Antarctic larvae: identification, community composition and distribution modelling

225 Pages·2014·14.5 MB·English

by  Ramón Gallego Simón

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Antarctic larvae:
identification, community
composition and

distribution modelling
Ramón Gallego Simón

A thesis submitted in fulfilment of the requirements for the degree of
Doctor of Philosophy in the Biological Sciences.
University of Auckland
July 2014

Abstract
This Thesis describes the variation of the meroplankton communities in oceanic and
coastal waters of the Ross Sea, Antarctica and hypothesizes the changes on a species
distribution with future climate conditions, combining information from adult and larval
environmental suitability.
This work relies on the accurate identification of larval specimens. Using a morphological
and molecular approach, DNA sequences obtained from specimens morphologically
identified as Operational Taxonomical Units (OTUs) were aligned with reference sequences
and a final identification was achieved using phylogenetic trees. In the oceanic Ross Sea, 68
of the original OTUs have been reclassified: we have been able to detect and discard from
further analysis 15 holoplanktonic molecular OTUs (mOTUs) and identified 43 mOTUs from
eight phyla.
In the oceanic Ross Sea - investigated as part of the IPY-CAML voyage to the Ross Sea –
the overall larval abundance was lower than in previous Antarctic studies (5.19 specimens per
100 m3) and was significantly higher in the first 200 m of the water column without showing
any variation across regions. Alpha diversity showed regional variation and it was
significantly higher over the Ross Sea Shelf than over the slope or the offshore Antarctic; and
without any depth variation. The community composition varied significantly across depth
and regions, and we found a weak but significant Spearman correlation between changes in
community composition and a combination of three environmental variables (temperature,
depth and latitude).
The coastal sampling scheme - part of the Latitudinal Gradient Project - studied three
sites in a latitudinal gradient along the Victoria Land coast: Cape Hallett, Terra Nova Bay and
Granite Harbour. We did not find any significant latitudinal pattern on larval abundance,
alpha diversity or number of OTUs, and it was in the community composition where a strong,
significant regional pattern arose. These differences were driven by a combination of locally
abundant and widespread species.
We found no evidence of a latitudinal variation in the feeding strategy of larvae. Terra
Nova Bay, the mid latitude site, showed the highest proportion of planktotrophic larvae
(0.95), while Cape Hallett and Granite Harbour showed similar proportions (0.73
I
planktotrophy in Cape Hallett and 0.7 in Granite Harbour), thus giving evidence of the
prevalence of planktotrophy at high latitudes.
The importance of dispersal stages on determining changes in a species distribution was
shown. Using georeferenced larval and adult records, two species distribution models were
constructed with MaxEnt, which were projected into future (2050) climate conditions. This
projection has revealed a decrease on suitability for both life stages, but the dramatic drop in
larval suitability in the Ross Sea predicts a population collapse in that area.

