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Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods.
We present a fully resolved phylogeny for ursids based on ten complete mitochondrial ge...
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... of this family are present on most continents and occupy a wide range of ecological niches from the arctic ice shelves to tropical rainforests (see Additional File 1, Figure S1a). Despite numerous morphological and molecular studies on the phylogenetic relationship among Ursidae members, no consensus exists with regard to either their phylogeny or their taxonomic nomenclature (Table 1). Most analyses have concentrated on the eight extant bear species: brown bear, American black bear, Asian black bear, polar bear, sun bear, sloth bear, spectacled bear and giant panda (for species names see Table 1). ...
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... numerous morphological and molecular studies on the phylogenetic relationship among Ursidae members, no consensus exists with regard to either their phylogeny or their taxonomic nomenclature (Table 1). Most analyses have concentrated on the eight extant bear species: brown bear, American black bear, Asian black bear, polar bear, sun bear, sloth bear, spectacled bear and giant panda (for species names see Table 1). Molecular studies based on mitochondrial and nuclear DNA from modern bears have recently provided convincing evidence about several of the controversial relationships among the bears, such as the basal positions of the giant panda and the spectacled bear in the bear tree [1][2][3][4] and the position of the polar bear within the brown bear tree making the later para- phyletic [5,6]. ...
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... phylogenetic uncertainty has resulted in major taxonomic confusion. Based on both morphologi- cal and molecular data up to six different genera (Ursus, Helarctos, Euarctos, Selenartos, Thalarctos and Melursus; i.e. one for each species) have been suggested for the extant ursine bears (Table 1). ...
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... mitogenomic data also has implications for bear tax- onomy. Six ursine bears and the sloth bear are mono- phyletic with absolute support, which agrees with Hall and Nowak's inclusion (Table 1) of the Asian black bear, American black bear, sun bear, polar bear and brown bear within the genus Ursus [28,29] and confirms the mitoge- nomic study by Yu et al [4]. Given the short divergence [4,28,29], that the sloth bear is grouped together with the other ursine bears in the genus Ursus and that the other genus names previously suggested for members of this radiation are discarded (Table 1). ...
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... ursine bears and the sloth bear are mono- phyletic with absolute support, which agrees with Hall and Nowak's inclusion (Table 1) of the Asian black bear, American black bear, sun bear, polar bear and brown bear within the genus Ursus [28,29] and confirms the mitoge- nomic study by Yu et al [4]. Given the short divergence [4,28,29], that the sloth bear is grouped together with the other ursine bears in the genus Ursus and that the other genus names previously suggested for members of this radiation are discarded (Table 1). ...
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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...
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... However, in our opinion, intergeneric hybridization within Diamesinae is an unlikely explanation, and the branching of lineages Boreoheptagyiini and Diamesini have significantly different histories (Figs 2 and 3). A third explanation, of explosive speciation (Krause et al. 2008, Chen et al. 2022, also is refuted in the tempo of the evolution of Diamesinae (Fig. 3). Thus, the reason for the incongruence of phylogeny between mtDNA and multi-locus data has not been established. ...
Diamesinae is a subfamily of Chironomidae, whose species live in cold lotic or oligotrophic lentic habitats with global distribution excepting Antarctica. The cool stenothermic ecology of nearly all diamesines produces a typical amphitropical pattern of absence at tropical latitudes, except at high elevation. Recent attention has focused on the species discovery, while evolutionary relationships at the generic and tribal level have remained inadequately understood. Current classification implies analogous evolutionary diversification in each hemisphere (boreal and austral). To test this concept, we used six genetic markers (18S, 28S, CAD1, COI-5p, COI-3p and COII) and fossil calibrations to produce a well-supported and resolved time-calibrated phylogeny of the subfamily. Austral and boreal diamesines indeed are reciprocally monophyletic lineages, with estimated Jurassic divergence (130-196, 164 Ma). The boreal Protanypodini, previously understood to be a tribe within Diamesinae, is excluded and elevated here to subfamily rank as Protanypodinae stat. nov. Ancestral austral diamesines probably originated in South America and successively reached New Zealand, Australia and South Africa during the Cretaceous-Paleogene. The Holarctic tribes Diamesini and Boreoheptagyiini probably originated in the Eastern Palaearctic with further dispersal/vicariance into the Western Palaearctic, Nearctic, East, and very likely dispersed southwards to montane East Africa and Borneo.
... The topology of our Bayesian tree based on mitogenome sequences ( Figure 3) agrees with previous phylogenies proposed for the family Ursidae [43,49,50]. The giant panda and the spectacled bear are the species that diverged the earliest,~20.0 ...
... The other six species diverged much more recently (~5 My) and, notably, two of the genus Ursus, the brown and the polar bears, diverged less than 1 My ago. The topology of our Bayesian tree based on mitogenome sequences ( Figure 3) agrees with previous phylogenies proposed for the family Ursidae [43,49,50]. The giant panda and the spectacled bear are the species that diverged the earliest, ~20.0 and 13.7 million years ago (My), respectively. ...
