linse and Phil Trathan who were most helpful in the production of the SOAntEco report for CCAMLR. Another expedition I shall never forget was the month I spent at Palmer Station. My time there was full of scientific excitement and incredible memories with my B301 course mates. I thank Professor Deneb Karentz for making such an amazing, once in a lifetime, experience possible. I dedicate this thesis to my overwhelmingly supportive family, they saw it all from start to finish; the excitements, the disappointments, the frustrations and the breakthroughs. So to my loving bungles; Julie, Alan, Jenna and Sam, here some words about worms. Thank you for always encouraging me to take on the world one Antarctic animal at a time. v Glossary and Acronyms 1M – 1 month 1W – 1 week 1Y – 1 year 6M – 6 months 3’ prime end – the end of a single-stranded nucleic acid molecule which terminates in a hydroxyl group. 5’ prime end - the end of a single-stranded nucleic acid molecule which terminates in a phosphate group. δ15N – denotes the isotopic ratio of 15N:14N AA – Amino Acid AIC – Akaike Information Criterion ACC – Antarctic Circumpolar Current Ala – Alanine (amino acid) ANDEEP - ANtarctic DEEP-sea benthic biodiversity Asp – Aspartic acid (amino acid) BAS – British Antarctic Survey BIC – Bayesian Information Criterion BIOPEARL - BIOdiversity dynamics: Phylogeography, Evolution, And Radiation of Life BLAST - Basic Local Alignment Search Tool BOLD – Barcode of Life Database bp – base pair vi CAML – Census of Antarctic Marine Life CCAMLR – Commission of the Conservation of Antarctic Marine Living Resources COI – Cytochrome c oxidase subunit 1 CSIA – Compound specific stable isotope analysis DNA Barcode – short sequence of DNA used to identify species EA/IRMS – Elemental Analyser Isotope Ratio Mass Spectrometry E – Ethanol FOODBANCS - FOOD for Benthos on the ANtarctic Continental Shelf F – Formalin Fr – Frozen GC – Gas Chromatography GC/C/IRMS – Gas Chromatography Combustion Isotope Ratio Mass Spectrometry GenBank – Online genetic database within the National Center for Biotechnology Information Glu – Glutamic acid (amino acid) Gly – Glycine (amino acid) GTR + I + G – General time reversible + invariable sites + gamma Iso – Isoleucine (amino acid) ITS – Internal transcribed spacer JR144 – BIOPEARL I expedition led by British Antarctic Survey on the RRS James Clarke Ross to sample the benthic communities of the Scotia Arc. JR179 – BIOPERAL II expedition led by British Antarctic Survey on the RRS James Clarke Ross to sample the benthic communities of the Amundsen Sea. vii JR275 – British Antarctic Survey expedition on the RRS James Clarke Ross to sample benthic communities of the eastern Weddell Sea. JR15005 – SOAntEco expedition led by British Antarctic Survey on the RRS James Clarke Ross to sample the benthic communities of