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Some typical clades within Laurasiatheria as suggested in the previous studies and their supports received from Bayesian PPs and BP analyses
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Although great progress has been made in resolving the relationships of placental mammals, the position of several clades in Laurasiatheria remain controversial. In this study, we performed a phylogenetic analysis of 97 orthologs (46,152 bp) for 15 taxa, representing all laurasiatherian orders. Additionally, phylogenetic trees of laurasiatherian ma...
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... likelihood scores from each gene were combined into a support value in two different ways, that is, the methods of Adachi and Hasegawa (1996) and Waddell, Cao, Hasegawa, and Mindell (1999), both shown in Waddell and Shelley (2003) as well. The Table 1 and SI Table 2). The BI tree was reconstructed for each gene and both SH and KH tests of all those 97 trees (SI Tree file) showed that no tree is identical to any of the others or to the resolved tree based on the combined genes alignment. ...
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... All of these factors have an impact on the estimation of species divergence time. The method used in this study for estimating divergence time has been widely used to estimate species divergence time based on whole-genome data [54][55][56]. Additionally, the fossil calibration points used to estimate the divergence time were obtained from TIMETREE (http://timetree.org/ ...
Cervidae represents a family that is not only rich in species diversity but also exhibits a wide range of karyotypes. The controversies regarding the phylogeny and classification of Cervidae still persist. The flourishing development of the genomic era has made it possible to address these issues at the genomic level. Here, the genomes of nine species were used to explore the phylogeny and chromosomal evolutionary events of Cervidae. By conducting whole-genome comparisons, we identified single-copy orthologous genes across the nine species and constructed a phylogenetic tree based on the single-copy orthologous genes sequences, providing new insights into the phylogeny of Cervidae, particularly the phylogenetic relationship among sika deer, red deer, wapiti and Tarim red deer. Gene family analysis revealed contractions in the olfactory receptor gene family and expansions in the histone gene family across eight Cervidae species. Furthermore, synteny analysis was used to explore the chromosomal evolutionary events of Cervidae species, revealing six chromosomal fissions during the evolutionary process from Bovidae to Cervidae. Notably, specific chromosomal fusion events were found in four species of Cervus, and a unique chromosomal fusion event was identified in Muntiacus reevesi. Our study further completed the phylogenetic relationship within the Cervidae and demonstrated the feasibility of inferring species phylogeny at the whole-genome level. Additionally, our findings on gene family evolution and the chromosomal evolutionary events in eight Cervidae species lay a foundation for comprehensive research of the evolution of Cervidae.
... Second, the phylogenetic isolation of the group from other mammalian orders, the limited fossil records, and the deep divergence within pangolins (Gaudin et al. 2009;Gaubert et al. 2018), pose methodological hurdles. Despite Pholidota being sister to the order Carnivora, the two orders are estimated to have started to diverge from around 78.9-76 million years ago (Zhou et al. 2011;Gaubert et al. 2018), thus making it difficult to incorporate outgroup taxa for genomic inferences of divergence and introgression. Compounded by this is the deep divergence (± 37.9 million years ago) of Asian and African pangolins (Gaubert et al. 2018) which may introduce ascertainment bias to genomic inferences depending on which continental clade the reference genome is a part of (Günther and Nettelblad 2019; Bohling 2020). ...
Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x–77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
... Laurasiatherian mammals have highly specialized anatomy and behavior; for example, they can fly, swim and run quickly, and they are insectivorous and carnivorous [68]. Rabies virus is a common virus of the genus RNA virus, and it is lethal to humans, wild mammals and domestic animals. ...
Many mammals risk damage from virus invasion due to frequent environmental changes. The oligoadenylate synthesis (OAS) gene family, which is an important component of the immune system, provides an essential response to the antiviral activities of interferons by regulating immune signal pathways. However, little is known about the evolutionary characteristics of OASs in Laurasiatherian mammals. Here, we examined the evolution of the OAS genes in 64 mammals to explore the accompanying molecular mechanisms of the antiviral ability of Laurasiatherian mammals living in different environments. We found that OAS2 and OAS3 were found to be pseudogenes in Odontoceti species. This may be related to the fact that they live in water. Some Antilopinae, Caprinae, and Cervidae species lacked the OASL gene, which may be related to their habitats being at higher altitudes. The OASs had a high number of positive selection sites in Cetartiodactyla, which drove the expression of strong antiviral ability. The OAS gene family evolved in Laurasiatherian mammals at different rates and was highly correlated with the species’ antiviral ability. The gene evolution rate in Cetartiodactyla was significantly higher than that in the other orders. Compared to other species of the Carnivora family, the higher selection pressure on the OAS gene and the absence of positive selection sites in Canidae may be responsible for its weak resistance to rabies virus. The OAS gene family was relatively conserved during evolution. Conserved genes are able to provide better maintenance of gene function. The rate of gene evolution and the number of positively selected sites combine to influence the resistance of a species to viruses. The positive selection sites demonstrate the adaptive evolution of the OAS gene family to the environment. Adaptive evolution combined with conserved gene function improves resistance to viruses. Our findings offer insights into the molecular and functional evolution of the antiviral ability of Laurasian mammals.
