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05-07-2020, 11:15 AM( This post was last modified: 05-07-2020, 11:16 AM by tigerluver )
(05-06-2020, 09:15 PM)OncaAtrox Wrote: Turns out that the cave lion diversification from the modern lion happened later than previously thought, with some researches considering subspecies of Panthera leo (in case there remained any doubts on their positions as true lions), but this is debatable.
Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
Previous studies based on partial fragments of the mitochondrial genome have estimated that cave and modern lions diverged ca. 500,000 y ago, using the appearance in the fossil record of the ancestral cave lion Panthera fossilis (5, 6). More recently, the divergence time was estimated to be 1.89 million years ago using full mitochondrial sequences and multiple fossil constraints (8). To investigate these discrepancies among estimates, and to fully resolve the position of cave lions in the phylogeny, we applied three independent methods that leverage the power of whole-genome sequences and do not rely on fossil record calibrations to estimate the divergence time between cave and modern lions.
First, we investigated the split time between the ancestral populations by estimating the probability F (Aderived|Bheterozygous) (17) of an individual A (such as the Siberian or Yukon cave lion) carrying a derived allele discovered as a heterozygote in a modern lion individual B. This summary statistic was then used to estimate the divergence time of the cave lion lineage given a model of population history in modern lions inferred using the pairwise sequential Markovian coalescent (PSMC) (18). We estimated that F(Cave lion|Modern lion) averaged at ∼0.15 (Fig. 2A), meaning that cave lions carry the derived allele in ∼15% of the heterozygous sites detected in modern lions (14.7 to 16.4%; SI Appendix, Table S2). From a simulation of the expected distribution pattern of F(Cave lion|Modern lion), given the population history of modern lions, a mutation rate (µ) of 4.5 × 10−9 per generation (11), and a generation time of 5 y (19),
*This image is copyright of its original author
We further explored the divergence time between cave and modern lions by exploiting the fact that the Siberian cave lion was a male (SI Appendix, Table S5). Male X chromosomes can be used to construct synthetic pseudodiploid genomes and estimate rates of coalescence between their ancestral populations. Since the effective population size (Ne) is inversely correlated with the amount of coalescing events occurring at a particular point in time, the Ne inferred from a pseudodiploid chromosome of two diverged populations should suddenly increase around the time of their divergence, as no coalescent events can happen after this estimated time assuming reproductive isolation occurred after the split. Indeed, we inferred from the PSMC of cave and each modern lion combined X chromosomes that there was a sharp increase in Ne to an unmeasurably large size ca. 495,000 y ago (Fig. 2B; 460,000 to 578,000 y ago, SI Appendix, Table S6). However, we caution that there may be added uncertainty around this estimate due to the low depth of coverage in the X-chromosome of the Siberian cave lion (1.96-fold, SI Appendix, Table S5).
We also assessed estimates of sequence divergence (dxy), which should be directly related to the split time (T) and the Ne of the common ancestor (Neanc) (dxy = 2Tµ + 4Nanc µ). We found that the mismatch rate between the Siberian cave lion and modern lions using only transversions was an average dxy = 0.00067 (SI Appendix, Fig. S6). Assuming that µ = 4.5 × 10−9 per generation (11), a transition/transversion ratio of 1.9 (SI section 4), a branch shortening in the Siberian cave lion of 6,000 generations (SI Appendix, Table S1) and Neanc of 55,000 individuals (Fig. 3A), we obtained a split time of ca. 108,000 generations [540,000 y assuming a generation time of 5 y (19)]. Given the general congruence among our estimates, we conclude that the most likely split time between cave and modern lions is ca. 500,000 y ago. This estimate is also remarkably consistent with the early Middle Pleistocene appearance of P. fossilis in the European fossil record (5).
Read this one moments after it came out, thanks for sharing. Nice study however they may've missed the mark with P. fossilis. Reading the main text and the supplement, not much detail is given in regards to the dates of P. fossilis. The earliest specimens come from at least around MIS 22-23, which is ~900 kya, from Kuznetsk basin per Sotnikova and Foronova (2014) and reviewed by Marciszak et al. (2019). There's also a possibly MIS 29-31 specimen (1 mya) from Greece (Sickenberg 1976). Essentially a little less than half of P. fossilis reviewed by Marciszak et al. (2019) falls outside of their confidence interval.
