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Genetic / taxonomic issues for the Cat Specialist Group

United Arab Emirates BorneanTiger Offline
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#1
( This post was last modified: 09-11-2019, 03:17 PM by BorneanTiger )

Different definitions of the term 'subspecies' exist, but the one that I will use here, derived from Study.com, is "a population of a species that is genetically and geographically different to another population of the same subspecies."

In 2017, the Cat Classification Taskforce of the Cat Specialist Group, which can be said to include a "who's who" of experts on of cats, such as Shu-Jin Luo and Urs Breitenmoser, published a revision of subspecies of felids: https://repository.si.edu/bitstream/hand...sAllowed=y

There are 2 main issues with the revision of 2017 that I can see:

1) The CSG admitted uncertainties regarding particular subspecies, such as for the bobcat and cheetah

2) Certain revisions, such a for the tiger and leopard, are controversial because they are not supported by all genetic assessments.
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United Arab Emirates BorneanTiger Offline
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#2
( This post was last modified: 09-11-2019, 03:58 PM by BorneanTiger )

Lion (Panthera leo)

Initially, several subspecies of African lions were described, including the Barbary lion (Panthera leo leo) of the Maghreb (Northwest Africa), the Senegal lion (Panthera leo senegalensis) of West Africa, and the Cape (Panthera leo melanochaita) and Kruger lions (Panthera leo krugeri) of South Africa, with the Asiatic lion (formerly Panthera leo persica) considered to be a separate subspecies. At some point, it was considered that all African lions belong to the same subspecies, Panthera leo leo, with the Asiatic lion being a separate subspecies. Eventually, genetic tests, like those of Barnett et al. and Antunes et al. in the 2000's, showed that genetically, certain African lions, such as the Barbary lion, were more closely related to the Asiatic lion than to other African lions, such as the Kruger lion, thus making the traditional recognition of the African and Asian lions as separate subspecies questionable.

In 2017, the CSG recognised lions in Asia and Northern, Western and Central Africa as belonging to the subspecies Panthera leo leo, and those in Eastern and Southern Africa as belonging to the subspecies Panthera leo melanochaita, but there is a problem, the 2 subspecies appear to overlap in the Northeast African country of Ethiopia, judging by the work of Bertola et al., which would mean that Ethiopian lions (formerly Panthera leo roosevelti or Felis leo roosevelti, in honor of the US President Theodore Roosevelt (https://archive.org/stream/smithsonianmi...3/mode/2up), but also treated as belonging to the Masai subspecies by Haas et al. and Wozencraft) are neither purely Panthera leo leo nor Panthera leo melanochaita, but a mixture (Panthera leo leo × Panthera leo melanochaita or Panthera leo leo + Panthera leo melanochaita), and the Cat Specialist Group put a question mark over the Horn of Africa in Page 72: 
   
   

As mentioned here, it's not necessarily the case that geneticists like Bertola found mixed up lions (Panthera leo leo × Panthera leo melanochaita), it's to do with where they found Northern (P. l. leo) and Southern lions (P. l. melanochaita) in Ethiopia or Northeast Africa, which suggests that their ranges overlap there:



*This image is copyright of its original author


*This image is copyright of its original author


*This image is copyright of its original author


An Ethiopian lion (formerly Panthera leo abyssinica or Panthera leo roosevelti) discovered in Bale Mountains National Park, Northeast Africa, image by The National Geographic

*This image is copyright of its original author


Additionally, not all Central African lions, particularly Northeast Congolese lions (formerly P. l. azandica) are of the Northern subspecies (P. l. leo), as indicated above. A number of them are of the Northern subspecies, but others are of the Southern subspecies (P. l. melanochaita).

Northeast Congolese lion (formerly Panthera leo azandica) at Virunga National Park, Central Africa, photo by Adrian Treves

*This image is copyright of its original author
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United Arab Emirates BorneanTiger Offline
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#3
( This post was last modified: 10-12-2019, 11:21 PM by BorneanTiger )

Tiger (Panthera tigris)
 
People would be familiar with the following 9 subspecies or types:
1) The Bengal tiger (Panthera tigris tigris) in South Asia
2) The Caspian tiger (Panthera tigris virgata) in Afghanistan (South Asia), and Central and Southwestern Asia, and possibly Eastern Europe, which is genetically similar to:
3) The Amur tiger (Panthera tigris altaica) in Northeast Asia
4) The Javan tiger (Panthera tigris sondaica) in the Sunda Islands
5) The South Chinese tiger (Panthera tigris amoyensis) in East Asia
6) The Balinese tiger (Panthera tigris balica) in the Sunda Islands
7) The Sumatran tiger (Panthera tigris sumatræ) in the Sunda Islands
8) The (Northern) Indochinese tiger (Panthera tigris corbetti) in Southeast Asia
9) The Malayan or Southern Indochinese tiger (Panthera tigris jacksoni synonym Panthera tigris malayensis) in Southeast Asia
 
