There is currently no clear agreement on how to relate geographically linked variation in morphology and genetics to the taxonomy and systematics of the widely distributed Wildcat (Felis silvestris) (Kitchener and Rees 2009). The latest phylogeographical analyses (Driscoll et al. 2007, 2009; Macdonald et al. 2010) suggest that the Wildcat consists of five subspecific groups and three traditional subspecies (Nowell and Jackson 1996, Stuart et al. 2013): including the recent recognition of the Southern African Wildcat (F. s. cafra Desmarest, 1822). Based on genetic, morphological and archaeological evidence, the familiar housecat was believed to have been domesticated from the Near Eastern Wildcat (F. s. lybica), probably 9,000-“10,000 years ago in the Fertile Crescent region (Vigne et al. 2004, Driscoll et al. 2007), coinciding with the first agricultural settlements (Driscoll et al. 2007, Macdonald et al. 2010). Although the domestic cat derived relatively recently from the Wildcat, in terms of biological processes and phylogeny, it can be taxonomically classified either as a subspecies (F. s. catus) of F. silvestris or as a separate species (F. catus) (Macdonald et al. 2010). Recent evidence supports the classification of domestic cats as genetically distinct from Wildcats (Driscoll et al. 2007). For the purposes of this assessment, although we recognise the potential validity of the Southern African Wildcat (F. s. cafra), we defer to the species level until further research can accurately delineate subspecific geographical boundaries.

The recognition of two externally distinct morphological forms of Finless Porpoises as separate biological species, the Indo-Pacific Finless Porpoise (Neophocaena phocaenoides) and the Narrow-ridged Finless Porpoise (N. asiaeorientalis), was accepted only recently when it was demonstrated that the two forms are reproductively isolated (and likely have been separated since the last glacial maximum) even though they occur sympatrically in a fairly large area of eastern Asia (Wang et al. 2008, Jefferson and Wang 2011). [Much of the literature published before ca 2010 refers to all Finless Porpoises (both species) as N. phocaenoides.] Differences in the external morphology of the dorsal aspect of the two species are distinguishable even amongst free-ranging animals (as opposed to only specimens in-hand) (Wang et al. 2010). Intermediates between the two main forms have never been reported even though several hundreds to thousands of carcasses have been examined. The two species also clearly differ in craniometry (Amano et al. 1992, Jefferson 2002). There is evidence to suggest subpopulation structure within Indo-Pacific Finless Porpoises in some areas (Jefferson 2002, Yang et al. 2008, Chen et al. 2010, Xu et al. 2010, Li et al. 2011, Ju et al. 2012, L. Li et al. 2013, S. Li et al. 2013, Jia et al. 2014, Lin et al. 2014) and this may apply throughout much of the species' distribution.

Although it was only recently described (Wada et al. 2003), the separate species identity of Omura's Whale, Balaenoptera omurai, is now well established phylogenetically (Sasaki et al. 2006). It was formerly regarded as a pygmy form of Bryde's Whale (B. brydei/edeni), but it is not closely related to that group, lying outside the clade formed by the Sei Whale (B. borealis) and two forms of Bryde's Whales). The morphology of Omura's Whale is quite distinct from those of Bryde's Whales and other known baleen whales, but its colouration resembles that of the Fin Whale (B. physalus) while lacking lateral rostral ridges (Wada et al. 2003). To date (December 2017), the only genetically confirmed observations of living Omura's Whales are of 18 biopsied individuals in an apparently resident population off northwestern Madagascar (Cerchio et al. 2015). Specimens collected in 1976 in the Solomon Sea (Ohsumi 1978) and in 1978 in the eastern Indian Ocean (Ohsumi 1980) were originally taken under a scientific permit for Bryde's Whales and were subsequently genetically identified as Omura's Whales (Wada et al. 2003). LeDuc and Dizon (2002) genetically analysed specimens of small Bryde's Whales from the Bohol Sea, Philippines, and found that they segregated phylogenetically outside the Sei/Bryde's Whale clade and basal to B. edeni/B. borealis. From a comparison of the published phylogenies, Sasaki et al. (2006) concluded that these specimens corresponded to Omura's Whale. Yamada et al. (2008) identified 24 skulls from a whaling operation in the Philippines as Omura's Whales.

Formerly considered a subspecies of Acomys cahirinus. See Musser and Carleton (2005) for details concerning the relationship between Acomys dimidiatus and A. cahirinus.

Although Physeter catodon is still occasionally used in the literature, P. macrocephalus is recommended (Rice 1989). Both names are listed on the same page of the original description by Linnaeus (1758), and priority is unclear. However, P. macrocephalus is preferable because it is used much more frequently, and this will support nomenclatural stability.

