Summary of research aims and objectives of the thesis

Underpinning the use of foraminifera in any applied taxonomic situation is the requirement of a robust taxonomic foundation. However, foraminiferal taxonomy is often challenging and interspecific boundaries are enigmatic. The overarching aim of this thesis is to conduct a detailed re-evaluation of the taxonomic boundaries of a number of key benthic foraminiferal taxa and to address some of the uncertainties faced by researchers in applied taxonomic situations.

Principally, this thesis aims to:

1) Address the utility of morphology in delineating between genetically distinct species of benthic foraminifera

2) Further the understanding of the biogeographic range and occurrence of benthic foraminifera

3) Explore patterns of intraspecific morphological variation within benthic foraminifera 4) Investigate whether classical morphospecies concepts and nomenclature can be

reconciled with new lines of taxonomic evidence

Ultimately, the primary aim of this thesis is to help to constrain species boundaries, enhance morphological characterisation and identification of foraminifera in applied taxonomic situations. The creation of a stable taxonomic framework would enhance the value of foraminifera in palaeoenvironmental and ecological investigations.

In order to address these aims two key taxonomic groups, the genus Ammonia and the Elphidiidae family, were selected for investigation. These were chosen because these taxa are some of the most ubiquitous and abundant species globally (Murray, 1991). Owing in part to their ubiquitous nature and extensive fossil record, species within these two taxonomic groups are important tools for understanding Quaternary climate and sea level cycles (e.g. Haslett, 2002; Murray, 2006). For example, numerous biological and geochemical proxies have been produced using these taxa (Sejrup et al., 2004; Horton and Edwards, 2005; Cage and Austin, 2010).However, these groups also represent two of the most taxonomically challenging and morphologically variable taxa within benthic foraminiferal taxonomy. Whilst recent advancements in molecular systematics have helped to elucidate some of the taxonomic relationships within these two groups (e.g. Hayward et al., 2004; Pillet et al., 2013), there remains a paucity of data on the genetic and morphological variability within these two taxonomic groups. Previous studies have been constrained due to the limited numbers of specimens analysed, or geographically constrained sampling. Given the ecological and palaeoenvironmental significance of these taxa, this necessitates a re-evaluation of morphological limits and a re-examination of their biodiversity and biogeography. The extensive sampling across the NE Atlantic shelf seas employed by this thesis presents an opportunity for a comprehensive assessment of the diversity (morphological and genetic) and biogeographical distributions of Elphidiidae and Ammonia across a range of environmental conditions.

This thesis is composed of seven chapters as follows:

Chapter 1 has presented a general introduction to foraminifera, taxonomy, classification, and a range of other topics that are addressed in this thesis. Chapter 2 introduces and provides an overview of the materials and methods, which were employed throughout this thesis.

Chapter 3 focuses upon the cryptic genus Ammonia which has a turbulent taxonomic history, owing in part to uncertain morphological boundaries and the prevalence of the taxonomic practice of ‘lumping’. This chapter examines the interspecific morphological relationships of seven distinct genotypes of Ammonia to establish if morphology, molecules and biogeography can be reconciled to provide a stable taxonomic framework for the identification of Ammonia in the NE Atlantic. This chapter also presents a case study conducted on Ammonia genotype S1 which assessed if any intraspecific morphological patterns could be identified across a large geographic spatial scale.

Chapter 4 examines the temporal dynamics of benthic foraminiferal assemblages from the NW Scottish shelf seas. The focus of this chapter is to assess whether any ecological/ seasonal partitioning of Ammonia species occurs. This chapter thereby provided an opportunity to assess the applicability of the taxonomic framework of Ammonia developed in Chapter 3 in an applied taxonomic situation. Additionally, the time-series study recorded changes in foraminiferal abundance and composition over the course of a year, thereby providing insights into the importance of having an understanding of the temporal variability when estimating biodiversity. Chapter 5 undertakes the first comprehensive effort to quantify the interspecific morphological boundaries within the Elphidiidae family in light of the new genetic evidence. This chapter comprises two components. The first component examines the interspecific morphological relationships and the biogeographic distributions of 17 genetically distinct genotypes identified within the Elphidiidaegroup by Darling et al. (in prep). The second component of this chapter employs two case studies to examine intraspecific morphological variability across a large geographic spatial scale.

In response to the taxonomic uncertainty encountered while trying to synthesise new lines of taxonomic evidence with classical taxonomy, Chapter 6 examines how traditional taxonomic species concepts and nomenclature can be reconciled with quantitative morphological boundaries and genetic sequences. This chapter focuses on the case study of Elphidium williamsoni (Haynes, 1972) to assess how these lines of taxonomic evidence can be reconciled

in practice. This chapter concludes by establishing a framework which aims to provide a new protocol to try to bridge the gap between classical taxonomy and new lines of taxonomic evidence.

Finally, Chapter 7 provides a synthesis of the thesis and conclusions. This chapter focuses on presenting the general conclusions and providing an outlook for future work.

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