Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication.

PubMed

Wood, Dustin A; Fisher, Robert N; Vandergast, Amy G

2014-01-01

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.

Fuzzy Boundaries: Color and Gene Flow Patterns among Parapatric Lineages of the Western Shovel-Nosed Snake and Taxonomic Implication

PubMed Central

Wood, Dustin A.; Fisher, Robert N.; Vandergast, Amy G.

2014-01-01

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process. PMID:24848638

Comparative Analysis of Leaf Trichome Structure and Composition of Epicuticular Flavonoids in Finnish Birch Species

PubMed Central

VALKAMA, ELENA; SALMINEN, JUHA‐PEKKA; KORICHEVA, JULIA; PIHLAJA, KALEVI

2003-01-01

The morphology, ultrastructure, density and distribution of trichomes on leaves of Betula pendula, B. pubescens ssp. pubescens, B. pubescens ssp. czerepanovii and B. nana were examined by means of light, scanning and transmission electron microscopy. The composition of flavonoids in ethanolic leaf surface extracts was analysed by high pressure liquid chromatography. All taxa examined contained both glandular and non‐glandular trichomes (short and/or long hairs) but differed from each other in trichome ultrastructure, density and location on the leaf. Leaves of B. pubescens were more hairy than those of B. pendula, but the latter species had a higher density of glandular trichomes. Of the two subspecies of B. pubescens, leaves of ssp. pubescens had more short hairs on the leaf surface and four times the density of glandular trichomes of leaves of ssp. czerepanovii, whereas, in the latter subspecies, short hairs occurred largely on leaf veins, as in B. nana. The glandular trichomes were peltate glands, consisting of medullar and cortical cells, which differed structurally. Cortical cells possessed numerous small, poorly developed plastids and small vacuoles, whereas medullar cells had several large plastids with well‐developed thylakoid systems and fewer vacuoles. In B. pubescens subspecies, vacuoles of the glandular cells contained osmiophilic deposits, which were probably phenolic, whereas in B. pendula, vacuoles of glandular trichomes were characterized by the presence of numerous myelin‐like membranes. The composition of epicuticular flavonoids also differed among species. The two subspecies of B. pubescens and B. nana shared the same 12 compounds, but five of these occurred only in trace amounts in B. nana. Leaf surface extracts of B. pendula contained just six flavonoids, three of which occurred only in this species. In summary, the structure, density and distribution of leaf trichomes and the composition of epicuticular flavonoids represent good taxonomic markers for Finnish birch species. PMID:12714363

Morphometric and molecular differentiation between quetzal subspecies of Pharomachrus mocinno (Trogoniformes: Trogonidae).

PubMed

Solórzano, Sofía; Oyama, Ken

2010-03-01

The resplendent Quetzal (Pharomachrus mocinno) is an endemic Mesoamerican bird species of conservation concern. Within this species, the subspecies P. m. costaricensis and P. m. mocinno, have been recognized by apparent morphometric differences; however, presently there is no sufficient data for confirmation. We analyzed eight morphometric attributes of the body from 41 quetzals: body length, tarsus and cord wing, as well as the length, wide and depth of the bill, body weight; and in the case of the males, the length of the long upper-tail cover feathers. We used multivariate analyses to discriminate morphometric differences between subspecies and contrasted each morphometric attribute between and within subspecies with paired non-parametric Wilcoxon test. In order to review the intraspecific taxonomic status of this bird, we added phylogenetic analysis, and genetic divergence and differentiation based on nucleotide variations in four sequences of mtDNA. The nucleotide variation was estimated in control region, subunit NDH6, and tRNAGlu and tRNAPhe in 26 quetzals from eight localities distributed in five countries. We estimated the genetic divergence and differentiation between subspecies according to a mutation-drift equilibrium model. We obtained the best mutation nucleotide model following the procedure implemented in model test program. We constructed the phylogenetic relationships between subspecies by maximum parsimony and maximum likelihood using PAUP, as well as with Bayesian statistics. The multivariate analyses showed two different morphometric groups, and individuals clustered according to the subspecies that they belong. The paired comparisons between subspecies showed strong differences in most of the attributes analyzed. Along the four mtDNA sequences, we identified 32 nucleotide positions that have a particular nucleotide according to the quetzals subspecies. The genetic divergence and the differentiation was strong and markedly showed two groups within P. mocinno that corresponded to the quetzals subspecies. The model selected for our data was TVM+G. The three phylogenetic methods here used recovered two clear monophyletic clades corresponding to each subspecies, and evidenced a significant and true partition of P. mocinno species into two different genetic, morphometric and ecologic groups. Additionally, according to our calculations, the gene flow between subspecies is interrupted at least from three million years ago. Thus we propose that P. mocinno be divided in two independent species: P. mocinno (Northern species, from Mexico to Nicaragua) and in P. costaricensis (Southern species, Costa Rica and Panama). This new taxonomic classification of the quetzal subspecies allows us to get well conservation achievements because the evaluation about the kind and magnitude of the threats could be more precise.

Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies

PubMed Central

2013-01-01

Background The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a Bos taurus or Bos indicus ancestor. Methods Phenotype data on one or more traits and SNP genotype data for 10 181 cattle from Bos taurus, Bos indicus and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. indicus or B. taurus on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin. Results Fitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies. Conclusions The results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. indicus and B. taurus cattle. Thus, the QTL that segregate in current populations likely resulted from mutations that occurred in one of the subspecies and can have both positive and negative effects on the traits. There was no evidence that selection has increased the frequency of alleles that increase body weight. PMID:24168700

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

DOE PAGES

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.; ...

2016-11-18

In order for a lignocellulosic bioenergy feedstock to be considered sustainable,it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application,it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin,glucan,and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) amongmore » parental and hybrid populations,whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age,with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase),and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%,respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass,with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass,respectively),with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate,biomass composition,and further optimization of enzymatic saccharification yield,high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.« less

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.

In order for a lignocellulosic bioenergy feedstock to be considered sustainable,it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application,it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin,glucan,and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) amongmore » parental and hybrid populations,whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age,with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase),and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%,respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass,with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass,respectively),with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate,biomass composition,and further optimization of enzymatic saccharification yield,high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.« less

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa.

PubMed

Healey, Adam L; Lee, David J; Lupoi, Jason S; Papa, Gabriella; Guenther, Joel M; Corno, Luca; Adani, Fabrizio; Singh, Seema; Simmons, Blake A; Henry, Robert J

2016-01-01

In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7-21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28-38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production.

Evaluation of Relationships between Growth Rate, Tree Size, Lignocellulose Composition, and Enzymatic Saccharification in Interspecific Corymbia Hybrids and Parental Taxa

PubMed Central

Healey, Adam L.; Lee, David J.; Lupoi, Jason S.; Papa, Gabriella; Guenther, Joel M.; Corno, Luca; Adani, Fabrizio; Singh, Seema; Simmons, Blake A.; Henry, Robert J.

2016-01-01

In order for a lignocellulosic bioenergy feedstock to be considered sustainable, it must possess a high rate of growth to supply biomass for conversion. Despite the desirability of a fast growth rate for industrial application, it is unclear what effect growth rate has on biomass composition or saccharification. We characterized Klason lignin, glucan, and xylan content with response to growth in Corymbia interspecific F1 hybrid families (HF) and parental species Corymbia torelliana and C. citriodora subspecies variegata and measured the effects on enzymatic hydrolysis from hydrothermally pretreated biomass. Analysis of biomass composition within Corymbia populations found similar amounts of Klason lignin content (19.7–21.3%) among parental and hybrid populations, whereas glucan content was clearly distinguished within C. citriodora subspecies variegata (52%) and HF148 (60%) as compared to other populations (28–38%). Multiple linear regression indicates that biomass composition is significantly impacted by tree size measured at the same age, with Klason lignin content increasing with diameter breast height (DBH) (+0.12% per cm DBH increase), and glucan and xylan typically decreasing per DBH cm increase (-0.7 and -0.3%, respectively). Polysaccharide content within C. citriodora subspecies variegata and HF-148 were not significantly affected by tree size. High-throughput enzymatic saccharification of hydrothermally pretreated biomass found significant differences among Corymbia populations for total glucose production from biomass, with parental Corymbia torelliana and hybrids HF-148 and HF-51 generating the highest amounts of glucose (~180 mg/g biomass, respectively), with HF-51 undergoing the most efficient glucan-to-glucose conversion (74%). Based on growth rate, biomass composition, and further optimization of enzymatic saccharification yield, high production Corymbia hybrid trees are potentially suitable for fast-rotation bioenergy or biomaterial production. PMID:27917179

Phylogeography of Canada Geese (Branta canadensis) in western North America

USGS Publications Warehouse

Scribner, K.T.; Talbot, S.L.; Pearce, J.M.; Pierson, Barbara J.; Bollinger, K.S.; Derksen, D.V.

2003-01-01

Using molecular genetic markers that differ in mode of inheritance and rate of evolution, we examined levels and partitioning of genetic variation for seven nominal subspecies (11 breeding populations) of Canada Geese (Branta canadensis) in western North America. Gene trees constructed from mtDNA control region sequence data show that subspecies of Canada Geese do not have distinct mtDNA. Large- and small-bodied forms of Canada Geese were highly diverged (0. 077 average sequence divergence) and represent monophyletic groups. A majority (65%) of 20 haplotypes resolved were observed in single breeding locales. However, within both large- and small-bodied forms certain haplotypes occurred across multiple subspecies. Population trees for both nuclear (microsatellites) and mitochondrial markers were generally concordant and provide resolution of population and subspecific relationships indicating incomplete lineage sorting. All populations and subspecies were genetically diverged, but to varying degrees. Analyses of molecular variance, nested-clade and coalescence-based analyses of mtDNA suggest that both historical (past fragmentation) and contemporary forces have been important in shaping current spatial genetic distributions. Gene flow appears to be ongoing though at different rates, even among currently recognized subspecies. The efficacy of current subspecific taxonomy is discussed in light of hypothesized historical vicariance and current demographic trends of management and conservation concern.

Genetic Ancestry of the Extinct Javan and Bali Tigers

PubMed Central

Xue, Hao-Ran; Yamaguchi, Nobuyuki; Driscoll, Carlos A.; Han, Yu; Bar-Gal, Gila Kahila; Zhuang, Yan; Mazak, Ji H.; Macdonald, David W.; O’Brien, Stephen J.

2015-01-01

The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1–2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers. PMID:25754539

[Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl (Gallus gallus gallus) in Thailand].

PubMed

Bao, Wen-Bin; Chen, Guo-Hong; Wu, Xin-Sheng; Xu, Qi; Wu, Sheng-Long; Shu, Jing-Ting; Weigend, Steffen

2007-05-01

Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl in Thailand (Gallus gallus gallus) was evaluated with 29 microstaellite loci, the genetic variability within subspecies and genetic differentiation between subspecies were estimated. The results showed that the 168 alleles were amplified with the number of alleles per locus from 2 to 13. The average expected heterozygosity and polymorphism information content (PIC) of all loci were 0.5780 and 0.53, respectively. The mean numbers of effective alleles of red jungle fowl in China and red jungle fowl in Thailand were 5.55 and 6.38. The heterozygosity and the genetic diversity of the two subspecies were high. Genetic differentiation index (FST) of these populations was 0.194 (P<0.01). Reynolds' genetic distance and gene flow between the two populations were 0.157 and 1.040, respectively. Based on these results, genetic structure and significant genetic differentiation of red jungle fowl in China were different from red jungle fowl in Thailand. The results of this study did not support to identify these red jungle fowl subspecies as the same subspecies, but supported the theory that Chinese domestic fowls have independent origin.

Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivas-Ubach, Albert; Sardans, Jordi; Hódar, José Antonio

The metabolome, the chemical phenotype of an organism, should be shaped by evolution. Metabolomes depend on genetic composition and expression, which can be sources of evolutionary inertia, so most aspects of metabolomes should be similar in closely related sympatric species. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), one introduced (ssp. iberica) and one autochthonous (ssp. nevadensis), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspeciesmore » were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results suggest that certain plant metabolic responses associated with folivory have been conserved throughout evolutionary history. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation, two recent severe issues in the Mediterranean Basin.« less

Polygamy slows down population divergence in shorebirds

USGS Publications Warehouse

Jackson, Josephine D'Urban; dos Remedios, Natalie; Maher, Kathryn; Zefania, Sama; Haig, Susan M.; Oyler-McCance, Sara J.; Blomqvist, Donald; Burke, Terry; Bruford, Michael W.; Székely, Tamás; Küpper, Clemens

2017-01-01

Sexual selection may act as a promotor of speciation since divergent mate choice and competition for mates can rapidly lead to reproductive isolation. Alternatively, sexual selection may also retard speciation since polygamous individuals can access additional mates by increased breeding dispersal. High breeding dispersal should hence increase gene flow and reduce diversification in polygamous species. Here, we test how polygamy predicts diversification in shorebirds using genetic differentiation and subspecies richness as proxies for population divergence. Examining microsatellite data from 79 populations in 10 plover species (Genus: Charadrius) we found that polygamous species display significantly less genetic structure and weaker isolation-by-distance effects than monogamous species. Consistent with this result, a comparative analysis including 136 shorebird species showed significantly fewer subspecies for polygamous than for monogamous species. By contrast, migratory behavior neither predicted genetic differentiation nor subspecies richness. Taken together, our results suggest that dispersal associated with polygamy may facilitate gene flow and limit population divergence. Therefore, intense sexual selection, as occurs in polygamous species, may act as a brake rather than an engine of speciation in shorebirds. We discuss alternative explanations for these results and call for further studies to understand the relationships between sexual selection, dispersal, and diversification.

Polygamy slows down population divergence in shorebirds

PubMed Central

D'Urban Jackson, Josephine; dos Remedios, Natalie; Maher, Kathryn H.; Zefania, Sama; Haig, Susan; Oyler‐McCance, Sara; Blomqvist, Donald; Burke, Terry; Bruford, Michael W.; Székely, Tamás; Küpper, Clemens

2017-01-01

Sexual selection may act as a promotor of speciation since divergent mate choice and competition for mates can rapidly lead to reproductive isolation. Alternatively, sexual selection may also retard speciation since polygamous individuals can access additional mates by increased breeding dispersal. High breeding dispersal should hence increase gene flow and reduce diversification in polygamous species. Here, we test how polygamy predicts diversification in shorebirds using genetic differentiation and subspecies richness as proxies for population divergence. Examining microsatellite data from 79 populations in 10 plover species (Genus: Charadrius) we found that polygamous species display significantly less genetic structure and weaker isolation‐by‐distance effects than monogamous species. Consistent with this result, a comparative analysis including 136 shorebird species showed significantly fewer subspecies for polygamous than for monogamous species. By contrast, migratory behavior neither predicted genetic differentiation nor subspecies richness. Taken together, our results suggest that dispersal associated with polygamy may facilitate gene flow and limit population divergence. Therefore, intense sexual selection, as occurs in polygamous species, may act as a brake rather than an engine of speciation in shorebirds. We discuss alternative explanations for these results and call for further studies to understand the relationships between sexual selection, dispersal, and diversification. PMID:28233288

Complete mitochondrial genome of the a rare subspecies of genus Bos, Tianzhu white yak from Tibetan area in China.

PubMed

E, Guangxin; Na, Ri-Su; Zhao, Yong-Ju; Gao, Hui-Jiang; An, Tian-Wu; Huang, Yong-Fu

2016-01-01

The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

USGS Publications Warehouse

Talbot, Sandra L.; Sage, Kevin; Sonsthagen, Sarah A.; Gravley, Megan C.; Swem, Ted; Williams, Jeffrey C.; Longmire, Jonathan L.; Ambrose, Skip; Flamme, Melanie J; Lewis, Stephen B.; Phillips, Laura M.; Anderson, Clifford; White, Clayton M

2017-01-01

Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)–each comprised of discrete populations that are variously intra-regionally connected.

Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing.

PubMed

Bataillon, Thomas; Duan, Jinjie; Hvilsom, Christina; Jin, Xin; Li, Yingrui; Skov, Laurits; Glemin, Sylvain; Munch, Kasper; Jiang, Tao; Qian, Yu; Hobolth, Asger; Wang, Jun; Mailund, Thomas; Siegismund, Hans R; Schierup, Mikkel H

2015-03-30

We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35× per individual. Central chimpanzees (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 per site) followed by Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P. t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses

PubMed Central

Hey, Jody

2010-01-01

The divergence of bonobos and three subspecies of the common chimpanzee was examined under a multipopulation isolation-with-migration (IM) model with data from 73 loci drawn from the literature. A benefit of having a full multipopulation model, relative to conducting multiple pairwise analyses between sampled populations, is that a full model can reveal historical gene flow involving ancestral populations. An example of this was found in which gene flow is indicated between the western common chimpanzee subspecies and the ancestor of the central and the eastern common chimpanzee subspecies. The results of a full analysis on all four populations are strongly consistent with analyses on pairs of populations and generally similar to results from previous studies. The basal split between bonobos and common chimpanzees was estimated at 0.93 Ma (0.68–1.54 Ma, 95% highest posterior density interval), with the split among the ancestor of three common chimpanzee populations at 0.46 Ma (0.35–0.65), and the most recent split between central and eastern common chimpanzee populations at 0.093 Ma (0.041–0.157). Population size estimates mostly fell in the range from 5,000 to 10,000 individuals. The exceptions are the size of the ancestor of the common chimpanzee and the bonobo, at 17,000 (8,000–28,000) individuals, and the central common chimpanzee and its immediate ancestor with the eastern common chimpanzee, which have effective size estimates at 27,000 (16,000–44,000) and 32,000 (19,000–54,000) individuals, respectively. PMID:19955478

The divergence of chimpanzee species and subspecies as revealed in multipopulation isolation-with-migration analyses.

PubMed

Hey, Jody

2010-04-01

The divergence of bonobos and three subspecies of the common chimpanzee was examined under a multipopulation isolation-with-migration (IM) model with data from 73 loci drawn from the literature. A benefit of having a full multipopulation model, relative to conducting multiple pairwise analyses between sampled populations, is that a full model can reveal historical gene flow involving ancestral populations. An example of this was found in which gene flow is indicated between the western common chimpanzee subspecies and the ancestor of the central and the eastern common chimpanzee subspecies. The results of a full analysis on all four populations are strongly consistent with analyses on pairs of populations and generally similar to results from previous studies. The basal split between bonobos and common chimpanzees was estimated at 0.93 Ma (0.68-1.54 Ma, 95% highest posterior density interval), with the split among the ancestor of three common chimpanzee populations at 0.46 Ma (0.35-0.65), and the most recent split between central and eastern common chimpanzee populations at 0.093 Ma (0.041-0.157). Population size estimates mostly fell in the range from 5,000 to 10,000 individuals. The exceptions are the size of the ancestor of the common chimpanzee and the bonobo, at 17,000 (8,000-28,000) individuals, and the central common chimpanzee and its immediate ancestor with the eastern common chimpanzee, which have effective size estimates at 27,000 (16,000-44,000) and 32,000 (19,000-54,000) individuals, respectively.

Investigating Concordance among Genetic Data, Subspecies Circumscriptions and Hostplant Use in the Nymphalid Butterfly Polygonia faunus

PubMed Central

Janz, Niklas; Leski, Michael; Slove, Jessica; Warren, Andrew; Nylin, Sören

2012-01-01

Subspecies are commonly used taxonomic units to formally describe intraspecific geographic variation in morphological traits. However, the concept of subspecies is not clearly defined, and there is little agreement about what they represent in terms of evolutionary units, and whether they can be used as reliably useful units in conservation, evolutionary theory and taxonomy. We here investigate whether the morphologically well-characterized subspecies in the North American butterfly Polygonia faunus are supported by genetic data from mitochondrial sequences and eight microsatellite loci. We also investigate the phylogeographic structure of P. faunus and test whether similarities in host-plant use among populations are related to genetic similarity. Neither the nuclear nor the mitochondrial data corroborated subspecies groupings. We found three well defined genetic clusters corresponding to California, Arizona and (New Mexico+Colorado). There was little structuring among the remaining populations, probably due to gene flow across populations. We found no support for the hypothesis that similarities in host use are related to genetic proximity. The results indicate that the species underwent a recent rapid expansion, probably from two glacial refugia in western North America. The mitochondrial haplotype network indicates at least two independent expansion phases into eastern North America. Our results clearly demonstrate that subspecies in P. faunus do not conform to the structuring of genetic variation. More studies on insects and other invertebrates are needed to better understand the scope of this phenomenon. The results of this study will be crucial in designing further experiments to understand the evolution of hostplant utilization in this species. PMID:22844425

Vitamin K epoxide reductase complex subunit 1 (Vkorc1) haplotype diversity in mouse priority strains

PubMed Central

Song, Ying; Vera, Nicole; Kohn, Michael H

2008-01-01

Background Polymorphisms in the vitamin K-epoxide reductase complex subunit 1 gene, Vkorc1, could affect blood coagulation and other vitamin K-dependent proteins, such as osteocalcin (bone Gla protein, BGP). Here we sequenced the Vkorc1 gene in 40 mouse priority strains. We analyzed Vkorc1 haplotypes with respect to prothrombin time (PT) and bone mineral density and composition (BMD and BMC); phenotypes expected to be vitamin K-dependent and represented by data in the Mouse Phenome Database (MPD). Findings In the commonly used laboratory strains of Mus musculus domesticus we identified only four haplotypes differing in the intron or 5' region sequence of the Vkorc1. Six haplotypes differing by coding and non-coding polymorphisms were identified in the other subspecies of Mus. We detected no significant association of Vkorc1 haplotypes with PT, BMD and BMC within each subspecies of Mus. Vkorc1 haplotype sequences divergence between subspecies was associated with PT, BMD and BMC. Conclusion Phenotypic variation in PT, BMD and BMC within subspecies of Mus, while substantial, appears to be dominated by genetic variation in genes other than the Vkorc1. This was particularly evident for M. m. domesticus, where a single haplotype was observed in conjunction with virtually the entire range of PT, BMD and BMC values of all 5 subspecies of Mus included in this study. Differences in these phenotypes between subspecies also should not be attributed to Vkorc1 variants, but should be viewed as a result of genome wide genetic divergence. PMID:19046458

Essential-oil composition of Daucus carota ssp. major (Pastinocello Carrot) and nine different commercial varieties of Daucus carota ssp. sativus fruits.

PubMed

Flamini, Guido; Cosimi, Elena; Cioni, Pier Luigi; Molfetta, Ilaria; Braca, Alessandra

2014-07-01

The chemical composition of the essential oils obtained by hydrodistillation from the pastinocello carrot, Daucus carota ssp. major (Vis.) Arcang. (flowers and achenes), and from nine different commercial varieties of D. carota L. ssp. sativus (achenes) was investigated by GC/MS analyses. Selective breeding over centuries of a naturally occurring subspecies of the wild carrot, D. carota L. ssp. sativus, has produced the common garden vegetable with reduced bitterness, increased sweetness, and minimized woody core. On the other hand, the cultivation of the pastinocello carrot has been abandoned, even if, recently, there has been renewed interest in the development of this species, which risks genetic erosion. The cultivated carrot (D. carota ssp. sativus) and the pastinocello carrot (D. carota ssp. major) were classified as different subspecies of the same species. This close relationship between the two subspecies urged us to compare the chemical composition of their essential oils, to evaluate the differences. The main essential-oil constituents isolated from the pastinocello fruits were geranyl acetate (34.2%), α-pinene (12.9%), geraniol (6.9%), myrcene (4.7%), epi-α-bisabolol (4.5%), sabinene (3.3%), and limonene (3.0%). The fruit essential oils of the nine commercial varieties of D. carota ssp. sativus were very different from that of pastinocello, as also confirmed by multivariate statistical analyses. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

Genetic ancestry of the extinct Javan and Bali tigers.

PubMed

Xue, Hao-Ran; Yamaguchi, Nobuyuki; Driscoll, Carlos A; Han, Yu; Bar-Gal, Gila Kahila; Zhuang, Yan; Mazak, Ji H; Macdonald, David W; O'Brien, Stephen J; Luo, Shu-Jin

2015-01-01

The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake (Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation

PubMed Central

Makowsky, Robert; Marshall, John C.; McVay, John; Chippindale, Paul T.; Rissler, Leslie J.

2012-01-01

Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrialgenes (NADH-II, Cyt-b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially-explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations. PMID:20302955

Subcarbonyl species of molybdenum hexacarbonyl supported on silica: A DRIFT study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurhinen, M.; Venaelaeinen, T.; Pakkanen, T.A.

1994-10-06

Subspecies of partially decarbonylated molybdenum hexacarbonyl supported on silica were studied by diffuse reflectance IR spectroscopy. Mo(CO)[sub 6]/SiO[sub 2] was prepared in a fluidized bed reactor by vapor-phase adsorption of molybdenum hexacarbonyl under nitrogen flow. Decarbonylation begins when Mo(CO)[sub 6] has adsorbed onto the silica. Dehydroxylation of the support during calcination facilitates the formation of subspecies of Mo(CO)[sub 6]. The activation energy needed for bond formation between a transition metal and silica and for decarbonylation is lower than the desorption energy of physisorbed Mo(CO)[sub 6], and this was seen in the IR spectra as a disappearance of bands due tomore » subspecies. When the supported Mo(CO)[sub 6] was reheated the physisorption bands were the last to disappear from the IR spectra. 37 refs., 6 figs., 2 tabs.« less

Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

PubMed Central

Besnard, G.; Garcia-Verdugo, C.; Rubio De Casas, R.; Treier, U. A.; Galland, N.; Vargas, P.

2008-01-01

Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors of subspp. guanchica and europaea. PMID:18024415

The role of the Ord Arid Intrusion in the historical and contemporary genetic division of long-tailed finch subspecies in northern Australia

PubMed Central

Rollins, Lee Ann; Svedin, Nina; Pryke, Sarah R; Griffith, Simon C

2012-01-01

The effect of separation by biogeographic features followed by secondary contact can blur taxonomic boundaries and produce complex genetic signatures. We analyzed population structure and gene flow across the range of the long-tailed finch (Poephila acuticauda) in northern Australia (1) to test the hypothesis that Ord Arid Intrusion acted as the causative barrier that led to divergence of P. acuticauda subspecies, (2) to determine whether genetic data support the presence of a gradual cline across the range or a sudden shift, both of which have been suggested based on morphological data, and (3) to estimate levels of contemporary gene flow within this species complex. We collected samples from 302 individuals from 10 localities. Analyses of 12 microsatellite loci and sequence data from 333 base pairs of the mitochondrial control region were used to estimate population structure and gene flow, using analysis of molecular variance (AMOVA), haplotype network analysis, frequency statistics, and clustering methods. Mitochondrial sequence data indicated the presence of three genetic groups (regions) across the range of P. acuticauda. Genetic diversity was highest in the east and lowest in the west. The Ord Arid Intrusion appears to have functioned as a biogeographic barrier in the past, according to mtDNA evidence presented here and evidence from previous studies. The absence of isolation by distance between adjacent regions and the lack of population genetic structure of mtDNA within regions indicates that genetic changes across the range of P. acuticauda subspecies are characterized by discrete breaks between regions. While microsatellite data indicate a complete absence of genetic structure across this species’ range, it appears unlikely that this results from high levels of gene flow. Mitochondrial data do not support the presence of contemporary gene flow across the range of this species. PMID:22833795

Using Molecular Genetic Markers to Resolve a Subspecies Boundary: The Northern Boundary of the Southwestern Willow Flycatcher in the Four-Corner States

USGS Publications Warehouse

Paxton, Eben H.; Sogge, Mark K.; Theimer, Tad C.; Girard, Jessica; Keim, Paul

2008-01-01

*Executive Summary* The northern boundary of the endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) is currently approximated as running through southern Colorado and Utah, but the exact placement is uncertain because this subspecies shares a border with the more northern and non-endangered E. t. adastus. To help resolve this issue, we evaluated the geographic distribution of mitochondrial and nuclear DNA by sampling breeding sites across the four-corner states (Arizona, Colorado, New Mexico, and Utah). We found that breeding sites clustered into two major groups generally consistent with the currently designated boundary, with the exception of three sites situated along the current boundary. However, delineating a precise boundary that would separate the two subspecies is made difficult because (1) we found evidence for a region of intergradation along the boundary area, suggesting the boundary is not discreet, and (2) the boundary region is sparsely populated, with too few extant breeding populations to precisely locate a boundary. The boundary region encompasses an area where elevation changes markedly over relatively short distances, with low elevation deserts to the south and more mesic, higher elevation habitats to the north. We hypothesized that latitudinal and elevational differences and their concomitant ecological effects could form an ecological barrier that inhibited gene flow between the subspecies, forming the basis for the subspecies boundary. We modeled changes in geographic patterns of genetic markers as a function of latitude and elevation finding significant support for this relationship. The model was brought into a GIS environment to create multiple subspecies boundaries, with the strength of each predicted boundary evaluated on the basis of how much genetic variation it explained. The candidate boundary that accounted for the most genetic variation was situated generally near the currently recognized subspecies boundary, but should be more biologically meaningful because it incorporates the landscape features that may be driving separation of the subspecies. Even so, we caution that using any narrow boundary line as an indicator of subspecies identity could be misleading because biologically the boundary is a region of intergradation rather than a discrete line. Designating, a boundary ultimately becomes a regulatory and management decision based on how much of the genetic variation unique to a subspecies should be protected. We discuss how the results of this study can help guide this decision process by wildlife policy makers.

Landscape Features Shape Genetic Structure in Threatened Northern Spotted Owls

USGS Publications Warehouse

Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

2008-01-01

Several recent studies have shown that landscape features can strongly affect spatial patterns of gene flow and genetic variation. Understanding landscape effects on genetic variation is important in conservation for defining management units and understanding movement patterns. The landscape may have little effect on gene flow, however, in highly mobile species such as birds. We tested for genetic breaks associated with landscape features in the northern spotted owl (Strix occidentalis caurina), a threatened subspecies associated with old forests in the U.S. Pacific Northwest and extreme southwestern Canada. We found little evidence for distinct genetic breaks in northern spotted owls using a large microsatellite dataset (352 individuals from across the subspecies' range genotyped at 10 loci). Nonetheless, dry low-elevation valleys and the Cascade and Olympic Mountains restrict gene flow, while the Oregon Coast Range facilitates it. The wide Columbia River is not a barrier to gene flow. In addition, inter-individual genetic distance and latitude were negatively related, likely reflecting northward colonization following Pleistocene glacial recession. Our study shows that landscape features may play an important role in shaping patterns of genetic variation in highly vagile taxa such as birds.

Mitochondrial-DNA variation among subspecies and populations of sea otters (Enhydra lutris)

USGS Publications Warehouse

Cronin, Matthew A.; Bodkin, James L.; Ballachey, Brenda E.; Estes, James A.; Patton, John C.

1996-01-01

We used restriction-enzyme analysis of polymerase-chain reaction-amplified, mitochondrial DNA (mtDNA) to assess genetic differentiation of subspecies and populations of sea otters, Enhydra lutris, throughout the range of the species. There were several haplotypes of mtDNA in each subspecies and geographically separate populations. MtDNA sequence divergence of haplotypes of sea otters was 0.0004–0.0041 base substitutions per nucleotide. E. L nereis appears to have monophyletic mitochondrial DNA, while E. I. lutris and E. I. kenyoni do not. Different frequencies of haplotypes of mtDNA among populations reflect current restriction of gene flow and the unique histories of different populations. There are two or three haplotypes of mtDNA and diversity of haplotypes is 0.1376–0.5854 in each population of otters. This is consistent with theoretical work, which suggests that population bottlenecks of sea otters probably did not result in major losses of genetic variation for individual populations, or the species as a whole.

Diversification in the South American Pampas: the genetic and morphological variation of the widespread Petunia axillaris complex (Solanaceae).

PubMed

Turchetto, Caroline; Fagundes, Nelson J R; Segatto, Ana L A; Kuhlemeier, Cris; Solís Neffa, Viviana G; Speranza, Pablo R; Bonatto, Sandro L; Freitas, Loreta B

2014-02-01

Understanding the spatiotemporal distribution of genetic variation and the ways in which this distribution is connected to the ecological context of natural populations is fundamental for understanding the nature and mode of intraspecific and, ultimately, interspecific differentiation. The Petunia axillaris complex is endemic to the grasslands of southern South America and includes three subspecies: P. a. axillaris, P. a. parodii and P. a. subandina. These subspecies are traditionally delimited based on both geography and floral morphology, although the latter is highly variable. Here, we determined the patterns of genetic (nuclear and cpDNA), morphological and ecological (bioclimatic) variation of a large number of P. axillaris populations and found that they are mostly coincident with subspecies delimitation. The nuclear data suggest that the subspecies are likely independent evolutionary units, and their morphological differences may be associated with local adaptations to diverse climatic and/or edaphic conditions and population isolation. The demographic dynamics over time estimated by skyline plot analyses showed different patterns for each subspecies in the last 100 000 years, which is compatible with a divergence time between 35 000 and 107 000 years ago between P. a. axillaris and P. a. parodii, as estimated with the IMa program. Coalescent simulation tests using Approximate Bayesian Computation do not support previous suggestions of extensive gene flow between P. a. axillaris and P. a. parodii in their contact zone. © 2013 John Wiley & Sons Ltd.

An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)

PubMed Central

Meyers, Stephen C.; Liston, Aaron; Meinke, Robert

2012-01-01

Limnanthes floccosa ssp. floccosa and L. floccosa ssp. grandiflora are two of five subspecies within Limnanthes floccosa endemic to vernal pools in southern Oregon and northern California. Three seasons of monitoring natural populations have quantified that L. floccosa ssp. grandiflora is always found growing sympatrically with L. floccosa ssp. floccosa and that their flowering times overlap considerably. Despite their subspecific rank within the same species crossing experiments have confirmed that their F1 hybrids are sterile. An analysis of twelve microsatellite markers, with unique alleles in each taxon, also shows exceedingly low levels of gene flow between populations of the two subspecies. Due to the lack of previous phylogenetic resolution among L. floccosa subspecies, we used Illumina next generation sequencing to identify single nucleotide polymorphisms from genomic DNA libraries of L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora. These data were used to identify single nucleotide polymorphisms in the chloroplast, mitochondrial, and nuclear genomes. From these variable loci, a total of 2772 bp was obtained using Sanger sequencing of ten individuals representing all subspecies of L. floccosa and an outgroup. The resulting phylogenetic reconstruction was fully resolved. Our results indicate that although L. floccosa ssp. floccosa and L. floccosa ssp. grandiflora are closely related, they are not sister taxa and therefore likely did not diverge as a result of a sympatric speciation event. PMID:22563502

Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi).

PubMed

Tan, Shuai; Zou, Dandan; Tang, Lei; Wang, Gaochao; Peng, Quekun; Zeng, Bo; Zhang, Chen; Zou, Fangdong

2012-06-01

Blue sheep (Pseudois nayaur), a Central Asian ungulate with restricted geographic distribution, exhibits unclear variation in morphology and phylogeographic structure. The composition of species and subspecies in the genus Pseudois is controversial, particularly with respect to the taxonomic designation of geographically restricted populations. Here, 26 specimens including 5 dwarf blue sheep (Pseudois schaeferi), which were collected from a broad geographic region in China, were analyzed for 2 mitochondrial DNA fragments (cytochrome b and control region sequences). In a pattern consistent with geographically defined subspecies, we found three deeply divergent mitochondrial lineages restricted to different geographic regions. The currently designated two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaur szechuanensis, were recognized in the phylogenetic trees. In addition, the Helan Mountain population showed distinct genetic characteristics from other geographic populations, and thus should be classified as a new subspecies. In contrast, dwarf blue sheep clustered closely with some blue sheep from Sichuan Province in the phylogenetic trees. Therefore, dwarf blue sheep appear to be a subset of Pseudois nayaur szechuanensis. After considering both population genetic information and molecular clock analysis, we obtained some relevant molecular phylogeographic information concerning the historical biogeography of blue sheep. These results also indicate that western Sichuan was a potential refugium for blue sheep during the Quaternary period.

Population Structure and Dispersal Patterns within and between Atlantic and Mediterranean Populations of a Large-Range Pelagic Seabird

PubMed Central

Genovart, Meritxell; Thibault, Jean-Claude; Igual, José Manuel; Bauzà-Ribot, Maria del Mar; Rabouam, Corinne; Bretagnolle, Vincent

2013-01-01

Dispersal is critically linked to the demographic and evolutionary trajectories of populations, but in most seabird species it may be difficult to estimate. Using molecular tools, we explored population structure and the spatial dispersal pattern of a highly pelagic but philopatric seabird, the Cory's shearwater Calonectris diomedea. Microsatellite fragments were analysed from samples collected across almost the entire breeding range of the species. To help disentangle the taxonomic status of the two subspecies described, the Atlantic form C. d. borealis and the Mediterranean form C. d. diomedea, we analysed genetic divergence between subspecies and quantified both historical and recent migration rates between the Mediterranean and Atlantic basins. We also searched for evidence of isolation by distance (IBD) and addressed spatial patterns of gene flow. We found a low genetic structure in the Mediterranean basin. Conversely, strong genetic differentiation appeared in the Atlantic basin. Even if the species was mostly philopatric (97%), results suggest recent dispersal between basins, especially from the Atlantic to the Mediterranean (aprox. 10% of migrants/generation across the last two generations). Long-term gene flow analyses also suggested an historical exchange between basins (about 70 breeders/generation). Spatial analysis of genetic variation indicates that distance is not the main factor in shaping genetic structure in this species. Given our results we recommend gathering more data before concluded whether these taxa should be treated as two species or subspecies. PMID:23950986

Intercontinental genetic structure and gene flow in Dunlin (Calidris alpina), a potential vector of avian influenza

USGS Publications Warehouse

Miller, Mark P.; Haig, Susan M.; Mullins, Thomas D.; Ruan, Luzhang; Casler, Bruce; Dondua, Alexei; Gates, River H.; Johnson, J. Matthew; Kendall, Steven J.; Tomkovich, Pavel S.; Tracy, Diane; Valchuk, Olga P.; Lanctot, Richard B.

2015-01-01

Waterfowl (Anseriformes) and shorebirds (Charadriiformes) are the most common wild vectors of influenza A viruses. Due to their migratory behavior, some may transmit disease over long distances. Migratory connectivity studies can link breeding and nonbreeding grounds while illustrating potential interactions among populations that may spread diseases. We investigated Dunlin (Calidris alpina), a shorebird with a subspecies (C. a. arcticola) that migrates from nonbreeding areas endemic to avian influenza in eastern Asia to breeding grounds in northern Alaska. Using microsatellites and mitochondrial DNA, we illustrate genetic structure among six subspecies: C. a. arcticola, C. a. pacifica, C. a. hudsonia, C. a. sakhalina, C. a. kistchinski, and C. a. actites. We demonstrate that mitochondrial DNA can help distinguish C. a. arcticola on the Asian nonbreeding grounds with >70% accuracy depending on their relative abundance, indicating that genetics can help determine whether C. a. arcticola occurs where they may be exposed to highly pathogenic avian influenza (HPAI) during outbreaks. Our data reveal asymmetric intercontinental gene flow, with some C. a. arcticola short-stopping migration to breed with C. a. pacifica in western Alaska. Because C. a. pacifica migrates along the Pacific Coast of North America, interactions between these subspecies and other taxa provide route for transmission of HPAI into other parts of North America.

Snake venomics and antivenomics of Crotalus durissus subspecies from Brazil: assessment of geographic variation and its implication on snakebite management.

PubMed

Boldrini-França, Johara; Corrêa-Netto, Carlos; Silva, Marliete M S; Rodrigues, Renata S; De La Torre, Pilar; Pérez, Alicia; Soares, Andreimar M; Zingali, Russolina B; Nogueira, Romildo A; Rodrigues, Veridiana M; Sanz, Libia; Calvete, Juan J

2010-08-05

We report the comparative proteomic and antivenomic characterization of the venoms of subspecies cascavella and collilineatus of the Brazilian tropical rattlesnake Crotalus durissus. The venom proteomes of C. d. collilineatus and C. d. cascavella comprise proteins in the range of 4-115 kDa belonging to 9 and 8 toxin families, respectively. Collilineatus and cascavella venoms contain 20-25 main toxins belonging to the following protein families: disintegrin, PLA(2), serine proteinase, cysteine-rich secretory protein (CRISP), vascular endothelial growth factor-like (VEGF), L-amino acid oxidase, C-type lectin-like, and snake venom metalloproteinase (SVMP). As judged by reverse-phase HPLC and mass spectrometry, cascavella and collilineatus share about 90% of their venom proteome. However, the relative occurrence of the toxin families departs among the two C. durissus subspecies venoms. The most notable difference is the presence of the myotoxin crotamine in some C. d. collilineatus specimens (averaging 20.8% of the total proteins of pooled venom), which is absent in the venom of C. d. cascavella. On the other hand, the neurotoxic PLA(2) crotoxin represents the most abundant protein in both C. durissus venoms, comprising 67.4% of the toxin proteome in C. d. collilineatus and 72.5% in C. d. cascavella. Myotoxic PLA(2)s are also present in the two venoms albeit in different relative concentrations (18.1% in C. d. cascavella vs. 4.6% in C. d. collilineatus). The venom composition accounts for the clinical manifestations caused by C. durissus envenomations: systemic neurotoxicity and myalgic symptoms and coagulation disturbances, frequently accompanied by myoglobinuria and acute renal failure. The overall compositions of C. d. subspecies cascavella and collilineatus venoms closely resemble that of C. d. terrificus, supporting the view that these taxa can be considered geographical variations of the same species. Pooled venom from adult C.d. cascavella and neonate C.d. terrificus lack crotamine, whereas this skeletal muscle cell membrane depolarizing inducing myotoxin accounts for approximately 20% of the total toxins of venom pooled from C.d. collilineatus and C.d. terrificus from Southern Brazil. The possible relevance of the observed venom variability among the tropical rattlesnake subspecies was assessed by antivenomics using anti-crotalic antivenoms produced at Instituto Butantan and Instituto Vital Brazil. The results revealed that both antivenoms exhibit impaired immunoreactivity towards crotamine and display restricted ( approximately 60%) recognition of PLA(2) molecules (crotoxin and D49-myotoxins) from C. d. cascavella and C. d. terrificus venoms. This poor reactivity of the antivenoms may be due to a combination of factors: on the one hand, an inappropriate choice of the mixture of venoms for immunization and, on the other hand, the documented low immunogenicity of PLA(2) molecules. C. durissus causes most of the lethal snakebite accidents in Brazil. The implication of the geographic variation of venom composition for the treatment of bites by different C. durissus subspecies populations is discussed. (c) 2010 Elsevier B.V. All rights reserved.

¹H NMR spectroscopy reveals the effect of genotype and growth conditions on composition of sea buckthorn (Hippophaë rhamnoides L.) berries.

PubMed

Kortesniemi, Maaria; Sinkkonen, Jari; Yang, Baoru; Kallio, Heikki

2014-03-15

¹H NMR spectroscopy and multivariate data analysis were applied to the metabolic profiling and discrimination of wild sea buckthorn (Hippophaë rhamnoides L.) berries from different locations in Finland (subspecies (ssp.) rhamnoides) and China (ssp. sinensis). Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) showed discrimination of the two subspecies and different growth sites. The discrimination of ssp. rhamnoides was mainly associated with typically higher temperature, radiation and humidity and lower precipitation in the south, yielding higher levels of O-ethyl β-d-glucopyranoside and d-glucose, and lower levels of malic, quinic and ascorbic acids. Significant metabolic differences (p<0.05) in genetically identical berries were observed between latitudes 60° and 67° north in Finland. High altitudes (> 2,000 m) correlated with greater levels of malic and ascorbic acids in ssp. sinensis. The NMR metabolomics approach applied here is effective for identification of metabolites, geographical origin and subspecies of sea buckthorn berries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Population structure and plumage polymorphism: the intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani

USGS Publications Warehouse

Hull, Joshua M.; Mindell, David P.; McCormick, C.R.; Kay, Emily H.; Hoekstra, Hopi E.; Ernest, Holly B.

