Tremarctinae Science

[brobear]

Topics on fossils, DNA, and other scientific discoveries focused on the Tremarctinae bears. 

[brobear]

www.sci-news.com/paleontology/stone-age-bear-genome-wide-data-chiquihuite-cave-09572.html

Genome-Wide Data from Stone Age Bears Recovered from Cave Sediments

Scientists have reconstructed the genomes of the extinct giant short-faced bear (Arctodus simus) and the American black bear (Ursus americanus) using environmental DNA fragments from the remote Chiquihuite Cave in Mexico.

[brobear]

For myself, I find the science of DNA to be interesting, yet exhausting and exasperating.

www.biorxiv.org/content/10.1101/2021.02.05.429853v1.full

Ancient genomes reveal hybridisation between extinct short-faced bears and the extant spectacled bear (Tremarctos ornatus).

Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae. Two of these species were giants, growing in excess of 1,000 kg, but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear (Tremarctos ornatus). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus. Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.

*Much more info on site.

[brobear]

WORLD OF PREHISTORIC CREATURES

Know your Cenozoic Predators.
Smilodon, Megalania, Amphicyon, Kelenken, Hyaenodon, Haast Eagle, Andrewsarchus, Purussaurus, Marsupial lion, Short-faced Bear and Megalodon by Roman Uchytel.
Titanoboa artist unknown as it is a stock image. 

[brobear]

royalsocietypublishing.org/doi/pdf/10.1098/rsbl.2016.0062

Ancient mitochondrial DNA reveals
convergent evolution of giant short-faced
bears (Tremarctinae) in North and South
America.

The Tremarctinae are a subfamily of bears endemic to the New World,
including two of the largest terrestrial mammalian carnivores that have
ever lived: the giant, short-faced bears Arctodus simus from North America
and Arctotherium angustidens from South America (greater than or equal to
1000 kg). Arctotherium angustidens became extinct during the Early
Pleistocene, whereas Arctodus simus went extinct at the very end of the
Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos
ornatus), a largely herbivorous bear that is today only found in South
America. The relationships among the spectacled bears (Tremarctos), South
American short-faced bears (Arctotherium) and North American shortfaced bears (Arctodus) remain uncertain. In this study, we sequenced a
mitochondrial genome from an Arctotherium femur preserved in a Chilean
cave. Our molecular phylogenetic analyses revealed that the South
American short-faced bears were more closely related to the extant South
American spectacled bear than to the North American short-faced bears.
This result suggests striking convergent evolution of giant forms in the
two groups of short-faced bears (Arctodus and Arctotherium), potentially as
an adaptation to dominate competition for megafaunal carcasses.

[brobear]

MORE: 3. Results
Our analyses recovered relationships among outgroup taxa
that were consistent with previous genetic studies,
but see. Within Tremarctinae, we recovered strong
support for a clade comprising Tremarctos ornatus and
Arctotherium to the exclusion of Arctodus simus (Bayesian
posterior probability ¼ 1.0, maximum-likelihood bootstrap
percentage ¼ 98%; figure 1). Our mean estimate for the time
of divergence between Tremarctos and Arctotherium was
4.1 Ma (95% highest posterior density, HPD ¼ 3.0–5.3 Ma),
and 4.8 Ma for the most recent common ancestor of Tremarctos,
Arctotherium and Arctodus (95% HPD ¼ 3.6–6.2 Ma). In general, node age estimates from our molecular dating analyses
were slightly younger than those of a previous study of ursid
mitochondrial DNA, although our 95% highest posterior
densities (HPDs) overlapped with theirs substantially for
equivalent nodes. These differences likely arise from our less
restrictive calibration on the root of the tree, which allowed
for the possibility that the Eocene Parictis is not a true
member of the bear lineage. Conversely, a study of nuclear
DNA obtained dates for the radiation of Ursinae that were
much younger than ours, likely as a result of our conservative constraint on the crown-age of Ursidae, which permitted
this node to substantially predate its first unequivocal fossil
representative (electronic supplementary material).

[brobear]

www.biorxiv.org/content/10.1101/2021.02.05.429853v1.full

Ancient genomes reveal hybridisation between extinct short-faced bears and the extant spectacled bear ( Tremarctos ornatus ).

