Evolutionary Biology

Two combinations (designated as options 1 and 2) of four plastid markers (matK, rpoC1, rpoB, psbA-trnH) that have been recommended for DNA barcoding were tested for utility in a putatively recently-diversified group: the primarily Canarian clade within the genus Tolpis (Asteraceae). Prior studies had indicated very little molecular variation in the group, and thus it was used to determine whether accepted taxa, segregate species, and morphological variants ostensibly deserving taxonomic recognition could be distinguished employing regions proposed as useful for DNA barcoding. The regions, particularly option 2, separated all morphologically distinct species of Tolpis except one, and distinguished one segregate species and certain variants in a morphologically variable and intergrading group (comprising both the T. laciniata and T. lagopoda species complexes). The barcoding sequences also revealed several variants that are worthy of additional study in order to further understand the diversity of Tolpis in the Canary Islands.

Two combinations (designated as options 1 and 2) of four plastid markers (matK, rpoC1, rpoB, psbA-trnH) that have been recommended for DNA barcoding were tested for utility in a putatively recently-diversified group: the primarily Canarian clade within the genus Tolpis (Asteraceae). Prior studies had indicated very little molecular variation in the group, and thus it was used to determine whether accepted taxa, segregate species, and morphological variants ostensibly deserving taxonomic recognition could be distinguished employing regions proposed as useful for DNA barcoding. The regions, particularly option 2, separated all morphologically distinct species of Tolpis except one, and distinguished one segregate species and certain variants in a morphologically variable and intergrading group (comprising both the T. laciniata and T. lagopoda species complexes). The barcoding sequences also revealed several variants that are worthy of additional study in order to further understand the diversity of Tolpis in the Canary Islands.

Recent genomic analyses show that the earliest peoples reaching Remote Oceania-associated with Austronesian-speaking Lapita culture-were almost completely East Asian, without detectable Papuan ancestry. However, Papuan-related genetic ancestry is found across present-day Pacific populations, indicating that peoples from Near Oceania have played a significant, but largely unknown, ancestral role. Here, new genome-wide data from 19 ancient South Pacific individuals provide direct evidence of a so-far undescribed Papuan expansion into Remote Oceania starting ~2,500 yr BP, far earlier than previously estimated and supporting a model from historical linguistics. New genome-wide data from 27 contemporary ni-Vanuatu demonstrate a subsequent and almost complete replacement of Lapita-Austronesian by Near Oceanian ancestry. Despite this massive demographic change, incoming Papuan languages did not replace Austronesian languages. Population replacement with language continuity is extremely rar...

A series of N,N-disubstituted piperazines were synthesized containing the structural elements of both methylenedioxybenzylpiperazine (MDBP) and trifluoromethylphenylpiperazine (TFMPP) in a single molecule. These six potential designer drug molecules having a regioisomeric relationship were compared in gas chromatography-mass spectrometry (GC-MS), gas chromatography-infrared spectroscopy and serotonin receptor affinity studies. These compounds were separated by capillary gas chromatography on an Rxi Ò -17Sil MS stationary phase film and the elution order appears to be determined by the position of aromatic ring substitution. The majority of electron ionization mass spectral fragment ions occur via processes initiated by one of the two nitrogen atoms of the piperazine ring. The major electron ionization mass spectrometry (EI-MS) fragment ions observed in all six of these regioisomeric substances occur at m/z = 364, 229, 163 and 135. The relative intensity of the various fragment ions is also equivalent in each of the six EI-MS spectra. The vapour phase infrared spectra provide a number of absorption bands to differentiate among the six individual compounds on this regioisomeric set. Thus, the mass spectra place these compounds into a single group and the vapour phase infrared spectra differentiate among the six regioisomeric possibilities. All of the TFMPP-MDBP regioisomers displayed significant binding to 5-HT 2B receptors and in contrast to 3-TFMPP, most of these TFMPP-MDBP isomers did not show significant binding at 5-HT 1 receptor subtypes. Only the 3-TFMPP-3,4-MDBP (Compound 5) isomer displayed affinity comparable to 3-TFMPP at 5-HT 1A receptors (K i = 188 nmol/L).

X&Y chromosomal aneuploidies are among the most common human whole-chromosomal copy number changes, but the population-based incidence and prevalence in the childbearing population is unclear. This retrospective analysis of prospectively collected data leveraged a routine non-invasive prenatal test (NIPT) using parental genotyping to estimate the population-based incidence of X&Y chromosome variations in this population referred for NIPT (generally due to advanced maternal age). From 141,916 women and 29,336 men, 119 X&Y chromosomal abnormalities (prevalence: 1 in 1,439) were identified. Maternal findings include: 43 cases of 45,X (40 mosaic); 30 cases of 47,XXX (12 mosaic); 3 cases of 46,XX uniparental disomy; 2 cases of 46,XY/46, XX; 23 cases of mosaicism of unknown type; 2 cases of 47,XX,i(X)(q10). Paternal findings include: 2 cases of 47,XXY (1 mosaic); 10 cases of 47,XYY (1 mosaic); 4 partial Y deletions. Single chromosome aneuploidy was present in one of every 1,439 individuals considered in this study, showing 47,XXX; 47,XX,i(X)(q10); 47,XYY; 47,XXY, partial Y deletions, and a high level of mosaicism for 45,X. This expands significantly our understanding of X&Y chromosomal variations and fertility issues, and is critical for families and adults affected by

Phytoliths are a class of microfossils produced in many, but not all, families of higher plants and composed of amorphous silica or opal. They are a class of microfossils that can be used as a proxy for reconstructing terrestrial vegetation, agricultural practices, and diets, especially in arid, semiarid, and oxidative contexts where pollen is scarce. Although phytoliths are especially abundant and have been well studied in grasses (Poaceae) and sedges (Cyperaceae), they are produced by over 50 families of higher plants. Given their relatively low level of taxonomic resolution they work particularly well in multiproxy projects complementing information from other sources.

We published a phylogenetic comparative analysis that found geckos had gained and lost adhesive toepads multiple times over their long evolutionary history (Gamble et al., PLoS One, 7, 2012, e39429). This was consistent with decades of morphological studies showing geckos had evolved adhesive toepads on multiple occasions and that the morphology of geckos with ancestrally padless digits can be distinguished from secondarily padless forms. Recently, Harrington & Reeder (J. Evol. Biol., 30, 2017, 313) reanalysed data from Gamble et al. (PLoS One, 7, 2012, e39429) and found little support for the multiple origins hypothesis. Here, we argue that Harrington and Reeder failed to take morphological evidence into account when devising ancestral state reconstruction models and that these biologically unrealistic models led to erroneous conclusions about the evolution of adhesive toepads in geckos.

Monographs are fundamental for progress in systematic botany. They are the vehicles for circumscribing and naming taxa, determining distributions and ecology, assessing relationships for formal classification, and interpreting long–term and short–term dimensions of the evolutionary process. Despite their importance, fewer monographs are now being prepared by the newer generation of systematic botanists, who are understandably involved principally with DNA data and analysis, especially for answering phylogenetic, biogeographic, and population genetic questions. As monographs provide hypotheses regarding species boundaries and plant relationships, new insights in many plant groups are urgently needed. Increasing pressures on biodiversity, especially in tropical and developing regions of the world, emphasize this point. The results from a workshop (with 21 participants) reaffirm the central role that monographs play in systematic botany. But, rather than advocating abbreviated models f...

Introduction: Characterized by the development of hundreds to thousands of colonic adenomas, classic familial adenomatous polyposis (FAP) is one of the most common hereditary syndromes associated with an increased risk of colorectal cancer. Several studies have attempted to correlate specific APC mutations with clinical phenotype. 6 However, there is considerable variability in the expression of specific phenotypes within families and among individuals with identical mutations. 7 Case presentation: A 30 year-old Hispanic female presented to the emergency department with a 2-week history of persistent, worsening, left lower quadrant abdominal pain. She had no family history of malignancy. Sigmoidoscopy revealed innumerable polyps in the rectum and sigmoid colon and a large mass in the sigmoid colon. Biopsy of the mass revealed a moderately differentiated adenocarcinoma invading the subserosa. Endoscopy revealed innumerable polyps. Genetic testing of the patient via southern blot revealed a germline APC mutation 3927del5, resulting in a premature truncation of the APC protein at amino acid position 1312. Conclusion: Genetic information has only recently started being incorporated into clinical care. More research and randomized clinical trials need to be conducted to definitively characterize random mutations. Once these mutations are further understood, FAP patients may be able to be risk stratified and this may ultimately improve the screening, diagnosis, and treatment of this rare condition.

Freshwater anostracans inhabit ephemeral water bodies in which as the water level decreases due to evaporation the salt concentration increases. Thus, for most anostracans salinity becomes the major stress factor. We tested five concentrations of NaCl (0 to 8 g/l) on the life table demography of Branchipus schaefferi fed Chlorella (alga). Age-specific survivorship curves of male and female B. schaefferi showed nearly a similar pattern in that increased salt concentration resulted in decreased survivorship. The age-specific reproduction (m(x)) of females showed several peaks of cyst production at 0 and 1 g/l salinity while in treatments containing salt at 4 or 8 g/l, there were fewer peaks. Average lifespan, life expectancy at birth, gross and net reproductive rates, generation time and the rate of population increase were all significantly influenced by the salt concentration in the medium. The highest value of net reproductive rate (970 cysts/female) was in treatments containing 0 ...

Six Artemia populations, one bisexual and five parthenogenetic, from different parts of Iran were compared using morphometric and genetic characteristics. The discriminant analysis based on 19 morphometric variables showed that there are significant differences between the studied populations based on their morphological characteristics, where 85.9% of original grouped cases were correctly classified. The bisexual Artemia urmiana however exhibited a 100% separation from the parthenogenetic populations. However, a 1500 bp mitochondrial rDNA fragment showed similar RFLP patterns for all Iranian populations confirming earlier reports of a close genetic relationship between A. urmiana and parthenogenetic Artemia. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

This study reports on male-biased sex ratios in west Mediterranean populations of the freshwater anostracan Branchipus schaefferi (Crustacea, Anostraca, Branchipodidae), in contrast to populations elsewhere. Crossing experiments over several generations indicate a clear paternal inheritance of the trait, possibly with a dosage effect. Various mechanisms

Sedimentological and paleontological study of the Man Aike Formation at the Estancia 25 de Mayo, SW of Santa Cruz Province, Argentina, represents the evolution of an incised valley from fluvial to marine environment during the late middle Eocene. At the base of the unit there is an unconformity that corresponds to fluvial channels which cut down into the underlying Maastrichtian sandstones of the Calafate Formation. The fauna of invertebrates (mostly molluscs) illustrated herein was collected from shell beds interpreted as tidal ravinement surfaces. The fauna includes terebratulid brachiopods, bivalves of the families Malletiidae, Mytilidae, Pinnidae, Ostreidae, Pectinidae, Carditidae, Crassatellidae, Lahillidae, Mactridae, Veneridae, and Hiatellidae, and gastropods of the families Trochidae and Calyptraeidae, and a member of Archaeogastropoda of uncertain affinities. The similarities of this fauna with that recorded in the Upper Member of the Río Turbio Formation, together with 87 Sr/ 86 Sr ages, suggest a late Middle Eocene age for the Man Aike Formation.

(ORDER ROSA-LES) FROM THE LA MESETA FORMATION (MIDDLE EOCENE), MARAMBIO ISLAND, ANTARCTICA, A new fossil flowcr with affinities to the family Grossulariaceae is described, It was collected from outcrops of La Meseta Formation, Marambio (Seyrnour) Island, Antarctica, together with other fossil plant rernains. The age of this unit has been calculated as lower Eocene to possibly lower Oligocene, although the fossil was collected from fine-grained heterolithic facies of estuarine origin dated as middle Eocene. The characters preserved in the flower suggest a close r.elationship with the family Grossulariaceae. Comparisons with living and fossil taxa are established. Based on these comparisons, we erect a new genus for this fossil flower.

Los materiales fósiles consisten en placas aisladas y un pequeño fragmento de la coraza, de naturaleza epitecal, correspondientes a diversos especímenes. Esta armadura epitecal es sólo conocida entre los miembros de la familia Dermochelyidae registrados desde el Eoceno medio hasta la Actualidad. Los especímenes antarticos son tentativamente referidos al género Psephophorus, taxón cuyas especies se registran desde el Eoceno mediosuperior hasta el Plioceno en Europa,

Las seis especies identificadas, tres de las cuales son citadas por vez primera, tienen afinidades con especies arbóreas que crecen actualmente en zonas boscosas de climas lluviosos, temperados-fríos, con estaciones diferencii-ias. Sobre la base de este conjunto florístico, se infieren condiciones paleocü.náticas similares para los depósitos de la isla Seymour durante el Eoceno-Oligoceno. Se discute las condiciones de depositación y se concluye que las maderas se petrificaron en un medio rico er. carbonatas. Las maderas habríanflotado en el mar, siendo depositadas en una zona protegida, probablememe una bahía.

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Resumen PANTI, Carolina; CESARI, Silvia N.; MARENSSI, Sergio A. y OLIVERO, Eduardo B.. Una nueva especie fósil de Araucaria del Paleógeno de Tierra del Fuego, Argentina. Ameghiniana [online]. 2007, vol. 44, n. 1, pp. 215-222. ISSN 1851-8044.

Formation fills an incised valley and comprises sediments that represent deltaic, estuarine and very shallow marine environments. Forests of both deciduous and evergreen trees were dominated by Nothofagus, podocarps, and araucarian conifers. The La Meseta paleoflora is distinctive in having a predominance of Antarctic taxa; this suggests a seasonal, cold-temperate, rainy c1imate and a latitudinal gradient. Among the terrestrial vertebrates, there are at least nine rnammal taxa, predominantly tiny marsupial s (mostly endemic and new genera). The presence of these marsupials suggests the existence of some form of isolating barrier (c1imatic and/or geographic), which must have allowed development of this endemic fauna. Cornparisons with faunas assigned to the Itaboraian (late Paleocene), Riochican (late Paleocene), Casamayoran (early Eocene), and Mustcrsan (tentatively assigned to the middle Eocene) ages of Patagonia were made. The assemblage of terrestrial vertebrates of the La Meseta Formation is unusual in the dominance of several endemic forms. The occurrence of protodidelphid and derorhynine marsupials, that had become extinct elsewhere in the Eocene of South America, on Seymour Island also indicates that isolation may have allowed extended survival ofthese taxa in theEocene of Antarctica. The nature, distribution, and composition ofthe La Meseta fauna firmly suggest a latitudinal differentiation in the middle Eocene. Paleogeographic evidence suggests that the terrestrial mammals of the La Meseta Formation probably lived under crepuscular and even extended noctumal conditions (assuming that the angle of the earth's spin axis was relatively the same as it is now) during part of the year. VERTEBRADOS EOCENOS TERRESTRES DE ALTAS LATITUDES DE ANTÁRTIDA COMO EVIDENCIA BIO-GEOGRÁFICA. Una biota moderadamente diversa es conocida en la Formación La Meseta (Eoceno-Oligoceno temprano"), isla Seymour, Península Antártica. La Formación La Meseta rellena un valle incidido y comprende sedimentos que representan ambientes estuáricos y marinos muy someros. Bosques con árboles deciduos y perennes estuvieron dominados por Nothofagus, y coníferas podocarpáceas y araucarias. La paleoflora de la Formación La Meseta es distintiva y predominan taxones antártico s que sugieren un clima templado frío, lluvioso, estacional y un gradiente latitudinal. Dentro de los vertebrados terrestres hay 9 taxones de mamíferos, predominantemente pequeños marsupiales, mayormente endémicos y novedosos, que sugieren que alguna forma de barrera de aislamiento, c1imática y/o geográfica, debió haber permitido el desarrollo de esta fauna endémica. Se realizaron comparaciones con las Iaunas asignadas a las edades mamífero Itaboraiense (Paleoceno tardío), Riochiquense (Paleoceno tardío), Casamayorense (Eoceno temprano) y Mustersense (tentativamente asignada al Eoceno medio). La fauna de la Fm. La Meseta es particular por el predominio de varias formas endémicas. La presencia de marsupiales protodidélfidos y derorhinchinos, los cuales ya no se registran en ninguna de las faunas del Eoceno de América del Sur, indica que el aislamiento pudo haber permitido la supervivencia de estos taxones en el Eoceno de Antártida. La naturaleza, distribución y composición de la fauna de la Fm. La Meseta firmemente sugiere una diferenciación latitudinal en el Eoceno medio. Finalmente, las evidencias paleogeográficas sugieren que los mamíferos terrestres de la Formación La Meseta probablemente vi vieron bajo condiciones crepusculares, aún nocturnas (asumiendo que la oblicuidad del eje de la Tierra fue relativamente la misma que la actual), durante parte del año.

Ichnological analysis of dark sediments of the Oceanic Anoxic Event at the Cenomanian-Turonian boundary interval (OAE-2) from the Betic Cordillera, southern Spain, reveals the presence of ichnofabrics containing trace fossils Chondrites isp., Palaeophycus heberti, Planolites isp., Thalassinoides isp., Trichichnus linearis, Zoophycos isp., and other bioturbational structures. Analysis of the ichnofabrics and trace fossil diversity allowed the reconstruction of relative oxygenation. Before the OAE-2, oxygenation of sediments was generally good, but it was punctuated by short anoxic events. During the OAE-2i, several longer anoxic intervals were interrupted by shorter dysaerobic and oxic periods. After the OAE-2, oxygenation improved and almost all trace fossils known before OAE-2 reappeared, although oxygenation dropped a few times to anoxia. Generally, the short oxygenation changes reveal a periodicity, which may suggest a Milankovitch control. h Betic Cordillera, OAE-2, Oceanic Anoxic Event, Spain, Trace Fossil.

Ichnological analysis of dark sediments of the Oceanic Anoxic Event at the Cenomanian-Turonian boundary interval (OAE-2) from the Betic Cordillera, southern Spain, reveals the presence of ichnofabrics containing trace fossils Chondrites isp., Palaeophycus heberti, Planolites isp., Thalassinoides isp., Trichichnus linearis, Zoophycos isp., and other bioturbational structures. Analysis of the ichnofabrics and trace fossil diversity allowed the reconstruction of relative oxygenation. Before the OAE-2, oxygenation of sediments was generally good, but it was punctuated by short anoxic events. During the OAE-2i, several longer anoxic intervals were interrupted by shorter dysaerobic and oxic periods. After the OAE-2, oxygenation improved and almost all trace fossils known before OAE-2 reappeared, although oxygenation dropped a few times to anoxia. Generally, the short oxygenation changes reveal a periodicity, which may suggest a Milankovitch control. h Betic Cordillera, OAE-2, Oceanic Anoxic Event, Spain, Trace Fossil.

Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major forms of environmental change - fertilisation and herbivore loss - are affected by species pool size and spatial compositional heterogeneity. Fertilisation led to higher rates of local extinction, whereas turnover in herbivore exclusion plots was driven by species replacement. Overall, sites with more spatially heterogeneous composition showed significantly higher rates of annual turnover, independent of species pool size and treatment. Taking into a...

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1 T as its type species, along with two other uncultivated metagenomeassembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-ofthe-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1 TS ), 'Igneacidithiobacillus siniensis' (S30A2 T ), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS ), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS ). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineagespecific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction.

The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42-80 • C, pH 6-9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.

Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are...

Fossil teeth are used for palaeoenvironmental reconstructions. Among the criteria used, the geochemical composition is favoured, because it is said that the enamel is exempt from diagenetic changes. The combined microstructural and chemical analyses of rodent incisors from the cave of El Hahroura 2 (Morocco, Middle Palaeolithic-Neolithic) using scanning electron microscopy, an electron microprobe and FTIR spectroscopy show that all teeth were preserved in apatite. Nevertheless, the microstructure of both dentine and enamel is altered, as well as their chemical composition. Teeth excavated from the upper layers are already diagenetically modified despite being from the Neolithic. Teeth from three older stratigraphic layers are also altered but with a different pattern. Up to now, a direct correlation of the morphological and structural/compositional preservation has not been possible, showing that to use only one criterion to infer the quality of the preservation is not sufficient. Moreover, palaeoecological or palaeoenvironmental reconstructions based on geochemical data without control of the dental microstructure may be biased.

Ellobius remains are common and often abundant in southeastern Europe, western and central Asia archaeological sites. A correct identification of species is crucial for our understanding of the evolution of species and communities through time, including biostratigraphic sequences to be established. This study applies geometric morphometric methods (GMM) to Ellobius first lower molars, with the objectives: 1) to discriminate modern species and explore morphological and size differences in reference samples; and 2) to identify fossil specimens recovered in archaeological sites, based on the aforementioned analysis. The reference dataset used in this paper includes specimens belonging to the three species that today occur in the southeastern Europe, western and central Asia: Ellobius fuscocapillus, E. lutescens and E. talpinus. The archaeological material comes from Late Pleistocene Iranian site of Kaldar Cave (Khorramabad valley, Lorestan Province, western Iran). Our study shows that the shape of the anterior cap and the arrangement of the following triangles allow discriminating the three studied extant Ellobius species. The shapes of E. fuscocapillus and E. lutescens m1 appear rather similar, whereas Ellobius talpinus is well separated from these two species. The total length and the anterior cap of m1 in E. fuscocapillus is greater than in Ellobius lutescens. The GMM analyses performed on the modern reference dataset allowed us to identify fossil specimens from Kaldar Cave as Ellobius lutescens and some as E. fuscocapillus, and excluding E. talpinus.

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Anomaluroidea, commonly known as the “scaly‐tailed squirrels,” are an emblematic group of tropical African mammals that includes gliding forms. The family Anomaluridae was until recently represented by three genera: the flying scaly‐tailed squirrels (Anomalurus), the flying mouse (Idiurus) and the flightless scaly‐tailed squirrels (Zenkerella). Idiurus and Zenkerella have long been grouped into the Zenkerellinae subfamily, and Zenkerella was interpreted as a rare case of evolutionary reversal to non‐gliding lifestyle. Recent studies have demonstrated that Zenkerella is sister to all other modern anomalurids, and represents in fact the monogeneric family Zenkerellidae. The Anomalurus genus was split into Anomalurus and Anomalurops, but no study has ever considered all Anomalurus species together in a phylogeny to test the status of Anomalurops. Here, we used mitogenomic next‐generation sequencing to infer the phylogenetic relationships among all extant anomalurids and to estimate the...

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, ...

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes—the Toll-like receptors (TLRs)—across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven ad...

Background Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results Here...

Phylogenetic trees give the information about the vertical relationships of ancestors and descendants but phylogenetic networks are used to visualize the horizontal relationships among the different organisms. In order to predict reticulate events there is a need to construct phylogenetic networks. Here, a Linear Programming (LP) model has been developed for the construction of phylogenetic network. The model is validated by using data sets of chloroplast of 16S rRNA sequences of photosynthetic organisms and Influenza A/H5N1 viruses. Results obtained are in agreement with those obtained by earlier researchers.

Phylogenetic networks are considered as the structures that are used to understand the evolutionary pathways among the different organisms. Evolutionary relations are due to the preservence of mutations in sequences, occurred due to non-tree like events like horizontal gene transfer, Homoplasy, sexual hybridization and recombination, etc. The effective and efficient reconstruction of the networks for these events is an challenging task in computational biology. In this article, a Fuzzy Weighted Least Squares (FWLS) approach is developed and employed to detect these events in commonly known species of grasses. The results obtained by the proposed method predicts the possibility of hybridization or recombination among the inter cluster species i.e., Oryza and Triticum and intra cluster species i.e. Bentgrass and Brachypodium. Results also provide the optimized values of Q

The extent and the nature of the constraints to evolutionary trajectories are central issues in biology. Constraints can be the result of systems dynamics causing a non-linear mapping between genotype and phenotype. How prevalent are these developmental constraints and what is their mechanistic basis? Although this has been extensively explored at the level of epistatic interactions between nucleotides within a gene, or amino acids within a protein, selection acts at the level of the whole organism, and therefore epistasis between disparate genes in the genome is expected due to their functional interactions within gene regulatory networks (GRNs) which are responsible for many aspects of organismal phenotype. Here we explore epistasis within GRNs capable of performing a common developmental function -converting a continuous morphogen input into discrete spatial domains. By exploring the full complement of GRN wiring designs that are able to perform this function, we analyzed all possible mutational routes between functional GRNs. Through this study we demonstrate that mechanistic constraints are common for GRNs that perform even a simple function. We demonstrate a common mechanistic cause for such a constraint involving complementation between counter-balanced gene-gene interactions. Furthermore we show how such constraints can be bypassed by means of ''permissive'' mutations that buffer changes in a direct route between two GRN topologies that would normally be unviable. We show that such bypasses are common and thus we suggest that unlike what was observed in protein sequence-function relationships, the ''tape of life'' is less reproducible when one considers higher levels of biological organization.

A Gram-positive, facultatively anaerobic, thermophilic bacterium, designated as ZQ18-1T, was isolated from a high temperature daqu sample collected from sesame-flavor liquor making process. Oval endospores were formed at the center of cells with swollen sporangia. The isolate was able to grow at the temperature of 20-60 °C (optimum at 50 °C), at pH 4-9 (optimum at pH 8), in the presence of 0-10% (w/v) NaCl (optimum at 2%). Glucose and galactose were major cell wall sugars and meso-diaminopimelic acid was the diagnostic amino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and three glycolipids. The major cellular fatty acids were anteiso-C17:0 and iso-C16:0, and the predominant menaquinone was MK-7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ18-1T was most closely related to Scopulibacillus darangshiensis DLS-06T, Pullulanibacillus pueri YN3T, Tuberibacillus calidus 607T, Pullulanibacillus naganoensis ATCC 539...

A Gram-stain-positive bacterial strain, designated as NR2T, isolated from Noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was recognized as a species of the genus Brachybacterium, to which seven closest neighbours being Brachybacterium squillarum M-6-3T (97.90% similarity), Brachybacterium faecium DSM 4810T (97.50%), Brachybacterium sacelli LMG 20345T (97.41%), Brachybacterium phenoliresistens phenol-AT (97.36%), Brachybacterium nesterenkovii DSM 9573T (97.36%) and Brachybacterium rhamnosum LMG 19848T (97.32%). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15:0 and iso-C15:0. St...

Two yellow-colored bacterial strains, designated as NBD5T and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. The cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was recognized as a species of the genus Sphingomonas, to which seven closest neighbours being Sphingomonas oligoaromativorans SY-6T (96.9% similarity), Sphingomonas polyaromaticivorans B2-7T (95.8%), Sphingomonas yantingensis 1007T (94.9%), Sphingomonas sanguinis IFO 13937T (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429T (94.6%), Sphingomonas wittichii RW1T (94.6%) and Sphingomonas formosensis CC-Nfb-2T (94.5%). NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-hom...

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune resp...

The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neandertals allows us to directly test for the presence of the ABO alleles in these extinct humans. We have analysed two male Neandertals that were retrieved under controlled conditions at the El Sidron site in Asturias (Spain) and that appeared to be almost free of modern human DNA contamination. We find a human specific diagnostic deletion for blood group O (O01 haplotype) in both Neandertal individuals. These results suggest that the genetic change responsible for the O blood group in humans predates the human and Neandertal divergence. A potential selective event associated with the emergence of the O allele may have therefore occurred after humans separated from their common ancestor with chimpanzees and before the human-Neandertal population divergence.

Xylaria is a widely distributed genus belong to the family Xylariaceae and grows on a wide variety of substrates in different habitats. Up to 60 species of Xylaria have been reported from the Indian subcontinent, while southwest India is known for about 30 species. Recently, four species of Xylaria (X. arbuscula, X. grammica, X. minuta and X. oxyacanthae) were found to grow on various habitats and substrates during an inventory of scrub jungles of southwest India during 2019-21. Xylaria arbuscula and X. grammica were confined to dead bark, while X. minuta and X. oxyacanthae were grown on the dead twigs and humus, respectively. This study reports description (of the above species), distribution, habitat specificity and substrate specificity of Xylaria spp. in southwest India based on the literature.

HIV-1 group M was transmitted to humans nearly one century ago. The virus has since diversified to form distinct clades, which spread to multiple regions worldwide. Of the different proteins encoded by HIV-1, the envelope glycoproteins (Envs) have diversified most rapidly in all infected populations. We compared the range of variants that emerged during the AIDS pandemic in diverse HIV-1 clades and distinct geographic regions. Our analyses focused on two components of Env that contain multiple epitopes of broadly-neutralizing antibodies: the glycan shield and apex domain. Interestingly, at each Env position, the amino acid in the inferred clade ancestor was replaced by a unique combination of emerging variants. Key antigenic sites and genetic signatures of vaccine protection have gradually evolved toward conserved frequency distributions (FDs) of all amino acids. FDs are specific for position and clade and are highly conserved in populations from different regions. Remarkably, found...

Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 0 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.