Assessing niche evolution remains an open question and an actively developing area of study. The family Ursidae consists of eight extant species for which, despite being the most studied family of carnivores, little is known about the influence of climate on their evolutionary history and diversification. We evaluated their evolutionary patterns based on a combined phylogeography and niche modeling approach. We used complete mitogenomes, estimated divergence times, generated ecological niche models and applied a phyloclimatic model to determine the species evolutionary and diversification patterns associated with their respective environmental niches. We inferred the family evolutionary path along the environmental conditions of maximum temperature and minimum precipitation, from around 20 million years ago to the present. Our findings show that the phyloclimatic niches of the bear species occupy most of the environmental space available on the planet, except for the most extreme warm conditions, in accordance with the wide geographic distribution of Ursidae. Moreover, some species exhibit broader environmental niches than others, and in some cases, they explore precipitation axes more extensively than temperature axes or vice versa, suggesting that not all species are equally adaptable to these variables. We were able to elucidate potential patterns of niche conservatism and evolution, as well as niche overlapping, suggesting interspecific competitive exclusion between some of the bear species. We present valuable insights into the ecological and evolutionary processes driving the diversification and distribution of the Ursidae. Our approach also provides essential information for guiding effective conservation strategies, particularly in terms of distribution limits in the face of climate change.
... Many typical Early Pleistocene Carnivora also went extinct or became much less abundant since the early Middle Pleistocene, including Pachycrocuta brevirostris in Europe (in eastern Asia it persisted longer) (Howell and Petter, 1980;Turner and Antón, 1996;Iannucci et al., 2021), Megantereon in eastern Asia (in Europe it went extinct earlier) (Teilhard de Chardin, 1939;Li and Sun, 2022), Xenocyon (Kretzoi, 1938;Jiangzuo et al., 2022c), Homotherium (Antón et al., 2014;Jiangzuo et al., 2022d) in Eurasia. Some species have experienced a high evolutionary rate since then, best exemplified by cave bear, with several morpho-species from Ursus savini to U. deningeri and U. kudarensis to various Late Pleistocene species (Baryshnikov, 1998;Vereschagin and Baryshnikov, 2000;Rabeder et al., 2004;Krause et al., 2008;Spassov et al., 2017;Barlow et al., 2021). At the same time, the inter-and intracontinental connection becomes stronger. ...
The fossil records of the cheetahs in eastern Asia are is rare, and mostly fragmented,
then and in theconsequence, the evolution of this lineage in eastern Asia remained
remains obscure. In this study, we report the new material from two early Middle
Pleistocene sites, the upper deposits (L2) of Jinyuan Cave (Dalian) and Zhoukoudian
Loc.13 (Beijing). These specimens are identified here as Acinonyx pleistocaenicus and
represent the latest and largest-sized member of the species. Acinonyx
pleistocaenicus shows a suit of craniodental traits that distinguishes it from the earlier
Early Pleistocene A. pardinensis but, and relates it closer to modern A. jubatus , and
should be regarded as a valid species. Shortly after the age represented by
Zhoukoudian Loc. 13 (0.6-0.7 Ma), the giant cheetah was replaced by much smaller
and morphologically different Acinonyx intermedius, supporting these two species as
independent, and the latter was likely a new immigrant from Africa around the Early-
Middle Pleistocene boundary, together with Panthera spelaea, Panthera pardus, and
Parahyaena prisca.
... is an herbivorous mammal belonging to the bear family (1,2). Giant pandas have undergone a series of evolution to adapt to the special bamboo diet, including ecological (3)(4)(5), morphological (6)(7)(8), and genetic (9)(10)(11) adaptations (4,12). ...
Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda’s gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p -coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas , as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas -associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro . A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism.
IMPORTANCE
Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p -coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas , as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas -associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas , as the main lignin-degrading bacteria.
... According to mitochondrial DNA, the Asiatic black bear and American black bear (Ursus americanus Pallas, 1780) diverged from each other 5 Ma ago (Talbot and Shields, 1996). Other scholars suggest later dates: Krause et al. (2008) propose the divergence of the black bears to the rest of the taxa between 5.89 and 3.51 Ma, and the split between American and Asiatic black bears between 5.27 and 3.11 Ma ago. Wu et al. (2015) indicated that black bears diverged from brown and cave bears 5.14 Ma ago, and U. thibetanus diverged from U. americanus 3.9 Ma ago. ...
... gr. minimusthibetanus (sensu Mazza and Rustioni, 1994) and appeared in the Early Pliocene (Krause et al., 2008;Wagner, 2010). By the beginning of MN17, however, they either evolved to or were replaced by the etruscan bears of Asiatic origin (Rustioni and Mazza, 1993), which likely in turn gave rise to the brown and spelaeoid lineages (Kurtén, 1968;Medin et al., 2017Medin et al., , 2019. ...