2010-01-01

These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

Checklists of Crustacea Decapoda from the Canary and Cape Verde Islands, with an assessment of Macaronesian and Cape Verde biogeographic marine ecoregions.

PubMed

GonzÁlez, JosÉ A

2018-04-23

The complete list of Canarian marine decapods (last update by González Quiles 2003, popular book) currently comprises 374 species/subspecies, grouped in 198 genera and 82 families; whereas the Cape Verdean marine decapods (now fully listed for the first time) are represented by 343 species/subspecies with 201 genera and 80 families. Due to changing environmental conditions, in the last decades many subtropical/tropical taxa have reached the coasts of the Canary Islands. Comparing the carcinofaunal composition and their biogeographic components between the Canary and Cape Verde archipelagos would aid in: validating the appropriateness in separating both archipelagos into different ecoregions (Spalding et al. 2007), and understanding faunal movements between areas of benthic habitat. The consistency of both ecoregions is here compared and validated by assembling their decapod crustacean checklists, analysing their taxa composition, gathering their bathymetric data, and comparing their biogeographic patterns. Four main evidences (i.e. different taxa; divergent taxa composition; different composition of biogeographic patterns; different endemicity rates) support that separation, especially in coastal benthic decapods; and these parametres combined would be used as a valuable tool at comparing biotas from oceanic archipelagos. To understand/predict south-north faunal movements in a scenario of regional tropicalization, special attention is paid to species having at the Canaries their southernmost occurrence, and also to tropical African warm-affinity species.

Genetic structure and gene flow in Beta vulgaris subspecies maritima along the Atlantic coast of France

USDA-ARS?s Scientific Manuscript database

Locating and quantifying genetic variation within crop wild relatives is an ongoing activity of gene banks tasked with ex situ conservation. Without detailed information about the population genetics of a species geography often serves as a reasonable proxy for differentiation. With this in mind, ...

Mitochondrial Divergence between Western and Eastern Great Bustards: Implications for Conservation and Species Status.

PubMed

Kessler, Aimee Elizabeth; Santos, Malia A; Flatz, Ramona; Batbayar, Nyambayar; Natsagdorj, Tseveenmyadag; Batsuur, Dashnyam; Bidashko, Fyodor G; Galbadrakh, Natsag; Goroshko, Oleg; Khrokov, Valery V; Unenbat, Tuvshin; Vagner, Ivan I; Wang, Muyang; Smith, Christopher Irwin

2018-06-02

The Great Bustard is the heaviest bird capable of flight and an iconic species of the Eurasian steppe. Populations of both currently recognized subspecies are highly fragmented and critically small in Asia. We used DNA sequence data from the mitochondrial cytochrome b gene and the mitochondrial control region to estimate the degree of mitochondrial differentiation and rates of female gene flow between the subspecies. We obtained genetic samples from 51 individuals of Otis tarda dybowskii representing multiple populations, including the first samples from Kazakhstan and Mongolia and samples from near the Altai Mountains, the proposed geographic divide between the subspecies, allowing for better characterization of the boundary between the two subspecies. We compared these with existing sequence data (n=66) from O. t. tarda. Our results suggest, though do not conclusively prove, that O. t. dybowskii and O. t. tarda may be distinct species. The geographic distribution of haplotypes, phylogenetic analysis, analyses of molecular variance, and coalescent estimation of divergence time and female migration rates indicate that O. t. tarda and O. t. dybowskii are highly differentiated in the mitochondrial genome, have been isolated for approximately 1.4 million years, and exchange much less than one female migrant per generation. Our findings indicate that the two forms should at least be recognized and managed as separate evolutionary units. Populations in Xinjiang, China and Khövsgöl and Bulgan, Mongolia exhibited the highest levels of genetic diversity and should be prioritized in conservation planning.

Spatiotemporal variation in the reproductive ecology of two parapatric subspecies of Oenothera cespitosa (Onagraceae).

PubMed

Artz, Derek R; Villagra, Cristian A; Raguso, Robert A

2010-09-01

• Flowering plants that rely on pollinators for most of their reproduction may experience unpredictable and inconsistent availability of effective pollinators throughout their reproductive lifetime. We investigated the reproductive ecology of two subspecies of the tufted evening primrose, Oenothera cespitosa, which occupy geographically and edaphically distinct habitats in western North America: O. cespitosa subsp. navajoensis inhabits sandstone soils on open sites or rocky slopes in the Colorado Plateau and O. cespitosa subsp. cespitosa grows in clay soils on talus slopes and exposed rocky ridges in the western Great Plains and northern Rocky Mountains of the United States. • Pollen augmentation and selfing experiments, floral visitor observations, and single-visit effectiveness experiments were conducted over 4 years to examine the breeding system and spatiotemporal variation in pollinator behavior, assemblage, and abundance at different populations for each subspecies. • Both subspecies of O. cespitosa were self-incompatible and pollen-limited, suggesting that the relative abundance, effectiveness, and movement patterns of different insects as pollinators influenced the quality and quantity of seed production in these plants. Medium-sized vespertine hawkmoths (Hyles lineata, Sphinx vashti) were effective pollinators when present, as were large matinal bees (Anthophora affabilis, A. dammersi, Xylocopa tabaniformis androleuca), whereas small oligolectic Lasioglossum bees primarily functioned as pollen thieves in the evening and morning. • These findings highlight the importance of variability of pollinator composition and abundance in the evolution of plant breeding systems and reproductive success at varying spatial and temporal scales.

Multiplex PCR-based identification of Streptococcus canis, Streptococcus zooepidemicus and Streptococcus dysgalactiae subspecies from dogs.

PubMed

Moriconi, M; Acke, E; Petrelli, D; Preziuso, S

2017-02-01

Streptococcus canis (S. canis), Streptococcus equi subspecies zooepidemicus (S. zooepidemicus) and Streptococcus dysgalactiae subspecies (S. dysgalactiae subspecies) are β-haemolytic Gram positive bacteria infecting animals and humans. S. canis and S. zooepidemicus are considered as two of the major zoonotic species of Streptococcus, while more research is needed on S. dysgalactiae subspecies bacteria. In this work, a multiplex-PCR protocol was tested on strains and clinical samples to detect S. canis, S. dysgalactiae subspecies and S. equi subspecies bacteria in dogs. All strains were correctly identified as S. canis, S. equi subspecies or S. dysgalactiae subspecies by the multiplex-PCR. The main Streptococcus species isolated from symptomatic dogs were confirmed S. canis. The multiplex-PCR protocol described is a rapid, accurate and efficient method for identifying S. canis, S. equi subspecies and S. dysgalactiae subspecies in dogs and could be used for diagnostic purposes and for epidemiological studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Serum proteins of Canada goose (Branta canadensis) subspecies

USGS Publications Warehouse

Morgan, R.P.; Sulkin, S.T.; Henny, C.J.

1977-01-01

Serum proteins from nine subspecies of Canada Geese (Brunta canadensis) were analyzed through the use of column and slab acrylamide electrophoresis. Variation was minimal within a subspecies, although all the subspecies were closely related. B. c. leucopareia appeared to be the most distinct subspecies, while maxima and moffitti were the most similar. Our preliminary findings suggest that the electrophoresis techniques are sensitive enough to identify some of the subspecies; however, baseline data from breeding ranges of all subspecies are required.

Red List of vascular plants of the Wadden Sea Area

NASA Astrophysics Data System (ADS)

Wind, P.; van der Ende, M.; Garve, E.; Schacherer, A.; Thissen, J. B. M.

1996-10-01

In the Wadden Sea area, a total of 248 (sub)species of vascular plants are threatened in at least one subregion. Of these, 216 (sub)species are threatened in the entire area and are therefore placed on the trialteral Red List. 17 (sub)species of the listed vascular plants are (probably) extinct in the entire Wadden Sea area. The status of 47 (sub)species of vascular plants is (probably) critical; 61 (sub)species are (probably) endangered; the status of 65 (sub)species is (probably) vulnerable and that of 26 (sub)species susceptible.

Migration of the Willow Flycatcher along the Middle Rio Grande

Treesearch

Wang Yong; Deborah M. Finch

1997-01-01

We studied timing, abundance, subspecies composition, fat stores, stopover length, and habitat use of Willow Flycatchers (Empidonax traillii) during spring and fall stopover along the Middle Rio Grande, New Mexico. Spring migration started in mid-May and lasted about a month. Fall migration started in early-August and also lasted about a month. The most abundant...

Growth, survival, and fatty acid composition of coppernose bluegill (Lepomis macrochirus subspecies) offered different winter feeding regimes

USDA-ARS?s Scientific Manuscript database

Winter fish losses are routinely reported by Arkansas sportfish producers in the spring. Juvenile centrarchid species (less than 7.6 cm) are quite susceptible to harsh winter conditions. While some of these winter fish losses can be attributed to predation by fish eating birds and water quality fact...

Collection and evaluation of wild perennial Helianthus pumilus achenes for oil concentration and fatty acid composition

USDA-ARS?s Scientific Manuscript database

The genus Helianthus consists of 51 species and 19 subspecies with 14 annual and 37 perennial species. The narrow genetic base of cultivated sunflower has been broadened by the infusion of genes from the wild species, which have provided a continued source of desirable agronomic traits. There has ...

Collection and evaluation of wild perennial Helianthus pumilus achenes for oil concentration and fatty acid composition

USDA-ARS?s Scientific Manuscript database

The genus Helianthus consists of 52 species and 19 subspecies with 14 annual and 38 perennial species. The narrow genetic base of cultivated sunflower has been broadened by the infusion of genes from the wild species, which have provided a continued source of desirable agronomic traits. There has ...

Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

PubMed

Vincent, Antony T; Trudel, Mélanie V; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger C; Charette, Steve J

2016-01-12

Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

PubMed Central

Brunelli, Joseph P.; Steele, Craig A.; Thorgaard, Gary H.

2010-01-01

Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout (Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish. PMID:20546904

EndoSd: an IgG glycan hydrolyzing enzyme in Streptococcus dysgalactiae subspecies dysgalactiae.

PubMed

Shadnezhad, Azadeh; Naegeli, Andreas; Sjögren, Jonathan; Adamczyk, Barbara; Leo, Fredrik; Allhorn, Maria; Karlsson, Niclas G; Jensen, Anders; Collin, Mattias

2016-06-01

The aim of this study was to identify and characterize EndoS-like enzymes in Streptococcus dysgalactiae subspecies dysgalactiae (SDSD). PCR, DNA sequencing, recombinant protein expression, lectin blot, ultra high performance liquid chromatography analysis and a chitinase assay were used to identify ndoS-like genes and characterize EndoSd. EndoSd were found in four SDSD strains. EndoSd hydrolyzes the chitobiose core of the glycan on IgG. The amino acid sequence of EndoSd is 70% identical to EndoS in S. pyogenes, but it has a unique C-terminal sequence. EndoSd secretion is influenced by the carbohydrate composition of the growth medium. Our findings indicate that IgG glycan hydrolyzing activity is present in SDSD, and that the activity can be attributed to the here identified enzyme EndoSd.

New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula.

PubMed

Pires, Ana Elisabete; Amorim, Isabel R; Borges, Carla; Simões, Fernanda; Teixeira, Tatiana; Quaresma, Andreia; Petrucci-Fonseca, Francisco; Matos, José

2017-06-01

This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies ( Canis lupus signatus ), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus . These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.

Male-Mediated Gene Flow in Patrilocal Primates

PubMed Central

Schubert, Grit; Stoneking, Colin J.; Arandjelovic, Mimi; Boesch, Christophe; Eckhardt, Nadin; Hohmann, Gottfried; Langergraber, Kevin; Lukas, Dieter; Vigilant, Linda

2011-01-01

Background Many group–living species display strong sex biases in dispersal tendencies. However, gene flow mediated by apparently philopatric sex may still occur and potentially alters population structure. In our closest living evolutionary relatives, dispersal of adult males seems to be precluded by high levels of territoriality between males of different groups in chimpanzees, and has only been observed once in bonobos. Still, male–mediated gene flow might occur through rare events such as extra–group matings leading to extra–group paternity (EGP) and female secondary dispersal with offspring, but the extent of this gene flow has not yet been assessed. Methodology/Principal Findings Using autosomal microsatellite genotyping of samples from multiple groups of wild western chimpanzees (Pan troglodytes verus) and bonobos (Pan paniscus), we found low genetic differentiation among groups for both males and females. Characterization of Y–chromosome microsatellites revealed levels of genetic differentiation between groups in bonobos almost as high as those reported previously in eastern chimpanzees, but lower levels of differentiation in western chimpanzees. By using simulations to evaluate the patterns of Y–chromosomal variation expected under realistic assumptions of group size, mutation rate and reproductive skew, we demonstrate that the observed presence of multiple and highly divergent Y–haplotypes within western chimpanzee and bonobo groups is best explained by successful male–mediated gene flow. Conclusions/Significance The similarity of inferred rates of male–mediated gene flow and published rates of EGP in western chimpanzees suggests this is the most likely mechanism of male–mediated gene flow in this subspecies. In bonobos more data are needed to refine the estimated rate of gene flow. Our findings suggest that dispersal patterns in these closely related species, and particularly for the chimpanzee subspecies, are more variable than previously appreciated. This is consistent with growing recognition of extensive behavioral variation in chimpanzees and bonobos. PMID:21747938

Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus).

PubMed

Schield, Drew R; Adams, Richard H; Card, Daren C; Corbin, Andrew B; Jezkova, Tereza; Hales, Nicole R; Meik, Jesse M; Perry, Blair W; Spencer, Carol L; Smith, Lydia L; García, Gustavo Campillo; Bouzid, Nassima M; Strickland, Jason L; Parkinson, Christopher L; Borja, Miguel; Castañeda-Gaytán, Gamaliel; Bryson, Robert W; Flores-Villela, Oscar A; Mackessy, Stephen P; Castoe, Todd A

2018-06-15

The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene. Copyright © 2018 Elsevier Inc. All rights reserved.

A call for tiger management using "reserves" of genetic diversity.

PubMed

Bay, Rachael A; Ramakrishnan, Uma; Hadly, Elizabeth A

2014-01-01

Tigers (Panthera tigris), like many large carnivores, are threatened by anthropogenic impacts, primarily habitat loss and poaching. Current conservation plans for tigers focus on population expansion, with the goal of doubling census size in the next 10 years. Previous studies have shown that because the demographic decline was recent, tiger populations still retain a large amount of genetic diversity. Although maintaining this diversity is extremely important to avoid deleterious effects of inbreeding, management plans have yet to consider predictive genetic models. We used coalescent simulations based on previously sequenced mitochondrial fragments (n = 125) from 5 of 6 extant subspecies to predict the population growth needed to maintain current genetic diversity over the next 150 years. We found that the level of gene flow between populations has a large effect on the local population growth necessary to maintain genetic diversity, without which tigers may face decreases in fitness. In the absence of gene flow, we demonstrate that maintaining genetic diversity is impossible based on known demographic parameters for the species. Thus, managing for the genetic diversity of the species should be prioritized over the riskier preservation of distinct subspecies. These predictive simulations provide unique management insights, hitherto not possible using existing analytical methods.

Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species.

PubMed

Kindler, Carolin; Chèvre, Maxime; Ursenbacher, Sylvain; Böhme, Wolfgang; Hille, Axel; Jablonski, Daniel; Vamberger, Melita; Fritz, Uwe

2017-08-07

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.

Body composition and weight dynamics of wintering greater white-fronted geese

USGS Publications Warehouse

Ely, Craig R.; Raveling, Dennis G.

1989-01-01

Adult greater white-fronted geese (Anser albifrons frontalis) wintering in southern Oregon and California increased or maintained body weight in autumn, lost weight from autumn through winter, and rapidly increased in weight before spring migration in late April. We documented significant annual differences in body weights for both sexes. We related seasonal changes in body weight to changes in lipid levels, which were lowest (12-13% of wet wt in M and F) in mid-March and highest in late April (24% in F). Greater white-fronted geese maintained lipid levels during winter similar to those reported for large subspecies of Canada geese (Branta canadensis), and greater than those reported for small subspecies of Canada geese and other small species of geese. Protein content of carcasses varied significantly in females; i.e., lowest in early October and highest in late October and late April. Differences among species in patterns of weight change and body composition during winter seem to be related to social organization, body size, food type, and foraging behavior. Females left spring staging areas weighing relatively less than most other species of geese and may have benefited from foraging opportunities on the nesting grounds.

Phylogeography of a vanishing North American songbird: The Painted Bunting (Passerina ciris)

USGS Publications Warehouse

Herr, C.A.; Sykes, P.W.; Klicka, J.

2011-01-01

The breeding distribution of Painted Buntings (Passerina ciris) is comprised of two allopatric populations separated by a 550-km distributional gap in the southeastern United States. Curiously, the boundary between the two recognized P. ciris subspecies does not separate the two allopatric breeding populations but instead runs roughly through the center of the interior population. Genetic relationships among these subspecies, and the allopatric breeding populations of Painted Bunting, have not been assessed. Given the recent decline in overall abundance of this species, such an assessment is warranted. We sampled birds from 15 localities (138 individuals) and identified 35 distinct haplotypes, six belonging to the Atlantic Coast population and 26 to the interior population, with three shared by both populations. AMOVA results showed that a significantly greater portion of the total genetic variance is explained when grouping birds by the interior and Atlantic Coast populations rather than by subspecies. Furthermore, our data indicate that the Atlantic Coast and interior populations represent independently evolving taxa, with no measureable gene flow between them. Although recently diverged (26,000-115,000 years ago), these isolated bunting populations represent incipient species. For development of conservation strategies, we suggest that the Atlantic Coast and interior populations be recognized as separate management units. ?? 2011 Springer Science+Business Media B.V.

Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.

PubMed

Torstrom, Shannon M; Pangle, Kevin L; Swanson, Bradley J

2014-07-01

The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes. Copyright © 2014 Elsevier Inc. All rights reserved.

Central nervous system effects and chemical composition of two subspecies of Agastache mexicana; an ethnomedicine of Mexico.

PubMed

Estrada-Reyes, Rosa; López-Rubalcava, C; Ferreyra-Cruz, Octavio Alberto; Dorantes-Barrón, Ana María; Heinze, G; Moreno Aguilar, Julia; Martínez-Vázquez, Mariano

2014-04-11

Agastache mexicana subspecies mexicana (Amm) and xolocotziana (Amx) are used in Mexican traditional medicine to relief cultural affiliation syndromes known as "susto" or "espanto", for "nervous" condition, and as a sleep aid. Despite its intensive use, neuropharmacological studies are scarce, and the chemical composition of the aqueous extracts has not been described. Aims of the study are: (1) To analyze the chemical composition of aqueous extracts from aerial parts of Amm and Amx. (2) To evaluate the anxiolytic-like, sedative, antidepressant-like effects. (3) Analyze the general toxic effects of different doses. Anxiolytic-like and sedative effects were measured in the avoidance exploratory behavior, burying behavior and the hole-board tests. The antidepressant-like actions were studied in the forced swimming and tail suspension tests. Finally, general activity and motor coordination disturbances were evaluated in the open field, inverted screen and rota-rod tests. The acute toxicity of Amm and Amx was determined by calculating their LD50 (mean lethal dose). The chemical analyses were performed employing chromatographic, photometric and HPLC-ESI-MS techniques. Low doses of Amm and Amx (0.1σ1.0mg/kg) induced anxiolytic-like actions; while higher doses (over 10mg/kg) induced sedation and reduced the locomotor activity, exerting a general inhibition in the central nervous system (CNS). Results support the use of Amm and Amx in traditional medicine as tranquilizers and sleep inducers. Additionally, this paper contributes to the knowledge of the chemical composition of the aqueous extracts of these plants. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus.

PubMed

Riyahi, Sepand; Vilatersana, Roser; Schrey, Aaron W; Ghorbani Node, Hassan; Aliabadian, Mansour; Senar, Juan Carlos

2017-11-01

Epigenetic modifications can respond rapidly to environmental changes and can shape phenotypic variation in accordance with environmental stimuli. One of the most studied epigenetic marks is DNA methylation. In the present study, we used the methylation-sensitive amplified polymorphism (MSAP) technique to investigate the natural variation in DNA methylation within and among subspecies of the house sparrow, Passer domesticus We focused on five subspecies from the Middle East because they show great variation in many ecological traits and because this region is the probable origin for the house sparrow's commensal relationship with humans. We analysed house sparrows from Spain as an outgroup. The level of variation in DNA methylation was similar among the five house sparrow subspecies from the Middle East despite high phenotypic and environmental variation, but the non-commensal subspecies was differentiated from the other four (commensal) Middle Eastern subspecies. Further, the European subspecies was differentiated from all other subspecies in DNA methylation. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We detected a correlation between methylation level and some morphological traits, such as standardized bill length, and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected 10 differentially methylated loci among subspecies and three loci that differentiated between commensal or non-commensal status. Therefore, the MSAP technique detected larger scale differences among the European and non-commensal subspecies, but did not detect finer scale differences among the other Middle Eastern subspecies. © 2017. Published by The Company of Biologists Ltd.

Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

PubMed Central

Muñoz, Irene; Henriques, Dora; Johnston, J. Spencer; Chávez-Galarza, Julio; Kryger, Per; Pinto, M. Alice

2015-01-01

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs. PMID:25875986

Chemical composition, larvicidal, and biting deterrent activity of essential oils of two subspecies of Tanacetum argenteum (Asterales: Asteraceae) and individual constituents against Aedes aegypti (Diptera: Culicidae)

USDA-ARS?s Scientific Manuscript database

Water distilled essential oils from the air dried aerial parts of Tanacetum argenteum (Lam.) Willd. subsp. argenteum (Lam.) and T. argenteum (Lam.) Willd. subsp. canum (C. Koch) Grierson were analyzed by gas chromatography (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Twenty-seven and 3...

A comprehensive review of non-enterica subspecies of Salmonella enterica.

PubMed

Lamas, Alexandre; Miranda, José Manuel; Regal, Patricia; Vázquez, Beatriz; Franco, Carlos Manuel; Cepeda, Alberto

2018-01-01

Salmonella is a major foodborne pathogen with a complex nomenclature. This genus is composed of two species, S. enterica and S. bongori. S. enterica is divided into six subspecies. S. enterica subspecies enterica is composed of more than 1500 serotypes with some of great importance, such as S. Typhimurium and S. Enteritidis. S. enterica subsp. enterica is responsible of more than 99% of human salmonellosis and therefore it is widely studied. However, the non-enterica subspecies of S. enterica have been little studied. These subspecies are considered to be related to cold-blooded animals and their pathogenicity is very limited. Phenotype and genotype information generated from different studies of non-enterica subspecies reveal poor ability to invade host cells and the absence or modification of important virulence factors. Also, the great majority of human infections due to non-enterica subspecies are related to a previous depressed immune system. Therefore, we propose to treat these subspecies only as opportunistic pathogens. For establish this premise, the present review evaluated, among other things, the genomic characteristics, prevalence, antimicrobial resistance and reported human cases of the non-enterica subspecies. Copyright © 2017 Elsevier GmbH. All rights reserved.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

PubMed

Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

2006-12-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

USGS Publications Warehouse

Beever, E.A.; Haig, S.M.; Chambers, Steven M.; Draheim, Hope M.; Dugger, Bruce D.; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B.; Kesler, Dylan C.; Knaus, Brian J.; Lopes, Iara F.; Loschl, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

2006-01-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Genetic Resources in the "Calabaza Pipiana" Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models.

PubMed

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma , known in Mexico as calabaza pipiana , and its wild relative C. argyrosperma ssp. sororia . The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia , and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia , in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies' distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies ( H E = 0.428 in sororia , and H E = 0.410 in argyrosperma ). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation ( F ST ) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.

So close and yet so far – Molecular Microbiology of Campylobacter fetus subspecies

PubMed Central

Sprenger, H.; Zechner, E. L.; Gorkiewicz, G.

2012-01-01

Campylobacter fetus comprises two subspecies, C. fetus subsp. fetus and C. fetus subsp. venerealis, which are considered emerging pathogens in humans and animals. Comparisons at the genome level have revealed modest subspecies-specific variation; nevertheless, these two subspecies show distinct host and niche preferences. C. fetus subsp. fetus is a commensal and pathogen of domesticated animals that can be transmitted to humans via contaminated food. The clinical features of human infection can be severe, especially in impaired hosts. In contrast, C. fetus subsp. venerealis is a sexually transmitted pathogen essentially restricted to cattle. Infections leading to bovine venereal campylobacteriosis cause substantial economic losses due to abortion and infertility. Recent genome sequencing of the two subspecies has advanced our understanding of C. fetus adaptations through comparative genomics and the identification of subspecies-specific gene regions predicted to be involved in pathogenesis. The most striking difference between the subspecies is the highly subspecies-specific association of a pathogenicity island in the C. fetus subsp. venerealis chromosome. The inserted region encodes a Type 4 secretion system, which contributes to virulence properties of this organism in vitro. This review describes the main differences in epidemiological, phenotypic, and molecular characteristics of the two subspecies and summarizes recent advances towards understanding the molecular mechanisms of C. fetus pathogenesis. PMID:24611123

Differentiation of subspecies and sexes of Beringian Dunlins using morphometric measures

USGS Publications Warehouse

Gates, H. River; Yezerinac, Stephen; Powell, Abby N.; Tomkovich, Pavel S.; Valchuk, Olga P.; Lanctot, Richard B.

2013-01-01

Five subspecies of Dunlins (Calidris alpina) that breed in Beringia are potentially sympatric during the non-breeding season. Studying their ecology during this period requires techniques to distinguish individuals by subspecies. Our objectives were to determine (1) if five morphometric measures (body mass, culmen, head, tarsus, and wing chord) differed between sexes and among subspecies (C. a. actites, arcticola, kistchinski, pacifica, and sakhalina), and (2) if these differences were sufficient to allow for correct classification of individuals using equations derived from discriminant function analyses. We conducted analyses using morphometric data from 10 Dunlin populations breeding in northern Russia and Alaska, USA. Univariate tests revealed significant differences between sexes in most morphometric traits of all subspecies, and discriminant function equations predicted the sex of individuals with an accuracy of 83–100% for each subspecies. We provide equations to determine sex and subspecies of individuals in mixed subspecies groups, including the (1) Western Alaska group of arcticola and pacifica (known to stage together in western Alaska) and (2) East Asia group of arcticola, actites, kistchinski, and sakhalina (known to winter together in East Asia). Equations that predict the sex of individuals in mixed groups had classification accuracies between 75% and 87%, yielding reliable classification equations. We also provide equations that predict the subspecies of individuals with an accuracy of 22–96% for different mixed subspecies groups. When the sex of individuals can be predetermined, the accuracy of these equations is increased substantially. Investigators are cautioned to consider limitations due to age and feather wear when using these equations during the non-breeding season. These equations will allow determination of sexual and subspecies segregation in non-breeding areas, allowing implementation of taxonomic-specific conservation actions.

Distinct subspecies or phenotypic plasticity? Genetic and morphological differentiation of mountain honey bees in East Africa.

PubMed

Gruber, Karl; Schöning, Caspar; Otte, Marianne; Kinuthia, Wanja; Hasselmann, Martin

2013-09-01

Identifying the forces shaping intraspecific phenotypic and genotypic divergence are of key importance in evolutionary biology. Phenotypic divergence may result from local adaptation or, especially in species with strong gene flow, from pronounced phenotypic plasticity. Here, we examine morphological and genetic divergence among populations of the western honey bee Apis mellifera in the topographically heterogeneous East African region. The currently accepted "mountain refugia hypothesis" states that populations living in disjunct montane forests belong to a different lineage than those in savanna habitats surrounding these forests. We obtained microsatellite data, mitochondrial sequences, and morphometric data from worker honey bees collected from feral colonies in three montane forests and corresponding neighboring savanna regions in Kenya. Honey bee colonies from montane forests showed distinct worker morphology compared with colonies in savanna areas. Mitochondrial sequence data did not support the existence of the two currently accepted subspecies. Furthermore, analyses of the microsatellite data with a Bayesian clustering method did not support the existence of two source populations as it would be expected under the mountain refugia scenario. Our findings suggest that phenotypic plasticity rather than distinct ancestry is the leading cause behind the phenotypic divergence observed between montane forest and savanna honey bees. Our study thus corroborates the idea that high gene flow may select for increased plasticity.

Ancient lakes, Pleistocene climates and river avulsions structure the phylogeography of a large but little-known rock scorpion from the Mojave and Sonoran deserts

USGS Publications Warehouse

Graham, Matthew R.; Wood, Dustin A.; Henault, Jonathan A.; Valois, Zachary J.; Cushing, Paula E.

2017-01-01

Recent syntheses of phylogeographical data from terrestrial animals in the Mojave and Sonoran deserts have revealed a complex history of geologic and climatic vicariance events. We studied the phylogeography of Smeringurus vachoni to see how vicariance events may have impacted a large, endemic rock scorpion. Additionally, we used the phylogeographical data to examine the validity of two subspecies of S. vachoni that were described using unconventional morphological characters. Phylogenetic, network and SAMOVA analyses indicate that S. vachoni consists of 11 clades mostly endemic to isolated desert mountain ranges. Molecular clock estimates suggest that clades diversified between the Miocene and early Pleistocene. Species distribution models predict a contraction of suitable habitat during the last glacial maximum. Landscape interpolations and Migrate-n analyses highlight areas of gene flow across the Colorado River. Smeringurus vachoni does not comprise two subspecies. Instead, the species represents at least 11 mitochondrial clades that probably diversified by vicariance associated with Pleistocene climate changes and formation of ancient lakes along the Colorado River corridor. Gene flow appears to have occurred from west to east across the Colorado River during periodic river avulsions.

Rice root-associated bacteria – insights in community structures across ten cultivars

PubMed Central

Hardoim, Pablo Rodrigo; Andreote, Fernando Dini; Reinhold-Hurek, Barbara; Sessitsch, Angela; van Overbeek, Leonard Simon; van Elsas, Jan Dirk

2015-01-01

In this study, the effect of plant genotype, soil type and nutrient use efficiency on the composition of different bacterial communities associated with rice roots were investigated. Thus, total bacteria, Alpha- and Beta-proteobacteria, Pseudomonas and Actinobacteria were studied using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE). Rice genotype determined to a large extent the composition of the different bacterial communities across cultivars. Several cultivars belonging to Oryza sativa subspecies indica tended to select similar bacterial communities, whereas those belonging to subspecies japonica and aromatica selected ones with divergent community structures. An effect of soil type was pronounced for the Actinobacteria communities, while a small effect of ‘improved’ and ‘traditional’ plants was noted for all communities analysed. A few dominant bands in PCR-DGGE, affiliated with Rhizobium radiobacter, Dickeya zeae, Mycobacterium bolletii and with members of the Rhizobiales, Rhodospirillaceae and Paenibacillaceae were spread across cultivars. In contrast, a majority of bands (e.g. affiliated with Enterobacter cloacae or Burkholderia kururiensis) was only present in particular cultivars or was erratically distributed amongst rice replicates. The data suggested that both bacterial adaptation and plant genotype contribute to the shaping of the dynamic bacterial communities associated with roots of rice plants. PMID:21426364

77 FR 56858 - Endangered and Threatened Wildlife and Plants; Draft Recovery Plan for Four Subspecies of Island Fox

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-14

...] Endangered and Threatened Wildlife and Plants; Draft Recovery Plan for Four Subspecies of Island Fox AGENCY... Plan for Four Subspecies of Island Fox (Urocyon littoralis) under the Endangered Species Act of 1973, as amended (Act). Each of the four subspecies, San Miguel Island fox (Urocyon littoralis littoralis...

A neo-W chromosome in a tropical butterfly links colour pattern, male-killing, and speciation.

PubMed

Smith, David A S; Gordon, Ian J; Traut, Walther; Herren, Jeremy; Collins, Steve; Martins, Dino J; Saitoti, Kennedy; Ireri, Piera; Ffrench-Constant, Richard

2016-07-27

Sexually antagonistic selection can drive both the evolution of sex chromosomes and speciation itself. The tropical butterfly the African Queen, Danaus chrysippus, shows two such sexually antagonistic phenotypes, the first being sex-linked colour pattern, the second, susceptibility to a male-killing, maternally inherited mollicute, Spiroplasma ixodeti, which causes approximately 100% mortality in male eggs and first instar larvae. Importantly, this mortality is not affected by the infection status of the male parent and the horizontal transmission of Spiroplasma is unknown. In East Africa, male-killing of the Queen is prevalent in a narrow hybrid zone centred on Nairobi. This hybrid zone separates otherwise allopatric subspecies with different colour patterns. Here we show that a neo-W chromosome, a fusion between the W (female) chromosome and an autosome that controls both colour pattern and male-killing, links the two phenotypes thereby driving speciation across the hybrid zone. Studies of the population genetics of the neo-W around Nairobi show that the interaction between colour pattern and male-killer susceptibility restricts gene flow between two subspecies of D. chrysippus Our results demonstrate how a complex interplay between sex, colour pattern, male-killing, and a neo-W chromosome, has set up a genetic 'sink' that keeps the two subspecies apart. The association between the neo-W and male-killing thus provides a 'smoking gun' for an ongoing speciation process. © 2016 The Authors.

Bacteraemia due to Streptococcus gallolyticus subspecies pasteurianus is associated with digestive tract malignancies and resistance to macrolides and clindamycin.

PubMed

Sheng, Wang-Huei; Chuang, Yu-Chung; Teng, Lee-Jene; Hsueh, Po-Ren

2014-08-01

This study was intended to delineate the association between digestive tract malignancies and bacteraemia due to Streptococcus gallolyticus subspecies pasteurianus. We reviewed the medical records and microbiological results of patients with bacteraemia due to Streptococcus bovis during the period 2000-2012. Species and subspecies identification of isolates originally classified as S. bovis was confirmed by 16S rRNA sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) assays. Minimum inhibitory concentrations of antimicrobial agents were determined by the broth microdilution method. Of the 172 S. bovis complex isolates obtained from 172 patients (age range, <1-94 years, median age, 66) with bacteraemia, 31 isolates were identified to be S. gallolyticus subspecies gallolyticus, 126 were S. gallolyticus subspecies pasteurianus, and 15 were shown to be Streptococcus infantarius. The majority (n = 104, 60%) of patients were male and had underlying malignancies (n = 87, 51%). Bacteraemia due to S. gallolyticus subspecies gallolyticus was significantly associated with endocarditis while S. gallolyticus subspecies pasteurianus was more likely to be associated with malignancies of the digestive tract, including gastric, pancreatic, hepatobiliary and colorectal cancers. Septic shock at presentation was the only factor associated with mortality among patients with bacteraemia due to either subspecies of S. bovis. Isolates of S. gallolyticus subspecies pasteurianus had higher rates of resistance to macrolides and clindamycin than isolates of S. gallolyticus subspecies gallolyticus. Extensive diagnostic work-up for digestive tract malignancies and trans-esophageal echocardiogram should be investigated in patients with bacteraemia caused by S. gallolyticus. Copyright © 2014 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

The original descriptions of reptiles and their subspecies.

PubMed

Uetz, Peter; Stylianou, Alexandrea

2018-01-24

By August 2017 an estimated 13,047 species and subspecies of extant reptiles have been described by a total of 6,454 papers and books which are listed in a supplementary file. For 1,052 species a total of 2,452 subspecies (excluding nominate subspecies) had been described by 2017, down from 1,295 species and 4,411 subspecies in 2009, due to the elevation of many subspecies to species. Here we summarize the history of these taxon description beginning with Linnaeus in 1758. While it took 80 years to reach the first 1,000 species in 1838, new species and subspecies descriptions since then have been added at a roughly constant rate of 1000 new taxa every 12-17 years. The only exception were the decades during World Wars I and II and the beginning of this millennium when the rate of descriptions increased to now about 7 years for the last 1,000 taxa. The top 101 most productive herpetologists (in terms of "taxon output") have described more than 8,000 species and subspecies, amounting to over 60% of all currently valid taxa. More than 90% of all species were described in either English (68.2%), German (12.7%) or French (9.3%).

A TaqMan-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies.

PubMed

Bach, H-J; Jessen, I; Schloter, M; Munch, J C

2003-01-01

Real-time TaqMan-PCR assays were developed for detection, differentiation and absolute quantification of the pathogenic subspecies of Clavibacter michiganensis (Cm) in one single PCR run. The designed primer pair, targeting intergenic sequences of the rRNA operon (ITS) common in all subspecies, was suitable for the amplification of the expected 223-nt DNA fragments of all subspecies. Closely related bacteria were completely discriminated, except of Rathayibacter iranicus, from which weak PCR product bands appeared on agarose gel after 35 PCR cycles. Sufficient specificity of PCR detection was reached by introduction of the additional subspecies specific probes used in TaqMan-PCR. Only Cm species were detected and there was clear differentiation among the subspecies C. michiganensis sepedonicus (Cms), C. michiganensis michiganensis (Cmm), C. michiganensis nebraskensis (Cmn), C. michiganensis insidiosus (Cmi) and C. michiganensis tessellarius (Cmt). The TaqMan assays were optimized to enable a simultaneous quantification of each subspecies. Validity is shown by comparison with cell counts.

Evidence of recent climate change within the historic range of Rio Grande cutthroat trout: implications for management and future persistence

USGS Publications Warehouse

Zeigler, Matthew P.; Todd, Andrew S.; Caldwell, Colleen A.

2012-01-01

Evidence of anthropogenically influenced climate change has motivated natural resource managers to incorporate adaptive measures to minimize risks to sensitive and threatened species. Detecting trends in climate variables (i.e., air temperature and hydrology) can serve as a valuable management tool for protecting vulnerable species by increasing our understanding of localized conditions and trends. The Rio Grande cutthroat trout Oncorhynchus clarkii virginalis has suffered a severe decline in its historical distribution, with the majority of current populations persisting in isolated headwater streams. To evaluate recent climate change within the subspecies' historical range, we examined trends in average air temperatures, biologically important hydrological variables (timing of snowmelt and seasonal flows), and the April 1 snow water equivalent over the last 45 years (1963–2007). While rates of change in all three metrics were variable across sites, rangewide patterns were evident. Across the subspecies' historical range, average annual air temperatures increased (0.29°C per decade) and the timing of snowmelt shifted 10.6 d earlier in the year (2.3 d/decade). Flows increased during biologically important periods, including winter (January 1–March 31; 6.6% increase per decade), prespawning (April 1–May 14; 6.9% increase per decade), and spawning (May 15–June 15; 4.2% increase per decade) and decreased in summer (June 16–September 15; 1.9% decrease per decade). Evidence of decreasing April 1 snow water equivalent (5.3% per decade) was also observed. While the impacts of these changes at the population level are equivocal, it is likely that negative effects would influence the subspecies by altering its distribution, decreasing available habitat, and altering the timing of important life history components. Continued monitoring and proactive management will be required to increase the resiliency of remaining populations to ensure long-term persistence and protection in a changing climate.

Nuclear DNA content and base composition in 28 taxa of Musa.

PubMed

Kamaté, K; Brown, S; Durand, P; Bureau, J M; De Nay, D; Trinh, T H

2001-08-01

The nuclear DNA content of 28 taxa of Musa was assessed by flow cytometry, using line PxPC6 of Petunia hybrida as an internal standard. The 2C DNA value of Musa balbisiana (BB genome) was 1.16 pg, whereas Musa acuminata (AA genome) had an average 2C DNA value of 1.27 pg, with a difference of 11% between its subspecies. The two haploid (IC) genomes, A and B, comprising most of the edible bananas, are therefore of similar size, 0.63 pg (610 million bp) and 0.58 pg (560 million bp), respectively. The genome of diploid Musa is thus threefold that of Arabidopsis thaliana. The genome sizes in a set of triploid Musa cultivars or clones were quite different, with 2C DNA values ranging from 1.61 to 2.23 pg. Likewise, the genome sizes of tetraploid cultivars ranged from 1.94 to 2.37 pg (2C). Apparently, tetraploids (for instance, accession I.C.2) can have a genome size that falls within the range of triploid genome sizes, and vice versa (as in the case of accession Simili Radjah). The 2C values estimated for organs such as leaf, leaf sheath, rhizome, and flower were consistent, whereas root material gave atypical results, owing to browning. The genomic base composition of these Musa taxa had a median value of 40.8% GC (SD = 0.43%).

Geographic variation in the plumage coloration of willow flycatchers Empidonax traillii

USGS Publications Warehouse

Paxton, Eben H.; Sogge, Mark K.; Koronkiewicz, Thomas J.; McLeod, Mary Anne; Theimer, Tad C.

2010-01-01

The ability to identify distinct taxonomic groups of birds (species, subspecies, geographic races) can advance ecological research efforts by determining connectivity between the non-breeding and breeding grounds for migrant species, identifying the origin of migrants, and helping to refine boundaries between subspecies or geographic races. Multiple methods are available to identify taxonomic groups (e.g., morphology, genetics), and one that has played an important role for avian taxonomists over the years is plumage coloration. With the advent of electronic devices that can quickly and accurately quantify plumage coloration, the potential of using coloration as an identifier for distinct taxonomic groups, even when differences are subtle, becomes possible. In this study, we evaluated the degree to which plumage coloration differs among the four subspecies of the willow flycatcher Empidonax traillii, evaluated sources of variation, and considered the utility of plumage coloration to assign subspecies membership for individuals of unknown origin. We used a colorimeter to measure plumage coloration of 374 adult willow flycatchers from 29 locations across their breeding range in 2004 and 2005. We found strong statistical differences among the mean plumage coloration values of the four subspecies; however, while individuals tended to group around their respective subspecies' mean color value, the dispersion of individuals around such means overlapped. Mean color values for each breeding site of the three western subspecies clustered together, but the eastern subspecies' color values were dispersed among the other subspecies, rather than distinctly clustered. Additionally, sites along boundaries showed evidence of intergradation and intermediate coloration patterns. We evaluated the predictive power of colorimeter measurements on flycatchers by constructing a canonical discriminant model to predict subspecies origin of migrants passing through the southwestern U.S. Considering only western subspecies, we found that individuals can be assigned with reasonable certainty. Applying the model to migrants sampled along the Colorado River in Mexico and the U.S. suggests different migration patterns for the three western subspecies. We believe that the use of plumage coloration, as measured by electronic devices, can provide a powerful tool to look at ecological questions in a wide range of avian species.

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies

PubMed Central

Tan, Joon L.; Ng, Kee P.; Ong, Chia S.; Ngeow, Yun F.

2017-01-01

Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex. PMID:29109707

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies.

PubMed

Tan, Joon L; Ng, Kee P; Ong, Chia S; Ngeow, Yun F

2017-01-01

Mycobacterium abscessus , a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex ( M. abscessus, M. massiliense , and M. bolletii ) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.

A new subspecies of sea snake, Hydrophis platurus xanthos, from Golfo Dulce, Costa Rica

PubMed Central

Bessesen, Brooke L.; Galbreath, Gary J.