The originally described 8 subspecies by Nowell and Jackson, pages 148–149:
   
 
A Malayan tiger, credit: Tigers-World 

*This image is copyright of its original author

 
A map of the distribution of tigers by Vratislav Mazák in 1981:
   
 
Now here is the history between the taxonomic disputes regarding the tiger that I know of:
 
In 2006, Mazák and Groves published a study on the Sumatran, Javan, Balinese and Indochinese tigers of Southeast Asia. They said "The taxonomic affinity of Southeast Asian tigers is re-investigated. Specimens of four traditionally recognized subspecies are examined using various craniological methods, including multivariate craniometric and phenetic analysis. Sumatran tigers differ absolutely (100%) from the geographically neighbouring mainland form P.t.corbetti; the Javanese tiger is also 100% distinguishable from the Sumatran. They are therefore regarded as two distinct species (P.sumatraeP.sondaica) under the Phylogenetic Species Concept (PSC). The Bali tiger is classified as a subspecies of the Javanese tiger, Panthera sondaica balica."
 
In 2015, Wilting et al. published a study on many sets of data on traits of tigers (morphological (craniodental and pelage), ecological, molecular) that were used to differentiate them into subspecies. They claimed "Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units," with the northern 'unit' of the mainland Asian subspecies being composed of the Amur and Caspian tigers (hence the name "Northern tigers" for them, collectively), and the southern 'unit' being the Bengal, Northern Indochinese, Malayan and South Chinese tigers. Kai Kupferschmidt then published an article in the same year, under the heading "Controversial study claims there are only two types of tiger", in which he mentioned differences in opinion about the study of Wilting et al. For instance, Urs Breitenmoser, a zoologist at the University of Bern, who was not involved in the study, and is a co-chair of the Cat Specialist Group of the International Union for Conservation of Nature (the organization that draws up the red list of threatened species) said that the paper would "surely cause a stir," but that he found "the work quite convincing and in keeping with other findings in recent years,” like a paper that suggested the Caspian and Siberian tigers were the same subspecies, and that the Cat Specialist Group would look at this proposal as well. However, Shu-Jin Luo, a geneticist at Peking University in Beijing who works on endangered species (and whom I will refer to later), was skeptical of the study, arguing that the 9 traditionally recognized subspecies could be distinguished genetically, and that that should be enough, saying "Genetic data is much more reliable and objective than morphology."
 
In 2017, the Cat Classification Taskforce of the Cat Specialist Group, in line with the work of Wilting et al., and what Breitenmoser said, decided to recognize only 2 subspecies of tigers (like with the lion): the Continental or Mainland Asian tiger (Panthera tigris tigris; comprising the Bengal, North Indochinese, Malayan, South Chinese, Amur and Caspian tigers), and the Sunda Island tiger (Panthera tigris sondaica; comprising the Javan, Sumatran and Balinese tigers), while recognizing that the Malayan tiger had a unique mtDNA haplotype, likely because it is close to the ancestral lineage. The border between the ranges of the Continental and Sunda tigers is the Strait of Malacca between the Malayan Peninsula (where the Malayan tiger is present) and the Sunda Island of Sumatra.
   
   
 
The Strait of Malacca between the Malayan Peninsula and Sumatra by Shizhao:

*This image is copyright of its original author

 
However, in 2018, CSG members Driscoll and Luo rebelled against the classification of tigers into only 2 subspecies, by contributing to a study which used the whole-genome sequencing approach for analysis, which was based on 32 tiger specimens. From this, they argued that tigers were divided into 6 monophyletic clades, and hence 6 living subspecies: the Bengal (P. t. tigris), North Indochinese (P. t. corbetti), Malayan (P. t. jacksoni), South Chinese (P. t. amoyensis), Amur (P. t. altaica) and Sumatran tigers (P. t. sumatræ).
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United Arab Emirates BorneanTiger Offline
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#4
( This post was last modified: 09-13-2019, 12:53 PM by BorneanTiger )

Leopard (Panthera pardus)

