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Background: The species M. melini has been observed in both the Pampa and Spinal ecoregions of Argentina. Researchers have underscored that distinguishing M. melini from other species within the same genus relies primarily on craniometric and molecular analyses. Morphological measurements alone do not offer a clear differentiation between M. melini and other members of this genus. This study aims to document the presence of M. melini within the Brazilian ecoregion, focusing on its morphological, morphometric and genetic characteristics. By undertaking a comprehensive examination, we seek to contribute valuable insights into the distribution and differentiation of M. melini in this region. New information: Molossus melini specimens exhibited a forearm length ranging from 39.9 to 40.08 mm. The average intraspecific divergence was 1.2%, with specimens from the Argentine Pampas clustering in the same clade with a 98% bootstrap support and a posterior probability of: Regarding dorsal colouration, the specimens displayed fur with two bands--a Snow White base colour and apex colours ranging from Olive Brown, Broccoli Brown, Wood Brown to Yellowish-Brown. This marks the first record of M. melini in Brazil, expanding its distribution 1,300 km northeastwards into the Curitiba, Paraná, Atlantic Forest Ecoregion. The findings contribute valuable information on the distribution, morphology, morphometrics and genetics of this species. [ABSTRACT FROM AUTHOR]

A study of taxonomic differentiation and transition bias of the cytb gene, focusing on the early stages of speciation, was carried out in 15 subfamilies/families of five orders of Palearctic mammals. It was confirmed that the genetic differentiation among taxa of small and large mammals is shifted by the same taxonomic level, in which connection the period of cryptic speciation of Micromammalia (semi- and allospecific levels) corresponds to the divergence of type species in their genus within Macromammalia. In all cases, both transition bias and its evolutionary compensation took place. The novelty of the study also lies in the proof that the alignment of the transitions and transversion rates in evolutionary lineages has the pattern of a phase transition, and the frequency of transversions in short-cycle species of the orders Insectivora and Rodentia is higher than in long-cycle orders Artiodactyla, Carnivora and Chiroptera while with relative equality of transitions. The latter circumstance might be associated with the traits of metabolism and determines the characteristics of the molecular evolution of mammalian groups with short and long life cycles. [ABSTRACT FROM AUTHOR]

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Mary Lyon's 1961 paper in the journal Nature offered an elegant solution to the dosage problem posed by the X and Y chromosomes in mammals. Lyon deduced from two observations in mice that one X chromosome is switched off early in embryonic development, and it is random whether the maternally or paternally inherited X is switched off in any given cell. This X inactivation leads to female mammals being genetically mosaic for genes in which parents contribute distinct variants, providing protection against adverse effects of mutant genes. Lyon's contribution to mammalian genetics is highly regarded and she serves as a role model for women in science. [Extracted from the article]

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolinCoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs. [ABSTRACT FROM AUTHOR]

The small-eared shrew genus Cryptotis is the third largest in the family Soricidae and occurs in North, Central, and northern South America. In Mexico and Central and South America, most species inhabit geographically isolated moist, montane habitats at middle and high elevations in a typical sky-island pattern. The 49 recognized species have been partitioned into as many as six species groups based on morphological and molecular phylogenetic studies. The relationships among these species groups are poorly resolved, and their evolutionary histories, including migration patterns and locomotor adaptations, remain unclear. Herein, we provide a new phylogeny incorporating complete mitochondrial genomes (mitogenomes) and supermatrix approach. We compared different evolutionary scenarios using approximately unbiased (AU), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH) statistical tests. The phylogenetic hypothesis based on mitogenomes revealed novel relationships supporting a basal position for the Cryptotis parvusgroup in the genus, and a close relationship between C. gracilis and one clade of the C. thomasi-group. The former relationship is consistent with the least derived humerus morphology and northern distribution of the species. The latter relationship implies multiple migrations between Central and South America. The lack of fine resolution for the species group relationships may be due partly to the lack of taxon sampling. In contrast, multi-approach analyses suggest that the unresolved relationships may be a result of rapid diversification during the early stages of Cryptotis evolution. [ABSTRACT FROM AUTHOR]

Proteins encoded by antigen-processing genes (APGs) provide major histocompatibility complex (MHC) class I (MHC-I) with antigenic peptides. In mammals, polymorphic multigenic MHC-I family is served by monomorphic APGs, whereas in certain nonmammalian species both MHC-I and APGs are polymorphic and coevolve within stable haplotypes. Coevolution was suggested as an ancestral gnathostome feature, presumably enabling only a single highly expressed classical MHC-I gene. In this view coevolution, while optimizing some aspects of adaptive immunity, would also limit its flexibility by preventing the expansion of classical MHC-I into a multigene family. However, some nonmammalian taxa, such as salamanders, have multiple highly expressed MHC-I genes, suggesting either that coevolution is relaxed or that it does not prevent the establishment of multigene MHC-I. To distinguish between these two alternatives, we use salamanders (30 species from 16 genera representing six families) to test, within a comparative framework, a major prediction of the coevolution hypothesis: the positive correlation between MHC-I and APG diversity. We found that MHC-I diversity explained both within-individual and species-wide diversity of two APGs, TAP1 and TAP2 , supporting their coevolution with MHC-I , whereas no consistent effect was detected for the other three APGs (PSMB8 , PSMB9 , and TAPBP). Our results imply that although coevolution occurs in salamanders, it does not preclude the expansion of the MHC-I gene family. Contrary to the previous suggestions, nonmammalian vertebrates thus may be able to accommodate diverse selection pressures with flexibility granted by rapid expansion or contraction of the MHC-I family, while retaining the benefits of coevolution between MHC-I and TAPs. [ABSTRACT FROM AUTHOR]

In mammals, the placenta mediates maternal–fetal nutrient and waste exchange and acts in an immunomodulatory way to facilitate maternal–fetal tolerance. The placenta is highly diverse across mammalian species, yet the molecular mechanisms that distinguish the placenta of human from other mammals are not fully understood. Using an interspecies transcriptomic comparison of human, macaque, and mouse late-gestation placentae, we identified hundreds of genes with lineage-specific expression—including dozens that are placentally enriched and potentially related to pregnancy. We further annotated the enhancers for different human tissues using epigenomic data and demonstrate that the placenta and chorion are unique in that their enhancers display the least conservation. We identified numerous lineage-specific human placental enhancers and found they highly overlap with specific families of endogenous retroviruses (ERVs), including MER21A, MER41A/B, and MER39B that were previously linked to immune response and placental function. Among these ERV families, we further demonstrate that MER41A/B insertions create dozens of lineage-specific serum response factor-binding loci in human, including one adjacent to FBN2 , a placenta-specific gene with increased expression in humans that produces the peptide hormone placensin to stimulate glucose secretion and trophoblast invasion. Overall, our results demonstrate the prevalence of lineage-specific placental enhancers which are frequently associated with ERV insertions and likely facilitate the lineage-specific evolution of the mammalian placenta. [ABSTRACT FROM AUTHOR]