2017-01-01

Abstract We describe a distinctive new subspecies of sea snake from the occasionally anoxic inner-basin waters of Golfo Dulce, Costa Rica, based on combined data garnered between 2010 and 2017 for 154 specimens, 123 free-ranging and 31 museum-held. The yellow sea snake, Hydrophis platurus xanthos Bessesen & Galbreath, subsp. n., is diagnosed by a notably smaller body size and nearly uniform yellow coloration, which contrasts with the black and yellow striae and tail spots or bands typical of the species. Within the modest geographic range (circa 320 km2), nearly all specimens possess both diagnostic character states. Bathymetrics appear to restrict genetic flow between this allopatric population and conspecifics in the broader Eastern Pacific. In perspicuous contrast to typical H. platurus, H. p. xanthos shows no association with drift lines, and feeds at night in turbulent waters, assuming a sinusoidal ambush posture never previously reported for the species. This evolutionarily significant unit (ESU) warrants taxonomic recognition and active protection. PMID:29200918

Guts don't fly: Small digestive organs in obese Bar-tailed Godwits

USGS Publications Warehouse

Piersma, Theunis; Gill, Robert E.

1998-01-01

We documented fat loads and abdominal organ sizes of Bar-tailed Godwits (Limosa lapponica baueri) that died after colliding against a radar dome on the Alaska Peninsula, most likely just after takeoff on a trans-Pacific flight of 11,000 km, and of birds of the same subspecies just before northward departure from New Zealand. We compared these data with data on body composition of godwits of the smaller lapponica subspecies obtained during a northward stopover in The Netherlands. As a consequence of high amounts of subcutaneous and intraperitoneal fat, and very small fat-free mass, Bar-tailed Godwits from Alaska had relative fat loads that are among the highest ever recorded in birds (ca. 55% of fresh body mass). Compared with northbound godwits from New Zealand, the Alaskan birds had very small gizzards, livers, kidneys, and guts. This suggests that upon departure, long-distance migrants dispense with parts of their "metabolic machinery" that are not directly necessary during flight, and rebuild these organs upon arrival at the migratory destination.

A Molecular Method for the Identification of Honey Bee Subspecies Used by Beekeepers in Russia

PubMed Central

Syromyatnikov, Mikhail Y.; Borodachev, Anatoly V.; Kokina, Anastasia V.; Popov, Vasily N.

2018-01-01

Apis mellifera L. includes several recognized subspecies that differ in their biological properties and agricultural characteristics. Distinguishing between honey bee subspecies is complicated. We analyzed the Folmer region of the COX1 gene in honey bee subspecies cultivated at bee farms in Russia and identified subspecies-specific SNPs. DNA analysis revealed two clearly distinct haplogroups in A. mellifera mellifera. The first one was characterized by multiple cytosine-thymine (thymine–cytosine) transitions, one adenine-guanine substitution, and one thymine–adenine substitution. The nucleotide sequence of the second haplogroup coincided with sequences from other subspecies, except the unique C/A SNP at position 421 of the 658-bp Folmer region. A. mellifera carnica and A. mellifera carpatica could be distinguished from A. mellifera mellifera and A. mellifera caucasica by the presence of the A/G SNP at position 99 of the 658-bp Folmer region. The G/A SNP at position 448 was typical for A. mellifera carnica. A. mellifera caucasica COX1 sequence lacked all the above-mentioned sites. We developed a procedure for rapid identification of honey bee subspecies by PCR with restriction fragment length polymorphism (RFLP) using mutagenic primers. The developed molecular method for honey bee subspecies identification is fast and inexpensive. PMID:29382048

Classification and phylogeny of sika deer (Cervus nippon) subspecies based on the mitochondrial control region DNA sequence using an extended sample set.

PubMed

Ba, Hengxing; Yang, Fuhe; Xing, Xiumei; Li, Chunyi

2015-06-01

To further refine the classification and phylogeny of sika deer subspecies, the well-annotated sequences of the complete mitochondrial DNA (mtDNA) control region of 13 sika deer subspecies from GenBank were downloaded, aligned and analyzed in this study. By reconstructing the phylogenetic tree with an extended sample set, the results revealed a split between Northern and Southern Mainland Asia/Taiwan lineages, and moreover, two subspecies, C.n.mantchuricus and C.n.hortulorum, were existed in Northern Mainland Asia. Unexpectedly, Dybowskii's sika deer that was thought to originate from Northern Mainland Asia joins the Southern Mainland Asia/Taiwan lineage. The genetic divergences were ranged from 2.1% to 4.7% between Dybowskii's sika deer and all the other established subspecies at the mtDNA sequence level, which suggests that the maternal lineage of uncertain sika subspecies in Europe had been maintained until today. This study also provides a better understanding for the classification, phylogeny and phylogeographic history of sika deer subspecies.

Colonisation and Diversification of the Zenaida Dove (Zenaida aurita) in the Antilles: Phylogeography, Contemporary Gene Flow and Morphological Divergence

PubMed Central

Monceau, Karine; Cézilly, Frank; Moreau, Jérôme; Motreuil, Sébastien; Wattier, Rémi

2013-01-01

Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six LA islands (Saint Barthélemy, Guadeloupe, Les Saintes, Martinique, Saint Lucia and Barbados). Eleven COI haplotypes were observed that could be assembled in two distinct lineages, with six specific to GA, four to LA, the remaining one occurring in all islands. However, the level of divergence between those two lineages was too moderate to fully corroborate the existence of two subspecies. Colonisation of the studied islands appeared to be a recent process. However, both phenotypic and microsatellite data suggest that differentiation is already under way between all of them, partly associated with the existence of limited gene flow. No isolation by distance was observed. Differentiation for morphological traits was more pronounced than for neutral markers. These results suggest that despite recent colonisation, genetic drift and/or restricted gene flow are promoting differentiation for neutral markers. Variation in selective pressures between islands may explain the observed phenotypic differentiation. PMID:24349217

Morphological traits of Pacific Flyway Canada Geese as an aid to subspecies identification and management

USGS Publications Warehouse

Pearce, John M.; Bollinger, Karen S.

2003-01-01

Subspecies of Canada Geese (Branta canadensis) exhibit wide variation in body size across their range. To monitor harvest levels in the Pacific Flyway, biologists commonly use culmen length and plumage color to differentiate among subspecies on sympatric wintering grounds. Among the four large-bodied Pacific subspecies (B. c. parvipes, B. c. occidentalis, B. c. fulva, and B. c. moffitti), overlap in culmen length and subjectivity of visually assessing color results in misclassification and inaccurate harvest estimates. We examined the morphology of Pacific large-bodied Canada Geese to characterize body size variation among subspecies and provide more discriminatory measures for harvest assessments. We found that culmen length, one of the most commonly used field measures, overlapped widely among subspecies, and it had little support for inclusion in discriminatory models. Morphological measures with greater explanatory power included bill width at nail, bill width at base, head length, and mid wing. If culmen length and plumage color continue to be used to assess winter harvest, we recommend the addition of at least one sex-specific measurement to reduce levels of misclassification among subspecies. If an additional morphological measure is included, further evaluation on the wintering grounds should be conducted as this measure's effectiveness may vary depending upon observer bias, temporal and spatial variation in subspecies abundance, and the proportion of birds accurately sexed by cloacal examination.

Experimental studies of adaptation in Clarkia xantiana. III. Phenotypic selection across a subspecies border.

PubMed

Anderson, Jill T; Eckhart, Vincent M; Geber, Monica A

2015-09-01

Sister taxa with distinct phenotypes often occupy contrasting environments in parapatric ranges, yet we generally do not know whether trait divergence reflects spatially varying selection. We conducted a reciprocal transplant experiment to test whether selection favors "native phenotypes" in two subspecies of Clarkia xantiana (Onagraceae), an annual plant in California. For four quantitative traits that differ between subspecies, we estimated phenotypic selection in subspecies' exclusive ranges and their contact zone in two consecutive years. We predicted that in the arid, pollinator-scarce eastern region, selection favors phenotypes of the native subspecies parviflora: small leaves, slow leaf growth, early flowering, and diminutive flowers. In the wetter, pollinator-rich, western range of subspecies xantiana, we expected selection for opposite phenotypes. We investigated pollinator contributions to selection by comparing naturally pollinated and pollen-supplemented individuals. For reproductive traits and for subspecies xantiana, selection generally matched expectations. The contact zone sometimes showed distinctive selection, and in ssp. parviflora selection sometimes favored nonnative phenotypes. Pollinators influenced selection on flowering time but not on flower size. Little temporal variation in selection occurred, possibly because of plastic trait responses across years. Though there were exceptions and some causes of selection remain obscure, phenotypic differentiation between subspecies appears to reflect spatially variable selection. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Complete genome sequence of Campylobacter fetus subsp. testudinum type strain 03-427T

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus subsp. testudinum has been isolated from reptiles and humans. This Campylobacter subspecies is genetically distinct from other C. fetus subspecies. Here we present the first whole genome sequence for this C. fetus subspecies....

Lipoprotein marker for hypertriglyceridemia

DOEpatents

Cubicciotti, Roger S.; Karu, Alexander E.; Krauss, Ronald M.

1986-01-01

Methods and compositions are provided for the detection of a particular low density lipoprotein which has been found to be a marker for patients suffering from type IV hypertriglyceridemia. A monoclonal antibody capable of specifically binding to a characteristic epitopic site on this LDL subspecies can be utilized in a wide variety of immunoassays. Hybridoma cell line SPL.IVA5A1 was deposited at the American Type Culture Collection on Mar. 29, 1984, and granted accession no. HB 8535.

Distinct subspecies or phenotypic plasticity? Genetic and morphological differentiation of mountain honey bees in East Africa

PubMed Central

Gruber, Karl; Schöning, Caspar; Otte, Marianne; Kinuthia, Wanja; Hasselmann, Martin

2013-01-01

Identifying the forces shaping intraspecific phenotypic and genotypic divergence are of key importance in evolutionary biology. Phenotypic divergence may result from local adaptation or, especially in species with strong gene flow, from pronounced phenotypic plasticity. Here, we examine morphological and genetic divergence among populations of the western honey bee Apis mellifera in the topographically heterogeneous East African region. The currently accepted “mountain refugia hypothesis” states that populations living in disjunct montane forests belong to a different lineage than those in savanna habitats surrounding these forests. We obtained microsatellite data, mitochondrial sequences, and morphometric data from worker honey bees collected from feral colonies in three montane forests and corresponding neighboring savanna regions in Kenya. Honey bee colonies from montane forests showed distinct worker morphology compared with colonies in savanna areas. Mitochondrial sequence data did not support the existence of the two currently accepted subspecies. Furthermore, analyses of the microsatellite data with a Bayesian clustering method did not support the existence of two source populations as it would be expected under the mountain refugia scenario. Our findings suggest that phenotypic plasticity rather than distinct ancestry is the leading cause behind the phenotypic divergence observed between montane forest and savanna honey bees. Our study thus corroborates the idea that high gene flow may select for increased plasticity. PMID:24223262

The Africanization of honeybees (Apis mellifera L.) of the Yucatan: a study of a massive hybridization event across time.

PubMed

Clarke, Kylea E; Rinderer, Thomas E; Franck, Pierre; Quezada-Euán, Javier G; Oldroyd, Benjamin P

2002-07-01

Until recently, African and European subspecies of the honeybee (Apis mellifera L.) had been geographically separated for around 10,000 years. However, human-assisted introductions have caused the mixing of large populations of African and European subspecies in South and Central America, permitting an unprecedented opportunity to study a large-scale hybridization event using molecular analyses. We obtained reference populations from Europe, Africa, and South America and used these to provide baseline information for a microsatellite and mitochondrial analysis of the process of Africanization of the bees of the Yucatan Peninsula, Mexico. The genetic structure of the Yucatecan population has changed dramatically over time. The pre-Africanized Yucatecan population (1985) comprised bees that were most similar to samples from southeastern Europe and northern and western Europe. Three years after the arrival of Africanized bees (1989), substantial paternal gene flow had occurred from feral Africanized drones into the resident European population, but maternal gene flow from the invading Africanized population into the local population was negligible. However by 1998, there was a radical shift with both African nuclear alleles (65%) and African-derived mitochondria (61%) dominating the genomes of domestic colonies. We suggest that although European mitochondria may eventually be driven to extinction in the feral population, stable introgression of European nuclear alleles has occurred.

Extensive population genetic structure in the giraffe

PubMed Central

Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

2007-01-01

Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations. PMID:18154651

Extensive population genetic structure in the giraffe.

PubMed

Brown, David M; Brenneman, Rick A; Koepfli, Klaus-Peter; Pollinger, John P; Milá, Borja; Georgiadis, Nicholas J; Louis, Edward E; Grether, Gregory F; Jacobs, David K; Wayne, Robert K

2007-12-21

A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

Demographic and growth responses of a guerrilla and a phalanx perennial grass in competitive mixtures

USGS Publications Warehouse

Humphrey, L. David; Pyke, David A.

1998-01-01

The advantages of guerrilla and phalanx growth for the guerrilla Elymus lanceolatus ssp. lanceolatus and phalanx E. l. ssp. wawawaiensis were evaluated over 2 years in two taxon mixtures with a range of densities of each subspecies and under two levels of watering. Ramet numbers and biomass of the guerrilla subspecies were higher than those of the phalanx grass in the first year but in the second year declined greatly, while the phalanx grass showed no change in biomass and an increase in ramet numbers. High neighbour densities affected the phalanx subspecies more strongly than the guerrilla subspecies in the first year, but in the second year there were few differences between subspecies. Biomass of the guerrilla grass remained greater than that of the phalanx grass but ramet numbers were similar in the second year. For both subspecies in both years, probability of flowering decreased at higher neighbour densities, indicating adaptation for competitive ability. In the first year, biomass was more strongly reduced by densities than flowering was, but in the second year, when crowding was apparently greater, flowering was more severely affected. Genet survival was high and similar for both subspecies. The presumed advantage of guerrilla subspecies in exploiting open space was supported. The guerrilla grass exploited resources more quickly in the first year by faster growth and greater ramet production, but its biomass, ramet numbers and rhizome growth, and thus its advantage, were reduced in the second year. The phalanx subspecies had slower growth, produced more ramets in later years, and delayed flowering until later years. Although less able to exploit open resources, it appeared adapted to more stressful conditions, and may be able to exploit temporal resource pulses more effectively.

Available data support protection of the Southwestern Willow Flycatcher under the Endangered Species Act

USGS Publications Warehouse

Theimer, Tad C.; Smith, Aaron D.; Mahoney, Sean M.; Ironside, Kirsten E.

2016-01-01

Zink (2015) argued there was no evidence for genetic, morphological, or ecological differentiation between the federally endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) and other Willow Flycatcher subspecies. Using the same data, we show there is a step-cline in both the frequency of a mtDNA haplotype and in plumage variation roughly concordant with the currently recognized boundary between E. t. extimus and E. t adastus, the subspecies with which it shares the longest common boundary. The geographical pattern of plumage variation is also concordant with previous song analyses differentiating those 2 subspecies and identified birds in one low-latitude, high-elevation site in Arizona as the northern subspecies. We also demonstrate that the ecological niche modeling approach used by Zink yields the same result whether applied to the 2 flycatcher subspecies or to 2 unrelated species, E. t. extimus and Yellow Warbler (Setophaga petechia). As a result, any interpretation of those results as evidence for lack of ecological niche differentiation among Willow Flycatcher subspecies would also indicate no differentiation among recognized species and would therefore be an inappropriate standard for delineating subspecies. We agree that many analytical techniques now available to examine genetic, morphological, and ecological differentiation would improve our understanding of the distinctness (or lack thereof) of Willow Flycatcher subspecies, but we argue that currently available evidence supports protection of the Southwestern Willow Flycatcher under the Endangered Species Act.

Cranial morphological homogeneity in two subspecies of water deer in China and Korea.

PubMed

Kim, Yung Kun; Koyabu, Daisuke; Lee, Hang; Kimura, Junpei

2015-11-01

The water deer (Hydropotes inermis) has conventionally been classified into two subspecies according to geographic distribution and pelage color pattern: H. i. inermis from China and H. i. argyropus from Korea. However, the results of a recent molecular study have called this into question. To further reappraise this classification, we examined morphological variation in craniodental measurements of these 2 subspecies. Results of univariate and multivariate analyses demonstrated that these 2 subspecies are not well-differentiated, suggesting that individuals of the 2 populations share common morphological traits. Despite the distribution of the subspecies at different latitudes, no clear morphocline was detected, suggesting that Bergmann's rule does not apply in this case. Discriminant analysis indicated that the characteristics of individuals are shared by both populations, suggesting that not all individuals can be assigned to their original population. Results of principal component analysis showed that the two populations shared more than 75% of individuals, congruent with the "75% rule" of subspecies classification. In both the neighbor-joining and unweighted pair group methods with arithmetic mean cluster analyses, specimens of H. i. argyropus and H. i. inermis were highly mixed within the cladograms. These results suggest that the overall morphological variation in the 2 subspecies overlaps considerably and that there is no coherent craniofacial difference between the 2 groups. The present findings combined with prior observations from molecular biogeography point out that the taxonomic division of water deer into 2 subspecies should be revisited.

Diurnal and Seasonal Variation in Sap Flow Among Different Sagebrush Species and Subspecies Along an Elevation Gradient in a Semi-Arid Ecosystem

NASA Astrophysics Data System (ADS)

Sharma, H.; Reinhardt, K.; Lohse, K. A.

2015-12-01

Sagebrush is a widespread and locally dominant shrub across much of western North America, occupying >66 million ha. Sagebrush steppe provides many important ecosystem services including carbon (C) storage, water storage, and providing critical habitat for several threatened and endangered animal species. At the Reynolds Creek Critical Zone Observatory (RC CZO) in southwestern Idaho, sagebrush is the dominant shrub species across most of the watershed. The research objectives of RC CZO are to quantify soil carbon storage and flux, and the environmental factors governing these from pedon to landscape scales. Sagebrush-steppe ecosystems have been identified as possible future C sinks, but C storage in these water-limited systems is tightly linked to hydroclimate, which is highly variable in space and time. Quantifying soil-plant water relations is essential to understanding C storage in these systems. Stem-heat-balance sap-flow sensors were installed in June 2015 at three sites in RC CZO that had existing meteorological stations and eddy covariance towers. These sites are situated along an elevation gradient from 1417 m to 2111 m. Artemisia tridentata ssp. wyomingenesis, A. arbuscula and A. tridentata ssp. vaseyana at dominate at the lower, middle, and upper sites, respectively. At all three sites, we installed sensors on 5-6 shrubs. Preliminary results indicate greater sap flow velocity in both wyomingenesis and tridentata species than arbuscula. The mean hourly sap flow rates were 2.05±0.12 g/h, 0.33±0.01 g/h and 3.02±0.14 g/h for wyomingenesis, arbuscula, and vaseyana, respectively, during June 26th to July 22nd, 2015. Daily sap flow averaged about 61.56±5.21 g/day, 7.60±0.88 g/day, and 74.60±5.44 g/day, respectively within same time period. Lower soil water content at the middle site seemed to be the cause of lower sap flow velocities in arbuscula. Diurnal patterns in sap flow were similar in all subspecies, with maximum flow velocities recorded between 11 AM to 4 PM. The data suggest that water use in tridentata dominated landscapes may be as much as 10 times greater compared to arbuscula dominated landscapes. Thus presumably, there is greater C storage capacity in tridentata dominated sites.

Introgression and dispersal among spotted owl (Strix occidentatlis) subspecies.

Treesearch

W.Chris Funk; Eric D. Forsman; Thomas D. Mullins; Susan M. Haig

2008-01-01

Population genetics plays an increasingly important role in the conservation and management of declining species, particularly for defining taxonomic units. Subspecies are recognized by several conservation organizations and countries and receive legal protection under the US Endangered Species Act (ESA). Two subspecies of spotted owls, northern (Strix...

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

USDA-ARS?s Scientific Manuscript database

Premise of study: Premise of study: The taxonomic classification of the subspecies of Daucus carota is unresolved. Intercrosses among traditionally recognized subspecies has been well-documented, as have intercrosses with other Daucus species containing 2n = 18 chromosomes (D. sahariensis and D. syr...

Building a DNA barcode reference library for the true butterflies (Lepidoptera) of Peninsula Malaysia: what about the subspecies?

PubMed

Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

2013-01-01

The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity.

Building a DNA Barcode Reference Library for the True Butterflies (Lepidoptera) of Peninsula Malaysia: What about the Subspecies?

PubMed Central

Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

2013-01-01

The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity. PMID:24282514

Calcium and other ions in blood and skeleton of Nicaraguan fresh-water shark.

PubMed

URIST, M R

1962-09-21

The bull shark, Carcharhinus leucas, employing archaic but effective means of regulating the physical-chemical composition of its body fluids, thrives in tropical fresh-water rivers and lakes. The ionic strength of the serum and the concentrations of total solutes, calcium, urea, and other ions are below the levels found in marine elasmobranchs but higher than the levels in teleosts. The patterns of the calcium deposits of the vertebrae are identical in marine and fresh-water subspecies.

Replacing and Additive Horizontal Gene Transfer in Streptococcus

PubMed Central

Choi, Sang Chul; Rasmussen, Matthew D.; Hubisz, Melissa J.; Gronau, Ilan; Stanhope, Michael J.; Siepel, Adam

2012-01-01

The prominent role of Horizontal Gene Transfer (HGT) in the evolution of bacteria is now well documented, but few studies have differentiated between evolutionary events that predominantly cause genes in one lineage to be replaced by homologs from another lineage (“replacing HGT”) and events that result in the addition of substantial new genomic material (“additive HGT”). Here in, we make use of the distinct phylogenetic signatures of replacing and additive HGTs in a genome-wide study of the important human pathogen Streptococcus pyogenes (SPY) and its close relatives S. dysgalactiae subspecies equisimilis (SDE) and S. dysgalactiae subspecies dysgalactiae (SDD). Using recently developed statistical models and computational methods, we find evidence for abundant gene flow of both kinds within each of the SPY and SDE clades and of reduced levels of exchange between SPY and SDD. In addition, our analysis strongly supports a pronounced asymmetry in SPY–SDE gene flow, favoring the SPY-to-SDE direction. This finding is of particular interest in light of the recent increase in virulence of pathogenic SDE. We find much stronger evidence for SPY–SDE gene flow among replacing than among additive transfers, suggesting a primary influence from homologous recombination between co-occurring SPY and SDE cells in human hosts. Putative virulence genes are correlated with transfer events, but this correlation is found to be driven by additive, not replacing, HGTs. The genes affected by additive HGTs are enriched for functions having to do with transposition, recombination, and DNA integration, consistent with previous findings, whereas replacing HGTs seen to influence a more diverse set of genes. Additive transfers are also found to be associated with evidence of positive selection. These findings shed new light on the manner in which HGT has shaped pathogenic bacterial genomes. PMID:22617954

Native Perennial Forb Variation Between Mountain Big Sagebrush and Wyoming Big Sagebrush Plant Communities

NASA Astrophysics Data System (ADS)

Davies, Kirk W.; Bates, Jon D.

2010-09-01

Big sagebrush ( Artemisia tridentata Nutt.) occupies large portions of the western United States and provides valuable wildlife habitat. However, information is lacking quantifying differences in native perennial forb characteristics between mountain big sagebrush [ A. tridentata spp. vaseyana (Rydb.) Beetle] and Wyoming big sagebrush [ A. tridentata spp. wyomingensis (Beetle & A. Young) S.L. Welsh] plant communities. This information is critical to accurately evaluate the quality of habitat and forage that these communities can produce because many wildlife species consume large quantities of native perennial forbs and depend on them for hiding cover. To compare native perennial forb characteristics on sites dominated by these two subspecies of big sagebrush, we sampled 106 intact big sagebrush plant communities. Mountain big sagebrush plant communities produced almost 4.5-fold more native perennial forb biomass and had greater native perennial forb species richness and diversity compared to Wyoming big sagebrush plant communities ( P < 0.001). Nonmetric multidimensional scaling (NMS) and the multiple-response permutation procedure (MRPP) demonstrated that native perennial forb composition varied between these plant communities ( P < 0.001). Native perennial forb composition was more similar within plant communities grouped by big sagebrush subspecies than expected by chance ( A = 0.112) and composition varied between community groups ( P < 0.001). Indicator analysis did not identify any perennial forbs that were completely exclusive and faithful, but did identify several perennial forbs that were relatively good indicators of either mountain big sagebrush or Wyoming big sagebrush plant communities. Our results suggest that management plans and habitat guidelines should recognize differences in native perennial forb characteristics between mountain and Wyoming big sagebrush plant communities.

Mapping Atheroprotective Functions and Related Proteins/Lipoproteins in Size Fractionated Human Plasma *

PubMed Central

Swertfeger, Debi K.; Li, Hailong; Rebholz, Sandra; Zhu, Xiaoting; Shah, Amy S.; Davidson, W. Sean; Lu, Long J.

2017-01-01

HDL has been shown to possess a variety of cardio-protective functions, including removal of excess cholesterol from the periphery, and inhibition of lipoprotein oxidation. It has been proposed that various HDL subparticles exist, each with distinct protein and lipid compositions, which may be responsible for HDL's many functions. We hypothesized that HDL functions will co-migrate with the operational lipoprotein subspecies when separated by gel filtration chromatography. Plasma from 10 healthy male donors was fractionated and the protein composition of the phospholipid containing fractions was analyzed by mass spectrometry (MS). Each fraction was evaluated for its proteomic content as well as its ability to promote cholesterol efflux and protect low density lipoprotein (LDL) from free radical oxidation. For each function, several peaks of activity were identified across the plasma size gradient. Neither cholesterol efflux or LDL antioxidation activity correlated strongly with any single protein across the fractions. However, we identified multiple proteins that had strong correlations (r values >0.7, p < 0.01) with individual peaks of activity. These proteins fell into diverse functional categories, including those traditionally associated with lipid metabolism, as well as alternative complement cascade, innate immunity and clotting cascades and immunoglobulins. Additionally, the phospholipid and cholesterol concentration of the fractions correlated strongly with cholesterol efflux (r = 0.95 and 0.82 respectively), whereas the total protein content of the fractions correlated best with antioxidant activity across all fractions (r = 0.746). Furthermore, two previously postulated subspecies (apoA-I, apoA-II and apoC-1; as well as apoA-I, apoC-I and apoJ) were found to have strong correlations with both cholesterol efflux and antioxidation activity. Up till now, very little has been known about how lipoprotein composition mediates functions like cholesterol efflux and antioxidation. PMID:28223350

Factors controlling shell carbon isotopic composition of land snail Acusta despecta sieboldiana estimated from laboratory culturing experiment

NASA Astrophysics Data System (ADS)

Zhang, N.; Yamada, K.; Suzuki, N.; Yoshida, N.

2014-10-01

The carbon isotopic composition (δ13C) of land snail shell carbonate derives from three potential sources: diet, atmospheric CO2, and ingested carbonate (limestone). However, their relative contributions remain unclear. Under various environmental conditions, we cultured one land snail subspecies, Acusta despecta sieboldiana, collected from Yokohama, Japan, and confirmed that all of these sources affect shell carbonate δ13C values. Herein, we consider the influences of metabolic rates and temperature on the carbon isotopic composition of the shell carbonate. Based on results obtained from previous works and this study, a simple but credible framework is presented to illustrate how each source and environmental parameter affects shell carbonate δ13C values. According to this framework and some reasonable assumptions, we estimated the contributions of different carbon sources for each snail individual: for cabbage-fed (C3 plant) groups, the contributions of diet, atmospheric CO2, and ingested limestone vary in the ranges of 66-80, 16-24, and 0-13%, respectively. For corn-fed (C4 plant) groups, because of the possible food stress (less ability to consume C4 plants), the values vary in the ranges of 56-64, 18-20, and 16-26%, respectively. Moreover, according to the literature and our observations, the subspecies we cultured in this study show preferences towards different plant species for food. Therefore, we suggest that the potential food preference should be considered adequately for some species in paleoenvironment studies. Finally, we inferred that only the isotopic exchange of the calcite-HCO3--aragonite equilibrium during egg laying and hatching of our cultured snails controls carbon isotope fractionation.

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

PubMed

King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

2006-12-01

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

Threatened and Endangered Subspecies with Vulnerable Ecological Traits Also Have High Susceptibility to Sea Level Rise and Habitat Fragmentation

PubMed Central

Benscoter, Allison M.; Reece, Joshua S.; Noss, Reed F.; Brandt, Laura A.; Mazzotti, Frank J.; Romañach, Stephanie S.; Watling, James I.

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success. PMID:23940614

Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act

USGS Publications Warehouse

King, Timothy L.; Switzer, John F.; Morrison, Cheryl L.; Eackles, Michael S.; Young, Colleen C.; Lubinski, Barbara A.; Cryan, Paul M.

2006-01-01

Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius. ?? 2006 The Authors.

Threatened and endangered subspecies with vulnerable ecological traits also have high susceptibility to sea level rise and habitat fragmentation.

PubMed

Benscoter, Allison M; Reece, Joshua S; Noss, Reed F; Brandt, Laura A; Mazzotti, Frank J; Romañach, Stephanie S; Watling, James I

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

Threatened and endangered subspecies with vulnerable ecological traits Also have high susceptibility to sea level rise and habitat fragmentation

USGS Publications Warehouse

Benscoter, Allison M.; Reece, Joshua S.; Noss, Reed F.; Brandt, Laura B.; Mazzotti, Frank J.; Romañach, Stephanie S.; Watling, James I.

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

A craniometric study of the black and white Colobus Illiger 1811 (Primates: Ceropithecoidea).

PubMed

Hull, D B

1979-08-01

This study examines the craniometry of Black and White Colobus monkeys using 1072 specimens representing all the recognized subspecies (after Rahm, '70) of the genus. Seventy-six measurements were taken on each individual, and examined using canonical variates analysis and clustering by Ward's Error Sum method. The assumptions of the analytical techniques are shown to be met, and the results demonstrated to be stable. Examination of the populations for statistical difference and taxonomic distinctiveness using a multivariate extension of Mayr's Rule indicates that the taxonomy presented by Rahm ('70) is essentially correct, except that the subspecies of guereza across the northern part of Central Africa should be lumped into a single group--C. g. occidentalis--and the subspecies of montane angolan colobus in Eastern Zaire should all be lumped into C. a. ruwenzorii. The systematic patterns of the genus illustrate the whole range of the process of speciation, from barely distinct subspecies, to subspecies almost as distinct as allopatric species of the genus, and on the fully sympatric species Three major zoogeographic areas may be delineated: an East African area dominated by the effects of the Rift Valley, with a large number of subspecies isolated in forest islands; a Central African area with little subspeciation and sympatric overlap of the major species of Colobus; and a West African area with a clinal pattern of distribution of subspecies, and secondary intergradation. The arbitrary nature of Mary's Rule is also apparent. Lastly, the CVA indicated major differences across the genus to be located in the teeth and jaws, suggesting diet might be an important distinguishing feature in Colobus.

77 FR 20773 - Endangered and Threatened Species; Proposed Threatened Status for Subspecies of the Ringed Seal

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-06

...-XZ59 Endangered and Threatened Species; Proposed Threatened Status for Subspecies of the Ringed Seal... conducted special independent peer review of the December 2010 status review report of the ringed seal... ochotensis), and Ladoga (Phoca hispida ladogensis) subspecies of ringed seals as threatened (75 FR 77476). On...

Conservation assessment for inland cutthroat trout

Treesearch

Michael K. Young

1995-01-01

This document focuses on the state of the science for five subspecies of cutthroat trout found largely on public lands in the Rocky Mountain and Intermountain West. These subspecies are restricted to a fragment of their former range, and primarily occupy small, high-elevation streams. Little is known about the three rarest subspecies (Bonneville, Colorado River, and...

Exogenous Methyl Jasmonate and Salicylic Acid Induce Subspecies-Specific Patterns of Glucosinolate Accumulation and Gene Expression in Brassica oleracea L.

PubMed

Yi, Go-Eun; Robin, Arif Hasan Khan; Yang, Kiwoung; Park, Jong-In; Hwang, Byung Ho; Nou, Ill-Sup

2016-10-24

Glucosinolates have anti-carcinogenic properties. In the recent decades, the genetics of glucosinolate biosynthesis has been widely studied, however, the expression of specific genes involved in glucosinolate biosynthesis under exogenous phytohormone treatment has not been explored at the subspecies level in Brassica oleracea . Such data are vital for strategies aimed at selective exploitation of glucosinolate profiles. This study quantified the expression of 38 glucosinolate biosynthesis-related genes in three B. oleracea subspecies, namely cabbage, broccoli and kale, and catalogued associations between gene expression and increased contents of individual glucosinolates under methyl jasmonate (MeJA) and salicylic acid (SA) treatments. Glucosinolate accumulation and gene expression in response to phytohormone elicitation was subspecies specific. For instance, cabbage leaves showed enhanced accumulation of the aliphatic glucoiberin, progoitrin, sinigrin and indolic neoglucobrassicin under both MeJA and SA treatment. MeJA treatment induced strikingly higher accumulation of glucobrassicin (GBS) in cabbage and kale and of neoglucobrassicin (NGBS) in broccoli compared to controls. Notably higher expression of ST5a (Bol026200), CYP81F1 (Bol028913, Bol028914) and CYP81F4 genes was associated with significantly higher GBS accumulation under MeJA treatment compared to controls in all three subspecies. CYP81F4 genes, trans-activated by MYB34 genes, were expressed at remarkably high levels in all three subspecies under MeJA treatment, which also induced in higher indolic NGBS accumulation in all three subspecies. Remarkably higher expression of MYB28 (Bol036286), ST5b , ST5c , AOP2 , FMOGS-OX5 (Bol031350) and GSL-OH (Bol033373) was associated with much higher contents of aliphatic glucosinolates in kale leaves compared to the other two subspecies. The genes expressed highly could be utilized in strategies to selectively increase glucosinolate compounds in B. oleracea subspecies. These results promote efforts to develop genotypes of B. oleracea and other species with enhanced levels of desired glucosinolates.

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops.

PubMed

Tambong, James T

2017-01-01

Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria.

Comparative genomics of Clavibacter michiganensis subspecies, pathogens of important agricultural crops

PubMed Central

2017-01-01

Subspecies of Clavibacter michiganensis are important phytobacterial pathogens causing devastating diseases in several agricultural crops. The genome organizations of these pathogens are poorly understood. Here, the complete genomes of 5 subspecies (C. michiganensis subsp. michiganensis, Cmi; C. michiganensis subsp. sepedonicus, Cms; C. michiganensis subsp. nebraskensis, Cmn; C. michiganensis subsp. insidiosus, Cmi and C. michiganensis subsp. capsici, Cmc) were analyzed. This study assessed the taxonomic position of the subspecies based on 16S rRNA and genome-based DNA homology and concludes that there is ample evidence to elevate some of the subspecies to species-level. Comparative genomics analysis indicated distinct genomic features evident on the DNA structural atlases and annotation features. Based on orthologous gene analysis, about 2300 CDSs are shared across all the subspecies; and Cms showed the highest number of subspecies-specific CDS, most of which are mobile elements suggesting that Cms could be more prone to translocation of foreign genes. Cms and Cmi had the highest number of pseudogenes, an indication of potential degenerating genomes. The stress response factors that may be involved in cold/heat shock, detoxification, oxidative stress, osmoregulation, and carbon utilization are outlined. For example, the wco-cluster encoding for extracellular polysaccharide II is highly conserved while the sucrose-6-phosphate hydrolase that catalyzes the hydrolysis of sucrose-6-phosphate yielding glucose-6-phosphate and fructose is highly divergent. A unique second form of the enzyme is only present in Cmn NCPPB 2581. Also, twenty-eight plasmid-borne CDSs in the other subspecies were found to have homologues in the chromosomal genome of Cmn which is known not to carry plasmids. These CDSs include pathogenesis-related factors such as Endocellulases E1 and Beta-glucosidase. The results presented here provide an insight of the functional organization of the genomes of five core C. michiganensis subspecies, enabling a better understanding of these phytobacteria. PMID:28319117

A novel multi-antigen virally vectored vaccine against Mycobacterium avium subspecies paratuberculosis.

PubMed

Bull, Tim J; Gilbert, Sarah C; Sridhar, Saranya; Linedale, Richard; Dierkes, Nicola; Sidi-Boumedine, Karim; Hermon-Taylor, John

2007-11-28

Mycobacterium avium subspecies paratuberculosis causes systemic infection and chronic intestinal inflammation in many species including primates. Humans are exposed through milk and from sources of environmental contamination. Hitherto, the only vaccines available against Mycobacterium avium subspecies paratuberculosis have been limited to veterinary use and comprised attenuated or killed organisms. We developed a vaccine comprising a fusion construct designated HAV, containing components of two secreted and two cell surface Mycobacterium avium subspecies paratuberculosis proteins. HAV was transformed into DNA, human Adenovirus 5 (Ad5) and Modified Vaccinia Ankara (MVA) delivery vectors. Full length expression of the predicted 95 kDa fusion protein was confirmed. Vaccination of naïve and Mycobacterium avium subspecies paratuberculosis infected C57BL/6 mice using DNA-prime/MVA-boost or Ad5-prime/MVA-boost protocols was highly immunogenic resulting in significant IFN-gamma ELISPOT responses by splenocytes against recombinant vaccine antigens and a range of HAV specific peptides. This included strong recognition of a T-cell epitope GFAEINPIA located near the C-terminus of the fusion protein. Antibody responses to recombinant vaccine antigens and HAV specific peptides but not GFAEINPIA, also occurred. No immune recognition of vaccine antigens occurred in any sham vaccinated Mycobacterium avium subspecies paratuberculosis infected mice. Vaccination using either protocol significantly attenuated pre-existing Mycobacterium avium subspecies paratuberculosis infection measured by qPCR in spleen and liver and the Ad5-prime/MVA-boost protocol also conferred some protection against subsequent challenge. No adverse effects of vaccination occurred in any of the mice. A range of modern veterinary and clinical vaccines for the treatment and prevention of disease caused by Mycobacterium avium subspecies paratuberculosis are needed. The present vaccine proved to be highly immunogenic without adverse effect in mice and both attenuated pre-existing Mycobacterium avium subspecies paratuberculosis infection and conferred protection against subsequent challenge. Further studies of the present vaccine in naturally infected animals and humans are indicated.

A distinctive new subspecies of Scytalopus griseicollis (Aves, Passeriformes, Rhinocryptidae) from the northern Eastern Cordillera of Colombia and Venezuela

PubMed Central

Avendaño, Jorge Enrique; Donegan, Thomas M.

2015-01-01

Abstract We describe a new subspecies of Pale-bellied Tapaculo Scytalopus griseicollis from the northern Eastern Cordillera of Colombia and Venezuela. This form differs diagnosably in plumage from described subspecies Scytalopus griseicollis griseicollis and Scytalopus griseicollis gilesi and from the latter in tail length. It is also differentiated non-diagnosably in voice from both these populations. Ecological niche modelling analysis suggests that the new subspecies is restricted to the Andean montane forest and páramo north of both the arid Chicamocha valley and the Sierra Nevada del Cocuy. PMID:26085800

Tigers of Sundarbans in India: is the population a separate conservation unit?

PubMed

Singh, Sujeet Kumar; Mishra, Sudhanshu; Aspi, Jouni; Kvist, Laura; Nigam, Parag; Pandey, Puneet; Sharma, Reeta; Goyal, Surendra Prakash

2014-01-01

The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate "evolutionarily significant unit" (ESU) following the adaptive evolutionary conservation (AEC) concept.

Trends in extramural consultation: comparison between subspecialized and general surgical pathology service models.

PubMed

Liu, Yong-Jun; Kessler, Meghan; Zander, Dani S; Karamchandani, Dipti M

2016-10-01

Academic and community hospital pathology groups are increasingly adopting subspecialized service models for surgical pathology (SP) practice. Reasons cited include improvements in sign-out efficiency, quality and accuracy, enhancement of clinician-pathologist communications, and augmentation of resident training quality. However, there is a paucity of published quantitative data regarding the outcomes of transitioning from general to subspecialized SP service coverage. Retrospective assessment of the frequencies and outcomes of SP extramural consultations requested by faculty at our institution was performed, encompassing 2 consecutive years each of subspecialized and general SP service models. The frequencies of extramural consultations between the 2 practice models were not significantly different (0.25% vs 0.21%, P = .142). Although more pathology cases were sent out in gastrointestinal (0.29% vs 0.14%, P = .007), gynecologic (0.16% vs 0.02%, P = .009), and pulmonary (1.73% vs 0.28%, P = .008) services during the "subspecialization" era, fewer pediatric cases were sent out (0.48% vs 1.69%, P = .008). Importantly, the transition to the subspecialized model was associated with a marked reduction in the frequency of major disagreements between the original diagnosis and the consultant's diagnosis (1.8% vs 9.3%, P = .018). Our study supports the value of the subspecialized SP sign-out model for increasing diagnostic accuracy and enhancing the quality of patient care. Copyright © 2016 Elsevier Inc. All rights reserved.

Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii.

PubMed

Tanigawa, Kana; Watanabe, Koichi

2011-03-01

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080(T), was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

Phylogenetic Position and Subspecies Divergence of the Endangered New Zealand Dotterel (Charadrius obscurus)

PubMed Central

Barth, Julia M. I.; Matschiner, Michael; Robertson, Bruce C.

2013-01-01

The New Zealand Dotterel (Charadrius obscurus), an endangered shorebird of the family Charadriidae, is endemic to New Zealand where two subspecies are recognized. These subspecies are not only separated geographically, with C. o. aquilonius being distributed in the New Zealand North Island and C. o. obscurus mostly restricted to Stewart Island, but also differ substantially in morphology and behavior. Despite these divergent traits, previous work has failed to detect genetic differentiation between the subspecies, and the question of when and where the two populations separated is still open. Here, we use mitochondrial and nuclear markers to address molecular divergence between the subspecies, and apply maximum likelihood and Bayesian methods to place C. obscurus within the non-monophyletic genus Charadrius. Despite very little overall differentiation, distinct haplotypes for the subspecies were detected, thus supporting molecular separation of the northern and southern populations. Phylogenetic analysis recovers a monophyletic clade combining the New Zealand Dotterel with two other New Zealand endemic shorebirds, the Wrybill and the Double-Banded Plover, thus suggesting a single dispersal event as the origin of this group. Divergence dates within Charadriidae were estimated with BEAST 2, and our results indicate a Middle Miocene origin of New Zealand endemic Charadriidae, a Late Miocene emergence of the lineage leading to the New Zealand Dotterel, and a Middle to Late Pleistocene divergence of the two New Zealand Dotterel subspecies. PMID:24205094

76 FR 30082 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To List the Spot...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-24

... laceratasubcaudalis as subspecies of the petitioned species, H. lacerata, because they were properly described in peer-reviewed literature and are recognized as subspecies by knowledgeable herpetologists: H. l. lacerata since 1880, and H. l. subcaudata since 1956 (ITIS 2009, p. 1). In addition to the two subspecies having...

Genetic Variability of the Grey Wolf Canis lupus in the Caucasus in Comparison with Europe and the Middle East: Distinct or Intermediary Population?