Interestingly, this data might support Hanko and Korsos (2007?) assertion of three waves of lion migration. According to them, first came P. fossilis to Eurasia, then P. spelaea, then P. leo. If P. spelaea shares a common ancestor with P. leo up until 500 kya, it's less likely it's just an advanced form in the lineage of P. fossilis.
(05-07-2020, 07:41 AM)Richardrli Wrote: I wonder if cave lions made it to Japan? There were tigers there at some point
The history of tigers on Japan is based on the follows:
1. Shikama and Okafuji (1958): Upper right canine, humerus, proximal ulna attributed to 'Felis tigris'.
2. Shikama and Okafuli (1963): Fragmentary maxilla and mandible attributed to 'Felis youngi'.
3. Takai and Hasegawa (1966): Multiple dentition, attributed to P. pardus but per the second author P. tigris (if the translation are right). The teeth are the size of small tigress but larger than those of P. pardus. The size is the cause of uncertainty.
4. Hemmer (1967) discussed P. palaeosinensis and is cited by Tilson and Nyhus as tiger. Unfortunately, I don't have the study to give my thoughts.
No literature that I am aware of ever refers to P. spelaea-type cats in Japan. All in all, the specimens don't identify themselves well. Looking into environmental context, Japan was composed of open boreal woodland during the Pleistocene, which is more of a tiger habitat. Looking into size, we know small tigers approaching the size of leopards existed for a good chunk of time historically and in the modern era (P. t. trinilensis, P. t. balica). We haven't seen any small-sized cave lions and certainly nothing so small that leopards come into the differential. If anything, cave lions never had it in them to be small as even 2 mya ancestor P. shawi was gigantic (at least as big as the largest P. atrox). I'm digressing now, but the point is small size points to tiger over lion-like cat as the former seems to have plasticity for dwarfism while the latter while doesn't.
(05-06-2020, 09:15 PM)OncaAtrox Wrote: Turns out that the cave lion diversification from the modern lion happened later than previously thought, with some researches considering subspecies of Panthera leo (in case there remained any doubts on their positions as true lions), but this is debatable.
Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
Previous studies based on partial fragments of the mitochondrial genome have estimated that cave and modern lions diverged ca. 500,000 y ago, using the appearance in the fossil record of the ancestral cave lion Panthera fossilis (5, 6). More recently, the divergence time was estimated to be 1.89 million years ago using full mitochondrial sequences and multiple fossil constraints (8). To investigate these discrepancies among estimates, and to fully resolve the position of cave lions in the phylogeny, we applied three independent methods that leverage the power of whole-genome sequences and do not rely on fossil record calibrations to estimate the divergence time between cave and modern lions.
First, we investigated the split time between the ancestral populations by estimating the probability F (Aderived|Bheterozygous) (17) of an individual A (such as the Siberian or Yukon cave lion) carrying a derived allele discovered as a heterozygote in a modern lion individual B. This summary statistic was then used to estimate the divergence time of the cave lion lineage given a model of population history in modern lions inferred using the pairwise sequential Markovian coalescent (PSMC) (18). We estimated that F(Cave lion|Modern lion) averaged at ∼0.15 (Fig. 2A), meaning that cave lions carry the derived allele in ∼15% of the heterozygous sites detected in modern lions (14.7 to 16.4%; SI Appendix, Table S2). From a simulation of the expected distribution pattern of F(Cave lion|Modern lion), given the population history of modern lions, a mutation rate (µ) of 4.5 × 10−9 per generation (11), and a generation time of 5 y (19),
*This image is copyright of its original author
We further explored the divergence time between cave and modern lions by exploiting the fact that the Siberian cave lion was a male (SI Appendix, Table S5). Male X chromosomes can be used to construct synthetic pseudodiploid genomes and estimate rates of coalescence between their ancestral populations. Since the effective population size (Ne) is inversely correlated with the amount of coalescing events occurring at a particular point in time, the Ne inferred from a pseudodiploid chromosome of two diverged populations should suddenly increase around the time of their divergence, as no coalescent events can happen after this estimated time assuming reproductive isolation occurred after the split. Indeed, we inferred from the PSMC of cave and each modern lion combined X chromosomes that there was a sharp increase in Ne to an unmeasurably large size ca. 495,000 y ago (Fig. 2B; 460,000 to 578,000 y ago, SI Appendix, Table S6). However, we caution that there may be added uncertainty around this estimate due to the low depth of coverage in the X-chromosome of the Siberian cave lion (1.96-fold, SI Appendix, Table S5).