Phylogenetic reconstruction and species delimitation are often challenging in the case of recent evolutionary radiations, especially when postspeciation gene flow is present. Leopardus is a Neotropical cat genus that has a long history of recalcitrant taxonomic problems, along with both ancient and current episodes of interspecies admixture. Here, we employ genome-wide SNP data from all presently recognized Leopardus species, including several individuals from the tigrina complex (representing Leopardus guttulus and two distinct populations of Leopardus tigrinus), to investigate the evolutionary history of this genus. Our results reveal that the tigrina complex is paraphyletic, containing at least three distinct species. While one can be assigned to L. guttulus , the other two remain uncertain regarding their taxonomic assignment. Our findings indicate that the "tigrina" morphology may be plesiomorphic within this group, which has led to a longstanding taxonomic trend of lumping these poorly known felids into a single species. [ABSTRACT FROM AUTHOR]

The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P  = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan. [ABSTRACT FROM AUTHOR]

The Yucatan Peninsula (YP) is a biotic province located in southeastern Mexico, delimited mainly by climatic variables. One endemic species of the YP is the Yucatan deer mouse Peromyscus yucatanicus. It is considered a member of the P. mexicanus species group, but some morphological characters and habitat preferences separate it from them. Herein, the DNA barcoding identification of P. yucatanicus, intraspecific relationships, and the level of genetic differentiation among its geographical distribution were examined. Sequences of the mitochondrial cytochrome c oxidase subunit 1 gene were used for the phylogenetic, demographic history, and genetic structure analysis. In addition, an ecological niche model was built and transferred to 6000 years ago in order to explore the current and past environmental suitability of the species. Results showed that P. yucatanicus was monophyletic and its phylogenetic relationships unresolved. Intraspecific analyses showed signatures of a scenario of demographic stability followed by population growth, and three genetic haplogroups were identified. Paleontological, paleoclimate, and the results presented here are useful to hypothesize that P. yucatanicus likely diverged in the Pleistocene and invaded the south of YP after the Last Glacial Period with the arrival of the current vegetation in the late Pleistocene—early-middle Holocene, and its demographic population was stable during the remaining Holocene epoch with slight growth at the late-middle Holocene resulting in the major precipitation changes that provided more plant coverage. [ABSTRACT FROM AUTHOR]

We addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends. [ABSTRACT FROM AUTHOR]

Several recent studies have suggested past gene flow between the Przewalski's horse and modern domestic horse and questioned the wild origin of the Przewalski's horse. Mitochondrial DNA has placed representatives of the Przewalski's horse into three among the eighteen haplogroups detected from the modern horse. Of these, two haplogroups have so far been found exclusively in the Przewalski's horse, while the one shared with the domestic horse includes captive individuals that have uncertain pedigrees. We recently found five domestic horse individuals of North European horse breeds to carry a mitochondrial haplogroup that was previously confined only to the Przewalski's horse. These individuals were sequenced for 6039 bp of mitochondrial DNA and used, together with domestic and Przewalski's horse sequences presenting all horse haplogroups, to examine the phylogenetic relationships and to date the divergence time between Przewalski's and domestic horse clusters within this haplogroup. The divergence was dated to have likely occurred about 13,300–11,400 years ago, which coincides with the time of the Younger Dryas. [ABSTRACT FROM AUTHOR]

The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted. We produced a highly contiguous male genome assembly, together with short-read genomes and transcriptomes for both sexes. We show that M. oregoni has lost an independently segregating Y chromosome and that the male-specific sex chromosome is a second X chromosome that is largely homologous to the maternally transmitted X. Both maternally inherited and male-specific sexchromosomes carry fragments of the ancestral Y chromosome. Consequences of this recently transformed sex chromosome system include Y-like degeneration and gene amplification on the male-specific X, expression of ancestral Y-linked genes in females, and X inactivation of the male-specific chromosome in male somatic cells. The genome of M. oregoni elucidates the processes that shape the gene content and dosage of mammalian sex chromosomes and exemplifies a rare case of plasticity in an ancient sex chromosome system. [ABSTRACT FROM AUTHOR]

Enamel microstructure of 34 species in eight odontocete families is described and categorized according to structural complexity (from no or prismless enamel to highly arranged enamel in decussating layers), then correlated with parameters of ecology, life history, and occlusal function. Overall, more complex dental structure in extant and extinct cetaceans is associated with smaller, more numerous teeth in taxa that bite or grasp smaller, harder prey with longer, narrower jaws and have more oral processing. Enamel complexity loosely correlates with mechanical properties, but measurement of compressive strength is complicated by the presence of cementum overlying or in place of crown enamel. Given the presence of Hunter-Schreger bands and other indices of high microstructural complexity in archaic cetaceans (with presumed plesiomorphic characters), the absence of complex enamel, as well as more generally of gross dental form, signals a loss of complexity in various cetacean lineages. Nonetheless, it is difficult to draw robust or reliable inferences regarding either cetacean phylogeny or dental function given the pattern of presumed loss of tooth complexity, and the confounding presence of numerous exceptions (taxa with complex teeth despite limited use, or with thin, weakly developed enamel and soft, simple teeth despite high occlusal function). Although retention of a complex feature implies its continued adaptive value, and thus selection for the underlying genetic and developmental bases for that complexity, loss of complexity can simply follow absence of function. Loss of complex traits presumably relates to accumulated mutations and economic efficiency, but unfolds with no distinct pattern of distribution. [ABSTRACT FROM AUTHOR]