PubMed Central

Pilot, Małgorzata; Dąbrowski, Michał J.; Hayrapetyan, Vahram; Yavruyan, Eduard G.; Kopaliani, Natia; Tsingarska, Elena; Bujalska, Barbara; Kamiński, Stanisław; Bogdanowicz, Wiesław

2014-01-01

Despite continuous historical distribution of the grey wolf (Canis lupus) throughout Eurasia, the species displays considerable morphological differentiation that resulted in delimitation of a number of subspecies. However, these morphological discontinuities are not always consistent with patterns of genetic differentiation. Here we assess genetic distinctiveness of grey wolves from the Caucasus (a region at the border between Europe and West Asia) that have been classified as a distinct subspecies C. l. cubanensis. We analysed their genetic variability based on mtDNA control region, microsatellite loci and genome-wide SNP genotypes (obtained for a subset of the samples), and found similar or higher levels of genetic diversity at all these types of loci as compared with other Eurasian populations. Although we found no evidence for a recent genetic bottleneck, genome-wide linkage disequilibrium patterns suggest a long-term demographic decline in the Caucasian population – a trend consistent with other Eurasian populations. Caucasian wolves share mtDNA haplotypes with both Eastern European and West Asian wolves, suggesting past or ongoing gene flow. Microsatellite data also suggest gene flow between the Caucasus and Eastern Europe. We found evidence for moderate admixture between the Caucasian wolves and domestic dogs, at a level comparable with other Eurasian populations. Taken together, our results show that Caucasian wolves are not genetically isolated from other Eurasian populations, share with them the same demographic trends, and are affected by similar conservation problems. PMID:24714198

Population history, gene flow, and bottlenecks in island populations of a secondary seed disperser, the southern grey shrike (Lanius meridionalis koenigi)

PubMed Central

Padilla, David P; Spurgin, Lewis G; Fairfield, Eleanor A; Illera, Juan Carlos; Richardson, David S

2015-01-01

Studying the population history and demography of organisms with important ecological roles can aid understanding of evolutionary processes at the community level and inform conservation. We screened genetic variation (mtDNA and microsatellite) across the populations of the southern grey shrike (Lanius meridionalis koenigi) in the Canary Islands, where it is an endemic subspecies and an important secondary seed disperser. We show that the Canarian subspecies is polyphyletic with L. meridionalis elegans from North Africa and that shrikes have colonized the Canary Islands from North Africa multiple times. Substantial differences in genetic diversity exist across islands, which are most likely the product of a combination of historical colonization events and recent bottlenecks. The Eastern Canary Islands had the highest overall levels of genetic diversity and have probably been most recently and/or frequently colonized from Africa. Recent or ongoing bottlenecks were detected in three of the islands and are consistent with anecdotal evidence of population declines due to human disturbance. These findings are troubling given the shrike's key ecological role in the Canary Islands, and further research is needed to understand the community-level consequences of declines in shrike populations. Finally, we found moderate genetic differentiation among populations, which largely reflected the shrike's bottleneck history; however, a significant pattern of isolation-by-distance indicated that some gene flow occurs between islands. This study is a useful first step toward understanding how secondary seed dispersal operates over broad spatial scales. PMID:25628862

The Sampling Scheme Matters: Pan troglodytes troglodytes and P. t. schweinfurthii Are Characterized by Clinal Genetic Variation Rather Than a Strong Subspecies Break

PubMed Central

Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B.; Sanz, Crickette; Reed, Patricia; Olson, Sarah H.; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

2015-01-01

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. PMID:25330245

Do mitochondrial properties explain intraspecific variation in thermal tolerance?

PubMed

Fangue, Nann A; Richards, Jeffrey G; Schulte, Patricia M

2009-02-01

As global temperatures rise, there is a growing need to understand the physiological mechanisms that determine an organism's thermal niche. Here, we test the hypothesis that increases in mitochondrial capacity with cold acclimation and adaptation are associated with decreases in thermal tolerance using two subspecies of killifish (Fundulus heteroclitus) that differ in thermal niche. We assessed whole-organism metabolic rate, mitochondrial amount and mitochondrial function in killifish acclimated to several temperatures. Mitochondrial enzyme activities and mRNA levels were greater in fish from the northern subspecies, particularly in cold-acclimated fish, suggesting that the putatively cold-adapted northern subspecies has a greater capacity for increases in mitochondrial amount in response to cold acclimation. When tested at the fish's acclimation temperature, maximum ADP-stimulated (State III) rates of mitochondrial oxygen consumption in vitro were greater in cold-acclimated northern fish than in southern fish but did not differ between subspecies at higher acclimation temperatures. Whole-organism metabolic rate was greater in fish of the northern subspecies at all acclimation temperatures. Cold acclimation also changed the response of mitochondrial respiration to acute temperature challenge. Mitochondrial oxygen consumption was greater in cold-acclimated northern fish than in southern fish at low test temperatures, but the opposite was true at high test temperatures. These differences were reflected in whole-organism oxygen consumption. Our data indicate that the plasticity of mitochondrial function and amount differs between killifish subspecies, with the less high-temperature tolerant, and putatively cold adapted, northern subspecies having greater ability to increase mitochondrial capacity in the cold. However, there were few differences in mitochondrial properties between subspecies at warm acclimation temperatures, despite differences in both whole-organism oxygen consumption and thermal tolerance at these temperatures.

The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break.

PubMed

Fünfstück, Tillmann; Arandjelovic, Mimi; Morgan, David B; Sanz, Crickette; Reed, Patricia; Olson, Sarah H; Cameron, Ken; Ondzie, Alain; Peeters, Martine; Vigilant, Linda

2015-02-01

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. Copyright © 2014 Wiley Periodicals, Inc.

Mating-Type Inheritance and Maturity Times in Crosses between Subspecies of TETRAHYMENA PIGMENTOSA

PubMed Central

Simon, Ellen M.

1980-01-01

Subspecies 6 and 8 of T. pigmentosa (formerly syngens 6 and 8 of T. pyriformis) share a mating-type system controlled by three alleles with "peck-order" dominance at a single locus. The system is apparently closed and limited to three mating types that are homologous, but not identical, in the subspecies. These relationships are reflected in new mating-type designations.—The viability in some intersyngenic crosses is excellent, and the inheritance of major mating types in first-generation hybrids and their progeny follows the pattern of subspecies 8.—The period of immaturity is shorter than that previously reported for subspecies 8, with 50% of the subclones maturing between 46 and 100 fissions after conjugation. Maturity curves are generally sigmoid, but some are apparently biphasic. The onset of maturity in triplicate sublines from the same synclone is usually highly correlated. PMID:17248998

Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies.

PubMed

Cronin, Matthew A; MacNeil, Michael D; Vu, Ninh; Leesburg, Vicki; Blackburn, Harvey D; Derr, James N

2013-01-01

The genetic relationship of American plains bison (Bison bison bison) and wood bison (Bison bison athabascae) was quantified and compared with that among breeds and subspecies of cattle. Plains bison from 9 herds (N = 136), wood bison from 3 herds (N = 65), taurine cattle (Bos taurus taurus) from 14 breeds (N = 244), and indicine cattle (Bos taurus indicus) from 2 breeds (N = 53) were genotyped for 29 polymorphic microsatellite loci. Bayesian cluster analyses indicate 3 groups, 2 of which are plains bison and 1 of which is wood bison with some admixture, and genetic distances do not show plains bison and wood bison as distinct groups. Differentiation of wood bison and plains bison is also significantly less than that of cattle breeds and subspecies. These and other genetic data and historical interbreeding of bison do not support recognition of extant plains bison and wood bison as phylogenetically distinct subspecies.

Molecular and antimicrobial susceptibility profiling of Streptococcus dysgalactiae isolated from swine.

PubMed

Moreno, Luisa Z; da Costa, Barbara L P; Matajira, Carlos E C; Gomes, Vasco T M; Mesquita, Renan E; Silva, Ana Paula S; Moreno, Andrea M

2016-10-01

Streptococcus dysgalactiae subspecies equisimilis and dysgalactiae were isolated from swine clinical specimens. The subspecies equisimilis presented 2 clonal patterns with 85% genetic similarity, whereas subspecies dysgalactiae presented distinct band pattern with less than 80% similarity with equisimilis genotypes. Isolates presented high MIC values to tetracyclines, danofloxacin, spectinomycin, tiamulin, and clindamycin. Copyright © 2016 Elsevier Inc. All rights reserved.

Novel molecular markers differentiate Oncorhynchus mykiss (rainbow trout and steelhead) and the O. clarki (cutthroat trout) subspecies

USGS Publications Warehouse

Ostberg, C.O.; Rodriguez, R.J.

2002-01-01

A suite of 26 PCR-based markers was developed that differentiates rainbow (Oncorhynchus mykiss) and coastal cutthroat trout (O. clarki clarki). The markers also differentiated rainbow from other cutthroat trout subspecies (O. clarki), and several of the markers differentiated between cutthroat trout subspecies. This system has numerous positive attributes, including: nonlethal sampling, high species-specificity and products that are easily identified and scored using agarose gel electrophoresis. The methodology described for developing the markers can be applied to virtually any system in which numerous markers are desired for identifying or differentiating species or subspecies.

Evolution of Compatibility Range in the Rice-Magnaporthe oryzae System: An Uneven Distribution of R Genes Between Rice Subspecies.

PubMed

Gallet, Romain; Fontaine, Colin; Bonnot, François; Milazzo, Joëlle; Tertois, Christophe; Adreit, Henri; Ravigné, Virginie; Fournier, Elisabeth; Tharreau, Didier

2016-04-01

Efficient strategies for limiting the impact of pathogens on crops require a good understanding of the factors underlying the evolution of compatibility range for the pathogens and host plants, i.e., the set of host genotypes that a particular pathogen genotype can infect and the set of pathogen genotypes that can infect a particular host genotype. Until now, little is known about the evolutionary and ecological factors driving compatibility ranges in systems implicating crop plants. We studied the evolution of host and pathogen compatibility ranges for rice blast disease, which is caused by the ascomycete Magnaporthe oryzae. We challenged 61 rice varieties from three rice subspecies with 31 strains of M. oryzae collected worldwide from all major known genetic groups. We determined the compatibility range of each plant variety and pathogen genotype and the severity of each plant-pathogen interaction. Compatibility ranges differed between rice subspecies, with the most resistant subspecies selecting for pathogens with broader compatibility ranges and the least resistant subspecies selecting for pathogens with narrower compatibility ranges. These results are consistent with a nested distribution of R genes between rice subspecies.

Fertility and reproductive rate of Varroa mite, Varroa destructor, in native and exotic honeybee, Apis mellifera L., colonies under Saudi Arabia conditions.

PubMed

Alattal, Yehya; AlGhamdi, Ahmad; Single, Arif; Ansari, Mohammad Javed; Alkathiri, Hussien

2017-07-01

Varroa mite is the most destructive pest to bee colonies worldwide. In Saudi Arabia, preliminary data indicated high infestation levels in the exotic honeybee colonies; such as Apis mellifera carnica and Apis mellifera ligustica , compared to native honeybee subspecies Apis mellifera jemenitica , which may imply higher tolerance to Varroasis . In this study, fertility and reproductive rate of Varroa mite, Varroa destructor , in capped brood cells of the native honeybee subspecies were investigated and compared with an exotic honeybee subspecies, A. m . carnica . Mite fertility was almost alike (87.5% and 89.4%) in the native and craniolan colonies respectively. Similarly, results did not show significant differences in reproduction rate between both subspecies ( F  = 0.66, Pr >  F  = 0.42). Number of adult Varroa daughters per fertile mother mite was 2.0 and 2.1 for native and craniolan honeybee subspecies respectively. This may indicate that mechanisms of keeping low infestation rates in the native honeybee colonies are not associated with Varroa reproduction. Therefore, potential factors of keeping lower Varroa infestation rates in native honey bee subspecies should be further investigated.

Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

PubMed Central

Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

2018-01-01

Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene. PMID:29662500

Comparison of venom composition and biological activities of the subspecies Crotalus lepidus lepidus, Crotalus lepidus klauberi and Crotalus lepidus morulus from Mexico.

PubMed

Martínez-Romero, Gerardo; Rucavado, Alexandra; Lazcano, David; Gutiérrez, José María; Borja, Miguel; Lomonte, Bruno; Garza-García, Yolanda; Zugasti-Cruz, Alejandro

2013-09-01

The rock rattlesnakes Crotalus lepidus comprise a group (lepidus, klauberi, morulus and maculosus) of poorly known mountain cold-tolerant snakes in Mexico. In particular, Crotalus lepidus morulus is a snake endemic of the northeast of Mexico, whereas Crotalus lepidus klauberi and C. l. lepidus are distributed in some regions of the north and central Mexico and southern U. S. Until now very little data are available from C. lepidus subspecies from Mexico, as the terrain inhabited by these snakes is generally steep and rugged. In this work, we have determined some biochemical and biological properties of C. l. morulus, C. l. klauberi and C. l. lepidus crude venoms. Some minor differences in venoms were noted in SDS-PAGE, HPLC profile and MALDI-TOF mass spectrometry analysis. Partial sequences of metalloproteinases, phospholipases A₂ (PLA₂) and galactose-specific lectins were identified in the venoms. Venoms of C. l. klauberi and C. l. lepidus had significantly higher hemorrhagic and lethal activities than C. l. morulus venom. Proteolytic activity in azocasein was higher in C. l. morulus venom, whereas gelatin hydrolysis was higher in C. l. klauberi. Fibrinogenolytic and PLA₂ activities were very similar in all venoms tested. The histological observations in the gastrocnemius muscle damaged by venoms from all the subspecies confirmed myonecrotic and hemorrhagic activities (at 3 and 24 h), which resulted in a poor regenerative response after 14 days. However, C. l. lepidus and C. l. klauberi venom induced a higher increase in the plasma activity of creatine kinase (CK), evidencing higher myotoxicity, whereas paw edema-inducing activity was higher in C. l. lepidus venom. The results indicate that the venoms from the three subspecies have similar protein profiles in electrophoresis, HPLC and molecular weight determinations. However, differences were found in the biological activities in mice. Notably, the venoms of C. l. lepidus and C. l. klauberi present higher toxicity (lower LD₅₀) and hemorrhagic activity than C. l. morulus venom. Copyright © 2013 Elsevier Ltd. All rights reserved.

Leopard (Panthera pardus) status, distribution, and the research efforts across its range.

PubMed

Jacobson, Andrew P; Gerngross, Peter; Lemeris, Joseph R; Schoonover, Rebecca F; Anco, Corey; Breitenmoser-Würsten, Christine; Durant, Sarah M; Farhadinia, Mohammad S; Henschel, Philipp; Kamler, Jan F; Laguardia, Alice; Rostro-García, Susana; Stein, Andrew B; Dollar, Luke

2016-01-01

The leopard's (Panthera pardus) broad geographic range, remarkable adaptability, and secretive nature have contributed to a misconception that this species might not be severely threatened across its range. We find that not only are several subspecies and regional populations critically endangered but also the overall range loss is greater than the average for terrestrial large carnivores. To assess the leopard's status, we compile 6,000 records at 2,500 locations from over 1,300 sources on its historic (post 1750) and current distribution. We map the species across Africa and Asia, delineating areas where the species is confirmed present, is possibly present, is possibly extinct or is almost certainly extinct. The leopard now occupies 25-37% of its historic range, but this obscures important differences between subspecies. Of the nine recognized subspecies, three (P. p. pardus, fusca, and saxicolor) account for 97% of the leopard's extant range while another three (P. p. orientalis, nimr, and japonensis) have each lost as much as 98% of their historic range. Isolation, small patch sizes, and few remaining patches further threaten the six subspecies that each have less than 100,000 km(2) of extant range. Approximately 17% of extant leopard range is protected, although some endangered subspecies have far less. We found that while leopard research was increasing, research effort was primarily on the subspecies with the most remaining range whereas subspecies that are most in need of urgent attention were neglected.

Genetic characterization of wild swamp deer populations: ex situ conservation and forensics implications.

PubMed

Kumar, Ved Prakash; Shrivastwa, Anupam; Nigam, Parag; Kumar, Dhyanendra; Goyal, Surendra Prakash

2017-11-01

Swamp deer (Rucervus duvaucelii) is an endemic, Scheduled I species under the Wildlife (Protection) Act 1972, India. According to variations in antler size, it has been classified into three subspecies, namely Western (R. duvaucelii duvaucelii), Central (R. duvaucelii branderi), and Eastern (R. duvaucelii ranjitsinhii). For planning effective ex situ and in situ conservation of a wide-ranging species in different bioclimatic regions and in wildlife forensic, the use of genetic characterization in defining morpho/ecotypes has been suggested because of the geographic clines and reproductive isolation. In spite of these morphotypes, very little is known about the genetic characteristics of the three subspecies, hence no strict subspecies-based breeding plan for retaining the evolutionary characteristics in captive populations for subsequent re-introduction is available except for a few studies. We describe the genetic characteristics of these three subspecies using cytochrome b of the mtDNA genome (400 bp). The DNA sequence data indicated 11 variable sites within the three subspecies. Two paraphyletic clades, namely the Central India and Western-Eastern populations were found, whereas the Western and Eastern populations are monophyletic with a bootstrap value of 69% within the clade. We suggest the need of sorting these three subspecies using different molecular mtDNA markers in zoos for captive breeding purposes so as to retain the genetic diversity of the separate geographic clines and to use a subspecies-specific fixed-state nucleotide to assess the extent of poaching to avoid any population demography stochastically in India.

Leopard (Panthera pardus) status, distribution, and the research efforts across its range

PubMed Central

Gerngross, Peter; Lemeris Jr., Joseph R.; Schoonover, Rebecca F.; Anco, Corey; Breitenmoser-Würsten, Christine; Durant, Sarah M.; Farhadinia, Mohammad S.; Henschel, Philipp; Kamler, Jan F.; Laguardia, Alice; Rostro-García, Susana; Stein, Andrew B.; Dollar, Luke

2016-01-01

The leopard’s (Panthera pardus) broad geographic range, remarkable adaptability, and secretive nature have contributed to a misconception that this species might not be severely threatened across its range. We find that not only are several subspecies and regional populations critically endangered but also the overall range loss is greater than the average for terrestrial large carnivores. To assess the leopard’s status, we compile 6,000 records at 2,500 locations from over 1,300 sources on its historic (post 1750) and current distribution. We map the species across Africa and Asia, delineating areas where the species is confirmed present, is possibly present, is possibly extinct or is almost certainly extinct. The leopard now occupies 25–37% of its historic range, but this obscures important differences between subspecies. Of the nine recognized subspecies, three (P. p. pardus, fusca, and saxicolor) account for 97% of the leopard’s extant range while another three (P. p. orientalis, nimr, and japonensis) have each lost as much as 98% of their historic range. Isolation, small patch sizes, and few remaining patches further threaten the six subspecies that each have less than 100,000 km2 of extant range. Approximately 17% of extant leopard range is protected, although some endangered subspecies have far less. We found that while leopard research was increasing, research effort was primarily on the subspecies with the most remaining range whereas subspecies that are most in need of urgent attention were neglected. PMID:27168983

Evolutionary history of Ichthyosaura alpestris (Caudata, Salamandridae) inferred from the combined analysis of nuclear and mitochondrial markers.

PubMed

Recuero, Ernesto; Buckley, David; García-París, Mario; Arntzen, Jan W; Cogălniceanu, Dan; Martínez-Solano, Iñigo

2014-12-01

Widespread species with morphologically and ecologically differentiated populations are key to understand speciation because they allow investigating the different stages of the continuous process of population divergence. The alpine newt, Ichthyosaura alpestris, with a range that covers a large part of Central Europe as well as isolated regions in all three European Mediterranean peninsulas, and with strong ecological and life-history differences among populations, is an excellent system for such studies. We sampled individuals across most of the range of the species, and analyzed mitochondrial (1442 bp) and nuclear (two nuclear genes -1554 bp- and 35 allozyme loci) markers to produce a time-calibrated phylogeny and reconstruct the historical biogeography of the species. Phylogenetic analyses of mtDNA data produced a fully resolved topology, with an endemic, Balkan clade (Vlasina) which is sister to a clade comprising an eastern and a western group. Within the former, one clade (subspecies I. a. veluchiensis) is sister to a clade containing subspecies I. a. montenegrina and I. a. serdara as well as samples from southern Romania, Bosnia-Herzegovina, Serbia and Bulgaria (subspecies I. a. reiseri and part of I. a. alpestris). Within the western group, populations from the Italian peninsula (subspecies I. a. apuana and I. a. inexpectata) are sister to a clade containing samples from the Iberian Peninsula (subspecies I. a. cyreni) and the remainder of the samples from subspecies I. a. alpestris (populations from Hungary, Austria, Poland, France, Germany and the larger part of Romania). Results of (∗)BEAST analyses on a combined mtDNA and nDNA dataset consistently recovered with high statistical support four lineages with unresolved inter-relationships: (1) subspecies I. a. veluchiensis; (2) subspecies I. a. apuana+I. a. inexpectata; (3) subspecies I. a. cyreni+part of subspecies I. a. alpestris (the westernmost populations, plus most Romanian populations); and (4) the remaining populations, including subspecies I. a. serdara, I. a. reiseri and I. a. montenegrina and part of subspecies I. a. alpestris, plus samples from Vlasina. Our time estimates are consistent with ages based on the fossil record and suggest a widespread distribution for the I. alpestris ancestor, with the split of the major eastern and western lineages during the Miocene, in the Tortonian. Our study provides a solid, comprehensive background on the evolutionary history of the species based on the most complete combined (mtDNA+nDNA+allozymes) dataset to date. The combination of the historical perspective provided by coalescent-based analyses of mitochondrial and nuclear DNA variation with individual-based multilocus assignment methods based on multiple nuclear markers (allozymes) also allowed identification of instances of discordance across markers that highlight the complexity and dynamism of past and ongoing evolutionary processes in the species. Copyright © 2014 Elsevier Inc. All rights reserved.

Stable hydrogen isotope analysis as a method to identify illegally trapped songbirds.

PubMed

Kelly, Andrew; Thompson, Richard; Newton, Jason

2008-06-01

We measured stable hydrogen isotope ratios in the primary feathers of two subspecies of goldfinches, confiscated by the Police and the Royal Society for the Prevention of Cruelty to Animals (RSPCA) on suspicion that they had been illegally taken from the wild. We found significant differences in the delta2H values of the two subspecies indicating that they were sourced from different geographical regions. Our results correlated with isotopic precipitation maps and with the known distribution of the two subspecies of goldfinch. We believe that this technique could be used by law enforcement agencies to determine the origin of birds in cases where the species or subspecies involved are geographically distinct.

Complex Population Patterns of Eunica tatila Herrich-Schäffer (Lepidoptera: Nymphalidae), with Special Emphasis on Sexual Dimorphism.

PubMed

Cavanzón-Medrano, L; Pozo, C; Hénaut, Y; Legal, L; Salas-Suárez, N; Machkour-M'Rabet, S

2016-04-01

The species Eunica tatila (Herrich-Schäffer) is present in the Neotropical region and comprises three subspecies. In Mexico, only one subspecies is reported: E. t. tatila (Herrich-Schäffer). The Yucatan Peninsula, in southeastern Mexico, is located in a transitional geographical position, between southern Florida, the West Indies and Central America. It is part of a transitional region, important for the dispersion of insects from southern Florida via Cuba and the Yucatan Peninsula. Considering the possibility of the overlapping and delimitation of described subspecies, we sampled different populations in the Yucatan Peninsula to possibly assign a subspecies name and evaluate the magnitude of sexual dimorphism. We collected 591 individuals (♀284, ♂307) in conserved areas. The study of male genitalia led to the identification of Eunica tatila tatilista (Kaye) as a subspecies; however, hypandrium structure and wing pattern analysis suggest a mix of E. t. tatila and E. t. tatilista characteristics. The analysis of sexual dimorphism provided evidence of more complex wing morphs for females, with 12 patterns instead of four as previously described. Our results demonstrate the complexity of characterizing E. tatila and suggest that the Yucatan Peninsula is a transitional zone for subspecies of some butterflies.

A new subspecies of Nitokra affinis Gurney, 1927 (Copepoda, Harpacticoida) from the Caribbean coast of Colombia

PubMed Central

Fuentes-Reinés, Juan M.; Suárez-Morales, Eduardo

2014-01-01

Abstract Plankton samples from Laguna Navio Quebrado, La Guajira, northern Colombia, yielded male and female specimens of an harpacticoid copepod that was first identified as the widely distributed species Nitokra affinis Gurney, 1927 for which at least four subspecies have been described from different geographic areas. A more detailed examination of the Colombian specimens revealed that it differs from the other morphs so far considered as subspecies. The Colombian specimens differ from the other four known subspecies in the following aspects: (1) rostrum with long projection, (2) relatively long exopod of P1, almost as long as first endopodal segment, (3) endopodal and exopodal rami of P2 equally long, (4) a reduced number of endopodal setal elements of the male P5. It also differs from N. a. californica Lang in details of the ornamentation of the urosomites. Descriptions and illustrations of this new subspecies, the first one described from the Neotropical region, are presented together with a key to the five known subspecies of Nitokra affinis. As in many other cases of presumedly widespread species of harpacticoids, it is possible that N. affinis represents a species complex with more restricted distributional patterns, a notion that certainly deserves further study. PMID:24574850

Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa)

PubMed Central

Wen, Ming; Xie, Munan; He, Lian; Wang, Yushuai; Shi, Suhua; Tang, Tian

2016-01-01

Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence. PMID:27797952

Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations.

PubMed

Luo, Shu-Jin; Johnson, Warren E; Martenson, Janice; Antunes, Agostinho; Martelli, Paolo; Uphyrkina, Olga; Traylor-Holzer, Kathy; Smith, James L D; O'Brien, Stephen J

2008-04-22

Tigers (Panthera tigris) are disappearing rapidly from the wild, from over 100,000 in the 1900s to as few as 3000. Javan (P.t. sondaica), Bali (P.t. balica), and Caspian (P.t. virgata) subspecies are extinct, whereas the South China tiger (P.t. amoyensis) persists only in zoos. By contrast, captive tigers are flourishing, with 15,000-20,000 individuals worldwide, outnumbering their wild relatives five to seven times. We assessed subspecies genetic ancestry of 105 captive tigers from 14 countries and regions by using Bayesian analysis and diagnostic genetic markers defined by a prior analysis of 134 voucher tigers of significant genetic distinctiveness. We assigned 49 tigers to one of five subspecies (Bengal P.t. tigris, Sumatran P.t. sumatrae, Indochinese P.t. corbetti, Amur P.t. altaica, and Malayan P.t. jacksoni tigers) and determined 52 had admixed subspecies origins. The tested captive tigers retain appreciable genomic diversity unobserved in their wild counterparts, perhaps a consequence of large population size, century-long introduction of new founders, and managed-breeding strategies to retain genetic variability. Assessment of verified subspecies ancestry offers a powerful tool that, if applied to tigers of uncertain background, may considerably increase the number of purebred tigers suitable for conservation management.

Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper.

PubMed

Oh, Eom-Ji; Bae, Chungyun; Lee, Han-Beoyl; Hwang, In Sun; Lee, Hyok-In; Yea, Mi Chi; Yim, Kyu-Ock; Lee, Seungdon; Heu, Sunggi; Cha, Jae-Soon; Oh, Chang-Sik

2016-10-01

Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies. One of these subspecies is C. michiganensis subsp. michiganensis, which causes bacterial canker disease in tomato. Bacterial strains showing very similar canker disease symptoms to those of a strain originally classified as C. michiganensis have been isolated from pepper. In this paper, we reclassified strains isolated from pepper. On the basis of phylogenetic analysis with 16S rRNA gene sequences, the strains isolated from pepper were grouped in a separate clade from other subspecies of C. michiganensis. Biochemical, physiological and genetic characteristics of strain PF008T, which is the representative strain of the isolates from pepper, were examined in this study. Based on multi-locus sequence typing and other biochemical and physiological features including colony color, utilization of carbon sources and enzyme activities, strain PF008T was categorically differentiated from eight subspecies of C. michiganensis. Moreover, genome analysis showed that the DNA G+C content of strain PF008T is 73.2 %. These results indicate that PF008T is distinct from other known subspecies of C. michiganensis. Therefore, we propose a novel subspecies, C. michiganensis subsp. capsici, causing bacterial canker disease in pepper, with a type strain of PF008T (=KACC 18448T=LMG 29047T).

Identical metabolic rate and thermal conductance in Rock Sandpiper (Calidris ptilocnemis) subspecies with contrasting nonbreeding life histories

USGS Publications Warehouse

Ruthrauff, Daniel R.; Dekinga, Anne; Gill, Robert E.; Piersma, Theunis

2013-01-01

Closely related species or subspecies can exhibit metabolic differences that reflect site-specific environmental conditions. Whether such differences represent fixed traits or flexible adjustments to local conditions, however, is difficult to predict across taxa. The nominate race of Rock Sandpiper (Calidris ptilocnemis) exhibits the most northerly nonbreeding distribution of any shorebird in the North Pacific, being common during winter in cold, dark locations as far north as upper Cook Inlet, Alaska (61°N). By contrast, the tschuktschorum subspecies migrates to sites ranging from about 59°N to more benign locations as far south as ~37°N. These distributional extremes exert contrasting energetic demands, and we measured common metabolic parameters in the two subspecies held under identical laboratory conditions to determine whether differences in these parameters are reflected by their nonbreeding life histories. Basal metabolic rate and thermal conductance did not differ between subspecies, and the subspecies had a similar metabolic response to temperatures below their thermoneutral zone. Relatively low thermal conductance values may, however, reflect intrinsic metabolic adaptations to northerly latitudes. In the absence of differences in basic metabolic parameters, the two subspecies’ nonbreeding distributions will likely be more strongly influenced by adaptations to regional variation in ecological factors such as prey density, prey quality, and foraging habitat.

Combination of Metabolomic and Proteomic Analysis Revealed Different Features among Lactobacillus delbrueckii Subspecies bulgaricus and lactis Strains While In Vivo Testing in the Model Organism Caenorhabditis elegans Highlighted Probiotic Properties

PubMed Central

Zanni, Elena; Schifano, Emily; Motta, Sara; Sciubba, Fabio; Palleschi, Claudio; Mauri, Pierluigi; Perozzi, Giuditta; Uccelletti, Daniela; Devirgiliis, Chiara; Miccheli, Alfredo

2017-01-01

Lactobacillus delbrueckii represents a technologically relevant member of lactic acid bacteria, since the two subspecies bulgaricus and lactis are widely associated with fermented dairy products. In the present work, we report the characterization of two commercial strains belonging to L. delbrueckii subspecies bulgaricus, lactis and a novel strain previously isolated from a traditional fermented fresh cheese. A phenomic approach was performed by combining metabolomic and proteomic analysis of the three strains, which were subsequently supplemented as food source to the model organism Caenorhabditis elegans, with the final aim to evaluate their possible probiotic effects. Restriction analysis of 16S ribosomal DNA revealed that the novel foodborne strain belonged to L. delbrueckii subspecies lactis. Proteomic and metabolomic approaches showed differences in folate, aminoacid and sugar metabolic pathways among the three strains. Moreover, evaluation of C. elegans lifespan, larval development, brood size, and bacterial colonization capacity demonstrated that L. delbrueckii subsp. bulgaricus diet exerted beneficial effects on nematodes. On the other hand, both L. delbrueckii subsp. lactis strains affected lifespan and larval development. We have characterized three strains belonging to L. delbrueckii subspecies bulgaricus and lactis highlighting their divergent origin. In particular, the two closely related isolates L. delbrueckii subspecies lactis display different galactose metabolic capabilities. Moreover, the L. delbrueckii subspecies bulgaricus strain demonstrated potential probiotic features. Combination of omic platforms coupled with in vivo screening in the simple model organism C. elegans is a powerful tool to characterize industrially relevant bacterial isolates. PMID:28702021

Combination of Metabolomic and Proteomic Analysis Revealed Different Features among Lactobacillus delbrueckii Subspecies bulgaricus and lactis Strains While In Vivo Testing in the Model Organism Caenorhabditis elegans Highlighted Probiotic Properties.

PubMed

Zanni, Elena; Schifano, Emily; Motta, Sara; Sciubba, Fabio; Palleschi, Claudio; Mauri, Pierluigi; Perozzi, Giuditta; Uccelletti, Daniela; Devirgiliis, Chiara; Miccheli, Alfredo

2017-01-01

Lactobacillus delbrueckii represents a technologically relevant member of lactic acid bacteria, since the two subspecies bulgaricus and lactis are widely associated with fermented dairy products. In the present work, we report the characterization of two commercial strains belonging to L. delbrueckii subspecies bulgaricus , lactis and a novel strain previously isolated from a traditional fermented fresh cheese. A phenomic approach was performed by combining metabolomic and proteomic analysis of the three strains, which were subsequently supplemented as food source to the model organism Caenorhabditis elegans , with the final aim to evaluate their possible probiotic effects. Restriction analysis of 16S ribosomal DNA revealed that the novel foodborne strain belonged to L. delbrueckii subspecies lactis . Proteomic and metabolomic approaches showed differences in folate, aminoacid and sugar metabolic pathways among the three strains. Moreover, evaluation of C. elegans lifespan, larval development, brood size, and bacterial colonization capacity demonstrated that L. delbrueckii subsp. bulgaricus diet exerted beneficial effects on nematodes. On the other hand, both L. delbrueckii subsp. lactis strains affected lifespan and larval development. We have characterized three strains belonging to L. delbrueckii subspecies bulgaricus and lactis highlighting their divergent origin. In particular, the two closely related isolates L. delbrueckii subspecies lactis display different galactose metabolic capabilities. Moreover, the L. delbrueckii subspecies bulgaricus strain demonstrated potential probiotic features. Combination of omic platforms coupled with in vivo screening in the simple model organism C. elegans is a powerful tool to characterize industrially relevant bacterial isolates.

GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter.

PubMed

Zaluga, Joanna; Heylen, Kim; Van Hoorde, Koenraad; Hoste, Bart; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

2011-09-01

The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens. Copyright © 2011 Elsevier GmbH. All rights reserved.

Life history attributes of Arizona Grasshopper Sparrow (Ammodramus savannarum ammolegus) and comparisons with other North American subspecies

USGS Publications Warehouse

Ruth, Janet M.

2017-01-01

Ammodramus savannarum ammolegus—commonly referred to as the Arizona Grasshopper Sparrow—occurs in the desert and plains grasslands of southeastern Arizona, southwestern New Mexico, and northern Sonora, Mexico. Although a subspecies of conservation concern, this is the first intensive study of its life history and breeding ecology, providing baseline data and facilitating comparisons with other North American Grasshopper Sparrow subspecies. Specifically, I found A. s. ammolegus males generally weighed less than other subspecies (16.0 ± 0.8 g) but with intermediate exposed culmen length (11.6 ± 0.5 mm) and wing chord length similar to the other two migratory subspecies (62.7 ± 1.5 mm). Territory size for A. s. ammolegus was 0.72 ± 0.37 ha, with some variation between sites and among years, possibly indicating variation in habitat quality across spatial and temporal scales. The return rate for A. s. ammolegus males was 39.2%. Nest initiation for A. s. ammolegus was early to mid-July after the monsoons had begun. Domed nests were constructed on the ground, primarily under native bunch grasses, and frequently with a tunnel extending beyond the nest rim, with nest openings oriented north. Clutch size was 3.97 ± 0.68, with no evidence of Brown-headed Cowbird (Molothrus ater) nest parasitism. Extreme climate factors in the arid Southwest may have affected the life history and morphology of A. s. ammolegus as compared to other subspecies, influencing body size and mass, culmen length, breeding phenology, and nest orientation. Other geographic variation occurred in return rates, clutch size, and nest parasitism rates. The baseline data for A. s. ammolegus obtained in this study will inform future taxonomic and ecological studies as well as conservation planning. Comparisons of A. s. ammolegus morphometrics with those of other subspecies will assist field biologists in distinguishing among subspecies where they overlap, especially on wintering grounds.

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA

PubMed Central

Wu, Jiaqi; Kohno, Naoki; Mano, Shuhei; Fukumoto, Yukio; Tanabe, Hideyuki; Hasegawa, Masami; Yonezawa, Takahiro

2015-01-01

The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear. PMID:26406587

Phylogeographic and Demographic Analysis of the Asian Black Bear (Ursus thibetanus) Based on Mitochondrial DNA.

PubMed

Wu, Jiaqi; Kohno, Naoki; Mano, Shuhei; Fukumoto, Yukio; Tanabe, Hideyuki; Hasegawa, Masami; Yonezawa, Takahiro

2015-01-01

The Asian black bear Ursus thibetanus is widely distributed in Asia and is adapted to broad-leaved deciduous forests, playing an important ecological role in the natural environment. Several subspecies of U. thibetanus have been recognized, one of which, the Japanese black bear, is distributed in the Japanese archipelago. Recent molecular phylogeographic studies clarified that this subspecies is genetically distantly related to continental subspecies, suggesting an earlier origin. However, the evolutionary relationship between the Japanese and continental subspecies remained unclear. To understand the evolution of the Asian black bear in relation to geological events such as climatic and transgression-regression cycles, a reliable time estimation is also essential. To address these issues, we determined and analyzed the mt-genome of the Japanese subspecies. This indicates that the Japanese subspecies initially diverged from other Asian black bears in around 1.46Ma. The Northern continental population (northeast China, Russia, Korean peninsula) subsequently evolved, relatively recently, from the Southern continental population (southern China and Southeast Asia). While the Japanese black bear has an early origin, the tMRCAs and the dynamics of population sizes suggest that it dispersed relatively recently in the main Japanese islands: during the late Middle and Late Pleistocene, probably during or soon after the extinction of the brown bear in Honshu in the same period. Our estimation that the population size of the Japanese subspecies increased rapidly during the Late Pleistocene is the first evidential signal of a niche exchange between brown bears and black bears in the Japanese main islands. This interpretation seems plausible but was not corroborated by paleontological evidence that fossil record of the Japanese subspecies limited after the Late Pleistocene. We also report here a new fossil record of the oldest Japanese black bear from the Middle Pleistocene, and it supports our new evolutionary hypothesis of the Japanese black bear.

Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

PubMed Central

Singh, Sujeet Kumar; Mishra, Sudhanshu; Aspi, Jouni; Kvist, Laura; Nigam, Parag; Pandey, Puneet; Sharma, Reeta; Goyal, Surendra Prakash

2015-01-01

The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate “evolutionarily significant unit” (ESU) following the adaptive evolutionary conservation (AEC) concept. PMID:25919139

Homologous Recombination and Xylella fastidiosa Host-Pathogen Associations in South America.

PubMed

Coletta-Filho, Helvécio D; Francisco, Carolina S; Lopes, João R S; Muller, Christiane; Almeida, Rodrigo P P

2017-03-01

Homologous recombination affects the evolution of bacteria such as Xylella fastidiosa, a naturally competent plant pathogen that requires insect vectors for dispersal. This bacterial species is taxonomically divided into subspecies, with phylogenetic clusters within subspecies that are host specific. One subspecies, pauca, is primarily limited to South America, with the exception of recently reported strains in Europe and Costa Rica. Despite the economic importance of X. fastidiosa subsp. pauca in South America, little is known about its genetic diversity. Multilocus sequence typing (MLST) has previously identified six sequence types (ST) among plant samples collected in Brazil (both subsp. pauca and multiplex). Here, we report on a survey of X. fastidiosa genetic diversity (MLST based) performed in six regions in Brazil and two in Argentina, by sampling five different plant species. In addition to the six previously reported ST, seven new subsp. pauca and two new subsp. multiplex ST were identified. The presence of subsp. multiplex in South America is considered to be the consequence of a single introduction from its native range in North America more than 80 years ago. Different phylogenetic approaches clustered the South American ST into four groups, with strains infecting citrus (subsp. pauca); coffee and olive (subsp. pauca); coffee, hibiscus, and plum (subsp. pauca); and plum (subsp. multiplex). In areas where these different genetic clusters occurred sympatrically, we found evidence of homologous recombination in the form of bidirectional allelic exchange between subspp. pauca and multiplex. In fact, the only strain of subsp. pauca isolated from a plum host had an allele that originated from subsp. multiplex. These signatures of bidirectional homologous recombination between endemic and introduced ST indicate that gene flow occurs in short evolutionary time frames in X. fastidiosa, despite the ecological isolation (i.e., host plant species) of genotypes.

Methods for Comparing Nutrients in Beebread Made by Africanized and European Honey Bees and the Effects on Hemolymph Protein Titers

PubMed Central

Degrandi-Hoffman, Gloria; Eckholm, Bruce; Huang, Ming

2015-01-01

Honey bees obtain nutrients from pollen they collect and store in the hive as beebread. We developed methods to control the pollen source that bees collect and convert to beebread by placing colonies in a specially constructed enclosed flight area. Methods were developed to analyze the protein and amino acid composition of the pollen and beebread. We also describe how consumption of the beebread was measured and methods used to determine adult worker bee hemolymph protein titers after feeding on beebread for 4, 7 and 11 days after emergence. Methods were applied to determine if genotype affects the conversion of pollen to beebread and the rate that bees consume and acquire protein from it. Two subspecies (European and Africanized honey bees; EHB and AHB respectively) were provided with the same pollen source. Based on the developed methods, beebread made by both subspecies had lower protein concentrations and pH values than the pollen. In general, amino acid concentrations in beebread made by either EHB or AHB were similar and occurred at higher levels in beebread than in pollen. Both AHB and EHB consumed significantly more of the beebread made by AHB than by EHB. Though EHB and AHB consumed similar amounts of each type of beebread, hemolymph protein concentrations in AHB were higher than in EHB. Differences in protein acquisition between AHB and EHB might reflect environmental adaptations related to the geographic region where each subspecies evolved. These differences could contribute to the successful establishment of AHB populations in the New World because of the effects on brood rearing and colony growth. PMID:25867246

Methods for comparing nutrients in beebread made by Africanized and European honey bees and the effects on hemolymph protein titers.

PubMed

Degrandi-Hoffman, Gloria; Eckholm, Bruce; Huang, Ming

2015-03-17

Honey bees obtain nutrients from pollen they collect and store in the hive as beebread. We developed methods to control the pollen source that bees collect and convert to beebread by placing colonies in a specially constructed enclosed flight area. Methods were developed to analyze the protein and amino acid composition of the pollen and beebread. We also describe how consumption of the beebread was measured and methods used to determine adult worker bee hemolymph protein titers after feeding on beebread for 4, 7 and 11 days after emergence. Methods were applied to determine if genotype affects the conversion of pollen to beebread and the rate that bees consume and acquire protein from it. Two subspecies (European and Africanized honey bees; EHB and AHB respectively) were provided with the same pollen source. Based on the developed methods, beebread made by both subspecies had lower protein concentrations and pH values than the pollen. In general, amino acid concentrations in beebread made by either EHB or AHB were similar and occurred at higher levels in beebread than in pollen. Both AHB and EHB consumed significantly more of the beebread made by AHB than by EHB. Though EHB and AHB consumed similar amounts of each type of beebread, hemolymph protein concentrations in AHB were higher than in EHB. Differences in protein acquisition between AHB and EHB might reflect environmental adaptations related to the geographic region where each subspecies evolved. These differences could contribute to the successful establishment of AHB populations in the New World because of the effects on brood rearing and colony growth.

Symbiotic regulation of plant growth, development and reproduction

USGS Publications Warehouse

Rodriguez, R.J.; Freeman, D. Carl; McArthur, E.D.; Kim, Y.-O.; Redman, R.S.