Summary
Two genera and multiple species of short-faced bear from the Americas went extinct during or toward the end of the Pleistocene, and all belonged to the endemic New World subfamily Tremarctinae [1–7]. Two of these species were giants, growing in excess of 1,000 kg [6, 8, 9], but it remains uncertain how these extinct bears were related to the sole surviving short-faced bear: the spectacled bear (Tremarctos ornatus). Ancient mitochondrial DNA has recently suggested phylogenetic relationships among these lineages that conflict with interpretations based on morphology [1, 10–12]. However, widespread hybridisation and incomplete lineage sorting among extant bears mean that the mitochondrial phylogeny frequently does not reflect the true species tree [13, 14]. Here we present ancient nuclear genome sequences from representatives of the two extinct short-faced bear genera, Arctotherium and Arctodus. Our new data support a third hypothesis for the relationships among short-faced bears, which conflicts with existing mitochondrial and morphological data. Based on genome-wide D-statistics, we suggest that the extant spectacled bear derives substantial ancestry from Pleistocene hybridisation with an extinct short-faced bear lineage, resulting in a discordant phylogenetic signal between the mitochondrion and portions of the nuclear genome.

[brobear]

Results and Discussion
The spectacled bear (Tremarctos ornatus) is the only extant species of short-faced bear (Tremarctinae), a once diverse subfamily endemic to the Americas. This subfamily also includes many species that became extinct during the Pleistocene, including the Florida cave bear (Tremarctos floridanus), two species of North American short-faced bears (Arctodus spp. [3, 4]), and as many as five species of South American short-faced bears (Arctotherium spp. [2, 6]), one of which (Arctotherium wingei) has recently been discovered as far north as the Yucatan of Mexico [5]. Notably, the genera Arctodus and Arctotherium both included giant (>1,000kg) forms [8, 9] — Arctodus simus and Arctotherium angustidens, respectively — and based on morphology it was hypothesised that these genera were closely related [1, 6, 10, 11]. However, recently published mitochondrial DNA data suggested that Arctotherium was most closely related to the extant spectacled bear, to the exclusion of North American Arctodus [12]. While this result supported the convergent evolution of giant bears in North and South America, the mitochondrial genome does not always reflect the true relationships among species [e.g. 15, 16–19]. Importantly, discordance between mitochondrial and nuclear loci has been previously noted in bears, and has been attributed to a combination of stochastic processes and the rapid evolution of bears [13], as well as hybridisation between species [13, 14, 20–25]. To further resolve the evolutionary history of short-faced bears, we applied ancient DNA techniques to retrieve and analyse whole genome data from both Arctodus and Arctotherium.

Ancient DNA (aDNA) was extracted and sequenced from three Arctodus simus specimens: one each from placer mines at Sixty Mile Creek (ACAD 438; Canadian Museum of Nature; CMN 42388) and Hester Creek (ACAD 344; Yukon Government; YG 76.4) in the Yukon Territory, Canada; and one from Natural Trap Cave in Wyoming, USA (ACAD 5177; University of Kansas; KU 31956). We also analysed one specimen of Arctotherium sp. from Cueva del Puma, Patagonia, Chile (ACAD 3599; complete right femur, no. 32104, Centro de Estudios del Hombre Austral, Instituto de la Patagonia, Universidad de Magallanes). The Arctotherium specimen was previously dated to 12,105 ± 175 cal yBP (Ua-21033) [26], while two of the Arctodus specimens have been dated: ACAD 438 at 47,621 ± 984 cal yBP (TO-2699) [27] and ACAD 5177 at 24,300 ± 208 cal yBP (OxA-37990) (Table S1). The Arctotherium specimen has yielded mitochondrial aDNA in a previous studies [12], however, here we shotgun sequenced this specimen, along with the three A. simus specimens, at much greater depth in order to reconstruct nuclear genome sequences. Mapping our new sequencing data from these specimens to the giant panda (Ailuropoda melanoleuca) reference genome (LATN01) yielded average depths of coverage between 0.12x to 5.9x (Table S3). We compared these new genomic data to previously published genomes from all extant species of bear (Table S2): spectacled bear, giant panda, brown bear (Ursus arctos), American black bear (U. americanus), Asian black bear (U. thibetanus), polar bear (U. maritimus), sloth bear (U. ursinus), and sun bear (U. malayanus).