Breeding management of small populations may have a critical influence on the development of population characteristics in terms of levels of genetic diversity and inbreeding. Two populations of antelope sister species – Critically Endangered Western Derby eland (Tauroragus derbianus derbianus) and non-native Least Concern Cape eland (Taurotragus oryx oryx) bred under different management strategies were studied in Senegal, Western Africa. The aims of the study were to compare the population genetic parameters of the two species and to test for the presence of interspecific hybrids. In total, blood and tissue samples from 76 Western Derby elands and 26 Cape elands were investigated, using 12 microsatellite markers. No hybrid individuals were detected in the sampled animals within the multispecies enclosure in Bandia Reserve, Senegal. The parameters of genetic polymorphism indicated much lower genetic diversity in Western Derby elands compared to Cape elands. On the other hand, the coefficient of inbreeding was low in both species. It is hypothesized that this could be a positive effect of strict population management of Western Derby elands, which, despite the loss of genetic diversity, minimizes inbreeding. [ABSTRACT FROM AUTHOR]

Bird remains are few compared to mammals at Neolithic Çatalhöyük, but thanks in part to an extensive flotation program, an assemblage of more than 1300 specimens from secure contexts has been recovered and studied, covering nearly the entire ca. 1100-year sequence from the Neolithic East Mound. The Çatalhöyük inhabitants heavily targeted water birds throughout the sequence. However, the overall relative stability in taxa through time conceals considerable household variation both in areas of the landscape exploited and particular species taken or avoided. As I have argued for the mammals, this may result in part from taboos on some birds, notably herons, that apply only to certain households or other social categories. Indeed, in contrast to earlier sites nearby, the meatier portions of the skeleton are underrepresented at Çatalhöyük, with legs and especially wings predominating. Feathers were likely a major motivation for taking many of the birds, some of them used for costumes. Some bird bones appear in special deposits indicating a symbolic role for, at least, cranes, vultures, crows, and spoonbills. [ABSTRACT FROM AUTHOR]

The aim of this experiment was to evaluate the significance of neonatal environment on feed efficiency. For that purpose, rabbits from a line selected for residual feed intake (RFI) during 10 generations (G10 kits) were cross‐fostered with non‐selected control does (i.e., G0 line), and reciprocally. In parallel, sibs were fostered by mothers from their original line. Nine hundred animals were raised in individual (N = 456) or collective (N = 320) cages. Traits analysed in this study were body weight at 32 days and at 63 days, average daily gain (ADG), feed intake between weaning and 63 days (FI), feed conversion ratio (FCR) and RFI. The maternal environment offered by does from the line selected for RFI deteriorated the FCR of the kits, independently of their line of origin, during fattening (+0.08 ± 0.02) compared to FCR of kits nursed by G0 does. The line, the type of housing and the batch were significant effects for all the measured traits: G10 kits were lighter than their G0 counterparts at 32 days (−82.9 ± 9 g, p < 0.0001) and at 63 days (−161 ± 16 g, p < 0.0001). They also had a lower ADG (−2.36 ± 0.36 g/day, p < 0.0001), RFI (−521 ± 24 g/day, p < 0.0001) and a lower FI (−855 ± 31 g, p < 0.0001), resulting in a more desirable feed efficiency (FCR: −0.35 ± 0.02). There was no significant difference in the contrast of G10 and G0 performances between collective and individual/digestive cages (p > 0.22): −2.35 g/day versus 2.94 g/day for ADG, −0.39 versus −0.40 for FCR, −577 g versus −565 g for RFI and −879 g versus −859 g for FI, respectively). Thus, no genotype‐by‐environment (housing) interaction is expected at the commercial level, that is, no re‐ranking of the animals due to collective housing. [ABSTRACT FROM AUTHOR]

Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock. [ABSTRACT FROM AUTHOR]

Abstract The BRCA1 gene is located on the human chromosome 17q21.31 and plays important role in biological processes. The aminoacyl-tRNA synthetases (AARS) are a family of heterogenous enzymes responsible protein synthesis and whose secondary functions include a role in autoimmune myositis. Our findings reveal that the compositional constraint and the preference of more A/T –ending codons determine the codon usage patterns in BRCA1 gene while more G/C-ending codons influence the codon usage pattern of AARS gene among mammals. The codon usage bias in BRCA1 and AARS genes is low. The codon CGC encoding arginine amino acid and the codon TTA encoding leucine were uniformly distributed in BRCA1 and AARS genes, respectively in mammals including human. Natural selection might have played a major role while mutation pressure might have played a minor role in shaping the codon usage pattern of BRCA1 and AARS genes. Highlights • Mammalian BRCA1 and AARS genes possess low codon bias. • A/T-ending codons determine the codon usage patterns in BRCA1 gene but G/C-ending codons in AARS gene. • Natural selection played a major role while mutation pressure played a minor role in shaping codon usage pattern of BRCA1 and AARS genes. [ABSTRACT FROM AUTHOR]

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ~ 170 MYR. Secondly, we identified the genomic outliers or "rebel genes" within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause. [ABSTRACT FROM AUTHOR]

Fin whales (Balaenoptera physalus) have a global distribution, but the population inhabiting the Gulf of California (GoC) is thought to be geographically and genetically isolated. However, their distribution and movements are poorly known. The goal of this study was to describe fin whale movements for the first time from 11 Argos satellite tags deployed in the southwest GoC in March 2001. A Bayesian Switching State-Space Model was applied to obtain improved locations and to characterize movement behavior as either “area-restricted searching” (indicative of patch residence, ARS) or “transiting” (indicative of moving between patches). Model performance was assessed with convergence diagnostics and by examining the distribution of the deviance and the behavioral parameters from Markov Chain Monte Carlo models. ARS was the predominant mode behavior 83% of the time during both the cool (December-May) and warm seasons (June-November), with slower travel speeds (mean = 0.84 km/h) than during transiting mode (mean = 3.38 km/h). We suggest ARS mode indicates either foraging activities (year around) or reproductive activities during the winter (cool season). We tagged during the cool season, when the whales were located in the Loreto-La Paz Corridor in the southwestern GoC, close to the shoreline. As the season progressed, individuals moved northward to the Midriff Islands and the upper gulf for the warm season, much farther from shore. One tag lasted long enough to document a whale’s return to Loreto the following cool season. One whale that was originally of undetermined sex, was tagged in the Bay of La Paz and was photographed 10 years later with a calf in the nearby San Jose Channel, suggesting seasonal site fidelity. The tagged whales moved along the western GoC to the upper gulf seasonally and did not transit to the eastern GoC south of the Midriff Islands. No tagged whales left the GoC, providing supporting evidence that these fin whales are a resident population. [ABSTRACT FROM AUTHOR]

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge. [ABSTRACT FROM AUTHOR]