II
Acknowledgements
I have been able to complete this thesis only because I have been surrounded by people
who have been as passionate as me about the work I was doing, who have given me their
time and knowledge, who have been there to cheer me up during the lows and to celebrate
during the highs. I will try to give everyone the credit they deserve for the help they have
given me, for teaching me so much, and for making my PhD and my stay in New Zealand the
most amazing journey, but please forgive me if I have forgotten to include you here.
I had the most amazing supervisors during this project. Shane, I am really thankful for
your help and patience, and for teaching me the entrails of the DNA world and being so
understanding when my English wasn’t particularly easy to understand. I am also grateful for
all the encouragement you gave me to go and apply for things. That made a difference.
Mary, I am sure you know how thankful I am for all the help you have given me during
this project. First of all, for remembering that guy that flicked you some emails in 2006 and
let me join this project. And since I started my thesis, you have always been there for me,
from coming to the microscope to see the latest weird thing that appeared in the plankton
tows and point me in the right direction, to giving me advice and directions on the Thesis as a
whole. Every piece of written work that I have sent you has come back to me with improved
perspective and clarity; and all really quickly. You have been an inspiration for me and have
made me more committed to pursue a scientific career. I am also forever grateful for letting
me join you in a trip of a lifetime to Antarctica.
This project could not have been possible without the commitment of the funding
agencies that made possible the collection of the samples. Antarctica is a remote, hazardous
place and organizing sampling campaigns in such locations doesn’t come cheap. Ministry of
Fisheries (now Ministry of Primary Industries) funded in 2008 the NZ IPY-CAML voyage to
the Ross Sea, which was carried out by NIWA o/b the RV Tangaroa. This project also funded
my stipend and my doctoral fees during three years, for which I am obviously grateful.
Antarctica New Zealand and Scott Base staff gave logistic support during the Latitudinal
Gradient Project. Sequencing and lab costs have been funded thanks to research grants from
the University of Auckland and from the Antarctic Science Bursary, which made possible the
molecular identification of the larvae and gave this project an increased impact. The
University of Auckland funded my stipend and fees for a further six months which were
extremely helpful. I am also thankful to Vertnet for funding my attendance to the
III
Biodiversity Informatics Training Workshop (BITW) in Boulder, Colorado, which opened
my mind and planted the seed for Chapter 5. My thanks to the SBS travel Fund and the Royal
Society of New Zealand Te Apārangi for funding trips to International Conferences.
Obtaining the samples during the IPY-CAML voyage is the work of Lisa Bryant and Julie
Hall, who did an amazing job under extreme circumstances. My thanks to all the crew and
scientists o/b the RV Tangaroa for making that sampling trip possible. The coastal campaign
was only possible thanks to the work of many people: thanks all for a great job and
particularly to those who were in Granite Harbour in 2009: Mary, Mike, Ian, Amy and Rhian,
thanks a lot for making it happen, those were really long hours of work and good fun.
Processing the samples in the lab was possible thanks to the tutoring of Mike and Mary
who showed great patience with me. I owe my knowledge on molecular techniques to Shane,
Vibha and Doro: thank you for not laughing at my questions. I have asked so many questions
of how to use ArcGIS and MaxEnt to Zeenatul Basher, and he was always very helpful and
patient, thanks for that. Thanks also to Adrian Turner for your help using all microscopy
resources, to Vivian Ward for her work on some figures, to Kristine Boxen for your help with
DNA sequencing, to Todd Dennis for your help on SDMs, and to Brian McArdle for
statistical advice.
I am really grateful to have shared my time at University with many people that I can call
my friends. Thanks to Emma, Richard, Lilly and Steen for your help with lab stuff and
troubleshooting and great conversation and coffees. And to Nick, Erica, Josefina, Mike,
Selena, Kate, Basher, Agnès and Jethro which made life in general way better, and helped
keep me sane.
And thanks to my parents and the rest of my family back in Spain, for asking and not
asking how I was, for being worried by any natural disaster in a 10,000 km radius, and for
giving support from the other side of the world. Also to my friends for cheering me up and
chatting as if I never left. Finally, I want to thank you Ana, for loving me, for helping me, for
making this adventure one to be remembered, and for what is to come.