We also assessed estimates of sequence divergence (dxy), which should be directly related to the split time (T) and the Ne of the common ancestor (Neanc) (dxy = 2Tµ + 4Nanc µ). We found that the mismatch rate between the Siberian cave lion and modern lions using only transversions was an average dxy = 0.00067 (SI Appendix, Fig. S6). Assuming that µ = 4.5 × 10−9 per generation (11), a transition/transversion ratio of 1.9 (SI section 4), a branch shortening in the Siberian cave lion of 6,000 generations (SI Appendix, Table S1) and Neanc of 55,000 individuals (Fig. 3A), we obtained a split time of ca. 108,000 generations [540,000 y assuming a generation time of 5 y (19)]. Given the general congruence among our estimates, we conclude that the most likely split time between cave and modern lions is ca. 500,000 y ago. This estimate is also remarkably consistent with the early Middle Pleistocene appearance of P. fossilis in the European fossil record (5).
Read this one moments after it came out, thanks for sharing. Nice study however they may've missed the mark with P. fossilis. Reading the main text and the supplement, not much detail is given in regards to the dates of P. fossilis. The earliest specimens come from at least around MIS 22-23, which is ~900 kya, from Kuznetsk basin per Sotnikova and Foronova (2014) and reviewed by Marciszak et al. (2019). There's also a possibly MIS 29-31 specimen (1 mya) from Greece (Sickenberg 1976). Essentially a little less than half of P. fossilis reviewed by Marciszak et al. (2019) falls outside of their confidence interval.
Interestingly, this data might support Hanko and Korsos (2007?) assertion of three waves of lion migration. According to them, first came P. fossilis to Eurasia, then P. spelaea, then P. leo. If P. spelaea shares a common ancestor with P. leo up until 500 kya, it's less likely it's just an advanced form in the lineage of P. fossilis.
(05-07-2020, 07:41 AM)Richardrli Wrote: I wonder if cave lions made it to Japan? There were tigers there at some point
The history of tigers on Japan is based on the follows:
1. Shikama and Okafuji (1958): Upper right canine, humerus, proximal ulna attributed to 'Felis tigris'.
2. Shikama and Okafuli (1963): Fragmentary maxilla and mandible attributed to 'Felis youngi'.
3. Takai and Hasegawa (1966): Multiple dentition, attributed to P. pardus but per the second author P. tigris (if the translation are right). The teeth are the size of small tigress but larger than those of P. pardus. The size is the cause of uncertainty.
4. Hemmer (1967) discussed P. palaeosinensis and is cited by Tilson and Nyhus as tiger. Unfortunately, I don't have the study to give my thoughts.
No literature that I am aware of ever refers to P. spelaea-type cats in Japan. All in all, the specimens don't identify themselves well. Looking into environmental context, Japan was composed of open boreal woodland during the Pleistocene, which is more of a tiger habitat. Looking into size, we know small tigers approaching the size of leopards existed for a good chunk of time historically and in the modern era (P. t. trinilensis, P. t. balica). We haven't seen any small-sized cave lions and certainly nothing so small that leopards come into the differential. If anything, cave lions never had it in them to be small as even 2 mya ancestor P. shawi was gigantic (at least as big as the largest P. atrox). I'm digressing now, but the point is small size points to tiger over lion-like cat as the former seems to have plasticity for dwarfism while the latter while doesn't.
I see your point, but 500k is not that much time of divergence between two groups to considerably make them completely different species. With the two species of clouded leopard, their divergence is believes to have happened short to 2 million years, and their morphological differences appear to be minimal.
With cave lions we are dealing with true lions, their ancestor might actually have been Panthera leo melanochaita that later gave rise to leo leo as well, if the study is accurate about the later diversion of the leo leo lineage. It would've been nice if the people in charge of the study would have tracked the genetic roots of Mosbach and American lions as well to determine their closeness to Panthera leo and spelaea, and maybe determine which one might the closet basal species that gave rise to them, or if it was a different ancient type of lion that gave rise to both lineages.