Karnezeika is a Lower Pleistocene locality in the Peloponnese, South Greece. More than 3000 specimens have been unearthed and studied, revealing the presence of a large mammal assemblage, which corresponds to the Middle Villafranchian biochronological unit. The bovid fauna of the site has already been presented, as well as the scarce remains of a large cercopithecid, which characterize Karnezeika as a primate-bearing fossil site. Herein, we describe the Carnivora of this locality. The carnivore guild of Karnezeika was found to consist of seven different taxa including Vulpes alopecoides, Felis sp., Megantereon cultridens, Ursus etruscus, Pachycrocuta brevirostris, Baranogale helbingi, and Mustelidae indet. Interestingly, the presence of the giant, short-faced hyena P. brevirostris among the assemblage shows that this species was present in SE Europe before the Olduvai subchron, similarly to West Europe. Furthermore, based on the new and relatively well-preserved specimens belonging to the rare mustelid B. helbingi, we discuss some possible taxonomic interpretations of this species. Finally, the majority of the carnivora taxa present in Karnezeika indicate a mixed habitat which agrees with previous palaeoenvironmental results concerning the site.
... The genus with the oldest occurrence in the subfamily is Plionarctos, from the Late Miocene-Early Pliocene of North America (Tedford and Martin, 2001;Mitchell et al., 2016). Arctodus has records from the Late Pliocene--Pleistocene of North America (Krause et al., 2008). Arctotherium, in turn, is a Pleistocene genus with occurrences from Central and South America and encompasses all South American Pleistocene ursids (Salis et al. 2021). ...
... savini-rossicus. Based on the methods of paleoDNA analysis, many species of cave bears are currently separated (Hofreiter et al. 2007;Krause et al. 2008;Knapp et al. 2009;Stiller et al. 2014;Barlow et al. 2016Barlow et al. , 2018Barlow et al. , 2019Barlow et al. , 2020. By the reason that not all cave bears from the Late Pleistocene have been genetically studied, we suppose that it is possible to consider them as U. ex. ...
The present work describes the dentognathic remains of Ursus etruscus Cuvier, 1823 from the recently discovered Taurida cave in central Crimea at the north Black Sea area. The bone-bearing layer of Taurida cave corresponds to the Psekupsian Faunal Assemblage of Eastern Europe and to the Late Villafranchian of Western Europe (ca. 1.8–1.5 Ma). Here, we describe unpublished ursid material unearthed during the excavations performed at the cave in 2020–2021, further comparing it with coeval chronologic and geographic sites around Europe. Our anatomical and biometrical analyses suggest the inclusion of the studied specimens in the hypodigm of the Early Pleistocene medium-sized species Ursus etruscus. The finds of the U. etruscus from the southern part of Eastern Europe provide a link between the western and eastern parts of the species range. Therefore, the finds from Crimea are important for understanding of the morphological diversity and evolution of U. etruscus which is the putative ancestor of both cave bears and brown bears. Furthermore, the study of these remains is also important for understanding the processes of the forming of the large mammal assemblages in the late Early Pleistocene and its relationships with the dispersal of the genus Homo.
... Tremarctos and Arctotherium are hypothesized to be sister taxa, diverging in the Pliocene. The estimated divergence estimation for Arctodus and Tremarctos is 5.66 million years ago (Krause et al. 2008). The Plionarctos linage is ancestral to Arctodus, Arctotherium, and Tremarctos but formed as a paraphyletic stem group (Tedford and Martin 2001). ...
Tremarctos ornatus (F.G. Cuvier, 1825) is a tremarctine bear commonly known as the Andean bear. It is a medium-sized bear with black to dark red-brown pelage with dense, long, coarse fur; creamy white marks occur on the chin, neck, and chest, and often white to creamy marks occur on the face, around the muzzle, and eyes. It is distributed in the tropical Andes of Venezuela, Colombia, Ecuador, Perú, Bolivia, and northern Argentina in South America. T. ornatus is catalogued as “Vulnerable” (VU) by the International Union for Conservation of Nature and Natural Resources and is included in CITES Appendix I. Main threats include habitat loss and fragmentation, illegal killing, human–bear conflicts, and most likely climate change.
... Aligning sequences helps to identify similar regions of DNA for easy comparison of genome sequences between multiple large vertebrates, making Progressive Cactus a great addition to the field of comparative genomics. Aligning and analyzing extinct and extant genomes may even help explain discordances in evolutionary history and answer how evolution impacted the flow of genetic information on extant Ursidae members (see Fig. 2) [33,34]. This also proves useful for identifying the genetic history of evolutionarily conserved traits that could hold biomedical importance. ...
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
