Taxonomy and classification: Implications for avian identification

There are over one million known species globally, of which approximately just over 10,000 are birds (Redding et al. 2015). Knowing this, a system of classification and identification is essential for the purpose of distinguishing phylogenetic lineages and morphological relationships comparatively between organisms. Without such a system, identification of an organism would be dependent on the observer’s description of its features, whilst understanding the organism’s relationship to its surrounding community would be increasingly difficult when trying to differentiate between organisms with similar morphology. The taxonomic system provides a standardised phylogenetic point of reference when establishing the identity of an organism. Currently, the modern taxonomic system is derived from the “Systema Naturae” developed by Carl Linnaeus in the 1700’s (Harris 2005). This system operates on the basis that organism classification occurs across levels whereby organisms are grouped not just to species level, but also in accordance to their relation to other organisms across all levels of life. The system approaches classification based on phylogenetic similarities and external morphology within a population. Morphologic traits which demonstrate relationships between individual taxa are grouped into a hierarchy from species to domain (Harris 2005). Each identified species is then formally described in a scientific journal and given a Latin binominal, with specimen types available for examination by peers (ICZN 2000).

Though Linnaeus’s methods form the foundations of taxonomic methods used today, fundamentally the basis of its creation is flawed. Linnaeus lacked any understanding of evolution and never acknowledged the findings of Darwin (Ereshfsky 2001). Thus many of his taxonomic classifications could not distinguish convergent evolutionary traits from species specific traits. The simple principle of grouping species based on external morphology has led to unnatural taxa classification (Jensen 2009) which in many cases is merely separate species that share a similar convergent, morphological trait (Dornburg er al. 2015). Consequently, due to the identified failings of Linnaeus’s hierarchy, a number of alternative classification methods were developed.

In an attempt to resolve the issue of misidentified species which share a phylogenetic trait, Willi Henning developed Cladistics classification in 1979. The method operates on the principles of classification based on common ancestry of an organism (Schmitt 2003). This method allows for clear, visual indication in phylogenetic divergence of an evolutionary trait as demonstrated by Noriega et al. (2011) who successfully reclassified Thegornis micrastur (a small falcon like bird) based on their common ancestral traits of the falconid family. However cladistic identification is flawed when paleoenvironments are considered for this species as historic morphology links this falcon to a temporal forest environment yet currently it is predominant in the Antarctic. Though Cladistics utilises phylogeny to establish an evolutionary tree relating traits between species, it fails to consider environmental factors limiting a species development by only focusing on one morphologic trait.

Numerical taxonomy was established by Sneath and Sokal in 1973 as statistical ecology’s popularity grew and computer technology became more advanced. This method hoped to eliminate observer bias and taxonomic error by implementing a statistical and systematic approach to identification. A number of measurements would be taken from an organism and multivariate analysis performed to group individuals on the basis of archived measurements of matching organisms (Sneath & Sokal 1973). This method allows for any scientist, regardless of taxonomic training, to adequately identify

an organism. Though, as highlighted by Blackwelder (1967) knowing what character measurements to take is dependent on experience of taxonomy and thus measurements cannot be performed by statisticians as their knowledge of an organism’s environmental range and potential environmental regulators on its development, is limited. As technology continued to evolve, Sibley and Ahlquist in 1986, developed the first method of identification to use DNA analysis as an indicator of species. DNA-DNA hybridisation determined species classification based on the melting points of hybrid DNA comprised from two separate dissociated and realigned base pair strands from two separate organisms (Gibson 1987). However, this method has not addressed melting point variation between genomes and possible effects of “junk DNA”, consequently modern techniques have since reversed some of the taxonomic classifications provided by this method. As an example Houde (1986) assessed various lineages of ratite birds in conjunction with analysis of fossils records and determined that ancestors of ostriches should be grouped with North American and European birds. This has since been proven to incorrect.

To date, DNA sequencing has become the dominant method of choice for identification. DNA barcoding or Mitochondrial gene sequencing, utilises a 648 base pair fragment located in the mitochondrial cytochrome c oxidase subunit I gene as a genetic marker in all organisms (Herbert et al. 2003). Mitochondrial DNA is abundant throughout many cells thus can easily be extracted, it is also inherited via the maternal gamete so genetic lineage is traceable throughout generations (Lefevre 2008). Identification is performed on an organism via PCR analysis of their mtDNA to establish the coding sequence within their mitochondrial cytochrome c oxidase subunit I (COI) sample. The sequence in which their base pairs occur is species specific thus is used to identify the organism via comparison to archives of known species sequences in public databases. Species separation is dependant of how far apart the evolutionary divergence occurred between the two species being compared and whether the sampled genes are paralogous or orthologous. This is due to levels of functional and non-functional sequencing changing in accordance to the sequences responsible for trait expression unique to the species (Frazer et al. 2003). Molecular clocks have demonstrated that modern organisms contain complex sequence variations of more primitive ancestors thus depending on the point of mutation or creation of a paralogous/orthologous gene, the similarities between sequenced DNA in two separate species will become increasingly less pronounced with increased distance and time between shared common ancestors (Wiemer & Fiedler 2007). Goncalves et al (2015) successfully utilised DNA barcoding, in conjunction with the GenBank database, in the identification of Graydidascalus brachyurus eggs confiscated from the illegal pet trade. Goncalves demonstrated the importance of this method in the identification of species when morphological traits are unclear or unavailable, as well as highlighting its use in identifying other cryptic species (Burns et al. 2007).

Techniques have also been developed to better understand the origins of phylogenetic traits. One such technique utilises microsatellites which consists of a repetitive base pair sequence known as a short tandem repeat (STR). STR markers can be used to produce higher resolution of an organism’s allelic diversity and phylogeny by performing PCR analysis with primers by flanking the repetitive sequence of the microsatellites. The number of times a sequence was repeated within a microsatellite locus, determines the size of the amplicons produced by the PCR, which in turn is measured and then assessed against recorded co-dominant alleles (Guichoux et al. 2011). Allentoft et al (2009) were successfully able use microsatellite 454 sequencing to identify a new set of genetic markers for an extinct species of moa. The study identified that microsatellite loci not only

demonstrated allelic diversity between species, it could be used to trace inherited lineages of an organism’s morphology.

Due to the popularity of DNA (mtDNA) sequencing in identification and the belief of some that DNA sequencing will replace the morphological based taxonomy (Herbert et al. 2003), the appeal and continued practice of taxonomy as a skill; has reduced significantly in number. However, the use of molecular methods such DNA barcoding as a replacement for modern taxonomy isn’t necessarily the step forward in identification and classification. Though DNA sequencing has its advantages, for example when assessing closely related species, sequence divergence if often significantly lower and thus differentiation of species can be does so more accurately (Herbert et al. 2004); DNA sequencing does have its weaknesses. The understanding that interspecific variation in the COI gene exceeds the variation seen in intraspecific (the barcode gap) is not always true. Wiemers & Fiedler (2007) found that the utilisation of only the COI gene is insufficient in sampling taxa due to increased sequence variation the longer a species has been established separately from its shared ancestor. In addition, our understanding of specific regions of DNA is still insufficient in the assessment of its expression and impacts on an organisms overall genome (Moritz & Cicero 2004).

Consequently, in order to yield an accurate and detailed understanding of the levels of biodiversity currently seen across the globe due to rapidly declining species populations and biodiversity as anthropogenic impacts become more widespread; the scientific world needs a combination of both phylogenetic/morphology based taxonomy and molecular methods. A so called “integrative taxonomy” is required to further advance the identification and classification process (Will et al. 2005)(Burns et al. 2007)(Miller 2007)

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