2009-01-01

The growth and development of rice (Oryzae sativa) seedlings was shown to be regulated epigenetically by a fungal endophyte. In contrast to un-inoculated (nonsymbiotic) plants, endophyte colonized (symbiotic) plants preferentially allocated resources into root growth until root hairs were well established. During that time symbiotic roots expanded at five times the rate observed in nonsymbiotic plants. Endophytes also influenced sexual reproduction of mature big sagebrush (Artemisia tridentata) plants. Two spatially distinct big sagebrush subspecies and their hybrids were symbiotic with unique fungal endophytes, despite being separated by only 380 m distance and 60 m elevation. A double reciprocal transplant experiment of parental and hybrid plants, and soils across the hybrid zone showed that fungal endophytes interact with the soils and different plant genotypes to confer enhanced plant reproduction in soil native to the endophyte and reduced reproduction in soil alien to the endophyte. Moreover, the most prevalent endophyte of the hybrid zone reduced the fitness of both parental subspecies. Because these endophytes are passed to the next generation of plants on seed coats, this interaction provides a selective advantage, habitat specificity, and the means of restricting gene flow, thereby making the hybrid zone stable, narrow and potentially leading to speciation. ?? 2009 Landes Bioscience.

POPULATION GENETICS OF THE MOSQUITO CULEX PIPIENS PALLENS REVEALS SEX-LINKED ASYMMETRIC INTROGRESSION BY CULEX QUINQUEFASCIATUS

PubMed Central

Fonseca, Dina M.; Smith, Julie L.; Kim, Heung-Chol; Mogi, Motoyoshi

2009-01-01

The Culex pipiens complex in Asia includes a temperate subspecies, Culex pipiens pallens, of uncertain taxonomic status. The shape of the male genitalia suggests it is a hybrid between Cx. pipiens and Cx. quinquefasciatus. We studied populations of Cx. p. pallens in Japan, Korea, and China and compared them to local populations of Cx. quinquefasciatus and Cx. p. pipiens. We examined variation in a nuclear intron in the acetylcholinesterase-2 gene [ACE] and eight microsatellite loci. We found a distinct microsatellite signature for Cx. p. pallens indicating restricted gene flow between Eastern and Western populations of Cx. pipiens, supporting the existence of two subspecies. Furthermore, a multilocus genotype analysis revealed current hybridization between Cx. p. pallens and Cx. quinquefasciatus in southern Japan, Republic of Korea, and China but not in Hokkaido, in northern Japan. Surprisingly, however, we found that the sex-linked ACE locus in chromosome I has introgressed asymmetrically through the males such that all male Cx. p. pallens have a copy of the Cx. quinquefasciatus ACE locus. This result highlights some of the potential consequences of hybridization between local and introduced species to disease transmission worldwide. PMID:19584006

Symbiotic regulation of plant growth, development and reproduction

PubMed Central

Freeman, D Carl; McArthur, E Durant; Kim, Yong Ok; Redman, Regina S

2009-01-01

The growth and development of rice (Oryzae sativa) seedlings was shown to be regulated epigenetically by a fungal endophyte. In contrast to un-inoculated (nonsymbiotic) plants, endophyte colonized (symbiotic) plants preferentially allocated resources into root growth until root hairs were well established. During that time symbiotic roots expanded at five times the rate observed in nonsymbiotic plants. Endophytes also influenced sexual reproduction of mature big sagebrush (Artemisia tridentata) plants. Two spatially distinct big sagebrush subspecies and their hybrids were symbiotic with unique fungal endophytes, despite being separated by only 380 m distance and 60 m elevation. A double reciprocal transplant experiment of parental and hybrid plants, and soils across the hybrid zone showed that fungal endophytes interact with the soils and different plant genotypes to confer enhanced plant reproduction in soil native to the endophyte and reduced reproduction in soil alien to the endophyte. Moreover, the most prevalent endophyte of the hybrid zone reduced the fitness of both parental subspecies. Because these endophytes are passed to the next generation of plants on seed coats, this interaction provides a selective advantage, habitat specificity, and the means of restricting gene flow, thereby making the hybrid zone stable, narrow and potentially leading to speciation. PMID:19704912

Review of the reticulated python (Python reticulatus Schneider, 1801) with the description of new subspecies from Indonesia

NASA Astrophysics Data System (ADS)

Auliya, M.; Mausfeld, P.; Schmitz, A.; Böhme, W.

2002-04-01

The geographically widespread Python reticulatus, the world's longest snake, has been largely neglected by taxonomists. Dwarfed individuals from Tanahjampea Island, Indonesia, differ strikingly in morphology. Phylogenetic relationships were analyzed using a 345-bp fragment of the cytochrome b gene for 12 specimens from different populations. Both genetic differences and morphological characters distinctly revealed two taxonomic subunits. The island populations of Tanahjampea and Selayar form two monophyletic lineages, supported by high bootstrap values, with distinct differences in color pattern and scalation. We consider these forms to represent two new subspecies. The Tanahjampea form is genetically related to populations of the Sunda Islands and mainland Southeast Asia, whereas the Selayar form is related to populations of Southwest Sulawesi. We conclude that, due to strong directional surface currents in this region, gene flow between Tanahjampea and Selayar is prevented. Sea-level changes during the Pleistocene probably contributed to the isolation of the two taxa described. Aspects of ecology and conservation status are briefly discussed. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00114-002-0320-4.

Overwintering strategy of wild free-ranging and enclosure-housed Japanese raccoon dogs ( Nyctereutes procyonoides albus)

NASA Astrophysics Data System (ADS)

Kitao, Naoya; Fukui, Daisuke; Hashimoto, Masaaki; Osborne, Peter G.

2009-03-01

The raccoon dog, Nyctereutes procyonoides, is a canid with a passive overwintering strategy in northern Europe. However, the behaviour and physiology of the Japanese subspecies, N. p. albus, which has fewer chromosomes than the other subspecies, remain unknown. We measured body temperature, body composition and blood biochemistry of wild free-ranging and fasted enclosure-housed N. p. albus during boreal winter in Hokkaido, Japan. Body temperature of N. p. albus decreased from 38°C in autumn to 35.9-36.7°C while maintaining a circadian rhythm in late February ( n = 3). A transient 18-36% decrease in resting heart rate occurred when body temperature was low ( n = 2). Despite a 33-45% decrease in body weight due to winter fasting, circulating glucose, total protein and triglyceride levels were maintained ( n = 4). Serum urea nitrogen dropped by 43-45% from autumn to spring, suggesting protein conservation during fasting. The overwintering survival strategy of N. p. albus in central Hokkaido is based upon large changes in seasonal activity patterns, winter denning and communal housing without the large decrease in body temperature that is characteristic of subarctic animals exhibiting hibernation or torpor.

Phylogeny of mitochondrial DNA clones in tassel-eared squirrels Sciurus aberti.

PubMed

Wettstein, P J; Lager, P; Jin, L; States, J; Lamb, T; Chakraborty, R

1994-12-01

The tassel-eared squirrel, Sciurus aberti, includes six subspecies which occupy restrictive and apparently identical habitats in Ponderosa pine forests in the south-western United States and Mexico; the strict habitat requirement of this species is based on dietary requirements which are only fulfilled in these forests. To examine evolutionary relationships among certain subspecies of S. aberti, we obtained estimates of nucleotide diversity within subspecies as well as nucleotide divergence between subspecies using mitochondrial DNA (mtDNA) analysis. Restriction site polymorphisms were identified in samples of the four US subspecies: S. a. aberti (Abert), S. a. kaibabensis (Kaibab), S. a. ferreus (Ferreus), and S. a. chuscensis (Chuska) Fourteen mtDNA clones were resolved that were, with one exception, uniquely subspecific. Dendrograms constructed by neighbour-joining and maximum parsimony methods revealed two major assemblages: (1) an Abert/Kaibab group; and (2) a Ferreus/Chuska group. The Abert vs. Ferreus clones exhibited the greatest net nucleotide divergence, with a lineage separation estimate approximating 572,000 years ago assuming a nucleotide substitution rate of 7.15 x 10(-9)/year/site. Five out of ten Chuska squirrels shared a clone with one Abert sample; the relative sizes of these two populations and their respective ranges as well as their close proximity support the proposal for relatively recent intermixing of Abert and Chuska populations resulting in what appears to be Abert-->Chuska migration. Nucleotide diversity within subspecies ranked as Kaibab < Ferreus < Abert < Chuska; the relatively high diversity for the Chuska sample is based on the apparent introgression of Abert mtDNA. The relative diversity exhibited by Kaibab, Ferreus and Aberti samples corresponds to the range size of the respective subspecies.

Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa).

PubMed

Parsons, Sandra K; Bull, C Michael; Gordon, David M

2015-09-01

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Efficiency of PCR-based methods in discriminating Bifidobacterium longum ssp. longum and Bifidobacterium longum ssp. infantis strains of human origin.

PubMed

Srůtková, Dagmar; Spanova, Alena; Spano, Miroslav; Dráb, Vladimír; Schwarzer, Martin; Kozaková, Hana; Rittich, Bohuslav

2011-10-01

Bifidobacterium longum is considered to play an important role in health maintenance of the human gastrointestinal tract. Probiotic properties of bifidobacterial isolates are strictly strain-dependent and reliable methods for the identification and discrimination of this species at both subspecies and strain levels are thus required. Differentiation between B. longum ssp. longum and B. longum ssp. infantis is difficult due to high genomic similarities. In this study, four molecular-biological methods (species- and subspecies-specific PCRs, random amplified polymorphic DNA (RAPD) method using 5 primers, repetitive sequence-based (rep)-PCR with BOXA1R and (GTG)(5) primers and amplified ribosomal DNA restriction analysis (ARDRA)) and biochemical analysis, were compared for the classification of 30 B. longum strains (28 isolates and 2 collection strains) on subspecies level. Strains originally isolated from the faeces of breast-fed healthy infants (25) and healthy adults (3) showed a high degree of genetic homogeneity by PCR with subspecies-specific primers and rep-PCR. When analysed by RAPD, the strains formed many separate clusters without any potential for subspecies discrimination. These methods together with arabionose/melezitose fermentation analysis clearly differentiated only the collection strains into B. longum ssp. longum and B. longum ssp. infantis at the subspecies level. On the other hand, ARDRA analysis differentiated the strains into the B. longum/infantis subspecies using the cleavage analysis of genus-specific amplicon with just one enzyme, Sau3AI. According to our results the majority of the strains belong to the B. longum ssp. infantis (75%). Therefore we suggest ARDRA using Sau3AI restriction enzyme as the first method of choice for distinguishing between B. longum ssp. longum and B. longum ssp. infantis. Copyright © 2011 Elsevier B.V. All rights reserved.

Clinal variation or validation of a subspecies? A case study of the Graptemys nigrinoda complex (Testudines: Emydidae)

USGS Publications Warehouse

Ennen, Joshua R.; Kalis, Marley E.; Patterson, Adam L.; Kreiser, Brian R.; Lovich, Jeffrey E.; Godwin, James; Qualls, Carl P.

2014-01-01

Widely distributed species often display intraspecific morphological variation due to the abiotic and biotic gradients experienced across their ranges. Historically, in many vertebrate taxa, such as birds and reptiles, these morphological differences within a species were used to delimit subspecies. Graptemys nigrinoda is an aquatic turtle species endemic to the Mobile Bay Basin. Colour pattern and morphological variability were used to describe a subspecies (G. n. delticola) from the lower reaches of the system, although it and the nominate subspecies also reportedly intergrade over a large portion of the range. Other researchers have suggested that these morphological differences merely reflect clinal variation. Our molecular data (mtDNA) did not support the existence of the subspecies, as the haplotypes were differentiated by only a few base pairs and one haplotype was shared between the putative subspecies. While there were significant morphological and pattern differences among putative specimens of G. n. nigrinoda, G. n. delticola and G. n. nigrinoda × delticola, these differences probably represent clinal variation as they were also related to environmental variables [i.e. cumulative drainage area and drainage (categorical)]. Specimens occupying slow-current, high-turbidity river reaches (e.g. the Tensaw River) exhibited greater relative carapace heights and more dark pigmentation, while specimens occupying fast-current, clearer rivers (e.g. the upper Alabama, Cahaba and Tallapoosa rivers) exhibited lower carapace heights and more yellow pigmentation. Given the absence of clear molecular and morphological differences that are related to drainage characteristics, we suggest that there is not sufficient evidence for the recognition of G. n. delticola as a distinct subspecies.

Seed-associated subspecies of the genus Clavibacter are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis.

PubMed

Yasuhara-Bell, Jarred; Alvarez, Anne M

2015-03-01

The genus Clavibacter contains one recognized species, Clavibacter michiganensis. Clavibacter michiganensis is subdivided into subspecies based on host specificity and bacteriological characteristics, with Clavibacter michiganensis subsp. michiganensis causing bacterial canker of tomato. Clavibacter michiganensis subsp. michiganensis is often spread through contaminated seed leading to outbreaks of bacterial canker in tomato production areas worldwide. The frequent occurrence of non-pathogenic Clavibacter michiganensis subsp. michiganensis-like bacteria (CMB) is a concern for seed producers because Clavibacter michiganensis subsp. michiganensis is a quarantine organism and detection of a non-pathogenic variant may result in destruction of an otherwise healthy seed lot. A thorough biological and genetic characterization of these seed-associated CMB strains was performed using standard biochemical tests, cell wall analyses, metabolic profiling using Biolog, and single-gene and multilocus sequence analyses. Combined, these tests revealed two distinct populations of seed-associated members of the genus Clavibacter that differed from each other, as well as from all other described subspecies of Clavibacter michiganensis. DNA-DNA hybridization values are 70 % or higher, justifying placement into the single recognized species, C. michiganensis, but other analyses justify separate subspecies designations. Additionally, strains belonging to the genus Clavibacter isolated from pepper also represent a distinct population and warrant separate subspecies designation. On the basis of these data we propose subspecies designations for separate non-pathogenic subpopulations of Clavibacter michiganensis: Clavibacter michiganensis subsp. californiensis subsp. nov. and Clavibacter michiganensis subsp. chilensis subsp. nov. for seed-associated strains represented by C55(T) ( = ATCC BAA-2691(T) = CFBP 8216(T)) and ZUM3936(T) ( = ATCC BAA-2690(T) = CFBP 8217(T)), respectively. Recognition of separate subspecies is essential for improved international seed testing operations. © 2015 IUMS.

Mitochondrial phylogeography, subspecific taxonomy, and conservation genetics of sandhill cranes (Grus canadensis; Aves: Gruidae)

USGS Publications Warehouse

Rhymer, J.M.; Fain, M.G.; Austin, J.E.; Johnson, D.H.; Krajewski, C.

2001-01-01

Six subspecies of sandhill cranes (Grus canadensis) have been denoted based on perceived morphological and/or breeding locality differences among them. Three subspecies are migratory, breeding from the high arctic in North America and Siberia (lesser sandhill, G. c. canadensis), south through central Canada (Canadian sandhill, G. c. rowani) and into the northern United States (greater sandhill, G. c. tabida). A review of sandhill crane taxonomy indicates that the size variation, on the basis of which these subspecies were named, may be clinal and not diagnostic. The other three subspecies, all listed as endangered or threatened, are non-migratory, resident in Florida (G. c. pratensis), Mississippi (G. c. pulla), and Cuba (G. c. nesiotes). We used analysis of mitochondrial DNA control region (CR) sequences to determine whether haplotypes representing current subspecies show any genetic cohesion or are more consistent with a pattern of clinal variation in morphology. CR sequences indicate that only two highly divergent (5.3%) lineages of sandhill cranes occur in North America: one lineage composed only of arctic-nesting G. c. canadensis, the other of the remaining North American subspecies (we lack data on the Cuban population). The deep split between lineages is consistent with an estimated isolation of approximately 1.5 Mya (mid-Pleistocene), while the distribution of mutational changes within lineages is consistent with an hypothesis of rapid, post-Pleistocene population expansions. No other phylogeographic structuring is concordant with subspecific boundaries, however, analysis of molecular variance indicates that there is significant population genetic differentiation among all subspecies except G. c. tabida and G. c. rowani, which are indistinguishable. We suggest that recognition of the recently named G. c. rowani be abandoned.

Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa)

PubMed Central

Parsons, Sandra K.; Bull, C. Michael

2015-01-01

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment. PMID:26092451

Global Patterns and Drivers of Avian Extinctions at the Species and Subspecies Level

PubMed Central

Szabo, Judit K.; Khwaja, Nyil; Garnett, Stephen T.; Butchart, Stuart H. M.

2012-01-01

Birds have long fascinated scientists and travellers, so their distribution and abundance through time have been better documented than those of other organisms. Many bird species are known to have gone extinct, but information on subspecies extinctions has never been synthesised comprehensively. We reviewed the timing, spatial patterns, trends and causes of avian extinctions on a global scale, identifying 279 ultrataxa (141 monotypic species and 138 subspecies of polytypic species) that have gone extinct since 1500. Species extinctions peaked in the early 20th century, then fell until the mid 20th century, and have subsequently accelerated. However, extinctions of ultrataxa peaked in the second half of the 20th century. This trend reflects a consistent decline in the rate of extinctions on islands since the beginning of the 20th century, but an acceleration in the extinction rate on continents. Most losses (78.7% of species and 63.0% of subspecies) occurred on oceanic islands. Geographic foci of extinctions include the Hawaiian Islands (36 taxa), mainland Australia and islands (29 taxa), the Mascarene Islands (27 taxa), New Zealand (22 taxa) and French Polynesia (19 taxa). The major proximate drivers of extinction for both species and subspecies are invasive alien species (58.2% and 50.7% of species and subspecies, respectively), hunting (52.4% and 18.8%) and agriculture, including non-timber crops and livestock farming (14.9% and 31.9%). In general, the distribution and drivers of subspecific extinctions are similar to those for species extinctions. However, our finding that, when subspecies are considered, the extinction rate has accelerated in recent decades is both novel and alarming. PMID:23056586

[Standard algorithm of molecular typing of Yersinia pestis strains].

PubMed

Eroshenko, G A; Odinokov, G N; Kukleva, L M; Pavlova, A I; Krasnov, Ia M; Shavina, N Iu; Guseva, N P; Vinogradova, N A; Kutyrev, V V

2012-01-01

Development of the standard algorithm of molecular typing of Yersinia pestis that ensures establishing of subspecies, biovar and focus membership of the studied isolate. Determination of the characteristic strain genotypes of plague infectious agent of main and nonmain subspecies from various natural foci of plague of the Russian Federation and the near abroad. Genotyping of 192 natural Y. pestis strains of main and nonmain subspecies was performed by using PCR methods, multilocus sequencing and multilocus analysis of variable tandem repeat number. A standard algorithm of molecular typing of plague infectious agent including several stages of Yersinia pestis differentiation by membership: in main and nonmain subspecies, various biovars of the main subspecies, specific subspecies; natural foci and geographic territories was developed. The algorithm is based on 3 typing methods--PCR, multilocus sequence typing and multilocus analysis of variable tandem repeat number using standard DNA targets--life support genes (terC, ilvN, inv, glpD, napA, rhaS and araC) and 7 loci of variable tandem repeats (ms01, ms04, ms06, ms07, ms46, ms62, ms70). The effectiveness of the developed algorithm is shown on the large number of natural Y. pestis strains. Characteristic sequence types of Y. pestis strains of various subspecies and biovars as well as MLVA7 genotypes of strains from natural foci of plague of the Russian Federation and the near abroad were established. The application of the developed algorithm will increase the effectiveness of epidemiologic monitoring of plague infectious agent, and analysis of epidemics and outbreaks of plague with establishing the source of origin of the strain and routes of introduction of the infection.

Genetic characterization of the Pacific sheath-tailed bat (Emballonura semicaudata rotensis) using mitochondrial DNA sequence data

USGS Publications Warehouse

Oyler-McCance, Sara J.; Valdez, Ernest W.; O'Shea, Thomas J.; Fike, Jennifer A.

2013-01-01

Emballonura semicaudata occurs in the southwestern Pacific and populations on many islands have declined or disappeared. One subspecies (E. semicaudata rotensis) occurs in the Northern Mariana Islands, where it has been extirpated from all but 1 island (Aguiguan). We assessed genetic similarity between the last population of E. s. rotensis and 2 other subspecies, and examined genetic diversity on Aguiguan. We sampled 12 E. s. rotensis, sequenced them at 3 mitochondrial loci, and compared them with published sequences from 2 other subspecies. All 12 E. s. rotensis had identical sequences in each of the 3 regions. Using cytochrome-b (Cytb) data E. s. rotensis was sister to E. s. palauensis in a clade separate from E. s. semicaudata. 12S ribosomal RNA (12S) sequences grouped all E. s. semicaudata in 1 clade with E. s. rotensis in a clade by itself. Genetic distances among the 3 subspecies at Cytb were smallest between E. s. palauensis and E. s. rotensis. Distance between E. s. semicaudata and the other 2 subspecies was not different from the distance between E. s. semicaudata and the full species E. raffrayana. A similar relationship was found using the 12S data. These distances are larger than those typically reported for mammalian subspecies using Cytb sequence and within the range of sister species.

Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa).

PubMed

Wen, Ming; Xie, Munan; He, Lian; Wang, Yushuai; Shi, Suhua; Tang, Tian

2016-12-31

Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA-mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sex-specific differences in the occurrence of Fusobacterium nucleatum subspecies and Fusobacterium periodonticum in the oral cavity

PubMed Central

Henne, Karsten; Schilling, Hildegard; Stoneking, Mark; Conrads, Georg; Horz, Hans-Peter

2018-01-01

The periodontitis-associated species Fusobacterium nucleatum (FN) has been implicated in several extra-oral diseases, including preterm birth and colorectal cancer. Due to its genetic and phenotypic heterogeneity, FN is classified in four subspecies which may differ in their disease potential. Here we compared the prevalence of FN subspecies and the close relative F. periodonticum (FP) via 16S rRNA gene analysis in saliva from 100 healthy individuals (60 females, and 40 males) from eleven countries spanning five continents. By focusing on the most abundant sequence types (i.e. analysis of approximately ten clone sequences each) the average number of FN/FP subspecies per individual differed significantly between females and males, i.e. 2.93 versus 2.5, respectively (P = 0.043). FN subsp. fusiforme/vincentii was significantly more prevalent in females vs males, with 2.85 vs. 1.68 sequence reads per individual, respectively (P = 0.012). A significant age-related difference was observed in females but not in males, i.e. 2.6 subspecies on average in females ≤ 30 years vs. 3.2 in females > 30 (P = 0.0076). Given the link between FN and systemic disorders our findings highlight the need for microbial studies at the subspecies level to further characterize the role of periodontal pathogens in diseases that affect females and males differently, e.g. colorectal cancer. PMID:29755677

Can changes in the distributions of resident birds in China over the past 50 years be attributed to climate change?

PubMed Central

Wu, Jianguo; Zhang, Guobin

2015-01-01

The distributions of bird species have changed over the past 50 years in China. To evaluate whether the changes can be attributed to the changing climate, we analyzed the distributions of 20 subspecies of resident birds in relation to climate change. Long-term records of bird distributions, gray relational analysis, fuzzy-set classification techniques, and attribution methods were used. Among the 20 subspecies of resident birds, the northern limits of over half of the subspecies have shifted northward since the 1960s, and most changes have been related to the thermal index. Driven by climate change over the past 50 years, the suitable range and latitude or longitude of the distribution centers of certain birds have exhibited increased fluctuations. The northern boundaries of over half of the subspecies have shifted northward compared with those in the 1960s. The consistency between the observed and predicted changes in the range limits was quite high for some subspecies. The changes in the northern boundaries or the latitudes of the centers of distribution of nearly half of the subspecies can be attributed to climate change. The results suggest that climate change has affected the distributions of particular birds. The method used to attribute changes in bird distributions to climate change may also be effective for other animals. PMID:26078858

To be or not to be a subspecies: description of Saperda populnea lapponica ssp. n. (Coleoptera, Cerambycidae) developing in downy willow (Salix lapponum L.)

PubMed Central

Wallin, Henrik; Kvamme, Torstein; Bergsten, Johannes

2017-01-01

Abstract A new subspecies of the European cerambycid Saperda populnea (Linnaeus, 1758) is described: Saperda populnea lapponica ssp. n. based on specimens from Scandinavia. The male genitalia characters were examined and found to provide support for this separation, as well as differences in morphology, geographical distribution and bionomy. The preferred host tree for the nominate subspecies S. populnea populnea is Populus tremula L., whereas S. populnea lapponica ssp. n. is considered to be monophagous on Salix lapponum L. DNA sequence data of mitochondrial cytochrome oxidase subunit I (COI) was generated from Scandinavian specimens of S. populnea populnea and specimens representing S. populnea lapponica ssp. n. The two subspecies were not reciprocally monophyletic and genetic distances in COI were small. All synonyms of S. populnea populnea have been considered, and species similar to S. populnea populnea have been examined, and not found to be related to S. populnea lapponica ssp. n. A male lectotype has been designated for each of the two following synonyms: Cerambyx decempunctatus De Geer, 1775, and Saperda salicis Zetterstedt, 1818. The synonymised species from Asia, S. balsamifera (Motshulsky, 1860), is elevated to subspecies: S. populnea balsamifera stat. n. We end with a discussion on the definition of subspecies under the unified species concept. PMID:29187784

Can changes in the distributions of resident birds in China over the past 50 years be attributed to climate change?

PubMed

Wu, Jianguo; Zhang, Guobin

2015-06-01

The distributions of bird species have changed over the past 50 years in China. To evaluate whether the changes can be attributed to the changing climate, we analyzed the distributions of 20 subspecies of resident birds in relation to climate change. Long-term records of bird distributions, gray relational analysis, fuzzy-set classification techniques, and attribution methods were used. Among the 20 subspecies of resident birds, the northern limits of over half of the subspecies have shifted northward since the 1960s, and most changes have been related to the thermal index. Driven by climate change over the past 50 years, the suitable range and latitude or longitude of the distribution centers of certain birds have exhibited increased fluctuations. The northern boundaries of over half of the subspecies have shifted northward compared with those in the 1960s. The consistency between the observed and predicted changes in the range limits was quite high for some subspecies. The changes in the northern boundaries or the latitudes of the centers of distribution of nearly half of the subspecies can be attributed to climate change. The results suggest that climate change has affected the distributions of particular birds. The method used to attribute changes in bird distributions to climate change may also be effective for other animals.

Streptococcal toxic-shock syndrome due to Streptococcus dysgalactiae subspecies equisimilis in breast cancer-related lymphedema: a case report.

PubMed

Sumazaki, Makoto; Saito, Fumi; Ogata, Hideaki; Yoshida, Miho; Kubota, Yorichika; Magoshi, Syunsuke; Kaneko, Hironori

2017-07-14

Breast cancer-related lymphedema often causes cellulitis and is one of the most common complications after breast cancer surgery. Streptococci are the major pathogens underlying such cellulitis. Among the streptococci, the importance of the Lancefield groups C and G is underappreciated; most cases involve Streptococcus dysgalactiae subspecies equisimilis. Despite having a relatively weak toxicity compared with group A streptococci, Streptococcus dysgalactiae subspecies equisimilis is associated with a mortality rate that is as high as that of group A streptococci in cases of invasive infection because Streptococcus dysgalactiae subspecies equisimilis mainly affects elderly individuals who already have various comorbidities. An 83-year-old Japanese woman with breast cancer-related lymphedema in her left upper limb was referred to our hospital with high fever and acute pain with erythema in her left arm. She showed septic shock with disseminated intravascular coagulation. Blood culture showed positive results for Streptococcus dysgalactiae subspecies equisimilis, confirming a diagnosis of streptococcal toxic-shock syndrome. She survived after successful intensive care. To the best of our knowledge, this case represents the first report of Streptococcus dysgalactiae subspecies equisimilis-induced streptococcal toxic-shock syndrome in a patient with breast cancer-related lymphedema. Breast cancer-related lymphedema is a common problem, and we must pay attention to invasive streptococcal soft tissue infections, particularly in elderly patients with chronic disease.

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations.

PubMed

Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

2013-03-01

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03-0.21, while the expected heterozygosity (He) ranged from 0.23-0.47. The genetic distances among populations ranged from 0.03-0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata.

Molecular and morphological differentiation of Secret Toad-headed agama, Phrynocephalus mystaceus, with the description of a new subspecies from Iran (Reptilia, Agamidae).

PubMed

Solovyeva, Evgeniya N; Dunayev, Evgeniy N; Nazarov, Roman A; Mehdi Radjabizadeh; Poyarkov, Nikolay A

2018-01-01

The morphological and genetic variation of a wide-ranging Secret Toad-headed agama, Phrynocephalus mystaceus that inhabits sand deserts of south-eastern Europe, Middle East, Middle Asia, and western China is reviewed. Based on the morphological differences and high divergence in COI (mtDNA) gene sequences a new subspecies of Ph. mystaceus is described from Khorasan Razavi Province in Iran. Partial sequences of COI mtDNA gene of 31 specimens of Ph. mystaceus from 17 localities from all major parts of species range were analyzed. Genetic distances show a deep divergence between Ph. mystaceus khorasanus ssp. n. from Khorasan Razavi Province and all other populations of Ph. mystaceus . The new subspecies can be distinguished from other populations of Ph. mystaceus by a combination of several morphological features. Molecular and morphological analyses do not support the validity of other Ph. mystaceus subspecies described from Middle Asia and Caspian basin. Geographic variations in the Ph. mystaceus species complex and the status of previously described subspecies were discussed.

Immobilization of human papillomavirus DNA probe for surface plasmon resonance imaging

NASA Astrophysics Data System (ADS)

Chong, Xinyuan; Ji, Yanhong; Ma, Suihua; Liu, Le; Liu, Zhiyi; Li, Yao; He, Yonghong; Guo, Jihua

2009-08-01

Human papillomavirus (HPV) is a kind of double-stranded DNA virus whose subspecies have diversity. Near 40 kinds of subspecies can invade reproductive organ and cause some high risk disease, such as cervical carcinoma. In order to detect the type of the subspecies of the HPV DNA, we used the parallel scan spectral surface plasmon resonance (SPR) imaging technique, which is a novel type of two- dimensional bio-sensing method based on surface plasmon resonance and is proposed in our previous work, to study the immobilization of the HPV DNA probes on the gold film. In the experiment, four kinds of the subspecies of the HPV DNA (HPV16, HPV18, HPV31, HPV58) probes are fixed on one gold film, and incubate in the constant temperature condition to get a HPV DNA probe microarray. We use the parallel scan spectral SPR imaging system to detect the reflective indices of the HPV DNA subspecies probes. The benefits of this new approach are high sensitive, label-free, strong specificity and high through-put.

Subspecies identification of captive Orang Utan in Melaka based on D-loop mitochondria DNA

NASA Astrophysics Data System (ADS)

Kamaluddin, Siti Norsyuhada; Yaakop, Salmah; Idris, Wan Mohd Razi; Rovie-Ryan, Jeffrine Japning; Md-Zain, Badrul Munir

2018-04-01

Mitochondrial DNA of Bornean Orang Utan populations suggests that there are three different subspecies (Pongo pygmaeus pygmaeus; Sarawak & Northwest Kalimantan, P. p. wurmbii; Southern West Kalimantan and Central Kalimantan, P. p. morio; East Kalimantan and Sabah). The subspecies of Orang Utans in captivity are difficult to determine through morphological observation. Thus, misidentification by ranger or zoo staffs leads to unwanted consequences especially towards conservation efforts of Orang Utan. The main objective of this study was to identify the subspecies and the geographic origin of 10 Orang Utans in Zoo Melaka and A' Famosa by using partial mitochondrial D-loop gene sequences. DNA of all individuals was extracted from FTA Card. Data analyses were performed using Maximum Parsimony, MP and Neighbor Joining, NJ. Molecular phylogeny analysis revealed that all the samples likely belong to one species of Sumatran Orang Utan (P. abelii) and three different subspecies of Bornean Orang Utans (P. p. pygmaeus, P. p. morio, and P. p. wurmbii). The results obtained in this study indirectly help the management of zoos in term of conservation and visitor's education.

The response of male and female black poplar (Populus nigra L. subspecies betulifolia (Pursh) W. Wettst.) cuttings to different water table depths and sediment types: implications for flow management and river corridor biodiversity

NASA Astrophysics Data System (ADS)

Hughes, Francine M. R.; Barsoum, Nadia; Richards, Keith S.; Winfield, Mark; Hayes, Adrian

2000-10-01

Management of river flows has altered the pattern of flood arrival times and reduced their frequency and duration on many European floodplains. Floodplain tree species depend on floods both to provide new sites for their regeneration and to recharge water tables at various depths in the rooting zone. A reduction in floods is one factor that has led to loss of river corridor biodiversity, with early successional tree species from the Salicaceae being particularly adversely affected. Members of the Salicaceae are dioecious and it is possible that the males and females of these species have measurably different water table requirements, which might lead to spatial segregation of the sexes on a floodplain. This paper describes an investigation that was carried out into the response of male and female black poplar (Populus nigra L. subspecies betulifolia (Pursh) W. Wettst.) to different soil moisture conditions. An experiment was set up on an alluvial island in the River Great Ouse (UK) in which cuttings of male and female black poplar were grown in different sediment types with different water table levels. The experiment was carried out over two field seasons in 1997 and 1998. Results showed that females tended to prefer wetter and more nutrient-rich sites than males but that there was considerable overlap in their requirements. A complementary genetic study showed very little genetic variation in the experimental population, which may also partially explain the relatively low level of variation between the two sexes found in the study. It is suggested that some limited spatial segregation of the sexes does occur in response to soil moisture availability and that river flow management which aims to maintain or increase river corridor biodiversity may need to take this into account.

Mapping Atheroprotective Functions and Related Proteins/Lipoproteins in Size Fractionated Human Plasma.

PubMed

Swertfeger, Debi K; Li, Hailong; Rebholz, Sandra; Zhu, Xiaoting; Shah, Amy S; Davidson, W Sean; Lu, Long J

2017-04-01

HDL has been shown to possess a variety of cardio-protective functions, including removal of excess cholesterol from the periphery, and inhibition of lipoprotein oxidation. It has been proposed that various HDL subparticles exist, each with distinct protein and lipid compositions, which may be responsible for HDL's many functions. We hypothesized that HDL functions will co-migrate with the operational lipoprotein subspecies when separated by gel filtration chromatography. Plasma from 10 healthy male donors was fractionated and the protein composition of the phospholipid containing fractions was analyzed by mass spectrometry (MS). Each fraction was evaluated for its proteomic content as well as its ability to promote cholesterol efflux and protect low density lipoprotein (LDL) from free radical oxidation. For each function, several peaks of activity were identified across the plasma size gradient. Neither cholesterol efflux or LDL antioxidation activity correlated strongly with any single protein across the fractions. However, we identified multiple proteins that had strong correlations (r values >0.7, p < 0.01) with individual peaks of activity. These proteins fell into diverse functional categories, including those traditionally associated with lipid metabolism, as well as alternative complement cascade, innate immunity and clotting cascades and immunoglobulins. Additionally, the phospholipid and cholesterol concentration of the fractions correlated strongly with cholesterol efflux ( r = 0.95 and 0.82 respectively), whereas the total protein content of the fractions correlated best with antioxidant activity across all fractions ( r = 0.746). Furthermore, two previously postulated subspecies (apoA-I, apoA-II and apoC-1; as well as apoA-I, apoC-I and apoJ) were found to have strong correlations with both cholesterol efflux and antioxidation activity. Up till now, very little has been known about how lipoprotein composition mediates functions like cholesterol efflux and antioxidation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Climate adaption and post-fire restoration of a foundational perennial in cold desert: Insights from intraspecific variation in response to weather

USGS Publications Warehouse

Brabec, Martha M.; Germino, Matthew; Richardson, Bryce A.

2017-01-01

1.The loss of foundational but fire-intolerant perennials such as sagebrush due to increases in fire size and frequency in semiarid regions has motivated efforts to restore them, often with mixed or even no success. Seeds of sagebrush Artemisia tridentata and related species must be moved considerable distances from seed source to planting sites, but such transfers have not been guided by an understanding of local climate adaptation. Initial seedling establishment and its response to weather are a key demographic bottleneck that likely varies among subspecies and populations of sagebrush. 2.We assessed differences in survival, growth, and physiological responses of sagebrush to weather among eleven seed sources that varied in subspecies, cytotype, and climates-of-origin over 18 months following outplanting. Diploid or polyploid populations of mountain, Wyoming, and basin big sagebrush (A.tridentata ssp. vaseyana, A.tridentata ssp. wyomingensis, and A.tridentata ssp. tridentata, respectively) were planted onto five burned sites that normally support A.t.wyomingensis with some A.t.tridentata. 3.A.t.wyomingensis had the most growth and survival, and tetraploid populations had greater survival and height than diploids. Seasonal timing of mortality varied among the subspecies/cytotypes and was more closely related to minimum temperatures than water deficit. 4.Temperatures required to induce ice formation were up to 6°C more negative in 4n-A.t.tridentata and A.t.wyomingensis than other subspecies/cytotypes, indicating greater freezing avoidance. In contrast, freezing resistance of photosynthesis varied only 1°C among subspecies/cytotypes, being greatest in A.t.wyomingensis and least in the subspecies normally considered most cold-adapted,A.t.vaseyana. A large spectrum of reliance on freezing-avoidance vs. freezing-tolerance was observed and corresponded to differences in post-fire survivorship among subspecies/cytotypes. Differences in water deficit responses among subspecies/cytotypes were not as strong and did not relate to survival patterns. 5.Synthesis and applications. Low temperature responses are a key axis defining climate adaptation in young sagebrush seedlings and vary more with cytotype than with subspecies, which contrasts with the traditional emphases on (i) water limitations to explain establishment in these deserts, and (ii) subspecies in selecting restoration seedings. These important and novel insights on climate adaptation are critical for seed selection and parameterizing seed transfer zones, and were made possible by incorporating weather data with survival statistics. The survival/weather statistics used here could be applied to any restoration planting or seeding to help elucidate factors contributing to success and enable adaptive management.

Taxonomy of Greater White-fronted Geese (Aves: Anatidae)

USGS Publications Warehouse

Banks, Richard C.

2011-01-01

Five subspecies of the Greater White-fronted Goose, Anser albifrons (Scopoli, 1769), have been named, all on the basis of wintering birds, and up to six subspecies have been recognized. There has been confusion over the application of some names, particularly in North America, because of lack of knowledge of the breeding ranges and type localities, and incorrect taxonomic decisions. There is one clinally varying subspecies in Eurasia, one that breeds in Greenland, and three in North America, one newly named herein.

Population connectivity of endangered Ozark big-eared bats (Corynorhinus townsendii ingens)

USGS Publications Warehouse

Lee, Dana N.; Stark, Richard C.; Puckette, William L.; Hamilton, Meredith J.; Leslie, David M.; Van Den Bussche, Ronald A.

2015-01-01

The endangered Ozark big-eared bat (Corynorhinus townsendii ingens) is restricted to eastern Oklahoma and western and north-central Arkansas, where populations may be susceptible to losses of genetic variation due to patchy distribution of colonies and potentially small effective population sizes. We used mitochondrial D-loop DNA sequences and 15 nuclear microsatellite loci to determine population connectivity among Ozark big-eared bat caves. Assessment of 7 caves revealed a haplotype not detected in a previous study (2002–2003) and gene flow among colonies in eastern Oklahoma. Our data suggest genetic mixing of individuals, which may be occurring at nearby swarming sites in the autumn. Further evidence of limited gene flow between caves in Oklahoma with a cave in Arkansas highlights the importance of including samples from geographically widespread caves to fully understand gene flow in this subspecies. It appears autumn swarming sites and winter hibernacula play an important role in providing opportunities for mating; therefore, we suggest protection of these sites, maternity caves, and surrounding habitat to facilitate gene flow among populations of Ozark big-eared bats.

Genetic relationships among some subspecies of the Peregrine Falcon (Falco peregrinus L.), inferred from mitochondrial DNA control-region sequences

USGS Publications Warehouse

White, Clayton M.; Sonsthagen, Sarah A.; Sage, George K.; Anderson, Clifford; Talbot, Sandra L.

2013-01-01

The ability to successfully colonize and persist in diverse environments likely requires broad morphological and behavioral plasticity and adaptability, and this may partly explain why the Peregrine Falcon (Falco peregrinus) exhibits a large range of morphological characteristics across their global distribution. Regional and local differences within Peregrine Falcons were sufficiently variable that ∼75 subspecies have been described; many were subsumed, and currently 19 are generally recognized. We used sequence information from the control region of the mitochondrial genome to test for concordance between genetic structure and representatives of 12 current subspecies and from two areas where subspecies distributions overlap. Haplotypes were broadly shared among subspecies, and all geographic locales shared a widely distributed common haplotype (FalconCR2). Haplotypes were distributed in a star-like phylogeny, consistent with rapid expansion of a recently derived species, with observed genetic patterns congruent with incomplete lineage sorting and/or differential rates of evolution on morphology and neutral genetic characters. Hierarchical analyses of molecular variance did not uncover genetic partitioning at the continental level, despite strong population-level structure (FST = 0.228). Similar analyses found weak partitioning, albeit significant, among subspecies (FCT = 0.138). All reconstructions placed the hierofalcons' (Gyrfalcon [F. rusticolus] and Saker Falcon [F. cherrug]) haplotypes in a well-supported clade either basal or unresolved with respect to the Peregrine Falcon. In addition, haplotypes representing Taita Falcon (F. fasciinucha) were placed within the Peregrine Falcon clade.

Multi-locus Analyses Reveal Four Giraffe Species Instead of One.

PubMed

Fennessy, Julian; Bidon, Tobias; Reuss, Friederike; Kumar, Vikas; Elkan, Paul; Nilsson, Maria A; Vamberger, Melita; Fritz, Uwe; Janke, Axel

2016-09-26

Traditionally, one giraffe species and up to eleven subspecies have been recognized [1]; however, nine subspecies are commonly accepted [2]. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies on mtDNA have shown reciprocal monophyly of the matrilines among seven of the nine assumed subspecies [3, 4]. Moreover, until now, genetic analyses have not been applied to biparentally inherited sequence data and did not include data from all nine giraffe subspecies. We sampled natural giraffe populations from across their range in Africa, and for the first time individuals from the nominate subspecies, the Nubian giraffe, Giraffa camelopardalis camelopardalis Linnaeus 1758 [5], were included in a genetic analysis. Coalescence-based multi-locus and population genetic analyses identify at least four separate and monophyletic clades, which should be recognized as four distinct giraffe species under the genetic isolation criterion. Analyses of 190 individuals from maternal and biparental markers support these findings and further suggest subsuming Rothschild's giraffe into the Nubian giraffe, as well as Thornicroft's giraffe into the Masai giraffe [6]. A giraffe survey genome produced valuable data from microsatellites, mobile genetic elements, and accurate divergence time estimates. Our findings provide the most inclusive analysis of giraffe relationships to date and show that their genetic complexity has been underestimated, highlighting the need for greater conservation efforts for the world's tallest mammal. Copyright © 2016 Elsevier Ltd. All rights reserved.

77 FR 76706 - Endangered and Threatened Species; Threatened Status for the Arctic, Okhotsk, and Baltic...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-28

...We, NMFS, issue a final determination to list the Arctic (Phoca hispida hispida), Okhotsk (Phoca hispida ochotensis), and Baltic (Phoca hispida botnica) subspecies of the ringed seal (Phoca hispida) as threatened and the Ladoga (Phoca hispida ladogensis) subspecies of the ringed seal as endangered under the Endangered Species Act (ESA). We will propose to designate critical habitat for the Arctic ringed seal in a future rulemaking. To assist us in this effort, we solicit information that may be relevant to the designation of critical habitat for Arctic ringed seals. In light of public comments and upon further review, we are withdrawing the proposed ESA section 4(d) protective regulations for threatened subspecies of the ringed seal because we have determined that such regulations are not necessary or advisable for the conservation of the Arctic, Okhotsk, or Baltic subspecies of the ringed seal at this time. Given their current population sizes, the long-term nature of the primary threat to these subspecies (habitat alteration stemming from climate change), and the existing protections under the Marine Mammal Protection Act, it is unlikely that the proposed protective regulations would provide appreciable conservation benefits.