The Indo-Pacific Bottlenose Dolphin (Tursiops aduncus) has been recognized as a different species from the more widely distributed Common Bottlenose Dolphin (Tursiops truncatus) since the late 1990's (Rice, 1998). Indo-Pacific Bottlenose Dolphins are distinct from Common Bottlenose Dolphins based on concordance among genetic, osteology, coloration and external morphology data (Wang et al. 1999, 2000a,b). No Indo-Pacific Bottlenose Dolphin subspecies are currently recognised by the Society for Marine Mammalogy's Committee on Taxonomy (2018). However, a recent re-assessment of Tursiops taxonomy worldwide (IWC 2019) and extensive genetic studies (Moura et al. 2013, Amaral et al. 2016, Gray et al. 2018) identified 4 or 5 different lineages (Africa, Pakistan, Bay of Bengal, China and Australia), including the recently described ""T. australis"" (Charlton-Robb et al., 2011) that may eventually be recognized as a subspecies. There is considerable population structure throughout the range of the species and multiple studies of morphology (Hale et al., 2000, Kemper 2004, Charlton-Robb et al., 2011) and genetics (Natoli et al. 2004, Särnblad et al. 2011, Charlton-Robb et al. 2011, Amaral et al. 2016) indicate that the taxonomic status for a number of populations in different regions should be re-evaluated.

This species is occasionally mistaken with Meller's Mongoose (Rhynchogale melleri), which also sometimes has a white tail. However, the White-tailed Mongoose is usually larger, and its body appears black, rather than brown (Skinner and Chimimba 2005). Further confusion in identification is sometimes created by the fact that Ichneumia albicauda individuals with black tails have been recorded in several areas of the African distribution range (A. Page pers. comm. 2014, C. Wright pers. comm. 2014). Only one subspecies has been listed, from southern Africa, I. a. grandis (Thomas 1890), but the nominate form has a wide distribution across much of the rest of Africa (Meester et al. 1986).

The entire taxonomy of Lepus capensis throughout its range is unclear. Taxonomic review of the species is urgently needed; otherwise, it is possible that some forms may go extinct before they are formally identified. Hoffmann and Smith (2005) restricted L. capensis to the South African distribution, citing no evidence of gene flow between the southern and northern ranges. A list of synonyms is provided based on four geographic locations (South Africa, East Africa, Arabia and Near East, and northwest Africa), which are informal subdivisions of L. capensis sensu lato. The authors suggested that these four groups might represent distinct species. In the Near East and Arabia L. c. arabicus; in South Africa L. c. capensis; L. c. aquilo, L. c. carpi, L. c. granti; East Africa L. c. aegyptius, L. c. hawkeri, L. c. isabellinus, L. c. sinaiticus; and L. c. atlanticus, L. c. schulmbergeri, L. c. whitakeri in northwest Africa (Hoffmann and Smith 2005, Schai-Braun and Hackländer 2018). According to Harrison and Bates (1991) there are eight subspecies in Arabia: L. c. syriacus (Syria, Lebanon, northern Israel); L. c. sinaiticus (southern Israel, Sinai); L. c. connori (east of the Euphrates in Iraq); L. c. arabicus (western Iraq, Kuwait, Saudi Arabia, Yemen); L. c. cheesmani (Saudi Arabia, Qatar, UAE, Yemen, Oman); L. c. omanensis (UAE, Oman); L. c. atallahi (Bahrain, Qatar?); L. c. jefferyi (Masirah Island, Oman). The taxonomic status of L. c. jefferyi needs clarification, as it may represent a good species. Hares present in Qatar also require taxonomic investigation. The taxonomic position of the Sardinian Hare is unresolved. Hoffmann and Smith (2005) include the Sardinian Hare as one of the unassigned synonyms of L. mediterraneus Wagner, 1841 or typicus Hilzheimer, 1906, in L. granatensis. Analysis of the mtCR-1 sequence indicated that Sardinian Hares form a monophyletic clade with North African Hares (Scandura et al. 2007). A genetic and morphometric analysis supports the hypothesis that the Sardinian Hare was introduced from North Africa (Canu et al. 2012). A phylogenetic analysis of mtCR-1 sequences from Tunisian and Egyptian Hares characterized them as monophyletic and separate from L. capensis (Ben Slimen et al. 2006). However, a study of the nuclear gene pool of L. capensis, L. europaeus and the North African Hare indicated that the North African Hare as well as L. europaeus belong to L. capensis (Ben Slimen et al. 2005), supporting Petter's (1959, 1961) hypothesis of the inclusion of L. europaeus in capensis. Ben Slimen et al. (2008a) suggest that in a case such as the genus Lepus, where evolution is ""rapid and to some extent reticulate"", species designation based solely on mtDNA is misleading without examination of the nuclear gene pool. Ben Slimen et al. (2008a) has shown that genetic differentiation between L. capensis and L. europaeus could be attributed to geographic distance rather than divergence. They speculate that gene flow may be occurring in the Near East where distributions meet resulting in the potential for intergraded populations. However, Ben Slimen et al. (2008b) propose that ""a combined phylogenetic, phylogeographic, and population genetic approach, based on various nuclear and mitochondrial markers and including other biological characters, such as phenotypic and morphometric data,"" is needed for conclusive evidence of a single species complex. A recent study looking at a partial transferrin nuclear gene and phylogenetic relationship of hares in Tunisia showed shared ancestral polymorphism between North African and Chinese hares (Awadi et al. 2016). It also concluded that the Tunisian Hare is well differentiated from hares considered belonging to brown hares L. europaeus from central Europe (Awadi et al. 2016). In light of this continuing uncertainty regarding the taxonomic status of the Sardinian and North African Hares, both will remain included in capensis and L. europaeus retains its taxonomic status as a distinct species. Many treatments indicate that the range of L. capensis extends into China, Mongolia and Russia; however, recognition of L. tibetanus and L. tolai as distinct species removes consideration of L. capensis as occurring in this region (Hoffmann and Smith 2005).