Faunal Analysis: Identification and Quantification

The zooarchaeological recording system used in this study follows a modification of categories and attributes in the York System (Harland et al. 2003) and Bonecode (Meadow 1978). Recording of element portions follows the zonation method by Dobney and Reilly (1988). All identifications are recorded in an excel file format from which pivot tables are derived. Identifications form the core of taxonomic work, and in turn, taxonomy underpins biodiversity studies and species discovery. In this thesis, the taxonomic studies are particularly crucial due to the discovery of novel species and rare fossil evidence for extinct large mammals.

Taxonomic and osteological identifiability can have relative levels of confidence from low to high (Gifford-Gonzalez 2018). In this study, specimens that are osteologically identifiable to element (or portion of element) and that had low levels of taxonomic identifiability (e.g. large mammal, fish or avian) were included as separate categories within tallies of NISP counts. Some typical examples coming from this study are identifications of ‘large mammal diaphysis (shaft)’ or ‘medium mammal vertebra fragment’. The cut-off used here for identifiability is when specimens could not be identified to element portion and nor could be assigned to a traditional vertebrate class of mammal, reptile, bird or fish. Such indeterminate fragments were sorted by size into categories of microvertebrate or macrovertebrate specimens. Within the mammal class, three main categories were used: large,

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intermediate (=medium) and small. The use of these categories is dependent on the nature of the endemic fauna of the archipelago. In most Philippine islands, the largest extant native species would be deer or pig, which are typically smaller (or dwarfed) forms compared to continental forms of the same taxa. Large mammals were further subdivided into two. Those in the size of deer and pig were tallied as ‘large mammal I’, and this is the most commonly observed mammal category in the assemblages. Mammals bigger than deer such as a cattle- sized bovid or tiger were tallied as ‘large mammal II’. Intermediate or medium- sized mammals were those in the size range of canids, macaques and small carnivores such as civet cats and otter. Small mammals typically contain murids and bats. However, due to the phenomenon of island gigantism, giant murid species are known in the oceanic Philippines. These animals can overlap in the size range of small carnivores, such that these giant rodents were classified under medium mammal.

Taxonomic identifications were aided by morphometric analysis. For large and medium mammals, standards for measurement and nomenclature followed von den Driesch (1976) unless otherwise stated. Standards and nomenclature for murid rodents typically followed Musser and Heaney (1992) and Heaney et al. (2011). Based on previous work, the author has a database of biometric measurements of teeth and postcranial material for pigs, deer and several other native mammal taxa of Palawan. Additional data, though, were necessary for pantherines and for the native murid rodents of Luzon Island. Reference measurements were gathered from museum comparative collections of the University of Cambridge Museum of Zoology and Zooarchaeology Laboratory, Oxford University Museum of Natural History, Natural History Museum (London), and the Field Museum of Natural History (Chicago).

The main unit of quantification used in the study is the NISP or number of identified specimens. The NISP is the most basic counting unit used by zooarchaeologists and employing it allows for comparison of faunal counts across sites. Following Grayson (1984: 16), a specimen is a bone or tooth or fragment thereof. A skeletal element is a complete discrete anatomical unit such as bone or tooth (Lyman 2008:5). The NISP includes specimens identified to both element (or portion of element) and taxon. It is generally used as an estimate of relative frequencies of taxa in a faunal assemblage (Reitz and Wing 1999).

Another counting unit that will be encountered in this study is the TNF or total number of fragments, following usage by O’Connor (2008). This unit is equivalent to the NSP, or number of specimens. In this study, the TNF is mainly used for taphonomic analyses, wherein counts of identified specimens (NISP) are combined with counts of indeterminate fragments. The TNF is usually aggregated per context, temporal unit or spatial unit within an assemblage.

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For various reasons, many specimens cannot be identified to either element or taxon and are considered indeterminate. Lyman (1994) notes that fragmentation has the initial effect of increasing NISP values, but as specimens are progressively broken, this leads to a reduction of NISP counts. Subsequently, fragmentation can produce an analytical absence of skeletal parts (Lyman 1994: 282). Nonetheless, what are considered indeterminate specimens retain useful taphonomic information, such as for carcass processing (Outram 2001).