IV
Contents
1 General Introduction ............................................................................................................... 1
1.1 The Southern Ocean ........................................................................................................... 3
1.1.1 Extent and physical environment .................................................................. 3
1.2 The Ross Sea ........................................................................................................................ 6
1.2.1 Extent and physical environment .................................................................. 6
1.2.2 Primary production and bentho-pelagic coupling ......................................... 8
1.3 Benthos assemblages in the Ross Sea ............................................................................... 10
1.4 Previous meroplankton studies ........................................................................................ 12
1.5 Larvae and species distribution ........................................................................................ 16
1.6 Thesis objectives ............................................................................................................... 18
1.7 Chapters overview and aims ............................................................................................. 19
1.7.1 Chapter 2: Identification of meroplankton specimens from the Ross Sea .. 19
1.7.2 Chapter 3: The meroplankton community of the oceanic Ross Sea during
the late austral summer ............................................................................... 19
1.7.3 Chapter 4: Latitudinal gradients in Victoria Land coast meroplankton ....... 20
1.7.4 Chapter 5: Differential sensitivity of larval and adult Antarctic acorn
barnacles to climate change ........................................................................ 21
1.7.5 Chapter 6: General conclusions and future directions ................................ 22
2 Identification of meroplankton specimens from the Ross Sea: a morphological and
molecular approach .............................................................................................................................. 23
2.1 Introduction ...................................................................................................................... 24
2.2 Methods ............................................................................................................................ 26
2.2.1 Sample collection, PCR amplification and DNA sequencing ........................ 26
2.2.2 Larval identification ..................................................................................... 27
2.3 Results ............................................................................................................................... 28
2.3.1 Phylum Echinodermata ................................................................................ 32
2.3.2 Phylum Arthropoda ..................................................................................... 39
2.3.3 Phylum Annelida .......................................................................................... 44
2.3.4 Phylum Mollusca .......................................................................................... 54
2.3.5 Phylum Cnidaria ........................................................................................... 57
2.3.6 Phylum Rotifera ........................................................................................... 60
2.3.7 Phylum Nemertea ........................................................................................ 61
2.3.8 Phylum Chordata ......................................................................................... 62
2.4 Discussion .......................................................................................................................... 66
2.4.1 Molecular Identification and marker selection ........................................... 67
2.4.2 Tree-based method ..................................................................................... 68
2.4.3 Future directions .......................................................................................... 69
V
2.4.4 Final remarks ................................................................................................ 69
3 The meroplankton community of the oceanic Ross Sea during the late austral summer ... 71
3.1 Introduction ...................................................................................................................... 72
3.2 Methods ............................................................................................................................ 73
3.2.1 Sample Collection ........................................................................................ 73
3.2.2 Genetic Analysis ........................................................................................... 77
3.2.3 Statistical analysis ........................................................................................ 80
3.3 Results ............................................................................................................................... 81
3.3.1 Meroplankton diversity ............................................................................... 82
3.3.2 Meroplankton distribution in the Ross Sea ................................................. 84
3.3.3 Multivariate analysis .................................................................................... 87
3.4 Discussion .......................................................................................................................... 94
3.5 Acknowledgements ......................................................................................................... 101
4 Latitudinal gradients in Victoria Land coast meroplankton ................................................ 103
4.1 Introduction .................................................................................................................... 104
4.2 Material and Methods .................................................................................................... 107
4.2.1 Sample collection ....................................................................................... 107
4.2.2 DNA extraction, PCR amplification and sequencing .................................. 108
4.2.3 Larval identification ................................................................................... 109
4.2.4 Statistical analysis ...................................................................................... 109
4.3 Results ............................................................................................................................. 111
4.3.1 Meroplankton diversity ............................................................................. 111
4.3.2 Feeding strategy in the coastal meroplankton .......................................... 120
4.3.3 Meroplankton community from three localities in Victoria Land ............. 120
4.3.4 Latitudinal variation in the Coastal Ross Sea meroplankton ..................... 133
4.4 Discussion ........................................................................................................................ 138
4.4.1 Latitudinal Gradient Project and meroplankton ........................................ 139
4.4.2 Developmental mode and latitude: Thorson’s Rule .................................. 141
4.4.3 Ross Sea meroplankton and the rest of Antarctica ................................... 142
5 Greater sensitivity of larvae to climate change predicts population collapse in the Antarctic
acorn barnacle .................................................................................................................................... 145
5.1 Introduction .................................................................................................................... 146
5.2 Methods .......................................................................................................................... 148
5.2.1 Observation records .................................................................................. 148
5.2.2 Environmental layers ................................................................................. 150
5.2.3 Model Development .................................................................................. 154
5.3 Results ............................................................................................................................. 155
5.3.1 Adult population model ............................................................................. 155
5.3.2 Larval population model ............................................................................ 158
VI