Molecular techniques provide new taxonomic perspectives

The introduction of molecular systematics has helped to clarify many of the taxonomic uncertainties surrounding Ammonia. The re-assessment of taxonomic relationships utilising molecular evidence based on LSU rRNA (large subunit of ribosomal DNA) and SSU rRNA (small subunit of ribosomal DNA) sequences has revealed previously unidentified diversity within

Ammonia across the globe (Holzmann, 1996; Holzmann and Pawlowski, 1997; Holzmann et al., 1998; Holzmann, 2000; Holzmann and Pawlowski, 2000; Langer and Leppig, 2000; Ertran et al.,2004; Hayward et al., 2004; Toyofuku et al., 2005; Pawlowski and Holzmann, 2009; Schweizer et al., 2011). On the basis of this new molecular evidence, it is estimated that there are likely to be as many as 40 genetically distinct species of Ammonia globally (Foissner and Pawlowski 2009). This highlights that the recognition of broad species concepts and many ecophenotypes within the literature lacks a genetic basis (Hayward et al., 2004).

Phylogenetics has also paved the way for the re-evaluation of classical morphospecies concepts and their associated biogeographic distributions; these interspecific boundaries can be tested through the integration of multiple lines of taxonomic evidence. To date the most comprehensive integrated study of Ammonia was conducted by Hayward et al. (2004). This taxonomic investigation revealed that 13 genetically distinct species of Ammonia were identified globally (Figure 3.1). The subsequent morphological analysis of these newly identified genotypes revealed that after extended morphological analysis subtle morphological test characters could be used to discriminate between the genotypes.

Figure 3.1 Phylogenetic tree of the 13 Ammonia genotypes (T1-T13) identified by the LSU rRNA collected worldwide by Hayward et al. (2004). The phylogeny is based on analysis of 267 partial LSU rRNA sequences using the Neighbour Joining method; the numbers shown on each of the branches illustrate the bootstrap percentage values based on 500 resamplings. Reproduced with the permission of the rights holder Elsevier from Hayward et al. (2004).

Figure 3.2 Global biogeographic distribution of Ammonia genotypes previously identified in Hayward et al. (2004). Reproduced with the permission of the rights holder Elsevier, taken from Hayward et al. (2004).

The analysis of the biogeographic distribution of Ammonia genotypes identified by Hayward et al. (2004) reveals that the majority of species exhibit a narrow biogeographic distribution (Figure 3.2). Only one Ammonia genotype (T1) has been identified as exhibiting a cosmopolitan distribution. Moreover, Hayward et al. (2004) revealed that up to two genetically distinct species of Ammonia can co-exist within a single site locality. This highlights that previous taxonomic investigations which delineate between Ammonia using classical morphospecies concepts may have overestimated the biogeographic distributions and/or have underestimated biodiversity and ecological preferences of Ammonia.

The integrated taxonomic investigation conducted by Hayward et al. (2004) has laid down the foundations for future taxonomic assignments and it provides a global overview of the genetic and morphological diversity found within the genus Ammonia. Nevertheless, whilst the study conducted by Hayward et al. (2004) represents an important step in the taxonomic re-evaluation of Ammonia, their study was not exhaustive. There are still some significant gaps in the taxonomic sampling regime, particularly within the NE Atlantic. Additionally, only a limited number of specimens of Ammonia have been jointly morphologically and genetically analysed at each site by Hayward et al. (2004). For example, although 178 specimens were morphometrically analysed in Hayward et al. (2004), only 79 of these specimens had an allied genetic sequence. Therefore it is unlikely that Hayward et al. (2004) have captured the entire range of interspecific and intraspecific morphological and genetic diversity within the genus

further taxonomic investigations are needed to assess the validity of the current genetic and morphological species boundaries identified in Hayward et al. (2004). Moreover, despite the significant taxonomic effort by Hayward et al. (2004), the taxonomic status of Ammonia within the literature remains controversial, as the classical morphological conservative framework with broad species concepts and open nomenclature continues to prevail. In part, this could be attributed to the uncertain nomenclatural placement of the newly delineated genotypes, and the current dearth of knowledge of the ecological preferences associated with each genotype. A concerted effort should therefore be given to improving our understanding of foraminiferal ecology, biology, morphological variability and biogeographic distribution of each of the extant genotypes of Ammonia; so that there is an improved understanding of the taxonomic ‘value’ of delineating between these genotypes in applied taxonomic situations.

In order to address some of these uncertainties and to clarify the interspecific boundaries, this chapter begins by examining the efficacy of morphology as a tool for discriminating between the seven genetically distinct species of Ammonia present in the NE Atlantic (these seven species were identified in Bird et al., in prep.). The detailed sampling regime employed within this study has provided an opportunity to develop a more comprehensive understanding of the biodiversity and biogeography of Ammonia within the NE Atlantic shelf seas. Additionally, it has enabled the collection of specimens from biogeographic regions not previously captured by Hayward et al. (2004). Moreover, the morphometric analysis of over 156 genetically sequenced specimens presented in this chapter provides an opportunity to analyse nearly double the number of genetically sequenced Ammonia specimens than has been previously analysed by Hayward et al. (2004). These new integrated lines of taxonomic evidence presented in this chapter are placed into a broader context, through examining the congruence of the interspecific morphological diversity and biogeographical distributions found in the NE Atlantic against the species boundaries identified in previous taxonomic investigations (e.g. Hayward et al., 2004; Schweizer et al., 2011). Overall, the integration of new lines of taxonomic evidence of

Ammonia provided in this chapter presents an opportunity to elucidate taxonomic relationships and to develop a stable taxonomic platform from which extant and fossil specimens can be robustly and consistently identified.

Aims

1. To test whether the seven genetically distinct genotypes of Ammonia identified in the North East Atlantic by Bird et al. (in prep.) can be robustly distinguished based upon their morphological characteristics.

2. To characterise in detail the interspecific and intraspecific morphological species boundaries of the seven genotypes and to identify any key diagnostic morphological features.

3. To evaluate the accuracy and utility of different numerical taxonomic approaches in accurately delineating specimens into their genetic groups.