Genetic divergence between Melipona quadrifasciata Lepeletier (Hymenoptera, Apidae) populations

PubMed Central

Tavares, Mara Garcia; Pietrani, Nathalia Teixeira; de Castro Durvale, Maxwell; Resende, Helder Canto; de Oliveira Campos, Lucio Antonio

2013-01-01

Melipona quadrifasciata is a stingless bee widely found throughout the Brazilian territory, with two recognized subspecies, M. quadrifasciata anthidioides, that exhibits interrupted metasomal stripes, and M. quadrifasciata quadrifasciata, with continuous metasomal stripes. This study aimed to estimate the genetic variability of these subspecies. For this purpose, 127 colonies from 15 Brazilian localities were analyzed, using nine species-specific microsatellite primers. At these loci, the number of alleles ranged from three to 15 (mean: 7.2), and the observed heterozygosity (Ho) ranged from 0.03–0.21, while the expected heterozygosity (He) ranged from 0.23–0.47. The genetic distances among populations ranged from 0.03–0.45. The FST multilocus value (0.23) indicated that the populations sampled were structured, and the clustering analysis showed the formation of two subgroups and two more distant populations. The first group contained the subspecies M. quadrifasciata quadrifasciata, and the other, the subspecies M. quadrifasciata anthidioides and the two M. quadrifasciata populations with continuous metasomal stripes from northern Minas Gerais. These results confirmed that the yellow metasomal stripes alone are not a good means for correctly identifying the different subspecies of M. quadrifasciata. PMID:23569416

Geographical variation in the skeletal morphology of red jungle fowl.

PubMed

Endo, H; Tsunekawa, N; Sonoe, M; Sasaki, Tї; Ogawa, H; Amano, T; Nguyen, T S; Phimphachanhvongsod, V; Kudo, K; Yonezawa, T; Akishinonomiya, F

2017-08-01

1. The skulls and postcranial skeletons of the red jungle fowl (Gallus gallus) were compared osteometrically between the populations from North and South Vietnam, North and Central Laos and Southeast Bangladesh. The populations include the three subspecies of G. g. spadiceus, G. g. gallus and G. g. murghi and were sampled to reveal the geographical morphological variations among populations in G. gallus. 2. The morphometric characteristics of subspecies murghi could be clearly distinguished from those of the other subspecies using a canonical discriminant analysis. However, the size and shape of the skull of the gallus population from South Vietnam were not statistically different from that of the subspecies spadiceus from North Laos. The canonical discriminant scores also clearly indicated that there were morphological similarities in the skulls of the populations from North Laos and South Vietnam. 3. From the results, therefore, it is concluded that red jungle fowls do not exhibit high levels of osteometric variation between geographical localities at least within the Indochinese Peninsula. 4. This contrasts with previous studies which have described these subspecies as having various external morphological differences and have argued that zoogeographical barriers exist between the north and south areas of the Indochinese Peninsula.

Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes.

PubMed

Hvilsom, C; Frandsen, P; Børsting, C; Carlsen, F; Sallé, B; Simonsen, B T; Siegismund, H R

2013-06-01

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.

Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

PubMed Central

Hvilsom, C; Frandsen, P; Børsting, C; Carlsen, F; Sallé, B; Simonsen, B T; Siegismund, H R

2013-01-01

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies. PMID:23531981

Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.

PubMed

Genthner, Fred J; James, Joseph B; Yates, Diane F; Friedman, Stephanie D

2005-07-01

Sources of Enterococcus faecalis isolates from Pensacola Beach, FL. were identified using a library-based approach by applying the statistical method of average similarity to single and composite data sets generated from separate analyses. Data sets included antibiotic resistance analysis (ARA), rep-fingerprints, and fatty acid methyl ester (FAME) profiles. Use of a composite data set composed of ARA and rep-fingerprints, added to the confidence of the identifications. The addition of FAME data to composite data sets did not add to the confidence of identifications. Source identification was performed to better understand risk associated with higher densities of enterococci found in swash zone interstitial water (SZIW) as compared to adjacent bathing water on Pensacola Beach, FL. The "swash zone" is that area of the beach continually washed over by waves. As the potential sources of enterococci were limited in this environment, only two library units, sea gull and human, were constructed. Identification of the beach isolates using a composite data set indicated a sea gull origin. The clonality of the beach isolates suggested that the beach environment selects certain subspecies of E. faecalis.

Investigating Seed Longevity of Big Sagebrush (Artemisia tridentata)

USGS Publications Warehouse

Wijayratne, Upekala C.; Pyke, David A.

2009-01-01

The Intermountain West is dominated by big sagebrush communities (Artemisia tridentata subspecies) that provide habitat and forage for wildlife, prevent erosion, and are economically important to recreation and livestock industries. The two most prominent subspecies of big sagebrush in this region are Wyoming big sagebrush (A. t. ssp. wyomingensis) and mountain big sagebrush (A. t. ssp. vaseyana). Increased understanding of seed bank dynamics will assist with sustainable management and persistence of sagebrush communities. For example, mountain big sagebrush may be subjected to shorter fire return intervals and prescribed fire is a tool used often to rejuvenate stands and reduce tree (Juniperus sp. or Pinus sp.) encroachment into these communities. A persistent seed bank for mountain big sagebrush would be advantageous under these circumstances. Laboratory germination trials indicate that seed dormancy in big sagebrush may be habitat-specific, with collections from colder sites being more dormant. Our objective was to investigate seed longevity of both subspecies by evaluating viability of seeds in the field with a seed retrieval experiment and sampling for seeds in situ. We chose six study sites for each subspecies. These sites were dispersed across eastern Oregon, southern Idaho, northwestern Utah, and eastern Nevada. Ninety-six polyester mesh bags, each containing 100 seeds of a subspecies, were placed at each site during November 2006. Seed bags were placed in three locations: (1) at the soil surface above litter, (2) on the soil surface beneath litter, and (3) 3 cm below the soil surface to determine whether dormancy is affected by continued darkness or environmental conditions. Subsets of seeds were examined in April and November in both 2007 and 2008 to determine seed viability dynamics. Seed bank samples were taken at each site, separated into litter and soil fractions, and assessed for number of germinable seeds in a greenhouse. Community composition data from each site, as well as several environmental variables, were used to evaluate seed viability within the context of habitat variation. Initial viability of seeds used in the seed retrieval experiment was 81 and 92 percent for mountain and Wyoming big sagebrush, respectively. After remaining in the field for 24 months, buried Wyoming big sagebrush seeds retained 28-58 percent viability,11-23 percent of seeds under litter remained viable, and no seeds remained viable on the surface (estimates are 95-percent confidence intervals). The odds of remaining viable did not change from 12 to 24 months. However, after 24 months the odds of seeds beneath litter being viable decreased to 75 percent of the odds of viability at 12 months. Similar to Wyoming big sagebrush, buried seeds of mountain big sagebrush were 31-68 percent viable, seeds under litter retained 10-22 percent of their viability, and no surface seeds were viable after 24 months. Both subspecies of big sagebrush had some portion of seed that remained viable for more than one growing season provided they were buried or under litter. Although seeds beneath litter may remain viable in intact communities, seeds are susceptible to incineration during fires. Nine months after seed dispersal, seed bank estimates for Wyoming big sagebrush ranged from 19 to 49 viable seeds/m2 in litter samples and 19-57 viable seeds/m2 in soil samples (95-percent confidence interval). For mountain big sagebrush, estimates were 27-75 viable seeds/m2 in litter samples and 54-139 viable seeds/m2 in soil (95-percent confidence interval). The number of viable seeds present in the seed bank 9 months after seed dispersal was not significantly different from the number present immediately after seed dispersal. Seed viability was highest in mountain big sagebrush sites for seeds on the surface and beneath litter, but decreased after one season. Buried seeds of both subspecies were in equal abundances and may be insulated from the effect

Climate-driven geographic distribution of the desert locust during recession periods: Subspecies' niche differentiation and relative risks under scenarios of climate change.

PubMed

Meynard, Christine N; Gay, Pierre-Emmanuel; Lecoq, Michel; Foucart, Antoine; Piou, Cyril; Chapuis, Marie-Pierre

2017-11-01

The desert locust is an agricultural pest that is able to switch from a harmless solitarious stage, during recession periods, to swarms of gregarious individuals that disperse long distances and affect areas from western Africa to India during outbreak periods. Large outbreaks have been recorded through centuries, and the Food and Agriculture Organization keeps a long-term, large-scale monitoring survey database in the area. However, there is also a much less known subspecies that occupies a limited area in Southern Africa. We used large-scale climatic and occurrence data of the solitarious phase of each subspecies during recession periods to understand whether both subspecies climatic niches differ from each other, what is the current potential geographical distribution of each subspecies, and how climate change is likely to shift their potential distribution with respect to current conditions. We evaluated whether subspecies are significantly specialized along available climate gradients by using null models of background climatic differences within and between southern and northern ranges and applying niche similarity and niche equivalency tests. The results point to climatic niche conservatism between the two clades. We complemented this analysis with species distribution modeling to characterize current solitarious distributions and forecast potential recession range shifts under two extreme climate change scenarios at the 2050 and 2090 time horizon. Projections suggest that, at a global scale, the northern clade could contract its solitarious recession range, while the southern clade is likely to expand its recession range. However, local expansions were also predicted in the northern clade, in particular in southern and northern margins of the current geographical distribution. In conclusion, monitoring and management practices should remain in place in northern Africa, while in Southern Africa the potential for the subspecies to pose a threat in the future should be investigated more closely. © 2017 John Wiley & Sons Ltd.

76 FR 61825 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To List 29 Mollusk...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-05

...We, the U.S. Fish and Wildlife Service announce a 90-day finding on a petition to list 29 mollusk species and subspecies as threatened or endangered, under the Endangered Species Act of 1973, as amended (Act). Based on our review, we find that the petition presents substantial scientific or commercial information indicating that listing 26 of the 29 species and subspecies may be warranted. Therefore, with the publication of this notice, we are initiating a review of the status of the 26 species and subspecies to determine if listing any of them is warranted. To ensure that the status review is comprehensive, we are requesting scientific and commercial data and other information regarding these 26 species and subspecies. Based on the status review, we will issue a 12-month finding on the petition, which will address whether the petitioned action is warranted, as provided in the Act.

A Revision of the Stylasteridae (Cnidaria, Hydrozoa, Filifera) from Alaska and Adjacent Waters

PubMed Central

Cairns, Stephen D.; Lindner, Alberto

2011-01-01

Abstract The stylasterid fauna of Alaska is revised, consisting of the description or redescription and illustration of 21 species, one additional subspecies, and a geographically adjacent species: Stylaster venustus. Six new species and one new subspecies are described: Errinopora fisheri, Errinopora undulata, Errinopora disticha, Errinopora dichotoma, Stylaster crassiseptum, Stylaster repandus, and Stylaster parageus columbiensis. Four subspecies are raised to species rank: Stylaster leptostylus, Stylaster trachystomus, Stylaster parageus, and Distichopora japonica, and five species and one subspecies were synonymized. A dichotomous key to the Errinopora species and tabular keys to the Errinopora and Alaskan Stylaster species are provided. The focus of the study was on the stylasterids from Alaska, primarily those from the diverse Aleutian Islands, but also including records from British Columbia. This is the first revisionary work on this fauna since the seminal report by Fisher in 1938. PMID:22303109

Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains.

PubMed

Brady, Jeff A; Faske, Jennifer B; Ator, Rebecca A; Castañeda-Gill, Jessica M; Mitchell, Forrest L

2012-04-01

Epidemiological studies of Pierce's disease (PD) can be confounded by a lack of taxonomic detail on the bacterial causative agent, Xylella fastidiosa (Xf). PD in grape is caused by strains of Xylella fastidiosa subsp. fastidiosa, but is not caused by other subspecies of Xf that typically colonize plants other than grape. Detection assays using ELISA and qPCR are effective at detecting and quantifying Xf presence or absence, but offer no information on Xf subspecies or strain identity. Surveying insects or host plants for Xf by current ELISA or qPCR methods provides only presence/absence and quantity information for any and all Xf subspecies, potentially leading to false assessments of disease threat. This study uses a series of adjacent-hybridizing DNA melt analysis probes that are capable of efficiently discriminating Xf subspecies and strain relationships in rapid real-time PCR reactions. Copyright © 2012 Elsevier B.V. All rights reserved.

Geographic variation in ultraviolet reflectance of the wings of the female cabbage butterfly, Pieris rapae.

PubMed

Obara, Yoshiaki; Ozawa, Gaku; Fukano, Yuya

2008-11-01

The British and Japanese subspecies of the cabbage butterfly, Pieris rapae , differ in terms of the UV reflectance of their wings ( Obara and Majerus, 2000 ). We studied the biogeographical distribution of the female cabbage butterfly having wings with UV reflectance around the Eurasian continent, and between Britain and Japan. For the study, we collected specimens from various locations. A gradient in the UV reflectance of the wings appears to exist along the west-east axis; reflectance was higher toward the east and reached a peak in butterflies in Japan. The UV-reflecting Japanese subspecies Pieris rapae crucivora was found exclusively along the east coast of the Eurasian continent. This suggests that the Japanese subspecies has evolved from a continental ancestor, with females having UV-absorbing wings. We discuss the results of our study with regard to the evolution and adaptive significance of UV coloration in the Japanese subspecies.

A revised key to the lizards of Iran (Reptilia: Squamata: Lacertilia).

PubMed

Nasrabadi, Reza; Rastegar-Pouyani, Nasrullah; Rastegar-Pouyani, Eskandar; Gharzi, Ahmad

2017-02-03

During recent years several lizard taxa have been added to the faunal list of Iran. Descriptions and new records are scattered in different publications in the herpetological literature. We here present species accounts for 152 species belonging to 43 genera and 10 families up to July 2016. The most diverse family is Lacertidae with 9 genera, 49 species and 2 subspecies, followed by Gekkonidae with 13 genera and 43 species, Agamidae with 5 genera, 18 species and 4 subspecies, Scincidae with 7 genera, 18 species and 2 subspecies, Phyllodactylidae with 1 genus and 10 species, Sphaerodactylidae with 2 genera and 4 species, Varanidae with 1 genus, 3 species and 2 subspecies, Uromastycidae with 2 genera and 3 species, Eublepharidae with 1 genus and 3 species, and Anguidae with 2 genera and 2 species. The current paper provides a dichotomous key including all of the currently recognized lizards of Iran.

Phylogeography of speciation: allopatric divergence and secondary contact between outcrossing and selfing Clarkia.

PubMed

Pettengill, James B; Moeller, David A

2012-09-01

The origins of hybrid zones between parapatric taxa have been of particular interest for understanding the evolution of reproductive isolation and the geographic context of species divergence. One challenge has been to distinguish between allopatric divergence (followed by secondary contact) versus primary intergradation (parapatric speciation) as alternative divergence histories. Here, we use complementary phylogeographic and population genetic analyses to investigate the recent divergence of two subspecies of Clarkia xantiana and the formation of a hybrid zone within the narrow region of sympatry. We tested alternative phylogeographic models of divergence using approximate Bayesian computation (ABC) and found strong support for a secondary contact model and little support for a model allowing for gene flow throughout the divergence process (i.e. primary intergradation). Two independent methods for inferring the ancestral geography of each subspecies, one based on probabilistic character state reconstructions and the other on palaeo-distribution modelling, also support a model of divergence in allopatry and range expansion leading to secondary contact. The membership of individuals to genetic clusters suggests geographic substructure within each taxon where allopatric and sympatric samples are primarily found in separate clusters. We also observed coincidence and concordance of genetic clines across three types of molecular markers, which suggests that there is a strong barrier to gene flow. Taken together, our results provide evidence for allopatric divergence followed by range expansion leading to secondary contact. The location of refugial populations and the directionality of range expansion are consistent with expectations based on climate change since the last glacial maximum. Our approach also illustrates the utility of combining phylogeographic hypothesis testing with species distribution modelling and fine-scale population genetic analyses for inferring the geography of the divergence process. © 2012 Blackwell Publishing Ltd.

Modeling sandhill crane population dynamics

USGS Publications Warehouse

Johnson, D.H.

1979-01-01

The impact of sport hunting on the Central Flyway population of sandhill cranes (Grus canadensis) has been a subject of controversy for several years. A recent study (Buller 1979) presented new and important information on sandhill crane population dynamics. The present report is intended to incorporate that and other information into a mathematical model for the purpose of assessing the long-range impact of hunting on the population of sandhill cranes.The model is a simple deterministic system that embodies density-dependent rates of survival and recruitment. The model employs four kinds of data: (1) spring population size of sandhill cranes, estimated from aerial surveys to be between 250,000 and 400,000 birds; (2) age composition in fall, estimated for 1974-76 to be 11.3% young; (3) annual harvest of cranes, estimated from a variety of sources to be about 5 to 7% of the spring population; and (4) age composition of harvested cranes, which was difficult to estimate but suggests that immatures were 2 to 4 times as vulnerable to hunting as adults.Because the true nature of sandhill crane population dynamics remains so poorly understood, it was necessary to try numerous (768 in all) combinations of survival and recruitment functions, and focus on the relatively few (37) that yielded population sizes and age structures comparable to those extant in the real population. Hunting was then applied to those simulated populations. In all combinations, hunting resulted in a lower asymptotic crane population, the decline ranging from 5 to 54%. The median decline was 22%, which suggests that a hunted sandhill crane population might be about three-fourths as large as it would be if left unhunted. Results apply to the aggregate of the three subspecies in the Central Flyway; individual subspecies or populations could be affected to a greater or lesser degree.

Temperature, energy metabolism, and adaptive divergence in two oyster subspecies.

PubMed

Li, Ao; Li, Li; Song, Kai; Wang, Wei; Zhang, Guofan

2017-08-01

Comparisons of related species that have diverse spatial distributions provide an efficient way to investigate adaptive evolution in face of increasing global warming. The oyster subjected to high environmental selections is a model species as sessile marine invertebrate. This study aimed to detect the adaptive divergence of energy metabolism in two oyster subspecies from the genus Crassostrea - C. gigas gigas and C. gigas angulata -which are broadly distributed along the northern and southern coasts of China, respectively. We examined the effects of acute thermal stress on energy metabolism in two oyster subspecies after being common gardened for one generation in identical conditions. Thermal responses were assessed by incorporating physiological, molecular, and genomic approaches. Southern oysters exhibited higher fluctuations in metabolic rate, activities of key energetic enzymes, and levels of thermally induced gene expression than northern oysters. For genes involved in energy metabolism, the former displayed higher basal levels of gene expression and a more pronounced downregulation of thermally induced expression, while the later exhibited lower basal levels and a less pronounced downregulation of gene expression. Contrary expression pattern was observed in oxidative stress gene. Besides, energy metabolic tradeoffs were detected in both subspecies. Furthermore, the genetic divergence of a nonsynonymous SNP ( SOD-132 ) and five synonymous SNPs in other genes was identified and validated in these two subspecies, which possibly affects downstream functions and explains the aforementioned phenotypic variations. Our study demonstrates that differentiations in energy metabolism underlie the plasticity of adaptive divergence in two oyster subspecies and suggest C. gigas angulata with moderate phenotypic plasticity has higher adaptive potential to cope with exacerbated global warming.

Comparative Morphological Analysis of the Immature Stages of the Grass Blue Butterflies Zizeeria and Zizina (Lepidoptera: Lycaenidae).

PubMed

Gurung, Raj D; Iwata, Masaki; Hiyama, Atsuki; Taira, Wataru; Degnan, Bernard; Degnan, Sandie; Otaki, Joji M

2016-08-01

The pale grass blue butterfly has been used to assess the biological effects of the Fukushima nuclear accident. Zizeeria and Zizina are two closely related genera of grass blue butterflies that are widely distributed in tropical to temperate Asia, Australia, and Africa, making them suitable environmental indicators for these areas. However, the morphological features of the immature stages have been examined only in fragmentary fashion. Here, we reared Zizeeria maha argia, Zizeeria maha okinawana, Zizeeria karsandra karsandra, Zizina emelina emelina, Zizina otis labradus, and Zizina otis riukuensis using a standard rearing method that was developed for Zizeeria maha, and comparatively identified morphological traits to effectively classify the immature stages of species or subspecies. Morphological information on these and other subspecies including Zizeeria knysna knysna and Zizina otis antanossa from Africa was also collected from literature. The subspecies were all reared successfully. The subspecies all had dorsal nectary and tentacle organs with similar morphology. For the subspecies of Zizeeria maha, only minor morphological differences were noted. Similarly, the subspecies of Zizina otis shared many traits. Most importantly, Zizeeria and Zizina differed in the shape of the sensory hairs that accompany the dorsal nectary organ; Zizeeriahad pointed hairs, and Zizina had blunt or rounded hairs. However, Zizina emelina exhibited several intermediate features between these two genera. Overall, the morphological traits did not completely reflect the conventional systematic relationships. This comparative study describes the efficient rearing of the grass blue butterflies and provides a morphological basis for the use of these species as environmental indicators.

Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA

PubMed Central

2010-01-01

Background Francisella (F.) tularensis is the causative agent of tularemia. Due to its low infectious dose, ease of dissemination and high case fatality rate, F. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. Microbiological diagnosis is cumbersome and time-consuming. Methods for the direct detection of the pathogen (immunofluorescence, PCR) have been developed but are restricted to reference laboratories. Results The complete 23S rRNA genes of representative strains of F. philomiragia and all subspecies of F. tularensis were sequenced. Single nucleotide polymorphisms on species and subspecies level were confirmed by partial amplification and sequencing of 24 additional strains. Fluorescent In Situ Hybridization (FISH) assays were established using species- and subspecies-specific probes. Different FISH protocols allowed the positive identification of all 4 F. philomiragia strains, and more than 40 F. tularensis strains tested. By combination of different probes, it was possible to differentiate the F. tularensis subspecies holarctica, tularensis, mediasiatica and novicida. No cross reactivity with strains of 71 clinically relevant bacterial species was observed. FISH was also successfully applied to detect different F. tularensis strains in infected cells or tissue samples. In blood culture systems spiked with F. tularensis, bacterial cells of different subspecies could be separated within single samples. Conclusion We could show that FISH targeting the 23S rRNA gene is a rapid and versatile method for the identification and differentiation of F. tularensis isolates from both laboratory cultures and clinical samples. PMID:20205957

76 FR 9733 - Endangered and Threatened Species; Proposed Threatened Status for Subspecies of the Ringed Seal

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-22

..., we, NMFS, published a proposed rule to list the Arctic (Phoca hispida hispida), Okhotsk (Phoca... the Arctic, Okhotsk, Baltic, and Ladoga subspecies of the ringed seal as threatened under the ESA...

76 FR 14882 - Endangered and Threatened Species; Proposed Threatened Status for Subspecies of the Ringed Seal

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-18

... rule to list the Arctic (Phoca hispida hispida), Okhotsk (Phoca hispida ochotensis), Baltic (Phoca... rule to list the Arctic, Okhotsk, Baltic, and Ladoga subspecies of the ringed seal as threatened under...

Small population size of Pribilof Rock Sandpipers confirmed through distance-sampling surveys in Alaska

USGS Publications Warehouse

Ruthrauff, Daniel R.; Tibbitts, T. Lee; Gill, Robert E.; Dementyev, Maksim N.; Handel, Colleen M.

2012-01-01

The Rock Sandpiper (Calidris ptilocnemis) is endemic to the Bering Sea region and unique among shorebirds in the North Pacific for wintering at high latitudes. The nominate subspecies, the Pribilof Rock Sandpiper (C. p. ptilocnemis), breeds on four isolated islands in the Bering Sea and appears to spend the winter primarily in Cook Inlet, Alaska. We used a stratified systematic sampling design and line-transect method to survey the entire breeding range of this population during springs 2001-2003. Densities were up to four times higher on the uninhabited and more northerly St. Matthew and Hall islands than on St. Paul and St. George islands, which both have small human settlements and introduced reindeer herds. Differences in density, however, appeared to be more related to differences in vegetation than to anthropogenic factors, raising some concern for prospective effects of climate change. We estimated the total population at 19 832 birds (95% CI 17 853–21 930), ranking it among the smallest of North American shorebird populations. To determine the vulnerability of C. p. ptilocnemis to anthropogenic and stochastic environmental threats, future studies should focus on determining the amount of gene flow among island subpopulations, the full extent of the subspecies' winter range, and the current trajectory of this small population.

Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group

PubMed Central

McDermott, Shannon R.; Noor, Mohamed A. F.

2011-01-01

Taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. Additionally, hybridization may spread alleles that confer barrier traits to other taxa. Historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. Here, we test for allelic variation within Drosophila persimilis and within the Bogota subspecies of D. pseudoobscura at regions previously shown to contribute to hybrid male sterility. We also test whether D. persimilis and the USA subspecies of D. pseudoobscura share an allele conferring hybrid sterility in a D. pseudoobscura bogotana genetic background. All loci conferred similar hybrid sterility effects across all strains studied, though we detected some statistically significant quantitative effect variation among D. persimilis alleles of some hybrid incompatibility QTLs. We also detected allelism between D. persimilis and D. pseudoobscura USA at a 2nd chromosome hybrid sterility QTL. We hypothesize that either the QTL is ancestral in D. persimilis and D. pseudoobscura USA and lost in D. pseudoobscura bogotana, or gene flow transferred the QTL from D. persimilis to D. pseudoobscura USA. We discuss our findings in the context of population features that may contribute to variation in hybrid incompatibilities. PMID:21729052

Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group.

PubMed

McDermott, Shannon R; Noor, Mohamed A F

2011-07-01

Taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. Additionally, hybridization may spread alleles that confer barrier traits to other taxa. Historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. Here, we test for allelic variation within Drosophila persimilis and within the Bogota subspecies of D. pseudoobscura at regions previously shown to contribute to hybrid male sterility. We also test whether D. persimilis and the USA subspecies of D. pseudoobscura share an allele conferring hybrid sterility in a D. pseudoobscura bogotana genetic background. All loci conferred similar hybrid sterility effects across all strains studied, although we detected some statistically significant quantitative effect variation among D. persimilis alleles of some hybrid incompatibility QTLs. We also detected allelism between D. persimilis and D. pseudoobscura USA at a second chromosome hybrid sterility QTL. We hypothesize that either the QTL is ancestral in D. persimilis and D. pseudoobscura USA and lost in D. pseudoobscura bogotana, or gene flow transferred the QTL from D. persimilis to D. pseudoobscura USA. We discuss our findings in the context of population features that may contribute to variation in hybrid incompatibilities. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Further clinical evidence for the existence of neurotoxicity in a population of the European adder (Vipera berus berus) in eastern Hungary: second authenticated case.

PubMed

Malina, Tamás; Babocsay, Gergely; Krecsák, László; Erdész, Csaba

2013-12-01

We report a recent case of common adder (Vipera berus) envenoming causing paralytic signs and symptoms. A 12-year-old girl was bitten by the nominate subspecies of the common adder (V. berus berus) in eastern Hungary on May 2, 2012, 22 km away from where the first neurotoxic V. berus berus envenoming was reported in 2008. The patient developed unambiguous cranial nerve disturbances, manifested in bilateral impairment characterized by oculomotor paralysis with partial ptosis, gaze paresis, and diplopia. Drowsiness and photophobia were her additional symptoms; both occurred only during the first day of envenoming. Until now among viper envenomings in Europe, photophobia has only been documented by victims of Vipera aspis. Supportive and symptomatic treatments were administered during 3 days of hospitalization. Although case reports of V. berus berus envenomings are often published, clinical experience with neurotoxicity by this subspecies still remains rare. Population-based and geographic variation of venom composition in V. berus berus seems to include neurotoxic envenomings in certain populations. This second authenticated case provides new clinical evidence for the existence of a possible neurotoxic V. berus berus population in a restricted geographical area in eastern Hungary. Wilderness Medical Society.

Three new species and one new subspecies of Deserticossus Yakovlev, 2006 (Lepidoptera: Cossidae) from Kazakhstan, Kyrgyzstan and Russia, with world catalogue of the genus.

PubMed

Yakovlev, Roman V; Witt, Thomas J

2017-05-23

Three new species and one new subspecies of the genus Deserticossus Yakovlev, 2006 are described: Deserticossus doroshkini Yakovlev & Witt sp. nov. from eastern Kazakhstan (Tarbagatai Mts.), D. selevini Yakovlev & Witt sp. nov. from southeastern Kazakhstan (Malye Boguty Mts.), D. kamelini Yakovlev & Witt sp. nov. from Kyrgyzstan (Fergana Valley), and D. tsingtauana didenkoi Yakovlev & Witt subsp. nov. from Russia (Southern Siberia, Buryatia Republic). The described species and subspecies of Deserticossus are listed, with notes on the type material, synonymies, and distribution for each taxon.

Eco-geographical diversification of bitter taste receptor genes (TAS2Rs) among subspecies of chimpanzees (Pan troglodytes).

PubMed

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires.

Eco-Geographical Diversification of Bitter Taste Receptor Genes (TAS2Rs) among Subspecies of Chimpanzees (Pan troglodytes)

PubMed Central

Hayakawa, Takashi; Sugawara, Tohru; Go, Yasuhiro; Udono, Toshifumi; Hirai, Hirohisa; Imai, Hiroo

2012-01-01

Chimpanzees (Pan troglodytes) have region-specific difference in dietary repertoires from East to West across tropical Africa. Such differences may result from different genetic backgrounds in addition to cultural variations. We analyzed the sequences of all bitter taste receptor genes (cTAS2Rs) in a total of 59 chimpanzees, including 4 putative subspecies. We identified genetic variations including single-nucleotide variations (SNVs), insertions and deletions (indels), gene-conversion variations, and copy-number variations (CNVs) in cTAS2Rs. Approximately two-thirds of all cTAS2R haplotypes in the amino acid sequence were unique to each subspecies. We analyzed the evolutionary backgrounds of natural selection behind such diversification. Our previous study concluded that diversification of cTAS2Rs in western chimpanzees (P. t. verus) may have resulted from balancing selection. In contrast, the present study found that purifying selection dominates as the evolutionary form of diversification of the so-called human cluster of cTAS2Rs in eastern chimpanzees (P. t. schweinfurthii) and that the other cTAS2Rs were under no obvious selection as a whole. Such marked diversification of cTAS2Rs with different evolutionary backgrounds among subspecies of chimpanzees probably reflects their subspecies-specific dietary repertoires. PMID:22916235

Genetic (RAPD) diversity between Oleria onega agarista and Oleria onega ssp. (Ithomiinae, Nymphalidae, Lepidoptera) in north-eastern Peru.

PubMed

Gallusser, S; Guadagnuolo, R; Rahier, M

2004-05-01

Oleria onega agarista Felder and Felder and Oleria onega ssp. nov. are two Ithomiinae subspecies from north-eastern Peru, that differ for some morphological and behavioural traits. Two contact zones are known near the town of Tarapoto: Ahuashiyacu, where both subspecies cohabit but do not seem to hybridise, and Estero (near the village of Shapaja), where they apparently hybridise. Genetic differences between the two subspecies and between populations were investigated with random amplified polymorphic DNA (RAPD) markers. Both Cluster and Principal Coordinates Analyses (CCoA and PCoA) performed using these data, provided a clear but weak discrimination between the two subspecies. Genetic diversity is much higher within the populations than between them. Moreover, the geographically more distant populations are grouped together by the genetic data. Morphological traits on the wing patterns of the hybrids are intermediary between the two butterflies subspecies, while RAPDs data place them closer to O. onega agarista than to O. onega ssp. The individuals of the Ahuashiyacu population are clearly separated into two groups, those of O. onega ssp. and O. onega agarista, by both morphology and RAPDs data. Moreover, none of those individuals show RAPD similarity with the hybrids, suggesting that hybridisation has not occurred in this population.

A new polytypic species of yellow-shouldered bats, genus Sturnira (Mammalia: Chiroptera: Phyllostomidae), from the Andean and coastal mountain systems of Venezuela and Colombia.

PubMed

Molinari, Jesús; Bustos, Xiomar E; Burneo, Santiago F; Camacho, M Alejandra; Moreno, S Andrea; Fermín, Gustavo

2017-03-13

Sturnira is the most speciose genus of New World leaf-nosed bats (Phyllostomidae). We name Sturnira adrianae, new species. This taxon is born polytypic, divided into a larger subspecies (S. a. adrianae) widespread in the mountains of northern and western Venezuela, and northern Colombia, and a smaller subspecies (S. a. caripana) endemic to the mountains of northeastern Venezuela. The new species inhabits evergreen, deciduous, and cloud forests at mainly medium (1000-2000 m) elevations. It has long been confused with S. ludovici, but it is more closely related to S. oporaphilum. It can be distinguished from other species of Sturnira by genetic data, and based on discrete and continuously varying characters. Within the genus, the new species belongs to a clade that also includes S. oporaphilum, S. ludovici, S. hondurensis, and S. burtonlimi. The larger new subspecies is the largest member of this clade. The two new subspecies are the most sexually dimorphic members of this clade. The smaller new subspecies is restricted to small mountain systems undergoing severe deforestation processes, therefore can be assigned to the Vulnerable (VU) conservation category of the International Union for Conservation of Nature (IUCN).

Inferences from the Historical Distribution of Wild and Domesticated Maize Provide Ecological and Evolutionary Insight

PubMed Central

Hufford, Matthew B.; Martínez-Meyer, Enrique; Gaut, Brandon S.; Eguiarte, Luis E.; Tenaillon, Maud I.

2012-01-01

Background The species Zea mays includes both domesticated maize (ssp. mays) and its closest wild relatives known as the teosintes. While genetic and archaeological studies have provided a well-established history of Z. mays evolution, there is currently minimal description of its current and past distribution. Here, we implemented species distribution modeling using paleoclimatic models of the last interglacial (LI; ∼135,000 BP) and the last glacial maximum (LGM; ∼21,000 BP) to hindcast the distribution of Zea mays subspecies over time and to revisit current knowledge of its phylogeography and evolutionary history. Methodology/Principal Findings Using a large occurrence data set and the distribution modeling MaxEnt algorithm, we obtained robust present and past species distributions of the two widely distributed teosinte subspecies (ssps. parviglumis and mexicana) revealing almost perfect complementarity, stable through time, of their occupied distributions. We also investigated the present distributions of primitive maize landraces, which overlapped but were broader than those of the teosintes. Our data reinforced the idea that little historical gene flow has occurred between teosinte subspecies, but maize has served as a genetic bridge between them. We observed an expansion of teosinte habitat from the LI, consistent with population genetic data. Finally, we identified locations potentially serving as refugia for the teosintes throughout epochs of climate change and sites that should be targeted in future collections. Conclusion/Significance The restricted and highly contrasting ecological niches of the wild teosintes differ substantially from domesticated maize. Variables determining the distributions of these taxa can inform future considerations of local adaptation and the impacts of climate change. Our assessment of the changing distributions of Zea mays taxa over time offers a unique glimpse into the history of maize, highlighting a strategy for the study of domestication that may prove useful for other species. PMID:23155371

Population structure of Salmonella enterica subspecies enterica (subspecies 1)

USDA-ARS?s Scientific Manuscript database

We sequenced and assembled 354 new Salmonella enterica ssp. enterica genomes. These genomes were chosen to maximize genetic diversity, representing at least 100 different serovars and distinct PFGE patterns within these serovars. 119 of the strains were of known antibiotic resistance,...

Hypothesis testing clarifies the systematics of the main Central American Chagas disease vector, Triatoma dimidiata (Latreille, 1811), across its geographic range.

PubMed

Dorn, Patricia L; de la Rúa, Nicholas M; Axen, Heather; Smith, Nicholas; Richards, Bethany R; Charabati, Jirias; Suarez, Julianne; Woods, Adrienne; Pessoa, Rafaela; Monroy, Carlota; Kilpatrick, C William; Stevens, Lori

2016-10-01

The widespread and diverse Triatoma dimidiata is the kissing bug species most important for Chagas disease transmission in Central America and a secondary vector in Mexico and northern South America. Its diversity may contribute to different Chagas disease prevalence in different localities and has led to conflicting systematic hypotheses describing various populations as subspecies or cryptic species. To resolve these conflicting hypotheses, we sequenced a nuclear (internal transcribed spacer 2, ITS-2) and mitochondrial gene (cytochrome b) from an extensive sampling of T. dimidiata across its geographic range. We evaluated the congruence of ITS-2 and cyt b phylogenies and tested the support for the previously proposed subspecies (inferred from ITS-2) by: (1) overlaying the ITS-2 subspecies assignments on a cyt b tree and, (2) assessing the statistical support for a cyt b topology constrained by the subspecies hypothesis. Unconstrained phylogenies inferred from ITS-2 and cyt b are congruent and reveal three clades including two putative cryptic species in addition to T. dimidiata sensu stricto. Neither the cyt b phylogeny nor hypothesis testing support the proposed subspecies inferred from ITS-2. Additionally, the two cryptic species are supported by phylogenies inferred from mitochondrially-encoded genes cytochrome c oxidase I and NADH dehydrogenase 4. In summary, our results reveal two cryptic species. Phylogenetic relationships indicate T. dimidiata sensu stricto is not subdivided into monophyletic clades consistent with subspecies. Based on increased support by hypothesis testing, we propose an updated systematic hypothesis for T. dimidiata based on extensive taxon sampling and analysis of both mitochondrial and nuclear genes. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of hybridization among wild and cultivated Vigna unguiculata subspecies revealed by arbitrarily primed polymerase chain reaction analysis

PubMed Central

Vijaykumar, Archana; Saini, Ajay; Jawali, Narendra

2012-01-01

Background and aims Intra-species hybridization and incompletely homogenized ribosomal RNA repeat units have earlier been reported in 21 accessions of Vigna unguiculata from six subspecies using internal transcribed spacer (ITS) and 5S intergenic spacer (IGS) analyses. However, the relationships among these accessions were not clear from these analyses. We therefore assessed intra-species hybridization in the same set of accessions. Methodology Arbitrarily primed polymerase chain reaction (AP-PCR) analysis was carried out using 12 primers. The PCR products were resolved on agarose gels and the DNA fragments were scored manually. Genetic relationships were inferred by TREECON software using unweighted paired group method with arithmetic averages (UPGMA) cluster analysis evaluated by bootstrapping and compared with previous analyses based on ITS and 5S IGS. Principal results A total of 202 (86 %) fragments were found to be polymorphic and used for generating a genetic distance matrix. Twenty-one V. unguiculata accessions were grouped into three main clusters. The cultivated subspecies (var. unguiculata) and most of its wild progenitors (var. spontanea) were placed in cluster I along with ssp. pubescens and ssp. stenophylla. Whereas var. spontanea were grouped with ssp. alba and ssp. tenuis accessions in cluster II, ssp. alba and ssp. baoulensis were included in cluster III. Close affinities of ssp. unguiculata, ssp. alba and ssp. tenuis suggested inter-subspecies hybridization. Conclusions Multi-locus AP-PCR analysis reveals that intra-species hybridization is prevalent among V. unguiculata subspecies and suggests that grouping of accessions from two different subspecies is not solely due to the similarity in the ITS and 5S IGS regions but also due to other regions of the genome. PMID:22619698

Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

PubMed Central

Loquasto, Joseph R.; Barrangou, Rodolphe; Dudley, Edward G.; Stahl, Buffy; Chen, Chun

2013-01-01

Many strains of Bifidobacterium animalis subsp. lactis are considered health-promoting probiotic microorganisms and are commonly formulated into fermented dairy foods. Analyses of previously sequenced genomes of B. animalis subsp. lactis have revealed little genetic diversity, suggesting that it is a monomorphic subspecies. However, during a multilocus sequence typing survey of Bifidobacterium, it was revealed that B. animalis subsp. lactis ATCC 27673 gave a profile distinct from that of the other strains of the subspecies. As part of an ongoing study designed to understand the genetic diversity of this subspecies, the genome of this strain was sequenced and compared to other sequenced genomes of B. animalis subsp. lactis and B. animalis subsp. animalis. The complete genome of ATCC 27673 was 1,963,012 bp, contained 1,616 genes and 4 rRNA operons, and had a G+C content of 61.55%. Comparative analyses revealed that the genome of ATCC 27673 contained six distinct genomic islands encoding 83 open reading frames not found in other strains of the same subspecies. In four islands, either phage or mobile genetic elements were identified. In island 6, a novel clustered regularly interspaced short palindromic repeat (CRISPR) locus which contained 81 unique spacers was identified. This type I-E CRISPR-cas system differs from the type I-C systems previously identified in this subspecies, representing the first identification of a different system in B. animalis subsp. lactis. This study revealed that ATCC 27673 is a strain of B. animalis subsp. lactis with novel genetic content and suggests that the lack of genetic variability observed is likely due to the repeated sequencing of a limited number of widely distributed commercial strains. PMID:23995933

Mitochondrial DNA variability in Giraffa camelopardalis: consequences for taxonomy, phylogeography and conservation of giraffes in West and central Africa.

PubMed

Hassanin, Alexandre; Ropiquet, Anne; Gourmand, Anne-Laure; Chardonnet, Bertrand; Rigoulet, Jacques

2007-03-01

The giraffe (Giraffa camelopardalis) still survives in four countries of West and central Africa. The populations of Niger and Cameroon are generally assigned to the subspecies peralta, but those of Chad and the Central African Republic are taxonomically problematic, as they are referred to as either peralta, or antiquorum, or congoensis. In this study, a mitochondrial fragment of 1765 nucleotide sites, covering the complete cytochrome b gene, three transfer RNAs and a large part of the control region, was sequenced to assess the relationships between several populations of giraffe. The phylogenetic analyses performed on the 12 identified haplotypes indicate that northern giraffes constitute a natural group, distinct from that of southern giraffes. Surprisingly, the giraffes of Niger are found to be more closely related to the giraffes of East Africa (subspecies rothschildi and reticulata) than to those of central Africa. We conclude therefore that the subspecies peralta contains only the Niger giraffes, whereas the subspecies antiquorum includes all populations living in Cameroon, Chad, the Central African Republic, and southwestern Sudan. We suggest that the ancestor of the Nigerian giraffe dispersed from East to North Africa during the Quaternary period and thereafter migrated to its current Sahelian distribution in West Africa, in response to the development of the Sahara desert. This hypothesis implies that Lake Mega-Chad acted as a strong geographical barrier during the Holocene, preventing any contact between the subspecies peralta and antiquorum. Our study has direct implications for conservation management, as we show that no subspecies peralta is represented in any European zoos, only in Niger, with a small population of less than 200 individuals.