My conclusion for that study is that there's still so much we don't know about lion evolution, I will be expectant on new studies done in the matter because it's fascinating. Thanks for your input in the matter too I'm sure we can all learn as time goes on more on this subject and construct a better picture on how lion lineages relate to each other.
05-07-2020, 05:38 PM( This post was last modified: 05-07-2020, 05:40 PM by Ashutosh )
@OncaAtrox, 500k years of divergence can be huge in terms of morphological differences between two organisms that branched out. One recent example is the difference between Indian and Sri Lankan leopard.
They have been separate for about 10,000 years since the land bridge submerged and there are already some major differences between them. They are classified as subspecies right now, but after 500,000 years if they continue on their paths (and the land bridge doesn’t appear), you would be looking at a different species entirely. There are obvious size differences as Sri Lankan leopard is the apex predator and considerably larger. Sri Lankan leopards spend a lot more time on the ground instead of on trees as there is no threat of tigers. These differences and other such details would only be magnified and exacerbated over hundreds of thousands of years.
As for the clouded leopard, the difference is marginal because of the habitats they occupy is very similar and the animals they share that habitat with are also very similar. The rainforest of Sumatra are comparable to forests of Northeastern India (which are the northernmost rainforest in the world latitudinally speaking). Before humans wiped out an insane amount of animals, most animals found in NorthEastern India were found all across South East Asia and into Sumatra And Java. For example, Javan Rhino and Sumatran Rhino habitat overlapped with Indian Rhino habitat in North East India. So, even though the Sunda clouded leopard and mainland clouded leopard diverged millions of years ago, they are very similar.
@Ashutosh there is actually no major morphological differences between Sri Lankan and mainland Indian leopards, definitely not in terms of size as both populations appear to peak their weight at around 80 kg. Sri Lankan leopards avoiding island dwarfism can be attributed to their role as the top cat which leopards in the mainland don't have, but besides that most of their changes appear to be related to behaviour rather than morphology, such as the lack to hoist prey in the absence of larger predators.
With cave lions their closeness to modern lions is even more marked than with the clouded leopards, in fact we have frozen cave lion cubs that clearly depict almost no morphological differences with modern lions. There is no reason to believe that they are completely different altogether with the *relative* short diversion time between both species. We are dealing with two closely related animals, which is why the researchers felt comfortable in grouping cave lions in the subspecies category of Panthera leo at the beginning of the study. Regardless of their classification as different subspecies with a close diversification from Panthera leo, or a subspecies of the latter, we are dealing with a true lion lineage.
You need better references and research if you think Indian leopards of South India and Sri Lankan leopards are of the same size. Most leopards tagged in India above 60 kilos are from Northern India not from Southern India (simple Bergmann’s Law). Whereas, Sri Lankan leopards have some exceptional specimens (weighing above 80 kilos) even though they are closer to the equator. The Sri Lankan leopard thread on this very site will confirm those specimens.
05-07-2020, 11:18 PM( This post was last modified: 05-08-2020, 02:12 AM by tigerluver )
Just some data on morphological difference. Two robust craniomandibular morphological studies found P. spelaea as distinct in this regard from P. leo (Sotnikova and Nikolsky 2006, Christiansen 2006). There is not much post-cranial analysis. Looking at limb ratios and proportions, the cave lion was similarly a long legged, tall, and lean (but likely more robust) cat akin to the modern lions.
Two, the new paper remarks that there was no significant genetic exchange between the two forms since 500 kya. Part of the definition of speciation is reproductive isolation. No definition of speciation takes into account the timeline. Time in itself has no value, it's the amount of change in the given time frame. Read into punctuated equilibrium if interested. Of course, the lion-like cats are most closely related to lions. The rest of discussion is due to man's necessity to neatly classify things. Remember that the idea of species is not a natural concept, it is just a man-made way of trying to fulfill our need for the rationalization of our surroundings.
So if scientists actually bring the cave lion/African lion hybrid back to life would that make it larger than all of the big cats except for ligers? And are cave lions actually a subspecies or not?
"In Europe, cave lions from Belgium and Germany show very individual prey preferences. Some seem to have preferred young, juicy cave bear cubs, while others specialised in hunting mature reindeer."
The Cave Lion (Panthera spelaea and Panthera fossilis)