As a raw counting unit, the NISP may appear to behave as a continuous, interval scale variable that has increments of one between each value (Gifford-Gonzalez 2018: 396). However, the NISP actually cannot guarantee specimen independence, since it can count more than one specimen for a fragmented element, and can also count more than one element per individual (Grayson 1984). This is the problem of interdependence, and accordingly, Lyman (1994) cautions that the NISP must be treated as an ordinal scale variable in statistical analyses. Based on this and other statistical criteria, non-parametric statistical tests can be more appropriate for zooarchaeological counting units.

To address the problem of interdependence, the MNI (minimum number of individuals) and MNE (minimum number of elements) are also used. The MNI is derived by identifying the most abundant element for each taxon. The MNE is an estimate of the lowest number of individual elements of a particular taxon. In this respect, the MNI estimate is based on the MNE (Lyman 2008; Marean et al. 2001). In the literature, there are a number of ways by which authors have computed the MNE (Marean et al. 2001). In this study, the MNE is calculated based on counting specimens with portions of an element that do not overlap with other specimens. The overlaps are primarily estimated based on the zonation system used. Factors such as siding, age, fusion and individual size are also taken into account when possible. Both MNI and MNE counts derive from the NISP and require a secondary calculation based on the primary quantitative data. In the case of the MNI, Lyman (2008: 70) notes that it is redundant with the NISP and that the information on taxonomic abundances within the MNI is found in the NISP. The strong linear relationship between these two units means that the MNI values can be closely predicted from NISP values. Both MNI and MNE suffer from the problem of aggregation, i.e. that different ways of aggregating or grouping specimens can produce different values. The MNE lends its main utility to the analysis of skeletal element representation and patterns of fragmentation. It is also used here to compute for another counting unit, the MAU or minimal animal unit. Following Lyman (2008:133), the MAU is derived by dividing MNE values for each anatomical part or portion by the number of times that element occurs in one complete skeleton. From the MAU, another counting unit is derived, the %MAU. Lyman (1994:255) observes that %MAU is equivalent to the value of

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%survivorship that Brain (1969) originally calculated. This measure is computed by dividing all MAU values by the greatest observed MAU value in the assemblage and multiplying the results by 100. The MAU and %MAU are units that are used for the analysis of skeletal part frequencies.

3.4.1 Measures of Taxonomic Diversity and Structure

Another set of quantification units involves measurement of taxonomic diversity. Zooarchaeologists have typically used alpha diversity measures derived from ecology and applied them to archaeological assemblages. Alpha diversity measures diversity at spatially defined units, often at the level of ecological communities (Magurran 1988, 2004). In archaeology, it is commonly applied to an assemblage or series of assemblages from particular geographic regions. Archaeologists deal with a subset of the death assemblage (taphoconoese), yet we are also interested in what this can tell us about the living biotic communities (biocoenose) from which they derived. Measures of taxonomic diversity allow the assessment of assemblage structure and faunal community structure, as well as inform patterns of human subsistence.

One of the most basic measures of diversity is taxonomic richness. In the ecological literature, this is also called numerical species richness or S, defined as the number of species per specified number of individuals (Magurran 2004: 75). In zooarchaeology, it is often referred to as the number of identified taxa or NTAXA (Lyman 2008). NTAXA or S is a nominal scale measure that is also used as an archaeological measure of ecological resources utilized by human groups, wherein the variation can be measured per geographic location and per temporal period.

Another important estimate looks at how abundant each of the identified taxa are within an assemblage. This is taxonomic evenness or equitability (Magurran 1988). I use Simpson’s index (D) and its reciprocal (1/D) as a measure of evenness. Faunas are said to be taxonomically even if each has the same number of individuals (Lyman 2008). The Simpson’s index provides a good estimate of diversity at relatively small sample sizes (Magurran 2004). The reciprocal of Simpson’s index (1/D) is attributed to be less sensitive to effects of taxonomic richness and more sensitive to dominance of the assemblage by one taxon (Lyman 2008). Low values of 1/D indicate that an assemblage is dominated by one taxon and consequently have less evenly distributed frequencies of taxa than those with higher values. Another measure, taxonomic heterogeneity, summarizes relative abundances of taxa and is a function of both

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richness and evenness. The conventional measure used is the Shannon-Weiner index (H). From the Shannon-Weiner index, the Shannon index of evenness (e) can also be derived, following the equation e= H/lnS. The values of this index fall between 0 and 1, and the lower the value of e, the less even the assemblage. Diversity indices (Section 3.4.1) were calculated in PAST version 3.19 (Hammer et al. 2001), following (Harper 1999).