A complete set of pika taxa, belonging to the subgenus Ochotona, was studied using craniometric and multilocus genetic analyses. We examined 1,007 skulls, covering the entire distribution range of the subgenus, as well as the mitochondrial COI gene and three nuclear introns in 31 specimens, representing nearly all taxa in question. An additional set of 167 COI gene sequences and 357 cytb gene sequences was analysed to enlarge the geographical extent of genetic data and to compare the results with previous publications. We found that the subgenus consists of eight species. One of them, Ochotona morosa, is elevated to the full species rank for the first time. The name of this species is given preliminarily and should be studied additionally. Several cases of interspecies hybridisation were found, which indicates that mitochondrial DNA cannot be used for species identification in this subgenus. Taxon Ochotona qionglaiensis, which was recently described as a separate species, represents a relic mitochondrial lineage of Ochotona thibetana. Another recently described species, Ochotona yarlungensis, is a Nubra pika with its native mitochondrial DNA, firstly found for this species. Intraspecies variation was analysed for several species for the first time. Thus, new subspecies (Ochotona thibetana fengii ssp. n.) was found within O. thibetana. [ABSTRACT FROM AUTHOR]

The human S100A7 resides in the epidermal differentiation complex (EDC) and has been described as a key effector of innate immunity. In humans, there are five S100A7 genes located in tandem—S100A7A, S100A7P1, S100AL2, S100A7, and S100AP2. The presence of several retroelements in the S100A7A/S100A7P1 and S100A7/S100A7P2 clusters suggests that these genes were originated from a duplication around ~ 35 million years ago, during or after the divergence of Platyrrhini and Catarrhini primates. To test this hypothesis, and taking advantage of the high number of genomic sequences available in the public databases, we retrieved S100A7 gene sequences of 12 primates belonging to the Cercopithecoidea and Hominoidea (Catarrhini species). Our results support the duplication theory, with at least one gene of each cluster being identified in both Cercopithecoidea and Hominoidea species. Moreover, given the presence of an ongoing gene conversion event between S100A7 and S100A7A, a high rate of mutation in S100A7L2 and the presence of pseudogenes, we proposed a model of concerted and birth-and-death evolution to explain the evolution of S100A7 gene family. Indeed, our results suggest that S100A7L2 most likely suffered a neofunctionalization in the Catarrhini group. Being S100A7 a major protein in innate defense, we believe that our findings could open new doors in the study of this gene family in immune system. [ABSTRACT FROM AUTHOR]

Abstract The Anatolian and the Lesser blind mole rats (Nannospalax xanthodon and N. leucodon) are widely distributed in Anatolia and Thrace and feature remarkable diversity of chromosomal races. The evolutionary relationship among various cytotypes has not been fully resolved, and little is known about the genetic diversity at the population level. Traditionally, N. xanthodon is divided into Western and Central Anatolian phylogenetic clades, but the inclusion of particular cytotypes into one or the other clade still causes controversy, and the relationship of N. leucodon from Thrace to other Turkish populations is not known. We genotyped 67 and 62 individuals, sampled across Western Turkey, respectively at one mtDNA (1048 bp long fragment of cyt b) and ten highly polymorphic microsatellite markers. The population genetic structure was analyzed (i) in respect to previously assigned karyotype (cytotypes 2n = 38, 50, 52, 56 and 60 of N. xanthodon and 2n = 56 of N. leucodon) and geographic locality data, and (ii) without assuming any prior grouping. Both the phylogeny constructed from the cyt b sequence and the population structure revealed by the microsatellite genotyping revealed the presence of two major clades. The first included the Western Anatolian populations of N. xanthodon (cytotypes 2n = 38, 2n = 50 and 2n = 52), but also N. leucodon from Thrace (2n = 56). The second clade included the Central Anatolian populations of N. xanthodon with cytotypes 2n = 56 and 2n = 60. These findings support and refine the previously suggested relationships between 2n = 38, Thracian N. leucodon and 2n = 60 (Hadid et al., 2012). We also revealed higher genetic diversity, particularly within cytotype 2n = 38 (race anatolicus), and stronger population structuring within the Western Anatolian clade. In contrast, the microsatellite genotypes of two races in Central Anatolian clade (2n = 60 and 2n = 56 from Manisa province), showed less diversity and weaker population structure. [ABSTRACT FROM AUTHOR]

Abstract We determined allelic variation at eleven microsatellite loci to study the effect of the Bosphorus, the Sea of Marmara, and the Dardanelles on the population genetic architecture of brown hares, Lepus europaeus , from Anatolia and Turkish Thrace in the southeastern most Balkans. The latter region was connected with Anatolia during periods of the late Pleistocene and the early Holocene (until ca. 8000 y BP) enabling natural gene flow. Following a recent mitochondrial (mt) DNA-based phylogeographic model that suggested unidirectional ancient gene flow from Anatolia to the SE Balkans, we expected lower genetic diversity in hares from Turkish Thrace than Anatolia. The Turkish Thrace population might have been established only relatively recently as natural northwestward expansion of a long existing Anatolian population. Alternatively, it might have received late Pleistocene or Holocene gene flow by hares from eastern Europe from north of the Black Sea, even after the formation of the marine barrier. This might have produced a notable genetic distinction between the hares from either side of the Bosphorus, the Sea of Marmara, and the Dardanelles. We found significantly lower allelic richness in hares from Turkish Thrace than Anatolia, very little genetic admixture in the Turkish Thrace population, and only one allele at low frequency in Turkish Thrace that was not observed in Anatolian hares. On the contrary, many alleles of Anatolian hares were not recovered in hares from Turkish Thrace. Nevertheless, genetic divergence (Fst , Cavalli-Sforza & Edwards distances, AMOVA) between the hares from either side of the current marine barrier was low (Fst values <10%). All findings accord to our initial hypothesis that the hares from Turkish Thrace represent merely a somewhat genetically depleted version of the Anatolian hares. Seemingly, no strong drift has occurred in the Turkish Thrace population since the break-up of the Holocene landbridge, and there is no indication of gene flow from other regions in (eastern) Europe into the Turkish Thrace population. Spatial genetic approaches and standard population genetics (BAPS, GENELAND, STRUCTURE, F-statistics, Cavalli-Sforza & Edwards distances) indicated significant spatial genetic differentiation of hares across Anatolia, but also on a very low level. Overall, our results are concordant with the latest mtDNA based model of ancient gene flow in hares only from Anatolia to the southeastern Balkans across the Pleistocene and early Holocene landbridge; this implies that most or all of the Balkans have been colonized by hares exclusively originating eventually from Anatolia. [ABSTRACT FROM AUTHOR]