Island Evolution and Systematic Revision of Comoran Snakes: Why and When Subspecies Still Make Sense

PubMed Central

Hawlitschek, Oliver; Nagy, Zoltán T.; Glaw, Frank

2012-01-01

Species delimitation and species concepts have been a matter of debate among biodiversity researchers in the last decades, resulting in integrative taxonomy approaches and the use of modern species concepts, such as the phylogenetic, evolutionary or general lineage species concepts. The discussion of subspecies status and concepts has been addressed much less extensively, with some researchers completely refraining from recognizing subspecies. However, allopatric insular populations that are particularly differentiated have traditionally been assigned subspecies status. We studied the molecular phylogeny and morphology of endemic Comoran tree snakes of the genus Lycodryas. Taking an integrative taxonomic approach, we used the concept of independent lines of evidence to discriminate between evidence for specific and subspecific status. Molecular (mtDNA) and morphological data provided sufficient evidence to support four different taxa within Comoran Lycodryas. In a revision of this group, we propose two species, each with two subspecies. We present a discussion of the strong sexual dichromatism unique to Comoran Lycodryas within the genus and related genera that may be explained by sexual selection in combination with the absence of major predators. Then, we discuss the effects of insular evolution and the “island rule” on morphological traits in Comoran Lycodryas and in Liophidium mayottensis, another snake endemic to the Comoros. The absence of larger-bodied snakes may have promoted an increase in body size and the number of dorsal scale rows in these species. Finally, we discuss the subspecies concept, its applications and its significance for integrative taxonomy and for limiting taxonomic inflation. We emphasize that taxon descriptions should be based on an integrative approach using several lines of evidence, preferably in combination with statements on the underlying species concepts or operational criteria, to increase the objectivity and comparability of descriptions. PMID:22937005

75 FR 46894 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To List the Mexican...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-04

... list the Mexican gray wolf (Canis lupus baileyi) (Mexican wolf) as an endangered subspecies and... subspecies on April 28, 1976 (41 FR 17742). The gray wolf species (Canis lupus) in North America south of...

[Morphological differentiations of the gills of two Gymnocypris przewa-lskii subspecies in different habitats and their functional adaptations].

PubMed

Zhang, Ren-Yi; Li, Guo-Gang; Zhang, Cun-Fang; Tang, Yong-Tao; Zhao, Kai

2013-08-01

Gill morphologies of two subspecies of Gymnocypris przewalskii (Gymnocypris przewalskii przewalskii and Gymnocypris przewalskii ganzihonensis) in different habitats were analyzed under scanning electron microscope. Results indicated that G. p. przewalskii had numerous long and dense-lined gill rakers while G. p. ganzihonensis had few short and scatter-lined gill rakers. There were no significant differences in distance between gill filaments (DBF) and distance gill lamella (DBL) between the two subspecies, but gill filaments of G. p. przewalskii were longer than in G. p. ganzihonensis. The electron microscopic study indicated that the pavement epithelium cells of G. p. przewalskii were well defined as irregular ovals, but were hexagonal in G. p. ganzihonensis. Moreover, G. p. przewalskii had more chloride cells than G. p. ganzihonensis, and mucous cells were only found on the surface of gill filaments of G. p. przewalskii. The morphological differences between the two subspecies of G. przewalskii are adaptations to their corresponding diets and habitats.

Application of a multiplex PCR assay for Campylobacter fetus detection and subspecies differentiation in uncultured samples of aborted bovine fetuses.

PubMed

Iraola, Gregorio; Hernández, Martín; Calleros, Lucía; Paolicchi, Fernando; Silveyra, Silvia; Velilla, Alejandra; Carretto, Luis; Rodríguez, Eliana; Pérez, Ruben

2012-12-01

Campylobacter (C.) fetus (epsilonproteobacteria) is an important veterinary pathogen. This species is currently divided into C. fetus subspecies (subsp.) fetus (Cff) and C. fetus subsp. venerealis (Cfv). Cfv is the causative agent of bovine genital Campylobacteriosis, an infectious disease that leads to severe reproductive problems in cattle worldwide. Cff is a more general pathogen that causes reproductive problems mainly in sheep although cattle can also be affected. Here we describe a multiplex PCR method to detect C. fetus and differentiate between subspecies in a single step. The assay was standardized using cultured strains and successfully used to analyze the abomasal liquid of aborted bovine fetuses without any pre-enrichment step. Results of our assay were completely consistent with those of traditional bacteriological diagnostic methods. Furthermore, the multiplex PCR technique we developed may be easily adopted by any molecular diagnostic laboratory as a complementary tool for detecting C. fetus subspecies and obtaining epidemiological information about abortion events in cattle.

Rattling the border wall: Pathophysiological implications of functional and proteomic venom variation between Mexican and US subspecies of the desert rattlesnake Crotalus scutulatus

PubMed Central

Dobson, James; Yang, Daryl C.; den Brouw, Bianca op; Cochran, Chip; Huynh, Tam; Kurrupu, Sanjaya; Sánchez, Elda E.; Massey, Daniel J.; Baumann, Kate; Jackson, Timothy N.W.; Nouwens, Amanda; Josh, Peter; Neri-Castro, Edgar; Alagón, Alejandro; Hodgson, Wayne C.; Fry, Bryan G.

2017-01-01

While some US populations of the Mohave rattlesnake (Crotalus scutulatus scutulatus) are infamous for being potently neurotoxic, the Mexican subspecies C. s. salvini (Huamantlan rattlesnake) has been largely unstudied beyond crude lethality testing upon mice. In this study we show that at least some populations of this snake are as potently neurotoxic as its northern cousin. Testing of the Mexican antivenom Antivipmyn showed a complete lack of neutralisation for the neurotoxic effects of C. s. salvini venom, while the neurotoxic effects of the US subspecies C. s. scutulatus were time-delayed but ultimately not eliminated. These results document unrecognised potent neurological effects of a Mexican snake and highlight the medical importance of this subspecies, a finding augmented by the ineffectiveness of the Antivipmyn antivenom. These results also influence our understanding of the venom evolution of Crotalus scutulatus, suggesting that neurotoxicity is the ancestral feature of this species, with the US populations which lack neurotoxicity being derived states. PMID:29074260

Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

PubMed

Marcelletti, Simone; Scortichini, Marco

2016-10-01

A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

Immunoreactivity of protein tyrosine phosphatase A (PtpA) in sera from sheep infected with Mycobacterium avium subspecies paratuberculosis.

PubMed

Gurung, Ratna B; Begg, Douglas J; Purdie, Auriol C; Bach, Horacio; Whittington, Richard J

2014-07-15

Evasion of host defense mechanisms and survival inside infected host macrophages are features of pathogenic mycobacteria including Mycobacterium avium subspecies paratuberculosis, the causative agent of Johne's disease in ruminants. Protein tyrosine phosphatase A (PtpA) has been identified as a secreted protein critical for survival of mycobacteria within infected macrophages. The host may mount an immune response to such secreted proteins. In this study, the humoral immune response to purified recombinant M. avium subsp. paratuberculosis PtpA was investigated using sera from a cohort of sheep infected with M. avium subsp. paratuberculosis and compared with uninfected healthy controls. A significantly higher level of reactivity to PtpA was observed in sera collected from M. avium subspecies paratuberculosis infected sheep when compared to those from uninfected healthy controls. PtpA could be a potential candidate antigen for detection of humoral immune responses in sheep infected with M. avium subspecies paratuberculosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Mitochondrial genome of the bullet tuna Auxis rochei from Indo-West Pacific collection provides novel genetic information about two subspecies.

PubMed

Li, Mingming; Guo, Liang; Zhang, Heng; Yang, Sen; Chen, Xinghan; Lin, Haoran; Meng, Zining

2016-09-01

Previously morphological studies supported the division of the bullet tuna into the two subspecies, Auxis rochei rochei and A. rochei eudorax. As a cosmopolitan species, A. rochei rochei ranges in the Indo-West Pacific and Atlantic oceans, while A. rochei eudorax inhabits in eastern Pacific region. Here, we used the HiSeq next-generation sequencing technique to determine the mitochondrial genome (mitogenome) of A. rochei from Indo-West Pacific collection, and then compared our data with mitogenomic sequences of the Atlantic and eastern Pacific retrieved from NCBI database. Results showed the mitogenome of A. rochei from three geographic collections shared the same genes and gene order, similar to typical teleosts. Also, we examined a low level of nucleotide diversity among these mitogenomic sequences. Interestingly, nucleotide diversity of intra-subspecies (Atlantic versus Indo-West) was higher than that of inter-subspecies (Atlantic versus eastern Pacific, Indo-West versus eastern Pacific).

Relative growth, ontogeny, and sexual dimorphism in gorilla (Gorilla gorilla gorilla and G. g. beringei): evolutionary and ecological considerations.

PubMed

Taylor, A B

1997-01-01

Gorillas are the largest and among the most sexually dimorphic of all extant primates. While gorillas have been incorporated in broad-level comparisons among large-bodied hominoids or in studies of the African apes, comparisons between gorilla subspecies have been rare. During the past decade, however, behavioral, morphological, and molecular data from a number of studies have indicated that the western lowland (Gorilla gorilla gorilla) and eastern mountain (Gorilla gorilla beringei) subspecies differ to a greater extent than has been previously believed. In this study I compare patterns of relative growth of the postcranial skeleton to evaluate whether differences between subspecies result from the differential extension of common patterns of relative growth. In addition, patterns of ontogeny and sexual dimorphism are also examined. Linear skeletal dimensions and skeletal weight were obtained for ontogenetic series of male and female G.g. gorilla (n = 315) and G.g. beringei (n = 38). Bivariate and multivariate methods of analysis were used to test for differences in patterns of relative growth, ontogeny, and sexual dimorphism between sexes of each subspecies and in same-sex comparisons between subspecies. Results indicate males and females of both subspecies are ontogenetically scaled for postcranial proportions and that females undergo an earlier skeletal growth spurt compared to males. However, results also indicate that the onset of the female growth spurt occurs at different dental stages in lowland and mountain gorillas and that mountain gorillas may be characterized by higher rates of growth. Finally, data demonstrate lowland and mountain gorilla females do not differ significantly in adult body size, but mountain gorilla males are significantly larger than lowland gorilla males, suggesting mountain gorillas are characterized by a higher degree of sexual dimorphism in body size. Thus, although lowland and mountain gorillas do not appear to have evolved novel adaptations of the postcranium which correlate with differences in locomotor behavior, the present investigation establishes subspecies differences in ontogeny and sexual dimorphism which may be linked with ecological variation. Specifically, these findings are evaluated in the context of risk aversion models which predict higher growth rates and increased levels of sexual dimorphism in extreme folivores.

Adaptive Zones Based on Phenotypic Data for a Newly Recognized Subspecies of Bottlebrush Squirreltail

USDA-ARS?s Scientific Manuscript database

Bottlebrush squirreltail (Elymus elymoides) is a highly ecotypic cool-season grass species that is prized for restoration applications in the Intermountain Region of the western U.S. Three major subspecies (elymoides, californicus, and brevifolius) have traditionally been recognized in this species...

Mycobacterium avium subspecies paratuberculosis recombinant proteins modulate antimycobacterial functions of bovine macrophages

USDA-ARS?s Scientific Manuscript database

It has been shown that Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) activates the Mitogen Activated Protein Kinase (MAPK) p38 pathway, yet it is unclear which components of M. paratuberculosis are involved in the process. Therefore, a set of 42 M. paratuberculosis recombinan...

Weight Loss Surgery in Adolescents Corrects High Density Lipoprotein Subspecies and their Function

PubMed Central

Davidson, W. Sean; Inge, Thomas H.; Sexmith, Hannah; Heink, Anna; Elder, Deborah; Hui, David Y.; Melchior, John T; Kelesidis, Theodoros; Shah, Amy S.

2016-01-01

Background/Objective Youth with obesity have an altered HDL subspecies profile characterized by depletion of large apoE rich HDL particles and an enrichment of small HDL particles. The goal of this study was to test the hypothesis that this atherogenic HDL profile would be reversed and that HDL function would improve with metabolic surgery. Methods Serum samples from adolescent males with severe obesity mean ± SD age of 17.4 ± 1.6 years were studied at baseline and 1 year following vertical sleeve gastrectomy (VSG). HDL subspecies and HDL function were evaluated pre and post VSG using paired t-tests. A lean group of adolescents was included as a reference group. Results After VSG, BMI decreased by 32% and insulin resistance as estimated by HOMA-IR decreased by 75% (both p<0.01). Large apoE rich HDL subspecies increased following VSG (p<0.01) and approached that of lean adolescents despite participants with considerable residual obesity. Additionally, HDL function improved compared to baseline (cholesterol efflux capacity increased by 12%, HDL lipid peroxidation potential decreased by 30%, and HDL anti-oxidative capacity improved by 25%, all p<0.01). Conclusions Metabolic surgery results in a significant improvement in the quantity of large HDL subspecies and HDL function. Our data suggest metabolic surgery may improve cardiovascular risk in adolescents and young adults. PMID:27780977

Cladistic analyses of behavioural variation in wild Pan troglodytes: exploring the chimpanzee culture hypothesis.

PubMed

Lycett, Stephen J; Collard, Mark; McGrew, William C

2009-10-01

Long-term field studies have revealed considerable behavioural differences among groups of wild Pan troglodytes. Here, we report three sets of cladistic analyses that were designed to shed light on issues relating to this interpopulation variation that are of particular relevance to palaeoanthropology. In the first set of analyses, we focused on the proximate cause of the variation. Some researchers have argued that it is cultural, while others have suggested that it is the result of genetic differences. Because the eastern and western subspecies of P. troglodytes are well differentiated genetically while groups within the subspecies are not, we reasoned that if the genetic hypothesis is correct, the phylogenetic signal should be stronger when data from the eastern and western subspecies are analysed together compared to when data from only the eastern subspecies are analysed. Using randomisation procedures, we found that the phylogenetic signal was substantially stronger with in a single subspecies rather than with two. The results of the first sets of analyses, therefore, were inconsistent with the predictions of the genetic hypothesis. The other two sets of analyses built on the results of the first and assumed that the intergroup behavioural variation is cultural in nature. Recent work has shown that, contrary to what anthropologists and archaeologists have long believed, vertical intergroup transmission is often more important than horizontal intergroup transmission in human cultural evolution. In the second set of analyses, we sought to determine how important vertical transmission has been in the evolution of chimpanzee cultural diversity. The first analysis we carried out indicated that the intergroup similarities and differences in behaviour are consistent with the divergence of the western and eastern subspecies, which is what would be expected if vertical intergroup transmission has been the dominant process. In the second analysis, we found that the chimpanzee cultural data are not only comparable to a series of modern human cultural data sets in terms of how tree-like they are, but are also comparable to a series of genetic, anatomical, and behavioural data sets that can be assumed to have been produced by a branching process. Again, this is what would be expected if vertical inter-group transmission has been the dominant process in chimpanzee cultural evolution. Human culture has long been considered to be adaptive, but recent studies have suggested that this needs to be demonstrated rather than assumed. With this in mind, in the third set of analyses we investigated whether chimpanzee culture is adaptive. We found the hypothesis that chimpanzee culture is adaptive was supported by an analysis of data from the Eastern African subspecies, but not by an analysis of data from the eastern and western subspecies. The results of our analyses have implications for the number of subspecies in Pan troglodytes, the relationship between hominin taxa and Palaeolithic industries, and the evolution of hominin cognition and behaviour.

Psychology Baccalaureates at Work: Major Area Subspecializations, Earnings, and Occupations

ERIC Educational Resources Information Center

Rajecki, D. W.

2012-01-01

A Census Bureau national survey identified baccalaureates aged up to 64 years having major area subspecializations labeled "psychology," "industrial/organizational (I/O) psychology," and "counseling psychology." Median 2009 earnings of all such types of baccalaureate psychology alumni were well below the distribution mean of the 153 fields in the…

Pangenome and taxonomic analysis of Salmonella enterica subspecies enterica

USDA-ARS?s Scientific Manuscript database

Salmonella enterica subspecies enterica (S. enterica ssp. I) contains almost all the major pathogens in this genus. We sequenced 354 new S. enterica ssp. I genomes using paired end 100 base reads to ~80-fold coverage. These genomes were chosen to maximize genetic diversity, representing at least 100...

Assessment of Food as a Source of Exposure to Mycobacterium avium Subspecies Paratuberculosis (MAP)

USDA-ARS?s Scientific Manuscript database

The National Advisory Committee on Microbiological Criteria for Foods (NACMCF or Committee) was asked to assess the importance of food as a source of exposure to Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne’s disease, which affects primarily the small intestin...

Characterization of the inflammatory phenotype of Mycobacterium avium subspecies paratuberculosis using a novel cell culture passage model

USDA-ARS?s Scientific Manuscript database

Understanding the pathogenic mechanisms and host responses to Johne’s disease, a chronic enteritis of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), is complicated by the multifaceted disease progression, late-onset host reaction, and the lack of ex vivo infection models ...

Characterizing the molecular variation among American marten (Martes americana) subspecies from Oregon and California

Treesearch

Keith M. Slauson; Bill Zielinski; Karen D. Stone

2009-01-01

We investigated the subspecific identity of a rediscovered population of American martens within the range of a presumed extinct subspecies (Martes americana humboldtensis) by comparing mitochondrial DNA sequence diversity from contemporary individuals within the described ranges of M. a. humboldtensis, nearby ranges of

Detection of Mycobacterium avium subspecies paratuberculosis in Drinking Water and Biofilms Using Quantitative PCR

EPA Science Inventory

Mycobacterium avium subspecies paratuberculosis (MAP) causes Johne’s disease in domestic animals and has been implicated in Crohn’s disease in humans. This bacterium is a slow growing, gram-positive, acid-fast organism which can be difficult to culture from the environment. For ...

NlpC/P60 domain-containing proteins of Mycobacterium avium subspecies paratuberculosis that differentially bind and hydrolyze peptidoglycan

USDA-ARS?s Scientific Manuscript database

While intense research is being conducted to develop faster and more reliable methods for diagnosis of Johne’s disease, there are still significant knowledge gaps concerning the molecular function of Mycobacterium avium subspecies paratuberculosis proteins. Therefore, we describe atomic resolution ...

Isolation of Mycobacterium avium subspecies paratuberculosis Reactive T-cells from Intestinal Biopsies of Crohn's Disease Patients

USDA-ARS?s Scientific Manuscript database

Crohn’s disease (CD) is a chronic granulomatous inflammation of the intestine. The etiology is still unknown. One hypothesis is that CD is caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP) in genetically predisposed individuals. MAP causes a similar disease in ruminants,...

Big sagebrush (Artemisia tridentata) communities: Ecology, importance and restoration potential

Treesearch

Stephen B. Monsen; Nancy L. Shaw

2000-01-01

Big sagebrush (Artemisia tridentata Nutt.) is the most common and widespread sagebrush species in the Intermountain region. Climatic patterns, elevation gradients, soil characteristics and fire are among the factors regulating the distribution of its three major subspecies. Each of these subspecies is considered a topographic climax dominant....

Folate content in fresh-cut vegetable packed products by 96-well microtiter plate microbiological assay.

PubMed

Fajardo, Violeta; Alonso-Aperte, Elena; Varela-Moreiras, Gregorio

2015-02-15

Ready-to-eat foods have nowadays become a significant portion of the diet. Accordingly, nutritional composition of these food categories should be well-known, in particular its folate content. However, there is a broad lack of folate data in food composition tables and databases. A total of 21 fresh-cut vegetable and fruit packed products were analysed for total folate (TF) content using a validated method that relies on the folate-dependent growth of chloramphenicol-resistant Lactobacillus casei subspecies rhamnosus (NCIMB 10463). Mean TF content ranged from 10.0 to 140.9μg/100g for the different matrices on a fresh weight basis. Higher TF quantity, 140.9-70.1μg/100g, was found in spinach, rocket, watercress, chard and broccoli. Significant differences were observed between available data for fresh vegetables and fruits from food composition tables or databases and the analysed results for fresh-cut packed products. Supplied data support the potential of folate-rich fresh-cut ready-to-eat vegetables to increase folate intake significantly. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

PubMed Central

Sousa, Vitor C.; Carneiro, Miguel; Ferrand, Nuno; Hey, Jody

2013-01-01

When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-with-migration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus). PMID:23457232

The systematic status of the Italian wolf Canis lupus

USGS Publications Warehouse

Nowak, Ronald M.; Federoff, Nicholas E.

2002-01-01

In the past, the gray wolf Canis lupus Linnaeus, 1758, has been recognized in Italy as either the subspecies lupus or italicus. It has also been postulated that this population has undergone introgression from the domestic dog Canis familiaris. In order to clarify these issues, multistatistical analyses were made of 10 skull measurements of 34 full grown male wolves from the Italian Peninsula, 91 other male Eurasian wolves, and 20 domestic dogs. The analyses, together with other morphological evidence and prior genetic research, support recognition of the Italian wolf as a separate subspecies, Canis lupus italicus. The same evidence indicates that the subspecies has not been affected through hybridization with the domestic dog.

Characterization of ten microsatellite loci in midget faded rattlesnake (Crotalus oreganus concolor)

USGS Publications Warehouse

Oyler-McCance, Sara J.; Parker, Joshua M.

2010-01-01

Primers for 10 microsatellite loci were developed for midget faded rattlesnake (Crotalus oreganus concolor), a small bodied subspecies of the Western Rattlesnake, which is found in the Colorado Plateau of eastern Utah, western Colorado and southwestern Wyoming. In a screen of 23 individuals from the most northern portion of the subspecies range in southwestern Wyoming, the 10 loci were found to have levels of variability ranging from 4 to 11 alleles. No loci were found to be linked, although one locus revealed significant departures from Hardy–Weinberg equilibrium. These microsatellite loci will be applicable for population genetic analyses, which will ultimately aid in management efforts for this rare subspecies of rattlesnake.

A catalogue of the scaleworm genus Lepidonotus (Polynoidae, Polychaeta) from South America, with two new records for Brazilian waters

PubMed Central

De Assis, José Eriberto; de Brito, Rafael Justino; Christoffersen, Martin Lindsey; de Souza, José Roberto Botelho

2015-01-01

Abstract The genus Lepidonotus is the largest in number of species within the Polynoidae, with more than 70 described species and subspecies. A catalogue of 18 nominal species and subspecies of Lepidonotus from South America is provided, with valid names, synonyms and original citations. Redescriptions and illustrations of two species based on new specimens collected along the littoral of the State of Paraíba, northeastern Brazil are included. Lepidonotus carinulatus and Lepidonotus natalensis are reported for the first time for Brazilian waters. A comparative table of characters for all reported species and subspecies of Lepidonotus from South America is provided. PMID:26668541

Phylogeography of the California mountain kingsnake, Lampropeltis zonata (Colubridae).

PubMed

Rodríguez-Robles, J A; Denardo, D F; Staub, R E

1999-11-01

The phylogeography of the California mountain kingsnake, Lampropeltis zonata, was studied using mitochondrial DNA sequences from specimens belonging to the seven recognized subspecies and collected throughout the range of the species. Maximum parsimony and maximum likelihood methods identified a basal split within L. zonata that corresponds to southern and northern segments of its distribution. The southern clade is composed of populations from southern California (USA) and northern Baja California, Mexico. The northern clade is divided into two subclades, a 'coastal' subclade, consisting of populations from the central coast of California and the southern Sierra Nevada Mountains of eastern California, and a 'northeastern' subclade, mainly comprised of populations north of the San Francisco Bay and from the majority of the Sierra Nevada. We suggest that past inland seaways in southwestern California and the embayment of central California constituted barriers to gene flow that resulted in the two deepest divergences within L. zonata. Throughout its evolutionary history, the northern clade apparently has undergone instances of range contraction, isolation, differentiation, and then expansion and secondary contact. Examination of colour pattern variation in 321 living and preserved specimens indicated that the two main colour pattern characters used to define the subspecies of L. zonata are so variable that they cannot be reliably used to differentiate taxonomic units within this complex, which calls into question the recognition of seven geographical races of this snake.

Is the Karyotype of Neotropical Boid Snakes Really Conserved? Cytotaxonomy, Chromosomal Rearrangements and Karyotype Organization in the Boidae Family

PubMed Central

Viana, Patrik F.; Ribeiro, Leila B.; Souza, George Myller; Chalkidis, Hipócrates de Menezes; Gross, Maria Claudia; Feldberg, Eliana

2016-01-01

Boids are primitive snakes from a basal lineage that is widely distributed in Neotropical region. Many of these species are both morphologically and biogeographically divergent, and the relationship among some species remains uncertain even with evolutionary and phylogenetic studies being proposed for the group. For a better understanding of the evolutionary relationship between these snakes, we cytogenetically analysed 7 species and 3 subspecies of Neotropical snakes from the Boidae family using different chromosomal markers. The karyotypes of Boa constrictor occidentalis, Corallus hortulanus, Eunectes notaeus, Epicrates cenchria and Epicrates assisi are presented here for the first time with the redescriptions of the karyotypes of Boa constrictor constrictor, B. c. amarali, Eunectes murinus and Epicrates crassus. The three subspecies of Boa, two species of Eunectes and three species of Epicrates exhibit 2n = 36 chromosomes. In contrast, C. hortulanus presented a totally different karyotype composition for the Boidae family, showing 2n = 40 chromosomes with a greater number of macrochromosomes. Furthermore, chromosomal mapping of telomeric sequences revealed the presence of interstitial telomeric sites (ITSs) on many chromosomes in addition to the terminal markings on all chromosomes of all taxa analysed, with the exception of E. notaeus. Thus, we demonstrate that the karyotypes of these snakes are not as highly conserved as previously thought. Moreover, we provide an overview of the current cytotaxonomy of the group. PMID:27494409

Is the Karyotype of Neotropical Boid Snakes Really Conserved? Cytotaxonomy, Chromosomal Rearrangements and Karyotype Organization in the Boidae Family.

PubMed

Viana, Patrik F; Ribeiro, Leila B; Souza, George Myller; Chalkidis, Hipócrates de Menezes; Gross, Maria Claudia; Feldberg, Eliana

2016-01-01

Boids are primitive snakes from a basal lineage that is widely distributed in Neotropical region. Many of these species are both morphologically and biogeographically divergent, and the relationship among some species remains uncertain even with evolutionary and phylogenetic studies being proposed for the group. For a better understanding of the evolutionary relationship between these snakes, we cytogenetically analysed 7 species and 3 subspecies of Neotropical snakes from the Boidae family using different chromosomal markers. The karyotypes of Boa constrictor occidentalis, Corallus hortulanus, Eunectes notaeus, Epicrates cenchria and Epicrates assisi are presented here for the first time with the redescriptions of the karyotypes of Boa constrictor constrictor, B. c. amarali, Eunectes murinus and Epicrates crassus. The three subspecies of Boa, two species of Eunectes and three species of Epicrates exhibit 2n = 36 chromosomes. In contrast, C. hortulanus presented a totally different karyotype composition for the Boidae family, showing 2n = 40 chromosomes with a greater number of macrochromosomes. Furthermore, chromosomal mapping of telomeric sequences revealed the presence of interstitial telomeric sites (ITSs) on many chromosomes in addition to the terminal markings on all chromosomes of all taxa analysed, with the exception of E. notaeus. Thus, we demonstrate that the karyotypes of these snakes are not as highly conserved as previously thought. Moreover, we provide an overview of the current cytotaxonomy of the group.

Campylobacter fetus subspecies contain conserved type IV secretion systems on multiple genomic islands and plasmids

USDA-ARS?s Scientific Manuscript database

The features contributing to the differences in pathogenicity of the C. fetus subspecies are unknown. Putative factors involved in pathogenesis are located in genomic islands that encode type IV secretion system (T4SS) and fic-domain (filamentation induced by cyclic AMP) proteins. In the genomes of ...

Spectrophotometry of Artemisia tridentata to quantitatively determine subspecies

Treesearch

Bryce A. Richardson; Alicia A. Boyd; Tanner Tobiasson; Matthew J. Germino

2018-01-01

Ecological restoration is predicated on our abilities to discern plant taxa. Taxonomic identification is a first step in ensuring that plants are appropriately adapted to the site. An example of the need to identify taxonomic differences comes from big sagebrush (Artemisia tridentata). This species is composed of three predominant subspecies occupying distinct...

A list of oribatid mites (Acari, Oribatida) of Vietnam

PubMed Central

Ermilov, Sergey G.

2015-01-01

Abstract A species list of identified oribatid mite taxa (Acari, Oribatida) in the fauna of Vietnam is provided. During 1967–2015, a total of 535 species/subspecies from 222 genera and 81 families was registered. Of these, 194 species/subspecies were described as new for science from Vietnam. PMID:26798306

50 CFR 14.53 - Detention and refusal of clearance.

Code of Federal Regulations, 2011 CFR

2011-10-01

... origin of the wildlife has not been established (in such cases, the burden is upon the owner, importer, exporter, consignor, or consignee to establish such identity by scientific name to the species level or, if any subspecies is protected by the laws of this country or the country of origin to the subspecies...

50 CFR 14.53 - Detention and refusal of clearance.

Code of Federal Regulations, 2012 CFR

2012-10-01

... origin of the wildlife has not been established (in such cases, the burden is upon the owner, importer, exporter, consignor, or consignee to establish such identity by scientific name to the species level or, if any subspecies is protected by the laws of this country or the country of origin to the subspecies...

50 CFR 14.53 - Detention and refusal of clearance.

Code of Federal Regulations, 2013 CFR

2013-10-01

... origin of the wildlife has not been established (in such cases, the burden is upon the owner, importer, exporter, consignor, or consignee to establish such identity by scientific name to the species level or, if any subspecies is protected by the laws of this country or the country of origin to the subspecies...

50 CFR 14.53 - Detention and refusal of clearance.

Code of Federal Regulations, 2014 CFR

2014-10-01

... origin of the wildlife has not been established (in such cases, the burden is upon the owner, importer, exporter, consignor, or consignee to establish such identity by scientific name to the species level or, if any subspecies is protected by the laws of this country or the country of origin to the subspecies...

Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

USDA-ARS?s Scientific Manuscript database

Genetic variation was quantified at 29 polymorphic microsatellite DNA loci in nine herds of plains bison (Bison bison bison), three herds of wood bison (B. b. athabascae), fourteen breeds of taurine cattle (Bos taurus taurus), and two breeds of indicine cattle (Bos taurus indicus). Genetic distances...

Genetic variation in bison (bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

USDA-ARS?s Scientific Manuscript database

Genetic variation was quantified at 29 polymorphic microsatellite DNA loci in nine herds of plains bison (Bison bison bison), three herds of wood bison (B.b. athabascae), fourteen breeds of taurine cattle (Bos Taurus Taurus), and two breeds of indicine cattle (Bos Taurus indicus). Genetic distances,...

Two subspecies and a hybrid of big sagebrush: Comparison of respiration and growth characteristics

Treesearch

L. D. Hansen; L. K. Farnsworth; N. K. Itoga; A. Nicholson; H. L. Summers; M. C. Whitsitt; E. D. McArthur

2008-01-01

Environmental temperatures and growth and respiratory characteristics of natural populations of two subspecies and a hybrid of sagebrush (Artemisia tridentata) that grow on a single hillside were measured to test a hypothesis that adaptation to microclimate temperature patterns restricts these taxa to their native locations and that plant-endophyte...

Multivariate analysis of morphological diversity among closely related Daucus species and subspecies in Tunisia

USDA-ARS?s Scientific Manuscript database

The genus Daucus includes about 20-25 species worldwide. Northern Africa represents a major center of diversity of Daucus, with Tunisia thought to contain 11 species and seven subspecies. We assessed morphological diversity from a Daucus germplasm collection of 103 accessions at the National Gene Ba...

A morphological review of subspecies of the Asian box turtle, Cuora amboinensis (Testudines, Geomydidae)

USGS Publications Warehouse

Ernst, Carl H.; Laemmerzahl, Arndt F.; Lovich, Jeffrey E.

2016-01-01

The turtle Cuora amboinensis has an extensive distribution covering most of southern mainland Asia, Indonesia, and extending to the Philippine Islands. Unlike many species, C. amboinensis occurs on both sides of Wallace's Line separating Asian and Australian flora and fauna. Four subspecies are currently recognized; Cuora a. kamaroma (southern continental Asia, Java and the northern Philippines [introduced]), C. a. lineata (Kachin Province, Myanmar [Burma] and adjacent Yunnan Province, China), C. a. couro (Sumatra, Java, Sumbawa, and adjacent smaller Indonesian islands); and C. a. amboinensis (Moluccas, Sulawesi, Philippines). Five pattern and 33 morphological characters were examined for variation in 691 individuals from throughout the species' range. Our analyses suggest that only two presently recognized subspecies are valid: amboinensis andkamaroma. Neither couro nor lineata are supported by our analysis. We recommend that C. a. couroshould be synonymized with the species C. amboinensis and C. a. lineata with the subspecies C. a. kamaroma.

Genetic variation in the midcontinental population of sandhill cranes, Grus canadensis.

PubMed

Petersen, Jessica L; Bischof, Richard; Krapu, Gary L; Szalanski, Allen L

2003-02-01

Three subspecies of sandhill crane (Grus canadensis) are recognized in the Midcontinental population, the lesser (Grus c. canadensis), Canadian (G. c. rowani), and greater (G. c. tabida). Blood samples collected on the population's primary spring staging area in Nebraska, U.S.A., were used to resolve the genetic relationship among these subspecies. Phylogenetic analysis of 27 G. canadensis, by DNA sequencing of a 675 bp region of the mtDNA, supports the subspecies designations of G. c. canadensis and G. c. tabida. G. c. rowani individuals were intermediate with each of the other two subspecies. Genetic divergence ranged from 6.5 to 14.5% between G. c. canadensis and G. c. tabida, 0.5 to 6.6% within G. c. canadensis, and 0.1 to 6.0% within G. c. tabida. Sufficient DNA for analysis was obtained from shed feathers indicating a source of genetic material that does not require the capture or sacrifice of the birds. Other genetic markers and methods, including satellite telemetry, are required for obtaining detailed information on crane distributions as needed to establish effective management units for the MCP.

Phylogeny and genetic structure of Erophaca (Leguminosae), a East-West Mediterranean disjunct genus from the Tertiary.

PubMed

Casimiro-Soriguer, Ramón; Talavera, María; Balao, Francisco; Terrab, Anass; Herrera, Javier; Talavera, Salvador

2010-07-01

The genus Erophaca comprises a single herbaceous perennial species with two subspecies distributed at opposite ends of the Mediterranean region. We used nrDNA ITS to investigate the phylogeny of the genus, and AFLP markers (9 primers, 20 populations) to establish the genetic relationship between subspecies, and among populations at each side of the Gibraltar Strait. According to nrDNA ITS, Erophaca is monophyletic, old (Miocene), and sister to the Astragalean clade. Life form attributes and molecular clock estimates suggest that Erophaca is one of the many Tertiary relicts that form part of the present Mediterranean flora. Within the occidental subspecies, European plants are clearly derived from North-African populations (Morocco) which, despite being rare on a regional scale, present the highest genetic diversity (as estimated by private and rare fragment numbers). In general, genetic diversity decreased with increasing distance from Morocco. AFLP and nrDNA ITS markers evidenced that the Eastern and the Western subspecies are genetically distinct. Possible causes for their disjunct distribution are discussed. Copyright 2010 Elsevier Inc. All rights reserved.

Rattling the border wall: Pathophysiological implications of functional and proteomic venom variation between Mexican and US subspecies of the desert rattlesnake Crotalus scutulatus.

PubMed

Dobson, James; Yang, Daryl C; Op den Brouw, Bianca; Cochran, Chip; Huynh, Tam; Kurrupu, Sanjaya; Sánchez, Elda E; Massey, Daniel J; Baumann, Kate; Jackson, Timothy N W; Nouwens, Amanda; Josh, Peter; Neri-Castro, Edgar; Alagón, Alejandro; Hodgson, Wayne C; Fry, Bryan G

2018-02-01

While some US populations of the Mohave rattlesnake (Crotalus scutulatus scutulatus) are infamous for being potently neurotoxic, the Mexican subspecies C. s. salvini (Huamantlan rattlesnake) has been largely unstudied beyond crude lethality testing upon mice. In this study we show that at least some populations of this snake are as potently neurotoxic as its northern cousin. Testing of the Mexican antivenom Antivipmyn showed a complete lack of neutralisation for the neurotoxic effects of C. s. salvini venom, while the neurotoxic effects of the US subspecies C. s. scutulatus were time-delayed but ultimately not eliminated. These results document unrecognised potent neurological effects of a Mexican snake and highlight the medical importance of this subspecies, a finding augmented by the ineffectiveness of the Antivipmyn antivenom. These results also influence our understanding of the venom evolution of Crotalus scutulatus, suggesting that neurotoxicity is the ancestral feature of this species, with the US populations which lack neurotoxicity being derived states. Copyright © 2017 Elsevier Inc. All rights reserved.

Activation of macrophages and interference with CD4+ T-cell stimulation by Mycobacterium avium subspecies paratuberculosis and Mycobacterium avium subspecies avium

PubMed Central

Lage, Susanne Zur; Goethe, Ralph; Darji, Ayub; Valentin-Weigand, Peter; Weiss, Siegfried

2003-01-01

Mycobacterium avium subspecies paratuberculosis (M. ptb) and M. avium subspecies avium (M. avium) are closely related but exhibit significant differences in their interaction with the host immune system. The macrophage line, J774, was infected with M. ptb and M. avium and analysed for cytokine production and stimulatory capacity towards antigen-specific CD4+ T cells. Under all conditions J774 cells were activated to produce proinflammatory cytokines. No influence on the expression of major histocompatibility complex (MHC) class II, intracellular adhesion molecule-1 (ICAM-1), B7.1, B7.2 or CD40 was found. However, the antigen-specific stimulatory capacity of J774 cells for a CD4+ T-cell line was significantly inhibited after infection with M. ptb, but not with M. avium. When a T-cell hybridoma expressing a T-cell receptor identical to that of the T-cell line was used, this inhibition was not observed, suggesting that costimulation which is essential for the CD4+ T-cell line is influenced by the pathogenic bacterium M. ptb. PMID:12519304

The New World whirligig beetles of the genus Dineutus Macleay, 1825 (Coleoptera, Gyrinidae, Gyrininae, Dineutini)

PubMed Central

Gustafson, Grey T.; Miller, Kelly B.

2015-01-01

Abstract All New World members of the whirligig beetle genus Dineutus Macleay, 1825 are treated. The New World Dineutus are found to be composed of 18 species and 6 subspecies: one species, Dineutus mexicanus Ochs, 1925, stat. n. is elevated from subspecies to species rank, and the subspecies Dineutus carolinus mutchleri Ochs, 1925, syn. n. is synonymized here with the typical form. Lectotypes are designated for Dineutus discolor Aubé, 1838, Dineutes metallicus Aubé, 1838, Dineutus solitarius Aubé, 1838, Dineutes analis Régimbart, 1883, and Gyrinus longimanus Olivier, 1795. Each taxonomic unit is provided with a taxonomic history, type locality, diagnosis, distribution, habitat information, and a discussion section. The aedeagus and male mesotarsal claws are illustrated, and dorsal and ventral habitus images of both sexes, for each species and subspecies are provided. General distribution maps are provided for all taxonimc units. A key to the genera of New World Gyrinidae, as well as all the New World Dineutus species is provided. General Dineutus anatomy as well as a clarification of homology and anatomical terms is included. PMID:25685002

Salmonella diversity associated with wild reptiles and amphibians in Spain.

PubMed

Briones, Víctor; Téllez, Sonia; Goyache, Joaquín; Ballesteros, Cristina; del Pilar Lanzarot, María; Domínguez, Lucas; Fernández-Garayzábal, José F

2004-08-01

During the spring and summer of 2001, faeces from 166 wild reptiles (94 individuals) and amphibians (72 individuals) from 21 different species found in central Spain were examined for the presence of Salmonella. Thirty-nine reptiles (41.5%) yielded 48 Salmonella isolates, whereas all the amphibians examined were negative. Subspecies Salmonella enterica enterica (I) accounted for up to 50% of isolates. Fourteen isolates (29.2%) belonged to subspecies diarizonae (IIIb), six isolates (12.5%) to subspecies salamae (II), and four isolates (8.3%) to subspecies arizonae (IIIa). Twenty-seven different serotypes were identified. Serotypes Anatum (12.5%), Herzliya (8.3%), Abony, 18:l,v:z, 9,12:z29:1,5 and 38:z10:z53 (6.2%/each) were the most frequently isolated. A high percentage (39.6%) of isolates belonged to serotypes previously associated with environmental sources. Also, 37.5% of isolates belonged to serotypes which had been related to human cases of salmonellosis. From these data, it is concluded that wild reptiles, but apparently not amphibians, may represent an important reservoir of Salmonella in nature and have potential implications for public health.

[Determination of genetic bases of auxotrophy in Yersinia pestis ssp. caucasica strains].

PubMed

Odinokov, G N; Eroshenko, G A; Kukleva, L M; Shavina, N Iu; Krasnov, Ia M; Kutyrev, V V

2012-04-01

Based on the results of computer analysis of nucleotide sequences in strains Yersinia pestis and Y. pseudotuberculosis recorded in the files of NCBI GenBank database, differences between genes argA, aroG, aroF, thiH, and thiG of strain Pestoides F (subspecies caucasica) were found, compared to other strains of plaque agent and pseudotuberculosis microbe. Using PCR with calculated primers and the method of sequence analysis, the structure of variable regions of these genes was studied in 96 natural Y. pestis and Y. pseudotuberculosis strains. It was shown that all examined strains of subspecies caucasica, unlike strains of plague-causing agent of other subspecies and pseudotubercolosis microbe, had identical mutations in genes argA (integration of the insertion sequence IS100), aroG (insertion of ten nucleotides), aroF (inserion of IS100), thiH (insertion of nucleotide T), and thiG (deletion of 13 nucleotides). These mutations are the reason for the absence in strains belonging to this subspecies of the ability to synthesize arginine, phenylalanine, tyrosine, and vitamin B1 (thiamine), and cause their auxotrophy for these growth factors.

Interest in Providing Multiple Sclerosis Care and Subspecializing in Multiple Sclerosis Among Neurology Residents

PubMed Central

Teixeira-Poit, Stephanie; Kane, Heather L.; Frost, A. Corey; Keating, Michael; Olmsted, Murrey

2014-01-01

Background: Although detailed knowledge regarding treatment options for multiple sclerosis (MS) patients is largely limited to neurologists, shortages in the neurologist workforce, including MS subspecialists, are predicted. Thus, MS patients may have difficulties in gaining access to appropriate care. No systematic evaluation has yet been performed of the number of neurology residents planning to pursue MS subspecialization. This study identifies factors affecting interest in providing MS patient care or MS subspecialization among current neurology residents. Methods: We randomly selected half of all Accreditation Council of Graduate Medical Education–certified neurology residency programs in the continental United States to receive the neurology resident survey. Completed surveys were received from 218 residents. Results: Residents were significantly more likely to have increased interest in MS care when they participated in MS research, were interested in teaching, and indicated that the “ability to improve patient outcomes and quality of life” was a positive factor influencing their desire to provide MS patient care. Residents who were interested in providing MS care, interested in teaching, and indicated that “research opportunities” was a positive factor for providing MS patient care were significantly more likely to express interest in MS subspecialization. Conclusions: Increasing opportunities to interact with MS patients, learn about MS care, and participate in MS research may increase interest in MS care and subspecialization among neurology residents. Opportunities to educate residents regarding MS patient care may affect residents’ attitudes. PMID:24688352

Planning tiger recovery: Understanding intraspecific variation for effective conservation

PubMed Central

Wilting, Andreas; Courtiol, Alexandre; Christiansen, Per; Niedballa, Jürgen; Scharf, Anne K.; Orlando, Ludovic; Balkenhol, Niko; Hofer, Heribert; Kramer-Schadt, Stephanie; Fickel, Jörns; Kitchener, Andrew C.

2015-01-01

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide. PMID:26601191

Identification of Francisella tularensis by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry: fast, reliable, robust, and cost-effective differentiation on species and subspecies levels.