Phylogenetic analyses on a concatenated dataset of genome-wide SNPs revealed relationships within Ursinae that were consistent with previous genomic studies: U. americanus, U. maritimus, and U. arctos formed a monophyletic clade sister to a clade consisting of U. thibetanus, U. malayanus, and U. ursinus [13, 14]. In contrast, within short-faced bears (Tremarctinae) we recovered strong support for a close relationship between the spectacled bear and the North American short-faced bear (Arctodus simus) to the exclusion of the South American Arctotherium (Figure 1A, Figure S2). This result conflicts with the mitochondrial tree, which instead supports a clade comprising Arctotherium and Tremarctos ornatus to the exclusion of Arctodus simus [12] (Figure 1B). As the radiation of bears is thought to have occurred rapidly during the Miocene - Pliocene transition, it is possible that this discordance could be explained by incomplete lineage sorting (ILS) [28], a process whereby pre-existing genetic variation in an ancestral species is randomly inherited and fixed in descendant species [29, 30]. Alternatively, given the observed propensity of bears for hybridisation [e.g. 13, 14, 20–22, 25, 31], mitochondrial/nuclear discordance within short-faced bears may instead result from gene flow between Tremarctos and either Arctodus or Arctotherium.

To test for potential phylogenetic discordance across our short-faced bear genomes, we constructed phylogenetic trees from 500 kb non-overlapping windows (n = 2622) across the 85 largest autosomal scaffolds of the giant panda reference genome (LATN01). Trees created from roughly 70% of windows agreed with the results from our genome-wide concatenated dataset (Topology 1; i.e. Tremarctos + Arctodus; Figure 2B & S3). However, approximately 30% of windows instead supported the mitochondrial tree topology (Topology 2; i.e. Tremarctos + Arctotherium; Figure 2B & S3), while the third possible topology where the two extinct genera form a clade — Arctodus + Arctotherium — was rejected for over 95% of windows. The frequencies of the three possible tree topologies are difficult to explain as a result of ILS, which we would expect to result in a more even representation of the two “minority” topologies (i.e. Topologies 2 and 3). Our results therefore suggest that introgression may be the most likely explanation for the observed phylogenetic discordance. Consequently, we calculated D-statistics [32, 33] using our concatenated genome-wide SNPs in order to identify signals of hybridisation between the bear species in our dataset.

Consistent with previous studies [i.e. 14], our D-statistics revealed compelling evidence for hybridisation between: Asian black bears and all North American ursine bears (including the polar bear); sun bears and North American ursine bears; and Asian black bear and sun bear (Table S4). In contrast, we did not obtain any significantly non-zero values for D-statistics calculated using our two extinct short-faced bear genomes, any member of Ursinae, and the panda outgroup (Table 1). This result suggests that no gene flow occurred between Arctodus or Arctotherium and the ancestors of any modern ursine bear, and also demonstrates a lack of any discernible reference bias in the ancient genomic data (which would result in asymmetrical allele sharing with the reference). Thus, it appears Arctodus and Arctotherium did not hybridise with brown and black bears in the Americas during the late Pleistocene, even though the distribution of Arctodus overlapped with both ursines, and Arctotherium may have encountered them in Mexico or Central America [5]

Contrary to previous studies, our D-statistics revealed signals consistent with gene flow between the spectacled bear and members of Ursinae (Table 1 & S5), suggesting the possibility that Tremarctos hybridised with ancestors of either the brown bear or American black bear during the Pleistocene. This signal is surprising given the deep divergence between ursine and short-faced bears, having split approximately 10 million years ago (mya) [12, 14, 28]. However, in support of this hypothesis, offspring between spectacled bear and American black bear have resulted from hybridisation in zoos, although whether these hybrids were fertile remains unknown [34]. Importantly, members of Tremarctos and the ancestors of modern American black bears had overlapping distributions throughout the Pleistocene in North America [4, 10], meaning that hybridisation may have occurred when the two lineages were less divergent and reproductive barriers had had less time to evolve.

In addition to evidence for hybridisation between Tremarctos and ursine bears, we also recovered convincing evidence for hybridisation between Arctotherium and Tremarctos (Table 1). These results are consistent with a model where the divergence between Arctodus and Tremarctos occurred in North America after the ancestors of Arctotherium dispersed southwards into South America, with subsequent hybridisation between Tremarctos and Arctotherium. This interpretation is supported by the presence of Arctodus and Tremarctos (and absence of Arctotherium) in the late Pliocene fossil record of North America [3, 4, 7, 10]. The fossil record further suggests that contact between Tremarctos and Arctotherium occurred during the late Pleistocene, when representatives of Arctotherium were distributed as far north as the Yucatan of Mexico [5], providing an opportunity for hybridisation.