The previously developed technology RNA enhancement (RNAe) is reported to increase specific gene expression at post-transcriptional level via a long noncoding RNA (lncRNA). The mechanism for SINEB2-dependent enhancement of translation remains not well understood. Here we present the result of experiments with the folded states of lncRNA in doubly deionized water obtained by slowcool method. These lncRNA were used in RNA pull-down assay that yielded six lncRNA-binding proteins potentially involved in RNAe. The direct interactions of lncRNA with interleukin enhancer-binding factor 3 (ILF3) and eukaryotic initiation factor 4A-I (eIF4A1) in vivo and in vitro were confirmed in RNA-binding protein affinity experiment and electrophoretic mobility shift assay (EMSA), respectively. These observations could explain RNAe phenomenon through lncRNA-dependent guiding of ILF3 protein, which, in turn, recruits polysomes or the factors for translation initiation, and attracting eIF4A1 proteins accelerating the unwinding of the secondary structure at the 5'-end of mRNA during translation initiation. Therefore, the hypothetical mechanism through which lncRNAs may regulate the translation of a specific mRNA is proposed. [ABSTRACT FROM AUTHOR]

In the northeastern Pacific Ocean, there are three "ecotypes" of killer whales that differ in diet, ecology, behavior, acoustics, genetics, and morphology. Previous attempts to describe the morphological differences among populations of killer whales (Orcinus orca) have been limited to descriptive accounts or categorical studies. We used elliptical Fourier analysis (EFA) to quantify shape differences of dorsal fins and pigmentation patterns among the ecotypes from photo‐identification data of more than 500 individuals. Variation in shapes of the dorsal fin, saddle patch, and eye patch were successfully quantified using EFA, and there were highly significant (P < 0.01) differences among the ecotypes in all three morphological traits. The ability of EFA to discriminate ecotypes based on dorsal fin and eye patch shapes was substantial, while it did not perform as well for saddle patches. Visualization of the shape variation along principal component axes mirrored previous descriptions of the differences among ecotypes. Although the degree of inheritance of morphology in killer whales has not been determined, these results are consistent with previous inference of reduced gene flow between the ecotypes, and introduces elliptical Fourier analysis to the study of cetacean morphometrics. [ABSTRACT FROM AUTHOR]

One of the hallmarks of cancer is the formation of oncogenic fusion genes as a result of chromosomal translocations. Fusion genes are presumed to form before fusion RNA expression. However, studies have reported the presence of fusion RNAs in individualswho were negative for chromosomal translocations. These observations give rise to "the cart before the horse" hypothesis, inwhich the genesis of a fusion RNA precedes the fusion gene. The fusion RNA then guides the genomic rearrangements that ultimately result in a gene fusion. However, RNA-mediated genomic rearrangements in mammalian cells have never been demonstrated. Here we provide evidence that expression of a chimeric RNA drives formation of a specified gene fusion via genomic rearrangement in mammalian cells. The process is: (i) specified by the sequence of chimeric RNA involved, (ii) facilitated by physiological hormone levels, (iii) permissible regardless of intrachromosomal (TMPRSS2-ERG) or interchromosomal (TMPRSS2-ETV1) fusion, and (iv) can occur in normal cells before malignant transformation. We demonstrate that, contrary to "the cart before the horse" model, it is the antisense rather than sense chimeric RNAs that effectively drive gene fusion, and that this disparity can be explained by transcriptional conflict. Furthermore, we identified an endogenous RNA AZI1 that functions as the "initiator" RNA to induce TMPRSS2-ERG fusion. RNA-driven gene fusion demonstrated in this report provides important insight in early disease mechanisms, and could have fundamental implications in the biology of mammalian genome stability, as well as gene-editing technology via mechanisms native to mammalian cells. [ABSTRACT FROM AUTHOR]

Range expansion is a widespread biological process, with well‐described theoretical expectations associated with the colonization of novel ranges. However, comparatively few empirical studies address the genomic outcomes accompanying the genome‐wide consequences associated with the range expansion process, particularly in recent or ongoing expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Using a restriction‐associated DNA sequencing (RADseq), we genotyped 394 coyotes at 22,935 SNPs and found that overall population structure corresponded to their 19th century historical range and two distinct populations that expanded during the 20th century. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front, which is likely due to hybridization with other Canis species. Furthermore, we identified 12 SNPs, located either within genes or putative regulatory regions, that were consistently associated with range expansion. Of these 12 genes, three (CACNA1C, ALK, and EPHA6) have putative functions related to dispersal, including habituation to novel environments and spatial learning, consistent with the expectations for traits under selection during range expansion. Although coyote colonization of eastern North America is well‐publicized, this study provides novel insights by identifying genes associated with dispersal capabilities in coyotes on the two eastern expansion fronts. Here, we evaluate two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been under selection during range expansion. Counter to theoretical expectations for populations to bottleneck during range expansions, we observed minimal evidence for decreased genomic diversity across coyotes sampled along either expansion front. Furthermore, we identified 12 SNPs, located either within genes or regulatory regions, that were consistently associated with range expansion, some of which have functions putatively associated with dispersal behavior. [ABSTRACT FROM AUTHOR]

Abstract It has been demonstrated that microRNAs (miRNAs) play important roles in the regulation of melanogenesis and hair color in mammals. Short tandem target mimic (STTM) has been used to effectively block small RNA functions in plants and animals. We previously showed that miR508-3p plays a functional role in regulating melanogenesis in alpaca melanocytes by directly targeting microphthalmia (MITF). To verify the effect of miR-508-3p function on melanogenesis in alpaca melanocytes, miR-508-3p was blocked using STTM technology in the present research. miR508-3p was predicted to target the gene encoding SRY-box6 (SOX6) by bioinformatics. The luciferase reporter assay indicated that miR508-3p regulates SRY-box6 (SOX6) expression by targeting its 3′UTR. Here, STTM-miR508-3p overexpression in alpaca melanocytes blocked the expression of miR-508-3p and up-regulated SOX6 expression at both the mRNA and protein levels, resulting in increasing the expression of key melanogenic genes, including cAMP responsive element (CRE) binding protein (CREB), MITF , tyrosinase (TYR) and tyrosinase-related protein 1 and 2 (TYRP1 and TYRP2). STTM-miR508-3p overexpression in melanocytes also resulted in increased melanin production, including total alkali soluble melanogenesis (ASM), eumelanogenesis (EM) and pheomelanogenesis (PM). Additionally, we identified melanin granules in alpaca melanocytes transfected with STTM-miR508-3p under Fontana-Masson staining. These results suggest that STTM-miR508-3p could up-regulate melanogenesis by effectively blocking miR508-3p. Highlights • SOX6 was one of the target genes of miR-508. • STTM-miR508-3p could up-regulate the melanogenesis by blocking miR508-3p effectively. • miR508-3p could act on SOX6 and downstream cyclin D1 to regulate melanogenesis through CREB/MITF pathway. [ABSTRACT FROM AUTHOR]