The CSGhad grouped the Zanzibari (formerly Panthera pardus adersi, possibly extant) and mainland African leopards (including the Barbary leopard (formerly Panthera pardus panthera) of the Maghreb (Northwest Africa)) into one subspecies (Panthera pardus pardus), and said that the Sinai (Panthera pardus jarvisi) and Arabian leopards (Panthera pardus nimr) could be the same subspecies as African leopards, and all other leopards in Asia and European Russia (which has Caucasian leopards (Panthera pardus ciscaucasia / tulliana)), including the Sri Lankan leopard (Panthera parsus kotiya), could be one subspecies (Panthera pardus fusca), with the exception of the Javan leopard (Panthera pardus melas):

"Luo et al. (2014) published a further molecular study which included more samples from Indochina and the Malay Peninsula. The phylogeographical patterns are not clear for all putative subspecies. For example, P. p. kotiya is close to East Asian leopards based on mtDNA, but groups with P. p. fusca based on microsatellites (Uphyrkina et al. 2001). P. p. saxicolor also seems to group differently depending on the analysis used (Uphyrkina et al. 2001, Luo et al. 2014). Luo et al. 2014 show that P. p. fusca is diphyletic based on mtDNA, which was not found in previous studies. Khorozyan et al. (2006) analysed the skull morphometrics of southwest Asian leopards, and concluded that saxicolor and ciscaucasica were consubspecific, but retained tulliana and millardi as distinct. However, sample sizes were very small for some of these putative subspecies. Rozhnov et al. (2011) examined sequences of mtDNA (NADH5) and 11 microsatellites from southwest Asian leopards. They concluded that all were consubspecific from Afghanistan through Iran to the Caucasus, but no western Turkish specimens (tulliana) were analysed. Here japonensis is included in orientalis; there is no clear biogeographical barrier between these two forms which appear to form a cline in northeastern Asia. As the molecular differences between continental Asian leopards are very small compared to differences in Javan leopards (P. p. melas; Wilting et al. 2016), there could be a case for including all Asian subspecies, excluding melas, in a single Asian subspecies. These conflicting results from different studies suggest that more comprehensive sampling is required from throughout the range, taking advantage of museum specimens of known provenance. Until such a study is carried out, we propose the following conservative arrangement of subspecies:

Panthera pardus pardus (Linnaeus, 1758). Distribution: Africa. Comment: Although there are two principal mtDNA clades in Africa, they both occur in southern Africa and appear to be partly sympatric. Thus it would appear that no subspecies can be distinguished within Africa. However, more comprehensive sampling is needed.

Panthera pardus tulliana (Valenciennes, 1856; 1039), including ciscaucasica, saxicolor. Type locality: Ninfi, village situé à huit lieues est de Smyrne [near Izmir, Turkey]. Holotype: MNHN-ZM-MO-1849-20 mounted skin (skull inside). Distribution: Turkey, Caucasus, Turkmenistan, Uzbekistan, Iran, Iraq, Afghanistan and Pakistan. Comment: This is the earliest name for leopards from South West Asia, and hence includes saxicolor and ciscaucasica. If tulliana proves to be distinct from other southwest Asian leopards, ciscaucasica is the earliest available name.

Panthera pardus fusca (Meyer, 1794). Distribution: Indian subcontinent, Burma and China.

Panthera pardus kotiya (Deraniyagala, 1949). Distribution: Sri Lanka.

Panthera pardus delacouri (Pocock, 1930b). Distribution: SE Asia and probably southern China

Panthera pardus orientalis (Schlegel, 1857), including japonensis. Distribution: Eastern Asia from Russian Far East to China.

Panthera pardus melas (Cuvier, 1809; 152). Distribution: Java. Comment: Distinct ancient island form (Meijaard 2004, Gippoliti & Meijaard 2007, Uphyrkina et al. 2001, Wilting et al. 2016).

Panthera pardus nimr (Hemprich and Ehrenberg, 1832). Distribution: Arabian Peninsula. Comment: Distinctively small form, but may prove to be consubspecific with subspecies pardus, although should be retained as a separate management unit if so."

   
   


As for Central Chinese leopards, like at Wolong Reserve in Sichuan, where they may attack sub-adult pandas, their exact taxonomic status is unclear, being alternatively grouped under the P. p. japonensisP. p. delacouri, or even P. p. fusca.

In 1993, Brakefield noted that just as there is a North Chinese leopard, there is also a South Chinese leopard, which was "much more golden yellow" in colour, had shorter fur, and which people thought might be of the Indian (Panthera pardus fusca) or Indochinese (Panthera pardus delacouri) subspecies, or a subspecies of its own (possibly Panthera pardus sinensis), and Uphyrikina et al. said "Teeth of ancient leopards found in southern China and dated from the Middle of Pleistocene were similar to the recent subspecies P. p. sinensis; this led to the hypothesis of local evolution in eastern and southeastern Asia (Hemmer 1976)."