... This clade is seen as the top of the challenges for the establishment of phylogenetic relationships between mammalian taxa (Hu et al., 2013), since, except for Eulipotyphla, all other orders diversified in a short period from 1 to 4 million years (Hallström & Janke, 2010;Zhou et al., 2012). In the absence of a few genes with a strong phylogenetic signal related to the divergence of laurasiatherians, many phylogenomic hypotheses have been proposed (for example, only in the last decade: Hallström et al., 2011;Mccomarck et al., 2012;Zhou et al., 2012;Nery et al., 2012;Romiguier et al., 2013;Benevento et al., 2019). ...
... This clade is seen as the top of the challenges for the establishment of phylogenetic relationships between mammalian taxa (Hu et al., 2013), since, except for Eulipotyphla, all other orders diversified in a short period from 1 to 4 million years (Hallström & Janke, 2010;Zhou et al., 2012). In the absence of a few genes with a strong phylogenetic signal related to the divergence of laurasiatherians, many phylogenomic hypotheses have been proposed (for example, only in the last decade: Hallström et al., 2011;Mccomarck et al., 2012;Zhou et al., 2012;Nery et al., 2012;Romiguier et al., 2013;Benevento et al., 2019). ...
The members of the Mammalia class experienced high ecological, morphological and taxonomic diversification during the Cenozoic Era. With technological advances in molecular paleontology in recent decades, many claims for the exceptional preservation of nonmineralized biomaterials have been made for this clade. However, these data are scattered in the literature and have associated such reports with unique and rare events. This study presents a review of the literature published in the last six decades, aiming to investigate the frequency with which vestigial of nonmineralized biomaterials are found in Mammalia fossils. The results identified 79 published studies describing endogenous biocomponents in Metatheria and Theria members. Of these, protein fragments were more frequent in sedimentary deposits (33.3%), and ancient DNA sequences were more frequent in depositional environments more favorable to exceptional preservation (53.1%), such as ice and cave deposits. The data on organic material for mammalian fossils are geographically and taxonomically comprehensive, with the superordinates Laurasiatheria and Afrotheria presenting the largest number of reports. With the emergence and improvement of new techniques for the recovery of organic material, it is believed that paleomolecular information for fossil mammals should increase, in addition to broadening the understanding of taphonomic factors related to exceptional preservation.
... Therefore, three different strategies were developed to design the MHC markers for the Formosan pangolin. Carnivora may be the closest related order to Pholidota, and some of the carnivore MHC genes have been widely studied, for example, cats and dogs [45][46][47] . In this study, the carnivore MHC gene sequence together with the draft genome sequence for the Chinese pangolin were used in the three different strategies. ...
The Formosan pangolin ( Manis pentadactyla pentadactyla ) is an endangered species in Taiwan. The polymorphisms at major histocompatibility complex (MHC) gene regions could provide an indicator for immunological fitness and genetic diversity of a population. In this study, seven different novel markers for MHC genotyping of Formosan pangolin were developed and used to evaluate the genetic diversity of 92 Formosan pangolins. In the MHC markers, six loci showed monomorphism or only two haplotypes. Only one marker, a DLA class II DR-1 beta chain-like locus, showed more diversity: four haplotypes were detected and their relative frequencies were 62.0, 37.0, 0.5 and 0.5%, with nine polymorphic sites in the nucleotide sequence and six variable sites in the amino acid sequence. The non-synonymous substitution rate (dN) and synonymous substitution rate (dS) were 0.026 and 0.017, and showed that this locus appears to be under positive selection (dN /dS >1). Observed heterozygosity (H O ) and expected heterozygosity (H E ) were 0.413 and 0.482, respectively. F IS was 0.144, indicating that the population might have an inbreeding tendency (F IS > 0). Haplotype diversity ( h ) was 0.482 and nucleotide diversity (π) was 0.010. Overall, the results indicated that the genetic diversity of MHC genes among Formosan pangolins in Taiwan was insufficient.