For polytypic mammal species, biogeographic barriers including rivers have often been used to delineate taxonomic units under the assumption that barriers have structured their distribution. We tested the importance of major riverine systems as biogeographic barriers in fox squirrels (Sciurus niger) across the state of Florida, where 4 currently recognized subspecies are delineated at major rivers. We also explored whether phylogeographic structure may be limited to ecologically divergent subspecies, specifically between S. n. avicennia and S. n. shermani. Using a multilocus approach to examine diversity, we found that restricted gene flow was only present between S. n. avicennia, located south of the Caloosahatchee River in south Florida, and the rest of S. niger, which is widespread across the state. Mitochondrial DNA revealed that 2 divergent groups of haplotypes are present and widespread across Florida, thus supporting the hypothesis that fox squirrels persisted in multiple refugia during the Pleistocene, and that S. n. avicennia diverged ecologically from other populations of fox squirrels relatively recently. This was supported by isolation with migration models that indicated matrilineal isolation since the onset of divergence between S. n. avicennia and S. n. shermani, which corresponds to the onset of ecological divergence in south Florida during the early Holocene. Isolation by distance at 8 microsatellite loci from the western panhandle to the southern end of the peninsula was significant only when S. n. avicennia was included; however, this was due to the hierarchical genetic patterns identified between S. n. avicennia and the other subspecies as determined by Bayesian clustering, and not due to spatially restricted dispersal. We postulate that the demographic isolation of S. n. avicennia is the result of adaptation to the unique ecological conditions of south Florida. [ABSTRACT FROM AUTHOR]

PLAC8 is a cysteine-rich protein described as a central mediator of tumor evolution in mammals; as such, it represents a promising candidate for diagnostic and therapeutic targeting. The human PLAC8 gene is also involved in contact hypersensitivity response and presents a role in psoriatic skin. In plants, PLAC8 motif-containing proteins are involved in the determination of organ size and growth, response to infection, Ca2+ influx, Cd resistance, and zinc detoxification. In general, PLAC8 motif-containing proteins present the conserved CCXXXXCPC or CLXXXXCPC region. However, there is no devised nomenclature for the PLAC8 motif-containing proteins. Here, through the analysis of 445 sequences, we show that PLAC8 motif-containing proteins constitute a unique gene family, and we propose a unified nomenclature. This is the first report indicating the existence of different groups of PLAC8 proteins, which we have called types I, II, and III. Type I genes are found in mammals, fungi, plants, and algae, and types II and III are exclusive to plants. Our study describes for the first time PLAC8 type III proteins. Whether these sequences maintain their known functional role or possess distinct functions of types I and II genes remains unclear. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Two species of bushbuck: T. scriptus in NW Africa and T. sylvaticus in SE Africa. • The two species have 2n = 57 M/58F and 2n = 33 M/34F chromosomes, respectively. • T. scriptus is related to T. angasii with mtDNA, and to T. sylvaticus with nuDNA. • Mitochondrial introgressive hybridization in the common ancestor of T. scriptus. • Evidence for chromosomal speciation after an event of interspecific hybridization. Abstract The bushbuck is the most widespread bovid species in Africa. Previous mitochondrial studies have revealed a polyphyletic pattern suggesting the possible existence of two distinct species. To assess this issue, we have sequenced 16 nuclear genes and one mitochondrial fragment (cytochrome b gene + control region) for most species of the tribe Tragelaphini, including seven bushbuck individuals belonging to the two divergent mtDNA haplogroups, Scriptus and Sylvaticus. Our phylogenetic analyses show that the Scriptus lineage is a sister-group of Sylvaticus in the nuclear tree, whereas it is related to Tragelaphus angasii in the mitochondrial tree. This mito-nuclear discordance indicates that the mitochondrial genome of Scriptus was acquired by introgression after one or several past events of hybridization between bushbuck and an extinct species closely related to T. angasii. The division into two bushbuck species is supported by the analyses of nuclear markers and by the karyotype here described for T. scriptus (2n = 57 M/58F), which is strikingly distinct from the one previously found for T. sylvaticus (2n = 33 M/34F). Molecular dating estimates suggest that the two species separated during the Early Pleistocene after an event of interspecific hybridization, which may have mediated massive chromosomal rearrangements in the common ancestor of T. scriptus. [ABSTRACT FROM AUTHOR]

The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years--longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution. [ABSTRACT FROM AUTHOR]

Reindeer (Rangifer tarandus L. 1758) are an essential element of the Russian Far North, providing a significant source of nutrition for the representatives of 18 ethnicities. The species has wild and domestic forms, which are in constant interaction. The aim of our study was to characterize the genetic structure of domestic and wild reindeer populations, using a genome-wide bovine genotyping array (BovineHD BeadChip). The wild reindeer samples were obtained from the western Taymyr Peninsula population and from the taiga and tundra populations in the Sakha Republic (Yakutia). The domestic populations included the Evenk, Even, and Chukotka-Khargin breeds of Yakutia and the Nenets breed from the Nenets Autonomous district and Murmansk region. The level of genetic diversity was higher for the wild population. Analyzing Neighbor-Net tree, multidimensional scaling, and Structure results, we observed strong genetic population structure and clear differentiation between domestic and wild populations. All regional populations of domestic reindeer were clearly separated, while wild reindeer showed similar genetic backgrounds. Nevertheless, we found contrasting patterns in the genetic structure of the tundra and taiga reindeer, in accordance with their morphological and ecological differences. Thus, our study revealed a clear genetic differentiation between domestic and wild reindeer populations. It provides novel insights into the genetic diversity and structure of reindeer populations, to support resource utilization and aid in the development of genetic improvement strategies and conservation programs for this species. [ABSTRACT FROM AUTHOR]