Stuffed leopard for testing pandas at Wolong Nature Reserve, Central China, credit: Alamy 

*This image is copyright of its original author



Back to African leopards, though the CSG grouped them into 1 subspecies, they admitted that 2 principal mtDNA clades in Africa, particularly in southern Africa, and thus that they appeared to be partly sympatric, so though they couldn't distinguish between African leopards as different subspecies, "more comprehensive sampling" was needed. That's not the only issue facing African leopards. In another thread, @chui_ posted excerpts from the study by Anco et al. (2017):

"Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens

Abstract 

Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.

...

Leopards exhibited population structuring at large geographic scales (West, Central-East/Central-Southern, and Southern Africa), suggesting strong evidence against panmixia in this species. AMOVA and pairwise FST analyses support differentiation in the ND-5 locus spanning five major haplogroups: West Africa, Coastal West-Central Africa, Central- East-Africa, Central-Southern Africa, and Southern Africa. Distinction between CEA and CSA as two independent regional populations is supported by pairwise FST analyses (Figure 4). Although still high, FST[CEA-CSA]¼0.40, was the lowest among all African leopard population comparisons. CSA showed higher levels of differentiation from WA and CWCA leopard populations, than the latter two did to CEA, indicating that CSA leopards are reproducing in isolation from neighbouring populations (Figure 4). Furthermore, CSA exhibited the highest levels of differentiation when compared with the two selected Asiatic subspecies: FST[CSA-nimr]¼0.98 and FST[CSA-saxicolor]¼0.97 (Figure 4).

The African leopard harbours a greater degree of genetic diversity than previously indicated and is partitioned in a pattern providing strong support for significant genetic subdivision. Our pairwise FST analyses using mtDNA revealed leopard populations throughout sub-Saharan Africa retain highly divergent copies of the ND-5 locus on levels approaching, and in some instances exceeding, FST values observed between Asiatic populations (Arabian and Persian leopards) presently recognized by the IUCN as separate subspecies (Figure 4). AMOVA revealed population structuring indicating a lack of gene flow between larger geographic regions (West Africa, Central-East/Central-Southern Africa, and Southern Africa) and among all the populations within regions. Two populations, CEA and CSA showed decreased pairwise differences relative to other populations, which could be an artifact of decreased sampling. Lastly, the star-like phylogeny, widespread distribution, and connectedness of the H10 haplotype points to a likely origin of diversity for the ancestral haplotype of this locus in Central and East Africa. We caution this work may not fully express the degree of genetic diversity present in African leopards, especially given sampling deficiencies in North Africa, parts of West Africa, and in Northeastern Africa.

This study has raised important questions regarding the taxonomic status of leopards in Africa. First, these findings support a distinction between African populations and Arabian and Persian leopard populations. We found additional strong support for an East-West split in African leopards, which may correspond to previously hypothesized taxonomic groupings (Figure 1, Table 1) and is congruent with numerous recent phylogeographic analyses of widespread African taxa (Moodley & Bruford 2007; Lorenzen et al. 2012; Dobigny et al. 2013; Smitz et al. 2013; Bertola et al. 2016; Fennessy et al. 2016). More sampling is needed to accurately delineate geographic features acting as potential barriers to gene flow (e.g. Sanaga River in Central Cameroon), while a suture zone has been identified between CWCA and CEA populations (Figures 2 and 3). In addition, we have identified previously unrecognized levels of genetic diversity in historical collections of African leopards not represented in contemporary leopard populations. While only based on mtDNA, the reconstruction of a haplotype network using novel samples of African leopards has reopened a >15-year-old conversation regarding African leopard diversity and taxonomy. We acknowledge that our results are limited by the use of mtDNA, and consequently single locus data. We therefore, strongly recommend multilocus sampling to investigate whether African leopards exhibit evidence of discordance between mitochondrial and nuclear markers (Toews & Brelsford 2012). These findings will provide the foundation for our ongoing analysis of temporal changes in phylogeographic patterns using sequence capture from historical collections, which will contribute to management and planning strategies to conserve remaining genetic diversity in the African leopard."

Image of the Atlas lion, brown bear and leopard from the Maghreb (Northwest Africa), by Joseph J. Ortega:

*This image is copyright of its original author


Video:



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