... The whole chloroplast genome has numerous features e.g., small in size, conserved structure, maternal inheritance, and species identification is broadly applied for evolutionary studies [6]. Recently, an extremely divergent region in plant plastome has been identified called "hotspot region" and served an useful genetic marker for phylogeny and evolutionary studies of genus Pinus [7]. Previous studies showed that the genus Pinus had shared several genomic sequence variations for cp DNAs owing to their recent divergence radiation, regular interspecific and introgression gene flow among species [8]. ...
Pinus is one of the most economical and ecological important conifers, model specie for studying sequence divergence and molecular phylogeney of gymnosperms. The less availability of information for genome resources enable researchers to conduct evolutionary studies of Pinus species. To improve understanding, we firstly reported, previously released chloroplast genome of 72 Pinus species, the sequence variations, phylogenetic relationships and genome divergence among Pinus species. The results displayed 7 divergent hotspot regions ( trnD-GUC , trnY-GUA , trnH-GUG , ycf1 , trnL-CAA , trnK-UUU and trnV-GAC ) in studied Pinus species, which holds potential to utilized as molecular genetic markers for future phylogenetic studies in Pinnus species. In addition, 3 types of repeats (tandem, palindromic and dispersed) were also studied in Pinus species under investigation. The outcome showed P . nelsonii had the highest, 76 numbers of repeats, while P . sabiniana had the lowest, 13 13 numbers of repeats. It was also observed, constructed phylogenetic tree displayed division into two significant diverged clades: single needle (soft pine) and double-needle (hard pine). Theoutcome of present investigation, based on the whole chloroplast genomes provided novel insights into the molecular based phylogeny of the genus Pinus which holds potential for its utilization in future studies focusing genetic diversity in Pinnus species.
... Modern genetics suggests that the superorder Laurasiatheria, of which bats (order Chiroptera) are a part, diverged from the rodent superorder Euarchontoglires during the mid-Cretaceous period (Murphy et al. 2004;Springer et al. 2004;Zhou et al. 2012). The earliest fossils representative of modern bats have been dated to 52.5 million years ago (Simmons et al. 2008;Veselka et al. 2010). ...
Bats (order Chiroptera) are the second largest group of mammals, diverging ~52.5 million years ago. Many species exhibit an unusual reproductive cycle and extreme longevity without reproductive senescence, yet steroid profiles exist for few bats. Big brown bats (Eptesicus fuscus) are temperate insectivores found throughout North America. They mate promiscuously in fall, store sperm during winter hibernation, and have delayed ovulation and fertilization in spring. Here, we report the first urinary steroid profile in bats by quantifying 17β-estradiol (E2) in captive male and female E. fuscus across their reproductive cycle. Male bats had higher urinary E2 levels than females, and adults had higher levels than yearlings following creatinine adjustment for hydration. In nonpregnant females, several seasonal differences in creatinine-adjusted and unadjusted urinary E2 levels were observed. Urinary E2 was higher in males than females in winter for both conditions and in autumn for creatinine-adjusted levels. We quantified progesterone (P4) in a subset of females. In nonpregnant females, urinary P4 was constant across seasons except for unadjusted levels, which were highest in the summer. In pregnant females, urinary E2 and P4 levels peaked beginning ~20 d before parturition, with both steroids returning to baseline in the following weeks. Knowing how urinary steroid levels fluctuate with age and sex and across the annual season is key to understanding reproductive cycling in bats. Our research furthers the potential for bats as a model for medical reproductive research. Moreover, it complements previous studies on the potential role of steroids in primer pheromonal effects in bats.
... Analyses of the selective pressure were performed based on the ratio of non-synonymous (d N ) to synonymous (d S ) substitutions (d N /d S or ω) in the CODEML program incorporated in the PAML 4.7a package (Yang 2007), where ω < 1, ω = 1 and ω > 1 indicate purifying selection, neutral selection and positive selection, respectively. The well-known species tree (Fig. 1) only served as a guide tree in subsequent PAML analyses (Flynn et al. 2005;Blanga-Kanfi et al. 2009;Kuntner et al. 2011;Polina et al. 2011;Zhou et al. 2012). Here, the premature stop codons were considered to be missing data (regarded as NNN or -) to maintain the sequence integrity for d N /d S analyses with CODEML. ...
Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.
... The absence of early Eocene bats in Asia, however, is striking in light of their laurasiatherian relationships and apparent rapid dispersal to such far flung continents as Australia and South America. Additionally, relationships among bats and other laurasiatherians are unsettled [21,24,25], obscuring the identification of unambiguously primitive characters among bats. ...
Bats dispersed widely after evolving the capacity for powered flight, and fossil bats are known from the early Eocene of most continents. Until now, however, bats have been conspicuously absent from the early Eocene of mainland Asia. Here, we report two teeth from the Junggar Basin of northern Xinjiang, China belonging to the first known early Eocene bats from Asia, representing arguably the most plesiomorphic bat molars currently recognized. These teeth combine certain bat synapomorphies with primitive traits found in other placental mammals, thereby potentially illuminating dental evolution among stem bats. The Junggar Basin teeth suggest that the dentition of the stem chiropteran family Onychonycteridae is surprisingly derived, although their postcranial anatomy is more primitive than that of any other Eocene bats. Additional comparisons with stem bat families Icaronycteridae and Archaeonycteridae fail to identify unambiguous synapomorphies for the latter taxa, raising the possibility that neither is monophyletic as currently recognized. The presence of highly plesiomorphic bats in the early Eocene of central Asia suggests that this region was an important locus for the earliest, transitional phases of bat evolution, as has been demonstrated for other placental mammal orders including Lagomorpha and Rodentia.
... 47 The Chiroptera order is a placental lineage of the middle Paleocene or early Eocene, evolved for more than 50 million years and which were initially classified in the super-order Archonta, together with the tree shrews (order Scandentia), colugos (arboreal climber) (Order Dermoptera) and primates, due to the apparent similarities between the current clate Megachiroptera and the other mammals. [48][49][50][51] Evolutionary studies with other groups of mammals and even among bats from different families can provide important clues in the investigation of physiological aspects that can favor disease dissemination events. Genetic, morphological and paleontological studies have shown that bats seem to be more related to fauna originating in the supercontinent Laurasia (Northern Hemisphere, including North America, Europe, North Asia and Japan), so bats are constituted in the super-order Laurasiatheria, comprising a monophyletic lineage 48 that includes together carnivores (Carnivorous Order), pangolins and scaly anteaters (Pholidota Order); ungulates of odd fingers; horses, tapirs, rinocentes etc. (Order Perissodactyla); and pigs, cattle, deer, etc. (Order Artiodactyla) with even fingers, and the Cetacean Order (dolphins and whales). ...
... Genetic, morphological and paleontological studies have shown that bats seem to be more related to fauna originating in the supercontinent Laurasia (Northern Hemisphere, including North America, Europe, North Asia and Japan), so bats are constituted in the super-order Laurasiatheria, comprising a monophyletic lineage 48 that includes together carnivores (Carnivorous Order), pangolins and scaly anteaters (Pholidota Order); ungulates of odd fingers; horses, tapirs, rinocentes etc. (Order Perissodactyla); and pigs, cattle, deer, etc. (Order Artiodactyla) with even fingers, and the Cetacean Order (dolphins and whales). [48][49][50] The nominal origin of the term "bat" originated from the Latin mure = mur, mouse with the word "blind", thus meaning "blind rat". Bats constitute the second largest order within the Mammalia Class, losing in diversity only to rodentia make up 20% of mammalia species. ...
Since recent findings on coronavirus, there are numerous outstanding questions about the recent emergence of these viruses, their relationship to bats, environmental issues, gene recombinations, reservoirs, evolution and the role of human coronavirus in human infection. This review aimed to gather information about the possible origin of the new coronavirus (SARS-CoV-2) and its relationship with the alated mammals and the new strains found. Selected studies indicate that SARS-CoV-2 is a chimeric virus between a bat coronavirus and a coronavirus of unknown origin. One of the possibilities points to bats as being a reservoir originating from SARS-CoV-2 (COVID-19), transmitting to man via host source. The records indicate that a recombination between the coronaviruses of pangolins and the bat coronavirus BatCoV RaTG13 and SARS-CoV-2 human there is a common ancestry among these Betacoronaviruses, which were even identified in other mammalian species, named Ptajacu-CoV. Several questions were raised about the artificial origin of the virus by laboratory manipulation. However, although remote, further investigations are needed to rule out a probable release and the real existence of SARS-CoV-2 and beta coronaviruses, which circulate for decades among the human species.