Cytochrome P450 (CYP) superfamily genes encode enzymes that play a role in metabolizing endogenous compounds and in detoxifying exogenous chemicals. The CYP2D subfamily is a member of the CYP2 family, and its gene expansion in herbivores is presumably linked with the need to detoxify abundant plant toxins in the diet, which indicates that CYP2D gene expansion is associated with dietary preferences. To test this hypothesis, the dietary information and CYP2D gene number for 73 vertebrates from different taxonomic groups including 22 mammals, 49 birds, 1 reptile, and 1 amphibian were collected, and correlation analysis and ANOVA were conducted. The results showed that most species (45/73) had only one CYP2D gene, despite their different diets, and dietary preferences were not correlated with CYP2D gene numbers. Specifically, the majority of birds and 7 mammals had only 1 CYP2D gene, and the CYP2D gene number of mammals ranged from 1 to 11, irrespective of their feeding habits. Species with a CYP2D gene number ≥5 included carnivores, herbivores, and omnivores. Furthermore, statistical analyses revealed that no significant correlation existed between dietary preferences and CYP2D gene number, and there was no significant CYP2D gene number variation among species with different dietary preferences, regardless of whether all vertebrates or specific lineages were considered. Furthermore, gene dynamics which indicated by gene duplication events and loss events showed that CYP2D gene number variation had no relationship with diet, suggesting that diet was not a driving force of CYP2D gene expansion and that CYP2D gene expansion was more complex than previously recognized. We tested the hypothesis that CYP2D gene expansion was associated with the dietary preferences and found that diet wasn't a driving force of CYP2D gene expansion, and CYP2D gene expansion was more complex than previously recognized. [ABSTRACT FROM AUTHOR]

The evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling pieces of evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I reanalyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that ∼60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with nonrodent mammals. These results led to an estimated rate of ∼12 de novo genes per million years in mouse. Contrary to a previous study (Wilson BA, Foy SG, Neme R, Masel J. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nat Ecol Evol. 1:0146), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes. [ABSTRACT FROM AUTHOR]

Recent advances in epigenomics have made it possible to map genome-wide regulatory regions using empirical methods. Subsequent comparative epigenomic studies have revealed that regulatory regions diverge rapidly between genome of different species, and that the divergence is more pronounced in enhancers than in promoters. To understand genomic changes underlying these patterns, we investigated if we can identify specific sequence fragments that are over-enriched in regulatory regions, thus potentially contributing to regulatory functions of such regions. Here we report numerous sequence fragments that are statistically over-enriched in enhancers and promoters of different mammals (which we refer to as ‘sequence determinants’). Interestingly, the degree of statistical enrichment, which presumably is associated with the degree of regulatory impacts of the specific sequence determinant, was significantly higher for promoter sequence determinants than enhancer sequence determinants. We further used a machine learning method to construct prediction models using sequence determinants. Remarkably, prediction models constructed from one species could be used to predict regulatory regions of other species with high accuracy. This observation indicates that even though the precise locations of regulatory regions diverge rapidly during evolution, the functional potential of sequence determinants underlying regulatory sequences may be conserved between species. [ABSTRACT FROM AUTHOR]

Although mammalian genomes encode genetic information in their linear sequences, their fundamental function with regard to gene expression depends on the higher-order structure of chromosomes. Current techniques for the evaluation of chromosomal structure have revealed that genomes are arranged at several hierarchical levels in three-dimensional space. The spatial organization of genomes involves the formation of chromatin loops that bypass a wide range of genomic distances, providing a connection between enhancers and chromosomal domains. Furthermore, they form chromatin domains that are arranged into chromosome territories in the three-dimensional space of the cell nucleus. Recent studies have shown that the spatial organization of the genome is essential for normal brain development and function. Activity-dependent alterations in the spatial organization of the genome can regulate transcriptional activity related to neuronal plasticity. Disruptions in the higher-order chromatin architecture have been implicated in neuropsychiatric disorders, such as cognitive dysfunction and anxiety. Here, we discuss the growing interest in the role of genome organization in brain development and neurological disorders. [ABSTRACT FROM AUTHOR]

Production of recombinant prion proteins is of crucial relevance in food technology (analytical standards, assay development) but also in basic research, most importantly structural biology (NMR, X-ray diffraction). Structural approaches conveniently allow for sophisticated investigation of prion disease pathogenesis, but usually require large amounts of sample material. Recently, working with recombinant prion proteins has been recategorized to biosafety levels > S1 as infectious prions may readily be generated de novo and become airborne via aerosols. Heterologous expression should therefore be established with appropriately adjusted safety precautions. We have developed a protocol for high-yield expression, purification and refolding of recombinant mammalian prion proteins at elevated biological safety levels by introducing means of abolishing aerosol formation and propagation. [ABSTRACT FROM AUTHOR]

Transposable elements are the largest individual constituent of mammalian genomes. These elements are highly diverse, a consequence of the multiplicity of genomic habitats that they inhabit and of the complex evolutionary histories that they have developed therein. Intriguingly, a surge of transposable element transcription occurs during mammalian preimplantation development, contributing to the establishment of totipotency and pluripotency and to the activation of the embryonic genome. However, it remains an open question how such an evolutionarily divergent set can mediate such conserved developmental processes. Here, we review transposable element diversity across mammals and their evolutionary significance. We also discuss the implications that their high evolutionary divergence has for the regulation of preimplantation development across mammals. Highlights Transposable elements are extensively transcribed during early development in a stage-specific manner in both mice and humans. Stage-specific transcriptional activity of transposable elements reflects a complex interplay between their co-option by host regulatory programs and their own selective pressure to replicate within the germline. Despite their limited conservation across mammals, transposable elements have been co-opted into regulatory functions during early development. The ERV-L family of endogenous retroviruses can function as alternative promoters during embryonic genome activation in both mice and humans, and despite its lack of sequence conservation, an orthologous transcription factor binds their long terminal repeat (LTR) in both species. The timely transcription of some transposable elements, such as L1 in mice, is necessary for developmental progression. [ABSTRACT FROM AUTHOR]