If the ancestors of the spectacled bear hybridised with Arctotherium somewhere in the American mid-latitudes during the migration of Tremarctos into South America, then signals of gene flow between members of these two genera could date to the latest Pleistocene or earliest Holocene, when spectacled bears are thought to have migrated into South America [6, 35, 36]. To test this hypothesis, we estimated divergence times among the three short-faced bear lineages for all 500 kb windows from the largest 40 scaffolds corresponding to either Topology 1 (n = 980) or Topology 2 (n = 413) and summarised the results (Figure 2c). The age of the most recent common ancestor (TMRCA) of Tremarctos, Arctodus, and Arctotherium was similar irrespective of topology (Topology 1: 3.6 mya; Topology 2: 3.6 mya), as was the subsequent divergence between the remaining two lineages (Topology 1: 3.1 mya; Topology 2: 3.1 mya). Assuming that members of Tremarctos migrated southward no earlier than the latest Pleistocene, our results superficially appear to be incompatible with late Pleistocene/Holocene hybridisation between Tremarctos and Arctotherium. The fossil record suggests two ways these observations may be explained.

Late Pleistocene fossil data indicate that the ancestors of the spectacled bear are likely to have encountered Arctotherium individuals from Mexico, Central America, and/or northern South America, which were comparable in size and diet to the spectacled bear [1, 5, 37] and which may have represented a different Arctotherium species from the Chilean specimen sequenced in the present study [1, 6, 12, 26]. Indeed, throughout the Pleistocene a number of Arctotherium species have been described across South and Central America, with putative species ranging from gigantic in the early-mid Pleistocene to relatively small in the late Pleistocene [1, 2, 6, 9]. If the ancestors of our sampled Patagonian Arctotherium specimen diverged from those of more northerly Arctotherium species during the Pliocene or early Pleistocene, then our molecular dating results remain consistent with hybridisation being the primary driver of phylogenetic discordance in our genomic data. Alternatively, hybridisation between Tremarctos and Arctotherium could have occurred in Central America during the Pleistocene. Tremarctos and Arctotherium have both been recorded in Central American cave deposits [5, 38], however, the extent of occupation by both genera in the region is unknown, and conceivably Central America represents a contact zone between the genera throughout the Pleistocene where hybridisation may have occurred.

An alternative interpretation of our phylogenetic results is that Topology 2 (Tremarctos + Arctotherium), which is supported by the mitochondrion and ~30% of our nuclear genome windows, is the pre-hybridisation tree. Recently, Li, et al. [39] suggested that under scenarios involving substantial gene flow the predominant phylogenetic signal across the genome may not reflect the pre-hybridisation tree. If this were the case for short-faced bears, the majority of support for Topology 1 would actually result from extensive hybridisation between Arctodus and Tremarctos in North America. Li, et al. [39] contend that the phylogenetic signal of the pre-hybridisation tree may be enriched in regions of low recombination, especially on the X-chromosome. In order to test this hypothesis, we identified panda scaffolds corresponding to the ~40 Mb recombination cold-spot on the X-chromosome highlighted by Li, et al. [39] and produced phylogenetic trees for each 500 kb window along this region (Figure S4). Interestingly, the majority of these fragments supported Topology 2 (Tremarctos + Arctotherium), the same topology as the mitochondrial phylogeny but contrasting with the majority of autosomal scaffolds.

Unlike felids [e.g. 40, 41, 42], a high-quality reference assembly and linkage map does not exist for any bear species, meaning scaffolds pertaining to high and low recombination areas of the genome could not be identified. Unfortunately, this currently makes it impossible to further explore the possibility that Topology 2 (Tremarctos + Arctotherium) may reflect the pre-hybridisation short-faced bear tree, rather than Topology 1 (Tremarctos + Arctodus). In the absence of a linkage map, sequencing aDNA from either the extinct Tremarctos floridanus or more northerly Arctotherium populations will be key to further resolving the evolutionary history of short-faced bears, though this will be challenging given that the core range of these species lies in the lower-latitudes where aDNA preservation is less reliable. For now we conclude that the weight of evidence supports a closer relationship between the spectacled bear and the extinct short-faced bears from North America (Arctodus) rather than South America (Arctotherium). In any case, our genomic data imply extensive hybridisation occurred between the spectacled bear and one of the extinct short-faced bear lineages. These results contribute to the growing consensus that hybridisation is widespread among carnivoran groups generally [13, 14, 39, 43].

[brobear]

Tremarctinae: