Systematics and Acceleration of Cranial Evolution in <Emphasis Type="Italic">Cerradomys</Emphasis> (Rodentia,Cricetidae, Sigmodontinae) of Quaternary Sandy Plains in Southeastern Brazil

The genus Cerradomys, comprising eight species, is distributed mainly in transitional, dry, open and inland South American biomes like Caatinga, Cerrado, and Chaco. However, Cerradomys goytaca is restricted to very harsh ecosystems along the Quaternary coast sandy plains (restingas) of the Rio de Janeiro and Espírito Santo states, in southeastern Brazil. Cytochrome b and IRBP DNA data were used for elucidating the phylogenetic relationships of Cerradomys and estimating the time of divergence of different evolutionary lineages, while morphometric analyses were carried out for analyzing the rate of phenotypic evolution. Our findings showed that the first speciation events occurred in the Pliocene and early Pleistocene, leading to the C. marinhus, C. maracajuensis, and C. scotti distributed in central and western Brazil while species from eastern Brazil (C. langguthi, C. vivoi, C. subflavus, and C. goytaca) originated in the middle to late Pleistocene. Cerradomys goytaca populations diverged from inland C. subflavus ca. 0.29 MYBP with an accelerated rate of phenotypic evolution resulting in unique craniometric attributes, likely due to the strong selective pressures imposed by harsh habitats.     

Nuclear mtDNA pseudogenes as a source of new variants of the mtDNA cytochrome <Emphasis Type="Italic">b</Emphasis> haplotypes: A case study of Siberian rubythroat <Emphasis Type="Italic">Luscinia calliope</Emphasis> (Muscicapidae,Aves)

Sequence polymorphism of the mitochondrial DNA cytochrome b gene fragment was analyzed in 21 specimens of subspecies Luscinia calliope calliope (Pallas, 1776) and two specimens of L. c. anadyrensis (Portenko, 1939). On sequence chromatograms, in 19 specimens of L. c. calliope, double peaks of heteroplasmy type in the taxon-specific positions were revealed. Moreover, two clone variants were identified. The first variant was the calliope mitochondrial cyt b gene and the second was the nuclear cyt b pseudogene, similar to the mitochondrial haplotype anadyrensis-camtschatkensis. In L. c. anadyrensis, four clone variants, represented by the mitochondrial calliope and anadyrensis-camtschatkensis cyt b genes and nuclear calliope and sachalinensis cyt b pseudogenes, were identified. Some nuclear cyt b pseudogenes were highly similar (98–99%) to the mitochondrial genes of the subspecies L. c. anadyrensis, L. c. camtschatkensis, and L. c. sachalinensis. In the same time, the majority of nuclear pseudogene sequences were characterized by a high level of polymorphism, caused by nonsynonymous substitutions (up to five substitutions per sequence), the presence of indels in some of the clones, and TAA and TGA stop codons. In our opinion, the mitochondrial haplotypes anadyrensis-camtschatkensis and sachalinensis occurred as a result of intergenomic homologous recombination. This finding provides a new insight into the colonization history of the northeastern part of the range by L. calliope, according to which populating the territory of Chukotka, Kamchatka, and Sakhalin took place at different times and along the independent pathways.     

A morphological and phylogenetic analysis of <Emphasis Type="Italic">Ornithodoros marinkellei</Emphasis> (Acari: Argasidae), with additional notes on habitat and host usage

Ornithodoros marinkellei was described from larvae collected on Pteronotus spp. bats in Colombia and Panama. More recently, this tick was reported in the Brazilian Amazon. Because some morphometric differences were observed between O. marinkellei larvae from Colombia and Brazil, it was proposed that further investigations were needed to assess whether the differences could be attributed to intra- or inter-specific polymorphism. Herein, we collected O. marinkellei specimens in the type locality of Colombia, in Brazil, and in a new locality in Nicaragua, expanding the distribution of the species to Nicaragua. Morphometric analysis of larvae and adults, corroborated by a principal component analysis (PCA), indicated that the Brazilian specimens were larger than specimens from Colombia and Nicaragua. Phylogenetic analysis inferred from the mitochondrial 16S rRNA gene showed ticks from Colombia and Nicaragua more genetically related than any of them with ticks from Brazil, although ticks from the three countries grouped in a clade sister to a major clade containing sequences of various Neotropical Ornithodoros species. We concluded that ticks identified as O. marinkellei from Colombia, Nicaragua, and Brazil represent the same taxon, and that the genetic and morphological differences between them are likely to have a geographical bias. We redescribed the nymph of O. marinkellei, which has a vestigial hypostome, probably incompatible with blood feeding. We also report human infestation by O. marinkellei adults. As all reports of O. marinkellei adults have been from hot caves (temperature?>?35 °C), this abiotic condition could be a limiting factor for the occurrence of this tick species.     

Genetic variation and phylogeography of the bank vole (<Emphasis Type="Italic">Clethrionomys glareolus</Emphasis>, Arvicolinae,Rodentia) in Russia with special reference to the introgression of the mtDNA of a closely related species,red-backed vole (<Emphasis Type="Italic">Cl. rutilus</Emphasis>)

Totally, 294 bank voles (Clethrionomys glareolus) and 18 red-backed voles (Cl. rutilus) from 62 sites of European Russia were studied. Incomplete sequences (967 bp) of the mitochondrial cytochrome b gene were determined for 93 Cl. glareolus individuals from 56 sites and 18 Cl. rutilus individuals from the same habitats. Analysis of the cytochrome b gene variation has demonstrated that practically the entire European part of Russia, Ural, and a considerable part of Western Europe are inhabited by bank voles of the same phylogroup, displaying an extremely low genetic differentiation. Our data suggest that Cl. glareolus very rapidly colonized over the presently occupied territory in the post-Pleistocene period from no more than two (central European and western European) refugia from ancestral populations with a small effective size. PCR typing of the mitochondrial cytochrome b gene allowed us to assess the scale of mtDNA introgression from a closely related species, Cl. rutilus, and to outline the geographical zone of this introgression. Comparison with the red-backed vole haplotypes in the habitats shared by both species favors the hypothesis of an ancient hybridization event (mid-Holocene) and a subsequent introgression. These results suggest that the hybridization took place in the southern and middle Pre-Ural region.     

A new primer set for amplification of the cytochrome <Emphasis Type="Italic">b</Emphasis> gene in lantern fishes (Myctophidae)

New universal primers are offered for amplification of complete sequence of mitochondrial cyt b gene in lantern fishes of the family Myctophidae. Analysis of cyt b variability in the species of seven genera (Bolinichthys, Ceratoscopelus, Diaphus, Diogenichthys, Lampanyctus, Lepidophanes, Nannobrachium) demonstrates considerable divergence between species: an average of 18.2% (p-distances). Diversity (nucleotide diversity, number of segregating and phylogenetically informative sites, average number of nucleotide differences) and divergence significantly exceed those of another widely used mitochondrial marker, a fragment of cytochrome c oxidase subunit 1 sequence (cox 1). The mitochondrial cyt b gene amplified with the developed primers can be recommended as an informative tool for phylogenetic and population studies of lantern fishes.     

Tashkent riffle minnow <Emphasis Type="Italic">Alburnoides oblongus</Emphasis> belongs to the genus <Emphasis Type="Italic">Alburnus</Emphasis> (Osteichthyes: Cyprinidae) as inferred from mitochondrial and nuclear DNA markers

Sequences of mitochondrial (cytochrome b) and nuclear (recombination activating gene 1–RAG1) DNA markers were obtained for two species of the genus Alburnoides, the Taskent riffle minnow A. oblongus Bulgakov 1923 and the Terek spirlin A. gmelini Bogutskaya and Coad 2009. Phylogenetic analysis revealed that A. oblongus belongs to the genus Alburnus.     

Comparative analysis of otolith morphology in three species of <Emphasis Type="Italic">Scomber</Emphasis>

Geometric morphometrics is a quick and reliable approach to differentiate fish stocks based on the variation of otolith shapes. In this study, morphometric analysis of otolith shapes was used to differentiate three species of Scomber. The sagittae morphology of S. scombrus otolith is totally different from that of S. japonicus and S. australasicus. Multivariate analysis consistently showed that S. japonicus was morphologically similar to S. australasicus, whereas a significant difference in otolith shapes was detected between S. scombrus and other two species of Scomber. The rostrum, antirostrum, excisural notch and dorsal-posterior margin of the otolith reflect the main variations between the three species of Scomber. Shape indices and Fourier coefficients were used to discriminate fish species using analysis of variance and Fisher discriminant analysis. The shape indices successfully differentiated 100%, 95.7% and 96.4% of otoliths in S. japonicus, S. australasicus and S. scombrus, respectively, while the Fourier coefficients only discriminated 70.0%, 61.9% and 91.3% of the sagittae in S. japonicus, S. australasicus and S. scombrus. This study indicates that the shape analysis on the sagittae morphometrics of otoliths is a better method to differentiate species of Scomber.     

Species complex delimitation and patterns of population structure at different geographic scales in Neotropical silver catfish (<Emphasis Type="Italic">Rhamdia</Emphasis>: Heptapteridae)

The Neotropical catfish genus Rhamdia inhabits rivers and lakes from Mexico to Argentina. Previous studies have found that the taxonomy of this genus, as well as that of R. quelen, remains controversial. The present study aims to contribute to the understanding of Rhamdia systematics by delimiting putative species, and to elucidate the pattern of genetic differentiation of Rhamdia at different geographic levels within the cis-andean region. Species boundaries were defined by Generalized Mixed Yule Coalescent and Automatic Barcode Gap Discovery methods, and by phylogenetic analyses of cytochrome b (cyt b) sequences. Moreover, we performed phylogeographic analyses based on cyt b sequences and microsatellite markers. Patterns of differentiation were analyzed at three nested geographic levels: in the main cis-andean basins (macrogeographic scale); in the second major Neotropical basin system (mesogeographic scale), which encompasses La Plata basin, Patos-Merin basin, and the coastal lagoons draining to SW Atlantic Ocean; and finally, in the three most important coastal lagoons for artisanal fisheries in Uruguay (microgeographic scale). Sixteen species were found within Rhamdia, divided into two clades (cis- and trans-andean clades), each composed of eight putative species. Cis-andean Rhamdia species have probably diverged due to vicariance events occurring between and within basins since late Miocene-Pleistocene. Microgeographic scale analysis based on cyt b and microsatellite data revealed a high genetic structuring among the studied coastal lagoons. Mitochondrial and microsatellite markers enabled to identify three different populations, corresponding to the three coastal lagoons analyzed, which would have diverged recently and could be considered as different Management Units.     

Length-weight and length-length relationships of <Emphasis Type="Italic">Cirrhinus mrigala</Emphasis> (Cyprinidae) and <Emphasis Type="Italic">Xenentodon cancila</Emphasis> (Belonidae) from the river Ganga

Length-weight and length-length relationships are presented for two fish species collected during May 2015 to August 2016 from Narora site of the river Ganga. The parameters a and b of the length-weight relationships were estimated after the logarithmic transformation of the equation: W = aL ^b . The lengthlength relationships were also estimated using linear regressions. The coefficients of determination (R ²) values were >0.9 for both target fish species and linear regressions were highly significant (p < 0.001). Length-weight relationship indicated positive allometric growth pattern for Cirrhinus mrigala and negative allometric growth pattern for Xenentodon cancila. Length-length relationships for the selected fish species were also highly significant (R ² > 0.9, p < 0.001).     

<Emphasis Type="Italic">Stemodia perfoliata</Emphasis> (Plantaginaceae): A 200 year old new species from the Caatinga of Minas Gerais,Brazil

A new species of Stemodia (Plantaginaceae) from the Caatinga of northern Minas Gerais, Brazil, is described and illustrated. Stemodia perfoliata was first collected by Auguste de Saint-Hilaire, ca. 200 years ago, and remained unnamed until now. The new species is characterized by the connate-perfoliate leaves, a unique feature in the genus. We provide notes on morphology, geographic distribution and conservation status of S. perfoliata, along with a key to differentiate it from the similar species that occur in Brazil: S. durantifolia, S. hyptoides, S. maritima, S. palustris and S. stricta.     

Evolutionary diversification of Western Atlantic <Emphasis Type="Italic">Bathygobius</Emphasis> species based on cytogenetic,morphologic and DNA barcode data

A number of fish groups, such as Gobiidae, are highly diversified and taxonomically complex. Extensive efforts are necessary to elucidate their cryptic diversity, since questions often arise about the phylogenetic aspects of new species. Clarifications about the diversity and phylogeny of the Bathygobius species from the southwestern Atlantic are particularly needed. Evidence has been accumulating on the Brazilian coast regarding the possible presence of new species while doubts remain about the taxonomic status of others. The taxonomic identification of some species of Bathygobius has been problematic, given their generally conservative external morphology, and several species are recognized as cryptic. This situation hinders understanding the real diversity in this taxon. Taken together, genetic, cytogenetic and morphometric analyses have been effective in identifying new species of this genus. Here we describe the karyotypic features and morphological patterns of three Western South Atlantic species of Bathygobius. Furthermore, its cytochrome c oxidase I (COI) gene sequences were compared with those of species from Central America, North America and the Caribbean. The broad analyses performed demonstrated an unsuspected diversity, leading to the identification of an un-described new species (Bathygobius sp.2) and the geographic redefinition of another, Bathygobius sp.1, undoubtedly a branch of B. geminatus, hitherto inaccurately identified as B. mystacium on the coast of Brazil.     

Fish assemblage structure in an estuary of the Atlantic Forest biodiversity hotspot (southern Brazil)

We described the fish assemblage in the estuary of the Guaraguaçu River (one of the largest tributaries of the Paranaguá Bay Estuary, located within Brazil’s Atlantic Forest Biosphere Reserve) from June 2005 to May 2006, and assessed the seasonal and spatial effects of abiotic environmental attributes on the fish assemblage structure. Despite some oscillations in salinity, the upper and lower estuaries had year-round persistent oligohaline and polyhaline conditions, respectively. Despite high species richness (55 species), the Guaraguaçu River Estuary fish community contains a few dominant taxa; 11% of the richness accounts for >60% of its density and biomass. The most abundant species (in terms of both biomass and density) was Atherinella brasiliensis. Species whose densities were most strongly associated with the upper estuary were Centropomus parallelus, Ctenogobius schufeldti, Eucinostomus melanopterus, Platanichthys platana, Trinectes paulistanus, and Eugerres brasilianus. Those whose densities were most strongly associated with the lower estuary were A. brasiliensis, Sphoeroides greeleyi, Eucinostomus argenteus, Sphoeroides testudineus, Diapterus rhombeus, and Harengula clupeola. Throughout the year, canonical correspondence analysis identified: (1) the pattern of horizontal stratification of salinity along the river as being the most important variable for explaining most of the fish fauna structure; and (2) a strong relationship between the fish fauna and the salinity gradient along the estuary. Analysis of similarity further confirmed that each estuarine zone supports a year-round persistent and relatively homogeneous fish species assemblage. Total mean density and biomass remained constant over time in each estuarine habitat, but density shifted in the most abundant species, which appears related to recruitment patterns. Such species and abundance persistence likely occurs because seasonal rainfall-induced changes in river discharge are not sufficient to significantly shift runoff and salinity and thus fish assemblage structure (species composition, density and biomass) along the estuary. Such a lack of seasonal fish fauna movement as a response to changes in river flow contrasts with other estuarine systems around the world.     

Unspecific histological and hematological alterations in anadromous and resident <Emphasis Type="Italic">Salvelinus malma</Emphasis> induced by volcanogenic pollution

Knowledge of larval dispersal and connectivity in coral reef species is crucial for understanding population dynamics, resilience, and evolution of species. Here, we use ten microsatellites and one mitochondrial marker (cytochrome b) to investigate the genetic population structure, genetic diversity, and historical demography of the powder-blue tang Acanthurus leucosternon across more than 1000 km of the scarcely studied Eastern African region. The global AMOVA results based on microsatellites reveal a low but significant F _ST value (F _ST = 0.00252 P < 0.001; D _EST = 0.025 P = 0.0018) for the 336 specimens sampled at ten sample sites, while no significant differentiation could be found in the mitochondrial cytochrome b dataset. On the other hand, pairwise F _ST, PCOA, and hierarchical analysis failed to identify any genetic breaks among the Eastern African populations, supporting the hypothesis of genetic homogeneity. The observed genetic homogeneity among Eastern African sample sites can be explained by the lengthy post-larval stage of A. leucosternon, which can potentiate long-distance dispersal. Tests of neutrality and mismatch distribution signal a population expansion during the mid-Pleistocene period.     

Genetic divergence of sympatric charrs of the genus <Emphasis Type="Italic">Salvelinus</Emphasis> from Nachikinskoe Lake (Kamchatka)

We studied genetic differentiation of two charr species, Dolly Varden Salvelinus malma malma Walbaum and resident lacustrine charr Salvelinus sp., which sympatrically inhabit Nachikinskoe Lake (the Bol’shaya River basin) in southwestern Kamchatka Peninsula. Using restriction analysis (RFLP), three mitochondrial DNA fragments (ND1/ND2, ND5/ND6, and Cyt b/D-loop) amplified in polymerase chain reaction (PCR) were compared. The divergence of the mtDNA sequences between Salvelinus sp. and S. malma malma was 2.8%; Salvelinus sp. and S. taranetzi, 0.36%; Salvelinus sp. and S. krogiusae, 0.21%; Salvelinus sp. and S. alpinus, 3.0%. These results point to reproductive isolation of charrs in Nachikinskoe Lake and support the earlier suggestion on a close relationship between Salvelinus sp., S. taranetzi, and S. krogiusae.     

<Emphasis Type="Italic">Paulogramma hydarnis</Emphasis> (n. comb.) (Nymphalidae: Biblidinae): Distribution,Systematic Position,and Conservation Status of a Rare and Endangered Butterfly

The nymphalid Paulogramma hydarnis (Godart) (n. comb., previously in the genus Callicore) is an endangered butterfly present in a few montane sites in the Atlantic Forest in the Southeastern Brazil. The precise systematic position of P. hydarnis was previously unknown. Based on molecular data, we find that it is sister to Paulogramma pygas (Godart) (n. comb., also previously in Callicore), a common and widespread species in the Neotropics. In addition, we find that Callicore is not monophyletic and that “Callicore” hydarnis (along with other species) is more related to the genus Paulogramma, and should thus be placed in that genus. The genus Paulogramma is now composed by the following species: Paulogramma pyracmon (Godart), Paulogramma eunomia (Hewitson) n. comb., Paulogramma hydarnis (Godart) n. comb., Paulogramma hystaspes (Fabricius) n. comb., Paulogramma pygas (Godart) n. comb., and Paulogramma tolima (Hewitson, 1852) n. comb. Museum specimens and field data report P. hydarnis in four sites in Southeastern Brazil. Recently, P. hydarnis was recorded for the first time at Parque Nacional do Caparaó, states of Espírito Santo and Minas Gerais, expanding its distribution about 200 km northward of the previously known limit. Although regularly recorded in some sites, most records are historic, before the 1960s, and the current conservation situation of this species is delicate, deserving attention.     

The High Divergence of Two Morphologically Similar Trematode Species of the Genus <Emphasis Type="Italic">Nanophyetus</Emphasis> of Salmonids from the Data of mtDNA <Emphasis Type="Italic">nad1</Emphasis> Gene Sequences

Intestinal flukes of fish (mainly salmonids) belonging to the genus Nanophyetus (Trematoda: Troglotrematidae) are the causative agents of nanophyetiasis, a zoonotic disease of animals and humans, which is widespread in countries in the northern Pacific. Two geographical forms, one from North America and the other from the eastern Eurasia were described within this genus; however, their taxonomic status was debatable. A multilocus analysis of nuclear rDNA sequences applied in this study has shown that these forms are independent nominal species: Nanophyetus salmincola and Nanophyetus schikhobalowi. This study, based on sequencing the mtDNA nad1 gene, has evaluated the genetic variability of N. schikhobalowi from eastern Eurasia (Russia) and compared our data with the results obtained for N. salmincola from North America (United States). The genetic differentiation within the Eurasian sample was 1.4%, that for the North American sample was 0.8%, and differentiation between the samples was 15.5%. High values of genetic divergence and completed sorting of mitochondrial haplotypes confirmed the species independence of the compared geographic forms of Nanophyetus.     

Authentication of five <Emphasis Type="Italic">Barilius</Emphasis> species from Indian waters using DNA barcoding

Authentic identification of fish species is essential for conserving them as a valuable genetic resource in our environment. DNA barcoding of living beings has become an important and ultimate tool for establishing their molecular identity. Among cyprinids, Barilius is an important genus having nearly 23 species in Indian region whose morphological identification is often difficult due to minute differences in their features. Five species collected from Indian waters and primarily identified as Opsarius bakeri (syn. Barilius bakeri), B. gatensis, B. vagra, B. bendelisis and B. ngawa were authenticated by their DNA barcoding based on mitochondrial COI gene sequences. Five individuals of each species were taken for barcode preparation by COI gene sequencing which yielded one barcode for B. ngawa, two barcodes each for O. bakeri, B. gatensis, B. bendelisis and three barcodes for B. vagra. The order of inter and intra-specific variation was estimated to know a preliminary status of variation prevailing in these cold stream fish species significant for evolution and conservation of these valued species of our ichthyofauna. Average variation within genera was found to be 13.6% with intra-specific variation ranging from 0.0% (B. ngawa) to 0.6% (B. gatensis). These distance data are in the same order found by various researchers globally using COI barcode sequences in different fish species. Phylogenetic relatedness among Barilius species and some other cyprinids validate their status of individual species as established by conventional taxonomy.     

Whole Mitochondrial Genome of Blakiston’s Fish Owl <Emphasis Type="Italic">Bubo</Emphasis> (<Emphasis Type="Italic">Ketupa</Emphasis>) <Emphasis Type="Italic">blakistoni</Emphasis> Suggests Its Redescription in the Genus <Emphasis Type="Italic">Ketupa</Emphasis>

The paper reports the whole mitochondrial genome (approximately 13 kb) sequencing in three individual representatives of the continental population of Blakiston’s fish owl Bubo blakistoni (Seebohm 1884), the IUCN Red List species in the family Strigidae. The analysis revealed extremely low mtDNA genetic diversity, which may be indicative of the critical state of the studied population. The phylogenetic analysis performed on the basis of the whole mitochondrial genome sequencing data showed that Blakiston’s fish owl is more closely related to the Strix genus than to the Bubo genus with the genetic divergence between blakistoni and either of the two genera being statistically significant and close to intergeneric level (p-distance of 0.135 in the case of the Strix genus and p-distance of 0.151 in the case of the Bubo genus). The results obtained in this work do not match the published data on the mitochondrial cytochrome b gene and the nuclear RAG-1 gene, which laid the basis for the assignment of Blackiston’s fish owl to the Bubo genus in the recent taxonomic bulletins, but rather support the earlier taxonomic classification according to which all four Asian forms, blakistoni, flavipes, zeylonensis, and ketupu, constituted a separate Ketupa genus.     

Molecular phylogeny of pectinase genes <Emphasis Type="Italic">PGU</Emphasis> in the yeast genus <Emphasis Type="Italic">Saccharomyces</Emphasis>

Using yeast genome databases and literature data, phylogenetic analysis of pectinase PGU genes from 112 Saccharomyces strains assigned to the biological species S. arboricola, S. bayanus (var. uvarum), S. cariocanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, and the hybrid taxon S. pastorianus (syn. S. carlsbergensis) was carried out. A superfamily of divergent PGU genes was found. Natural interspecies transfer of the PGU gene both from S. cerevisiae to S. bayanus and from S. paradoxus to S. cerevisiae may, however, occur. Within the Saccharomyces species, identity of the PGU nucleotide sequences was 98.8–100% for S. cerevisiae, 86.1–95.7% for S. bayanus (var. uvarum), 94–98.3% for S. kudriavzevii, and 96.8–100% for S. paradoxus/S. cariocanus. For the first time, a family of polymeric PGU1b, PGU2b, PGU3b and PGU4b genes is documented for the yeast S. bayanus var. uvarum, a variety important for winemaking.