In domestic cats, the AB blood group system consists of the three types A, B, and C (usually called AB), which vary in frequency among breeds and geographic regions. Mismatches cause acute hemolytic transfusion reactions and hemolysis of the newborn due to the presence of naturally occurring anti-A alloantibodies. Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) converts N-acetylneuraminic acid (type B) to N-glycolylneuraminic acid (type A), and type C erythrocytes express both antigens. We examined the feline CMAH coding regions and genotyped cats to characterize type A, B, and C animals. Of 421 phenotypically typed cats, 60% were A, 35% B and 5% C. Among the 70 cats for which the CMAH coding region was sequenced, 13 new variants were identified in addition to 16 of the previously reported 18 variants. The CMAH variant c.268T>A is seen in type B cats of most breeds, and the variant c.179G>T results in type B in Turkish breeds. The variants c.1322delT and c.933delA cause frameshifts with early stop codons and thereby type B in some Ragdolls and domestic shorthair cats, respectively. Protein modeling with PROVEAN affirmed their deleterious effects. No type A and C cats had more than one allele with one of the above variants. Variant analysis of three SNVs (c.142G>A, c.268T>A and Δ-53) and blood typing of an additional 351 typed cats showed complete phenotype-genotype concordance. In conclusion, the three CMAH variants c.179G>T, c.268T>A and c.1322delT are the main reasons for the defective NeuGc synthesis causing blood type B in domestic purebred and non-pedigreed cats. Together with the variant c.364C>T for type C in Ragdolls they offer a molecular screening scheme for clinical diagnostics to assure blood type compatibility. [ABSTRACT FROM AUTHOR]

ABSTRACT: Caves and abandoned mines provide roosting habitat for bat species that depend on subterranean conditions. Disturbances at caves (e.g., commercial development, recreation) limit their availability to bats, in some cases shifting use to abandoned mines. However, abandoned mines pose public safety hazards and often are gated to reduce risk to humans while maintaining access to bats. To date there is limited information on species‐specific acceptance of gates at abandoned mines. We designed our research objectives to determine short‐term (1 week) behavioral responses of bats to gating, including gate material and height above ground, mid‐term (<1 yr) changes in bat use before and after gate installation, and long‐term changes (≥4 yrs) in use and factors influencing species presence. We used an in situ mock gate experiment, comparison of bat use before and after gating, and genetic identification of guano in gated mines for our short‐, mid‐, and long‐term studies, respectively. In our short‐term study, bats increased energetically demanding behaviors following gate installation. Although we detected no difference in responses to gate material or height, a less maneuverable bat species circled, collided, and landed more frequently on gates than did an agile species. In the mid‐term study, activity remained stable or increased at 73% of mines after gating compared to before gating, although number of maternity colonies decreased. In the long‐term study, elevation, portal area, number of mine levels, and entrances were more important than gates in predicting presence of 4 bat species, including 2 subterranean obligates. Species‐specific responses to gates appeared based on morphology and vocalization characteristics. Responses to gates shifted from negative in our short‐term study to positive in our long‐term study. Gate age and mine characteristics were more important predictors of use for most species than gate design. Although the complexity of subterranean habitats makes them difficult to replicate and many factors may influence how bats use this habitat, gates designed for bats (bat‐compatible) appear effective for many species. © 2018 The Wildlife Society. [ABSTRACT FROM AUTHOR]

In recent years, retrotransposons have gained increasing attention as a source of binding motifs for transcription factors (TFs). Despite the substantial roles of these mobile genetic elements in the regulation of gene expression, a comprehensive resource enabling the investigation of retrotransposon species that are bound by TFs is still lacking. Herein, I introduce for the first time a novel database called RTFAdb, which allows exploring computationally predicted associations between retrotransposons and TFs in diverse cell lines and tissues of human and mouse. My database, using over 3.000 TF ChIP-seq binding profiles collected from human and mouse samples, makes possible searching more than 1.500 retrotransposon species in the binding sites of a total of 596 TFs. RTFAdb is freely available at http://tools.ibg.deu.edu.tr/rtfa/ and has the potential to offer novel insights into mammalian transcriptional networks by providing an additional layer of information regarding the regulatory roles of retrotransposons. [ABSTRACT FROM AUTHOR]

The goitered gazelle, Gazella subgutturosa, is a medium-sized ungulate inhabiting arid and semi-arid regions in the Middle East and central Asia. The intraspecific classification of the species remains unclear. We analysed the genetic diversity in mitochondrial DNA control region (CR) sequences (976 bp) from 104 wild samples from the Xinjiang Uyghur Autonomous Region (XUAR) in north-west China, and reconstructed phylogeny with additional sequences from across the species’ range. We detected 58 haplotypes in XUAR populations, all but three of which were specific to single sampling sites. The phylogenetic analysis displayed two obvious clades of mtDNA haplotypes and the other haplotypes differed from the two clades. A median-joining network showed three groups of haplotypes were to a high extent concordant with the phylogenetic tree. The haplotype clustering was consistent with their geographic distribution. Nei’s net sequence divergences amongst the three groups ranged from 0.010 to 0.018 and indicated three subspecies, two of which inhabit XUAR. We detected strong differentiation between northern (NX) and southern (SX) XUAR populations overall (FST = 0.4448, P < 0.001), but the Mantel test showed no correlation between the genetic distance and geographic distance. Our results indicate that the NX and SX populations represent different subspecies that might be managed separately. [ABSTRACT FROM AUTHOR]

Polygyny in mammals, as in other groups, is related to sexual dimorphism, with males being larger than females or with elaborate weaponry as a response to sexual selection. However, sexual selection can also act on females, leading to cases where dimorphism is reversed or absent and females mate with several males, leading to a promiscuous mating system. In this study, we analyzed the mating system of a monomorphic mammalian species, the white-lipped peccary ( Tayassu pecari ), using microsatellite molecular markers and parentage tests. The white-lipped peccary mating system is predicted to be polygyny, but so far, no systematic study exists. To verify their mating behavior, 131 individuals of a herd from the Brazilian Pantanal were genotyped for 11 microsatellite loci and parentage tests were performed for all the sampled young. We determined that both males and females had offspring with more than one partner which is compatible with a promiscuous mating system. Promiscuity in this species could be related to competition among females as a result of the female-biased sex ratio leading to sexual and/or natural selection not only on males but also females. [ABSTRACT FROM AUTHOR]

Abstract: Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co‐amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large‐scale variation in vampire bat diet and bat population structure would empower locality‐ and species‐specific projections of disease transmission risks. However, previously used methods are not cost‐effective and efficient for large‐scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure. [ABSTRACT FROM AUTHOR]