PubMed

Seibold, E; Maier, T; Kostrzewa, M; Zeman, E; Splettstoesser, W

2010-04-01

Francisella tularensis, the causative agent of tularemia, is a potential agent of bioterrorism. The phenotypic discrimination of closely related, but differently virulent, Francisella tularensis subspecies with phenotyping methods is difficult and time-consuming, often producing ambiguous results. As a fast and simple alternative, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was applied to 50 different strains of the genus Francisella to assess its ability to identify and discriminate between strains according to their designated species and subspecies. Reference spectra from five representative strains of Francisella philomiragia, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. holarctica, Francisella tularensis subsp. mediasiatica, and Francisella tularensis subsp. novicida were established and evaluated for their capability to correctly identify Francisella species and subspecies by matching a collection of spectra from 45 blind-coded Francisella strains against a database containing the five reference spectra and 3,287 spectra from other microorganisms. As a reference method for identification of strains from the genus Francisella, 23S rRNA gene sequencing was used. All strains were correctly identified, with both methods showing perfect agreement at the species level as well as at the subspecies level. The identification of Francisella strains by MALDI-TOF MS and subsequent database matching was reproducible using biological replicates, different culture media, different cultivation times, different serial in vitro passages of the same strain, different preparation protocols, and different mass spectrometers.

The uncharacterized gene 1700093K21Rik and flanking regions are correlated with reproductive isolation in the house mouse, Mus musculus.

PubMed

Kass, David H; Janoušek, Václav; Wang, Liuyang; Tucker, Priscilla K

2014-06-01

Reproductive barriers exist between the house mouse subspecies, Mus musculus musculus and M. m. domesticus, members of the Mus musculus species complex, primarily as a result of hybrid male infertility, and a hybrid zone exists where their ranges intersect in Europe. Using single nucleotide polymorphisms (SNPs) diagnostic for the two taxa, the extent of introgression across the genome was previously compared in these hybrid populations. Sixty-nine of 1316 autosomal SNPs exhibited reduced introgression in two hybrid zone transects suggesting maladaptive interactions among certain loci. One of these markers is within a region on chromosome 11 that, in other studies, has been associated with hybrid male sterility of these subspecies. We assessed sequence variation in a 20 Mb region on chromosome 11 flanking this marker, and observed its inclusion within a roughly 150 kb stretch of DNA showing elevated sequence differentiation between the two subspecies. Four genes are associated with this genomic subregion, with two entirely encompassed. One of the two genes, the uncharacterized 1700093K21Rik gene, displays distinguishing features consistent with a potential role in reproductive isolation between these subspecies. Along with its expression specifically within spermatogenic cells, we present various sequence analyses that demonstrate a high rate of molecular evolution of this gene, as well as identify a subspecies amino acid variant resulting in a structural difference. Taken together, the data suggest a role for this gene in reproductive isolation.

Planning tiger recovery: Understanding intraspecific variation for effective conservation.

PubMed

Wilting, Andreas; Courtiol, Alexandre; Christiansen, Per; Niedballa, Jürgen; Scharf, Anne K; Orlando, Ludovic; Balkenhol, Niko; Hofer, Heribert; Kramer-Schadt, Stephanie; Fickel, Jörns; Kitchener, Andrew C

2015-06-01

Although significantly more money is spent on the conservation of tigers than on any other threatened species, today only 3200 to 3600 tigers roam the forests of Asia, occupying only 7% of their historical range. Despite the global significance of and interest in tiger conservation, global approaches to plan tiger recovery are partly impeded by the lack of a consensus on the number of tiger subspecies or management units, because a comprehensive analysis of tiger variation is lacking. We analyzed variation among all nine putative tiger subspecies, using extensive data sets of several traits [morphological (craniodental and pelage), ecological, molecular]. Our analyses revealed little variation and large overlaps in each trait among putative subspecies, and molecular data showed extremely low diversity because of a severe Late Pleistocene population decline. Our results support recognition of only two subspecies: the Sunda tiger, Panthera tigris sondaica, and the continental tiger, Panthera tigris tigris, which consists of two (northern and southern) management units. Conservation management programs, such as captive breeding, reintroduction initiatives, or trans-boundary projects, rely on a durable, consistent characterization of subspecies as taxonomic units, defined by robust multiple lines of scientific evidence rather than single traits or ad hoc descriptions of one or few specimens. Our multiple-trait data set supports a fundamental rethinking of the conventional tiger taxonomy paradigm, which will have profound implications for the management of in situ and ex situ tiger populations and boost conservation efforts by facilitating a pragmatic approach to tiger conservation management worldwide.

Streptococcus dysgalactiae subsp. equisimilis Isolated From Infections in Dogs and Humans: Are Current Subspecies Identification Criteria accurate?

PubMed

Ciszewski, Marcin; Zegarski, Kamil; Szewczyk, Eligia M

2016-11-01

Streptococcus dysgalactiae is a pyogenic species pathogenic both for humans and animals. Until recently, it has been considered an exclusive animal pathogen causing infections in wild as well as domestic animals. Currently, human infections are being reported with increasing frequency, and their clinical picture is often similar to the ones caused by Streptococcus pyogenes. Due to the fact that S. dysgalactiae is a heterogeneous species, it was divided into two subspecies: S. dysgalactiae subsp. equisimilis (SDSE) and S. dysgalactiae subsp. dysgalactiae (SDSD). The first differentiation criterion, described in 1996, was based on strain isolation source. Currently applied criteria, published in 1998, are based on hemolysis type and Lancefield group classification. In this study, we compared subspecies identification results for 36 strains isolated from clinical cases both in humans and animals. Species differentiation was based on two previously described criteria as well as MALDI-TOF and genetic analyses: RISA and 16S rRNA genes sequencing. Antimicrobial susceptibility profiles were also determined according to CLSI guidelines. The results presented in our study suggest that the subspecies differentiation criteria previously described in the above two literature positions seem to be inaccurate in analyzed group of strains, the hemolysis type on blood agar, and Lancefield classification should not be here longer considered as criteria in subspecies identification. The antimicrobial susceptibility tests indicate emerging of multiresistant human SDSE strains resistant also to vancomycin, linezolid and tigecycline, which might pose a substantial problem in treatment.

Genetic differentiation and inferred dynamics of a hybrid zone between Northern Spotted Owls (Strix occidentalis caurina) and California Spotted Owls (S. o. occidentalis) in northern California

USGS Publications Warehouse

Miller, Mark P.; Mullins, Tom; Forsman, Eric D.; Haig, Susan M.

2017-01-01

Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls (NSO: S. o. caurina) and California Spotted Owls (CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mtDNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region. Our analyses revealed that a NSO population close to the northern edge of the CSO range in northern California (the NSO Contact Zone population) is highly differentiated relative to other NSO populations throughout the remainder of their range. Phylogenetic analyses identified a unique lineage of mtDNA in the NSO Contact Zone, and Bayesian clustering analyses of the microsatellite data identified the Contact Zone as a third distinct population that is differentiated from CSO and NSO found in the remainder of the subspecies' range. Hybridization between NSO and CSO was readily detected in the NSO Contact Zone, with over 50% of individuals showing evidence of hybrid ancestry. Hybridization was also identified among 14% of CSO samples, which were dispersed across the subspecies' range in the Sierra Nevada Mountains. The asymmetry of hybridization suggested that the hybrid zone may be dynamic and moving. Although evidence of hybridization existed, we identified no F1 generation hybrid individuals. We instead found evidence for F2 or backcrossed individuals among our samples. The absence of F1 hybrids may indicate that (1) our 10 microsatellites were unable to distinguish hybrid types, (2) primary interactions between subspecies are occurring elsewhere on the landscape, or (3) dispersal between the subspecies' ranges is reduced relative to historical levels, potentially as a consequence of recent regional fires.

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep.

PubMed

Johnson, Heather E; Mills, L Scott; Wehausen, John D; Stephenson, Thomas R; Luikart, Gordon

2011-12-01

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations. ©2011 Society for Conservation Biology.

Fine Analysis of Genetic Diversity of the tpr Gene Family among Treponemal Species, Subspecies and Strains

PubMed Central

Centurion-Lara, Arturo; Giacani, Lorenzo; Godornes, Charmie; Molini, Barbara J.; Brinck Reid, Tara; Lukehart, Sheila A.

2013-01-01

Background The pathogenic non-cultivable treponemes include three subspecies of Treponema pallidum (pallidum, pertenue, endemicum), T. carateum, T. paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme (Simian isolate). These treponemes are morphologically indistinguishable and antigenically and genetically highly similar, yet cross-immunity is variable or non-existent. Although all of these organisms cause chronic, multistage skin and systemic disease, they have historically been classified by mode of transmission, clinical presentations and host ranges. Whole genome studies underscore the high degree of sequence identity among species, subspecies and strains, pinpointing a limited number of genomic regions for variation. Many of these “hot spots” include members of the tpr gene family, composed of 12 paralogs encoding candidate virulence factors. We hypothesize that the distinct clinical presentations, host specificity, and variable cross-immunity might reside on virulence factors such as the tpr genes. Methodology/Principal Findings Sequence analysis of 11 tpr loci (excluding tprK) from 12 strains demonstrated an impressive heterogeneity, including SNPs, indels, chimeric genes, truncated gene products and large deletions. Comparative analyses of sequences and 3D models of predicted proteins in Subfamily I highlight the striking co-localization of discrete variable regions with predicted surface-exposed loops. A hallmark of Subfamily II is the presence of chimeric genes in the tprG and J loci. Diversity in Subfamily III is limited to tprA and tprL. Conclusions/Significance An impressive sequence variability was found in tpr sequences among the Treponema isolates examined in this study, with most of the variation being consistent within subspecies or species, or between syphilis vs. non-syphilis strains. Variability was seen in the pallidum subspecies, which can be divided into 5 genogroups. These findings support a genetic basis for the classification of these organisms into their respective subspecies and species. Future functional studies will determine whether the identified genetic differences relate to cross-immunity, clinical differences, or host ranges. PMID:23696912

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data

PubMed Central

Laidò, Giovanni; Mangini, Giacomo; Taranto, Francesca; Gadaleta, Agata; Blanco, Antonio; Cattivelli, Luigi; Marone, Daniela; Mastrangelo, Anna M.; Papa, Roberto; De Vita, Pasquale

2013-01-01

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles. PMID:23826256

Mexorchestia: a new genus of talitrid amphipod (Crustacea, Amphipoda, Talitridae) from the Gulf of Mexico and Caribbean Sea, with the description of a new species and two new subspecies.

PubMed

Wildish, David J; Lecroy, Sara E

2014-08-26

Two species of supralittoral Tethorchestia were reported by Bousfield (1984) to occur on the shores of the Gulf of Mexico and closely adjacent waters: T. antillensis Bousfield, 1984 from Quintana Roo, Mexico and an undescribed species, Tethorchestia sp. B of Bousfield (1984), from Florida and the U.S. Gulf coast. In this paper, we rediagnose and illustrate the former taxon based on material from Goodland Bay, Florida, which represents a range extension for that species. We examined the latter taxon from many locations throughout the Gulf of Mexico using classical morphology, epidermal pigment pattern recognition and allometry, reinforced by molecular markers (mitochondrial cytochrome oxidase I, Radulovici 2012), determining that Tethorchestia sp. B represents a new genus and species, comprising two subspecies. The nominate subspecies, Mexorchestia carpenteri carpenteri n. gen., sp. and subsp., is described from Tiger Tail Beach, Florida, based on conventional morphological criteria and its distinctive epidermal pigment patterns. The Tiger Tail Beach ecotope of M. c. carpenteri n. gen., sp. and subsp. was distinct from that of other locations examined in Florida and was associated with epidermal pigment pattern polymorphism, absent at other locations. A second subspecies, distinguished by differences in size, number of articles in the flagellum of antenna 2, the number of marginal setae on oostegite 2 of the female and the number of distal dorsolateral robust setae on the telson, was found in samples from Belize and Mexico. This subspecies is described from material collected at Turneffe Island, Belize, as Mexorchestia carpenteri raduloviciae n. gen., sp. and subsp. Like M. c. carpenteri n. gen., sp. and subsp., this taxon is also associated with epidermal pigment pattern polymorphism. A key is provided for the three currently described species of Tethorchestia (two extant) and two new subspecies of Mexorchestia n.gen. 

The effect of omega-3 carboxylic acids on apolipoprotein CIII-containing lipoproteins in severe hypertriglyceridemia.

PubMed

Morton, Allyson M; Furtado, Jeremy D; Lee, Jane; Amerine, William; Davidson, Michael H; Sacks, Frank M

Lipoprotein subspecies containing apoCIII adversely affect cardiovascular disease (CVD) risk; for example, low density lipoprotein (LDL) with apoCIII is a stronger CVD predictor than LDL without apoCIII. The Epanova for Lowering Very High Triglycerides (EVOLVE) trial showed that Epanova (omega-3 carboxylic acids [OM3-CA]) significantly lowered TG and apoCIII but raised LDL-C. However, it is unknown what subspecies of LDL were affected by treatment. To determine how lipoprotein subspecies are affected by omega-3 fatty acid treatment, we studied the effect of OM3-CA on apoCIII concentrations in high density lipoprotein (HDL), LDL, and very low density lipoprotein (VLDL) and on the concentrations of subspecies of HDL, LDL, and VLDL that contain or do not contain apoCIII. We analyzed plasma from a subset of subjects from the EVOLVE trial, a 12-week double-blind study of 399 subjects with fasting TG of 500 to 2000 mg/dL who were randomized to OM3-CA 2, 3, or 4 g/d or olive oil (placebo). OM3-CA significantly reduced plasma apoCIII relative to placebo, as well as apoCIII in HDL, and apoCIII in LDL. Treatment did not significantly affect the concentration of LDL with apoCIII, a subspecies highly associated with CVD risk. OM3-CA increased selectively the concentration of LDL that does not contain apoCIII, a subspecies with a weak relation to coronary heart disease. The reduction in apoCIII was associated with plasma increases in eicosapentaenoic acid, docosahexaenoic acid, and arachidonic acid and decreases in linoleic, palmitic, and oleic acids. Reduction in apoCIII may be a mechanism for the TG-lowering effects of OM3-CA. The increase in LDL-C seen in the EVOLVE trial may not be associated with increased risk of CVD. Copyright © 2016 National Lipid Association. Published by Elsevier Inc. All rights reserved.

Intraspecific variation buffers projected climate change impacts on Pinus contorta

PubMed Central

Oney, Brian; Reineking, Björn; O'Neill, Gregory; Kreyling, Juergen

2013-01-01

Species distribution modeling (SDM) is an important tool to assess the impact of global environmental change. Many species exhibit ecologically relevant intraspecific variation, and few studies have analyzed its relevance for SDM. Here, we compared three SDM techniques for the highly variable species Pinus contorta. First, applying a conventional SDM approach, we used MaxEnt to model the subject as a single species (species model), based on presence–absence observations. Second, we used MaxEnt to model each of the three most prevalent subspecies independently and combined their projected distributions (subspecies model). Finally, we used a universal growth transfer function (UTF), an approach to incorporate intraspecific variation utilizing provenance trial tree growth data. Different model approaches performed similarly when predicting current distributions. MaxEnt model discrimination was greater (AUC – species model: 0.94, subspecies model: 0.95, UTF: 0.89), but the UTF was better calibrated (slope and bias – species model: 1.31 and −0.58, subspecies model: 1.44 and −0.43, UTF: 1.01 and 0.04, respectively). Contrastingly, for future climatic conditions, projections of lodgepole pine habitat suitability diverged. In particular, when the species' intraspecific variability was acknowledged, the species was projected to better tolerate climatic change as related to suitable habitat without migration (subspecies model: 26% habitat loss or UTF: 24% habitat loss vs. species model: 60% habitat loss), and given unlimited migration may increase amount of suitable habitat (subspecies model: 8% habitat gain or UTF: 12% habitat gain vs. species model: 51% habitat loss) in the climatic period 2070–2100 (SRES A2 scenario, HADCM3). We conclude that models derived from within-species data produce different and better projections, and coincide with ecological theory. Furthermore, we conclude that intraspecific variation may buffer against adverse effects of climate change. A key future research challenge lies in assessing the extent to which species can utilize intraspecific variation under rapid environmental change. PMID:23467191

Spread of Aedes japonicus japonicus (Theobald, 1901) in Austria, 2011-2015, and first records of the subspecies for Hungary, 2012, and the principality of Liechtenstein, 2015.

PubMed

Seidel, Bernhard; Nowotny, Norbert; Bakonyi, Tamás; Allerberger, Franz; Schaffner, Francis

2016-06-24

The Asian bush mosquito, Aedes (Hulecoeteomyia) japonicus japonicus (Theobald, 1901) (Diptera: Culicidae), was first identified in Austria in August 2011 in the federal state of Styria at the border to Slovenia. Between 2011 and 2015 the spread of Ae. j. japonicus was monitored in southern, eastern and western Austrian provinces as well as in neighbouring countries by checking natural and man-made container habitats for the aquatic stages. The search concentrated around the most recent occurrence of Ae. j. japonicus and extended up to several kilometres until the subspecies could not be found anymore. Between May and July 2012 the distribution area of Ae. j. japonicus was found to be extended westwards into Carinthia, and eastwards towards the federal state of Burgenland. In August 2012, the subspecies was found in Hungary, representing the first record of an invasive mosquito species in this country. In 2013 its expansion was confirmed at several sites in Austria. Additionally, between April and July 2015, the subspecies was detected in all districts of the westernmost Austrian state Vorarlberg reaching the alpine Montafon valley at the end of October 2015, at all three examined sites in southern Bavaria bordering Vorarlberg, and in the adjacent Principality of Liechtenstein, for which it also represents the first record of an invasive mosquito species. One remarkable finding of the subspecies was located close to the city of Kufstein in the lower Inn valley of the Tyrol in September 2015, which is an isolated occurrence without spatial connection to any known established population. Our findings demonstrate the ongoing spread of Ae. j. japonicus towards all directions within Austria and beyond. Together with the absence of supposed natural barriers, e.g. high mountain chains, at the borders of the current subspecies' distribution area in south-eastern Austria, these findings suggest a further spread to the Austrian capital Vienna and the Hungarian tourist region of Lake Balaton within the upcoming few years. The observed intrusions in western Austria represent most probably extensions of the population established and spreading in eastern Switzerland and southern Germany. The putative role of the subspecies in pathogen transmission together with its rapid spread observed argues for the implementation of comprehensive nation-wide surveillance and response preparedness.

CD4 T Cells From Intestinal Biopsies of Crohn's Disease Patients React to Mycobacterium avium subspecies paratuberculosis

USDA-ARS?s Scientific Manuscript database

The role of Mycobacterium avium subspecies paratuberculosis (MAP) in Crohn’s disease (CD) remains controversial. One issue that has been raised is the lack of data showing a cellular immune response to MAP. Earlier studies have mostly focused on responses in peripheral blood which have several limit...

76 FR 66255 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition to Delist the Coastal...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-26

... subspecies recognition for the coastal California gnatcatcher. We subsequently made these data available to... support recognition of the coastal California gnatcatcher as a subspecies. Zink et al. (2000) does not... adaptation. Other molecular markers with higher mutation rates may reveal more recent patterns of divergence...

Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires re-evaluation of current diagnostics

USDA-ARS?s Scientific Manuscript database

Classification of the Campylobacter fetus subspecies fetus and venerealis was first described in 1959 and was based on the source of isolation (intestinal vs genital) and the ability of the strains to proliferate in cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described...

76 FR 61531 - Endangered and Threatened Wildlife and Plants; 90-Day Finding on a Petition To List 10 Subspecies...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-04

... that listing the following 4 of the 10 subspecies as threatened or endangered may be warranted: Baking...: Baking Powder Flat blue butterfly (Euphilotes bernardino minuta), Mono Basin skipper (Hesperia uncas.... The Baking Powder Flat blue butterfly was added as Euphilotes battoides ssp., now known as Euphilotes...

Serotypes of Salmonella enterica subspecies I isolated from mice caught on US poultry farms 1995 through 1998

USDA-ARS?s Scientific Manuscript database

Whole genome analysis of foodborne pathogens is standard practice for regulatory agencies in the US, and a goal of 1 million genomes for Salmonella enterica is currently 76% complete. Inclusion of a range of Salmonella enterica subspecies I serotypes is important because only 30 of approximately 150...

Genetic and environmental effects on seed weight in subspecies of big sagebrush: Applications for restoration

Treesearch

Bryce A. Richardson; Hector G. Ortiz; Stephanie L. Carlson; Deidre M. Jaeger; Nancy L. Shaw

2015-01-01

The sagebrush steppe is a patchwork of species and subspecies occupying distinct environmental niches across the intermountain regions of western North America. These ecosystems face degradation from disturbances and exotic weeds. Using sagebrush seed that is matched to its appropriate niche is a critical component to successful restoration, improving habitat for the...

Development and characterization of microsatellite markers in the Point Arena mountain beaver Aplodontia rufa nigra

Treesearch

Kristine L. Pilgrim; William J. Zielinski; Mary J. Mazurek; Frederick V. Schlexer; Michael K. Schwartz

2006-01-01

The Point Arena mountain beaver (Aplodontia rufa nigra) is an endangered subspecies. Efforts to recover this sub-species will be aided by advances in molecular genetics, specifically the ability to estimate population size using noninvasive genetic sampling. Here we report on the development of nine polymorphic loci for the Point Arena mountain...

A Novel Cell Wall Lipopeptide Is Important for Biofilm Formation and Pathogenicity of Mycobacterium avium subspecies paratuberculosis

USDA-ARS?s Scientific Manuscript database

Biofilm formation by pathogenic bacteria plays a key role in their pathogenesis. Previously, the pstA gene was shown to be involved in the virulence of Mycobacterium avium subspecies paratuberculosis (M. ap), the causative agent of Johne's disease in cattle and a potential risk factor for Crohn's d...

The Medicago sativa Gene Index 1.2: A web-accessible expression atlas of two Medicago sativa sub-species

USDA-ARS?s Scientific Manuscript database

Alfalfa is an important crop, both financially and ecologically, in the agricultural system of the United States. Using Illumina RNA-seq technology we have developed a de-novo transcriptome assembly from two Medicago sativa sub-species, sativa (B47) and falcata (F56). These two genotypes have proven...

Atypical den use of Carolina Northern Flying Squirrels (Glaucomys sabrinus coloratus) in the southern Appalachian Mountains

USGS Publications Warehouse

Diggins, Corinne A.; Kelly, Christine A.; Ford, W. Mark

2015-01-01

Glaucomys sabrinus coloratus (Carolina Northern Flying Squirrel) is a federally endangered subspecies that occurs in high elevation forests of the southern Appalachian Mountains. Denning sites may be a limiting factor for this subspecies in areas where cavity trees are not abundant or where interspecific competition from other tree squirrels occurs. This shortage can result in use of unusual denning sites, such as subterranean dens. Herein, we report atypical denning habits of radio-collared Carolina Northern Flying Squirrels in southwestern Virginia and western North Carolina from 2008 to 2011 and 2014. Increased knowledge of denning habitats may be beneficial for conservation and habitat management of this subspecies, particularly in sub-optimal or degraded habitats.

Nuclear and Mitochondrial DNA Analyses of Golden Eagles (Aquila chrysaetos canadensis) from Three Areas in Western North America; Initial Results and Conservation Implications

PubMed Central

Craig, Erica H.; Adams, Jennifer R.; Waits, Lisette P.; Fuller, Mark R.; Whittington, Diana M.

2016-01-01

Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles. Our results indicate high genetic diversity, low genetic structure and high connectivity. Nuclear DNA Fst values between Idaho and California were low but significantly different from zero (0.026). Bayesian clustering methods indicated a single population, and we were unable to distinguish summer breeding residents from different regions. Results of the mtDNA AMOVA showed that most of the haplotype variation (97%) was within the geographic populations while 3% variation was partitioned among them. One haplotype was common to all three areas. One region-specific haplotype was detected in California and one in Idaho, but additional sampling is required to determine if these haplotypes are unique to those geographic areas or a sampling artifact. We discuss potential sources of the high gene flow for this species including natal and breeding dispersal, floaters, and changes in migratory behavior as a result of environmental factors such as climate change and habitat alteration. Our preliminary findings can help inform the USFWS in development of golden eagle management strategies and provide a basis for additional research into the complex dynamics of the North American subspecies. PMID:27783687

Long-Distance Dispersal by Sea-Drifted Seeds Has Maintained the Global Distribution of Ipomoea pes-caprae subsp. brasiliensis (Convolvulaceae)

PubMed Central

Miryeganeh, Matin; Takayama, Koji; Tateishi, Yoichi; Kajita, Tadashi

2014-01-01

Ipomoea pes-caprae (Convolvulaceae), a pantropical plant with sea-drifted seeds, is found globally in the littoral areas of tropical and subtropical regions. Unusual long-distance seed dispersal has been believed to be responsible for its extraordinarily wide distribution; however, the actual level of inter-population migration has never been studied. To clarify the level of migration among populations of I. pes-caprae across its range, we investigated nucleotide sequence variations by using seven low-copy nuclear markers and 272 samples collected from 34 populations that cover the range of the species. We applied coalescent-based approaches using Bayesian and maximum likelihood methods to assess migration rates, direction of migration, and genetic diversity among five regional populations. Our results showed a high number of migrants among the regional populations of I. pes-caprae subsp. brasiliensis, which suggests that migration among distant populations was maintained by long-distance seed dispersal across its global range. These results also provide strong evidence for recent trans-oceanic seed dispersal by ocean currents in all three oceanic regions. We also found migration crossing the American continents. Although this is an apparent land barrier for sea-dispersal, migration between populations of the East Pacific and West Atlantic regions was high, perhaps because of trans-isthmus migration via pollen dispersal. Therefore, the migration and gene flow among populations across the vast range of I. pes-caprae is maintained not only by seed dispersal by sea-drifted seeds, but also by pollen flow over the American continents. On the other hand, populations of subsp. pes-caprae that are restricted to only the northern part of the Indian Ocean region were highly differentiated from subsp. brasiliensis. Cryptic barriers that prevented migration by sea dispersal between the ranges of the two subspecies and/or historical differentiation that caused local adaptation to different environmental factors in each region could explain the genetic differentiation between the subspecies. PMID:24755614

Nuclear and Mitochondrial DNA Analyses of Golden Eagles (Aquila chrysaetos canadensis) from Three Areas in Western North America; Initial Results and Conservation Implications.

PubMed

Craig, Erica H; Adams, Jennifer R; Waits, Lisette P; Fuller, Mark R; Whittington, Diana M

2016-01-01

Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles. Our results indicate high genetic diversity, low genetic structure and high connectivity. Nuclear DNA Fst values between Idaho and California were low but significantly different from zero (0.026). Bayesian clustering methods indicated a single population, and we were unable to distinguish summer breeding residents from different regions. Results of the mtDNA AMOVA showed that most of the haplotype variation (97%) was within the geographic populations while 3% variation was partitioned among them. One haplotype was common to all three areas. One region-specific haplotype was detected in California and one in Idaho, but additional sampling is required to determine if these haplotypes are unique to those geographic areas or a sampling artifact. We discuss potential sources of the high gene flow for this species including natal and breeding dispersal, floaters, and changes in migratory behavior as a result of environmental factors such as climate change and habitat alteration. Our preliminary findings can help inform the USFWS in development of golden eagle management strategies and provide a basis for additional research into the complex dynamics of the North American subspecies.

Nuclear and mitochondrial DNA analyses of golden eagles (Aquila chrysaetos canadensis) from three areas in western North America; initial results and conservation implications

USGS Publications Warehouse

Craig, Erica H; Adams, Jennifer R.; Waits, Lisette P.; Fuller, Mark R.; Whittington, Diana M.

2016-01-01

Understanding the genetics of a population is a critical component of developing conservation strategies. We used archived tissue samples from golden eagles (Aquila chrysaetos canadensis) in three geographic regions of western North America to conduct a preliminary study of the genetics of the North American subspecies, and to provide data for United States Fish and Wildlife Service (USFWS) decision-making for golden eagle management. We used a combination of mitochondrial DNA (mtDNA) D-loop sequences and 16 nuclear DNA (nDNA) microsatellite loci to investigate the extent of gene flow among our sampling areas in Idaho, California and Alaska and to determine if we could distinguish birds from the different geographic regions based on their genetic profiles. Our results indicate high genetic diversity, low genetic structure and high connectivity. Nuclear DNA Fst values between Idaho and California were low but significantly different from zero (0.026). Bayesian clustering methods indicated a single population, and we were unable to distinguish summer breeding residents from different regions. Results of the mtDNA AMOVA showed that most of the haplotype variation (97%) was within the geographic populations while 3% variation was partitioned among them. One haplotype was common to all three areas. One region-specific haplotype was detected in California and one in Idaho, but additional sampling is required to determine if these haplotypes are unique to those geographic areas or a sampling artifact. We discuss potential sources of the high gene flow for this species including natal and breeding dispersal, floaters, and changes in migratory behavior as a result of environmental factors such as climate change and habitat alteration. Our preliminary findings can help inform the USFWS in development of golden eagle management strategies and provide a basis for additional research into the complex dynamics of the North American subspecies.

Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis

PubMed Central

Goldstone, Robert J.; McLuckie, Joyce; Smith, David G. E.

2015-01-01

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates. PMID:26677250

Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

PubMed Central

Fausser, Jean-Luc; Prosper, Prosper; Donati, Giuseppe; Ramanamanjato, Jean-Baptiste; Rumpler, Yves

2002-01-01

Background Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and particularly in the cytogenetic distinct subspecies group of Hapalemur griseus, 357 bp sequence of cytochrome b and 438 bp of 12S mitochondrial DNAs were analyzed on a sample of animals captured in areas extending from the north to the south-east of Madagascar. This sample covers all cytogenetically defined types recognized of the genus Hapalemur. Results Phylogenetic trees and distances analyses demonstrate a first emergence of Hapalemur simus followed by H. aureus which is the sister clade of the H. griseus subspecies. Hapalemur griseus is composed of 4 subspecies separated into two clades. The first contains H. g. griseus, H. g. alaotrensis and H. g. occidentalis. The second consists of H. g. meridionalis. A new chromosomal polymorphic variant from the region of Ranomafana, H. griseus ssp, has been analysed and was found in both clades. Conclusions Our results support the raising of H. g. meridionalis to the specific rank H. meridionalis, while neither cytogenetic nor molecular evidences support the raising of H. g. alaotrensis to a species rank despite its morphological characteristics. The new cytotype H. g. ssp which has been previously characterized by cytogenetic studies contains animals clustering either with the group of Hapalemur griseus griseus or with that of Hapalemur meridionalis. This suggests the existence of an ancestral polymorphism or an introgression of mitochondrial DNA between subspecies. PMID:11914128

Deep Genetic Divergence between Disjunct Refugia in the Arctic-Alpine King’s Crown, Rhodiola integrifolia (Crassulaceae)

PubMed Central

DeChaine, Eric G.; Forester, Brenna R.; Schaefer, Hanno; Davis, Charles C.

2013-01-01

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King’s Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome. PMID:24282505

The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America

PubMed Central

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A.; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa. PMID:25379725

The complex biogeography of the plant pathogen Xylella fastidiosa: genetic evidence of introductions and Subspecific introgression in Central America.

PubMed

Nunney, Leonard; Ortiz, Beatriz; Russell, Stephanie A; Ruiz Sánchez, Rebeca; Stouthamer, Richard

2014-01-01

The bacterium Xylella fastidiosa is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies, X. fastidiosa subsp. fastidiosa. The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies Xylella fastidiosa subsp. pauca which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of X. fastidiosa. Four isolates, classified as X. fastidiosa subsp. fastidiosa, showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from X. fastidiosa subsp. pauca while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of X. fastidiosa subsp. pauca in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of X. fastidiosa.

Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso.

PubMed

Adimpong, David B; Nielsen, Dennis S; Sørensen, Kim I; Vogensen, Finn K; Sawadogo-Lingani, Hagrétou; Derkx, Patrick M F; Jespersen, Lene

2013-10-01

Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9(T), was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA-DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii. The genome sequence of isolate ZN7a-9(T) was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9(T) together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9(T) as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii. Strain ZN7a-9(T) additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9(T) represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9(T) = DSM 26046(T) = LMG 27067(T).

Deep genetic divergence between disjunct Refugia in the Arctic-Alpine King's Crown, Rhodiola integrifolia (Crassulaceae).

PubMed

DeChaine, Eric G; Forester, Brenna R; Schaefer, Hanno; Davis, Charles C

2013-01-01

Despite the strength of climatic variability at high latitudes and upper elevations, we still do not fully understand how plants in North America that are distributed between Arctic and alpine areas responded to the environmental changes of the Quaternary. To address this question, we set out to resolve the evolutionary history of the King's Crown, Rhodiola integrifolia using multi-locus population genetic and phylogenetic analyses in combination with ecological niche modeling. Our population genetic analyses of multiple anonymous nuclear loci revealed two major clades within R. integrifolia that diverged from each other ~ 700 kya: one occurring in Beringia to the north (including members of subspecies leedyi and part of subspecies integrifolia), and the other restricted to the Southern Rocky Mountain refugium in the south (including individuals of subspecies neomexicana and part of subspecies integrifolia). Ecological niche models corroborate our hypothesized locations of refugial areas inferred from our phylogeographic analyses and revealed some environmental differences between the regions inhabited by its two subclades. Our study underscores the role of geographic isolation in promoting genetic divergence and the evolution of endemic subspecies in R. integrifolia. Furthermore, our phylogenetic analyses of the plastid spacer region trnL-F demonstrate that among the native North American species, R. integrifolia and R. rhodantha are more closely related to one another than either is to R. rosea. An understanding of these historic processes lies at the heart of making informed management decisions regarding this and other Arctic-alpine species of concern in this increasingly threatened biome.

Ways to be different: foraging adaptations that facilitate higher intake rates in a northerly-wintering shorebird compared to a low-latitude conspecific

USGS Publications Warehouse

Ruthrauff, Daniel R.; Dekinga, Anne; Gill, Robert E.; van Gils, Jan A.; Piersma, Theunis

2015-01-01

At what phenotypic level do closely related subspecies that live in different environments differ with respect to food detection, ingestion, and processing? This question motivated an experimental study on rock sandpipers (Calidris ptilocnemis). The species' nonbreeding range spans 20 degrees of latitude, the extremes of which are inhabited by two subspecies: Calidris p. ptilocnemis that winters primarily in upper Cook Inlet, Alaska (61°N), and C. p. tschuktschorum that overlaps slightly with C. p. ptilocnemis but whose range extends much farther south (~40°N). In view of the strongly contrasting energetic demands of their distinct nonbreeding distributions, we conducted experiments to assess the behavioural, physiological, and sensory aspects of foraging, and we used the bivalve Macoma balthica for all trials. Ptilocnemis consumed a wider range of prey sizes, had higher maximum rates of energy intake, processed shell waste at higher maximum rates, and handled prey more quickly. Notably, however, the two subspecies did not differ in their abilities to find buried prey. The subspecies were similar in size and had equally sized gizzards, but the more northern ptilocnemis individuals were 10-14% heavier than their same-sex tschuktschorum counterparts. The higher body mass in ptilocnemis likely resulted from hypertrophy of digestive organs (e.g. intestine, liver) related to digestion and nutrient assimilation. Given the previously established equality of the two subspecies' metabolic capacities, we propose that the high-latitude nonbreeding range of ptilocnemis rock sandpipers is primarily facilitated by digestive (i.e. physiological) aspects of their foraging ecology rather than behavioural or sensory aspects.

Comparative analysis of mitochondrial genomes of geographic variants of the gypsy moth, Lymantria dispar, reveals a previously undescribed genotypic entity

USDA-ARS?s Scientific Manuscript database

The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the European gypsy moth (L. dispar dispar), whose females are flightless, the two Asian subspecies, L. dispar asiatica and L. dispar japonica, have flig...

Description of a new species and subspecies of Idalus Walker from Costa Rica, Honduras and Guatemala (Lepidoptera, Erebidae, Arctiinae, Arctiini)

PubMed Central

Espinoza, Bernardo A.; Janzen, Daniel H.; Winnie Hallwachs;  J. Bolling Sullivan

2013-01-01

Abstract A new species and subspecies of Idalus Walker are described from Costa Rica, Honduras and Guatemala. Images of males and females and their genitalia are provided. Locality information and distribution maps for Costa Rica and for Guatemala are included. The biology and phylogeny of Idalus are discussed. PMID:23730178

Whole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production

USDA-ARS?s Scientific Manuscript database

Campylobacter fetus can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (Cfv) and C. fetus subsp. testudinum. Subspecies identification of C. fetus strains is crucial in the control of Bovine Genital C...

Late winter and early spring home range and habitat use of the endangered Carolina northern flying squirrel in western North Carolina

Treesearch

W. Mark Ford; Christine A. Kelly; Jane L. Rodrigue; Richard H. Odom; Douglas Newcomb; L. Michelle Gilley; Corrine A. Diggins

2014-01-01

The Carolina northern flying squirrel Glaucomys sabrinus coloratus is an endangered subspecies that is restricted to high elevation forests in the southern Appalachian Mountains. Owing to rugged terrain and nocturnal habits, the subspecies' natural history, home range characteristics and habitat preferences are poorly known. We radio-tracked 3...

A range-wide occupancy estimate and habitat model for the endangered Point Arena mountain beaver (Aplodontia rufa nigra)

Treesearch

William J. Zielinski; Fredrick V. Schlexer; Jeffrey R. Dunk; Matthew J. Lau; James J. Graham

2015-01-01

The mountain beaver (Aplodontia rufa) is notably the most primitive North American rodent with a restricted distribution in the Pacific Northwest based on its physiological limits to heat stress and water needs. The Point Arena subspecies (A. r. nigra) is federally listed as endangered and is 1 of 2 subspecies that have extremely...

Revision of the genus Bradyporus Charpentier, 1825 (Orthoptera: Tettigoniidae: Bradyporinae).

PubMed

Ünal, Mustafa

2017-05-31

The genus Bradyporus Charpentier is taxonomically revised using information obtained from numerous recently collected specimens. Bradyporus is divided into two subgenera Bradyporus Charpentier s.str. and Callimenus Fischer von Waldheim. Five species groups are distinguished in the latter subgenus. Sixteen species and subspecies are listed. Bradyporus (Callimenus) multituberculatus multituberculatus (Fischer von Waldheim, 1833) and Bradyporus (Callimenus) multituberculatus montandoni (Burr, 1898) are designated subspecies for the first time. Previously synonymized Bradyporus (Callimenus) macrogaster skopjensis Karaman, 1961 is reinstated as a valid species. A new species, Bradyporus (Callimenus) gocmeni Ünal, sp. nov. from Eastern Turkey and the previously unknown female of Bradyporus (Callimenus) skopjensis Karaman, 1961 are described. A Neotype for Bradyporus (Callimenus) macrogaster longicollis (Fieber, 1853) is designated. Nomenclatural and taxonomical problems are discussed under the relevant taxa. Phylogenetic relationships based on morphology of the subgenera, species groups, and the species and subspecies of each species group are proposed. Morphological derived and ancestral characters are discussed. A key to the lower taxa of the genus is provided with 207 original figures including 3 distributional maps. A check-list of the lower taxa of the genus is given. Additionally the IUCN Red List statuses of the species and subspecies are included.

Leukotriene signaling in the extinct human subspecies Homo denisovan and Homo neanderthalensis. Structural and functional comparison with Homo sapiens.

PubMed

Adel, Susan; Kakularam, Kumar Reddy; Horn, Thomas; Reddanna, Pallu; Kuhn, Hartmut; Heydeck, Dagmar

2015-01-01

Mammalian lipoxygenases (LOXs) have been implicated in cell differentiation and in the biosynthesis of pro- and anti-inflammatory lipid mediators. The initial draft sequence of the Homo neanderthalensis genome (coverage of 1.3-fold) suggested defective leukotriene signaling in this archaic human subspecies since expression of essential proteins appeared to be corrupted. Meanwhile high quality genomic sequence data became available for two extinct human subspecies (H. neanderthalensis, Homo denisovan) and completion of the human 1000 genome project provided a comprehensive database characterizing the genetic variability of the human genome. For this study we extracted the nucleotide sequences of selected eicosanoid relevant genes (ALOX5, ALOX15, ALOX12, ALOX15B, ALOX12B, ALOXE3, COX1, COX2, LTA4H, LTC4S, ALOX5AP, CYSLTR1, CYSLTR2, BLTR1, BLTR2) from the corresponding databases. Comparison of the deduced amino acid sequences in connection with site-directed mutagenesis studies and structural modeling suggested that the major enzymes and receptors of leukotriene signaling as well as the two cyclooxygenase isoforms were fully functional in these two extinct human subspecies. Copyright © 2014 Elsevier Inc. All rights reserved.

Ubiquity of Polynucleobacter necessarius subspecies asymbioticus results from ecological diversification

PubMed Central

Jezbera, Jan; Jezberová, Jitka; Brandt, Ulrike; Hahn, Martin W

2011-01-01

The subspecies Polynucleobacter necessarius asymbioticus (> 99% 16S rRNA similarity) has a cosmopolitan distribution and a ubiquitous occurrence in lentic freshwater habitats. We tested if the observed ubiquity of these free-living planktonic freshwater bacteria results from a euryoecious (generalist) adaptation of P. n. asymbioticus strains, or from ecological diversification within the subspecies. We developed a reverse line blot hybridization assay enabling the cultivation-independent detection of 13 groups within the subspecies in environmental samples. A set of 121 lentic freshwater habitats, spanning a broad variety of habitat types (e.g. pH levels ranging from 3.8 to 8.5) was investigated for the presence of these 13 P. n. asymbioticus groups. Statistical analyses of the reverse line blot hybridization detections revealed pronounced differences in habitat preferences of several of the groups. Their preferences differed regarding pH, conductivity, dissolved organic carbon and oxygen concentration of habitats. For some groups, differences in environmental preferences resulted even in complete niche separation between them. The revealed differences in habitat preferences suggest that the previously reported ubiquity of P. n. asymbioticus results from ecological diversification within the taxon and not from generalist adaptation of strains. PMID:21208356

Screening of the antioxidative properties and total phenolic contents of three endemic Tanacetum subspecies from Turkish flora.

PubMed

Tepe, Bektas; Sokmen, Atalay

2007-11-01

Methanolic extracts of three different Tanacetum subspecies [Tanacetum densum (Lab.) Schultz Bip. subsp. sivasicum Hub-Mor and Grierson, Tanacetum densum (Lab.) Schultz Bip. subsp. eginense Heywood and Tanacetum densum (Lab.) Schultz Bip. subsp. amani Heywood] which are endemic to Turkish flora were screened for their possible antioxidant activities by two complementary test systems namely DPPH free radical scavenging and beta-carotene/linoleic acid. In DPPH system, the most active plant was T. densum subsp. amani with an IC(50) value of 69.30+/-0.37 microg/ml. On the other hand, T. densum subsp. sivasicum exerted greater antioxidant activity than those of other subspecies in beta-carotene/linoleic acid system (79.10%+/-1.83). Antioxidant activities of BHT, curcumine and ascorbic acid were also determined as positive controls in parallel experiments. Total phenolic constituents of the extracts of Tanacetum subspecies were performed employing the literature methods involving Folin-Ciocalteu reagent and gallic acid as standard. The amount of total phenolics was highest in subsp. sivasicum (162.33+/-3.57 microg/mg), followed by subsp. amani (158.44+/-2.17 microg/mg). Especially, a positive correlation was observed between total phenolic content and antioxidant activity of the extracts.

Changes of Tight Junction Protein Claudins in Small Intestine and Kidney Tissues of Mice Fed a DDC Diet.

PubMed

Abiko, Yukie; Kojima, Takashi; Murata, Masaki; Tsujiwaki, Mitsuhiro; Takeuchi, Masaya; Sawada, Norimasa; Mori, Michio

2013-12-01

DDC (3,5-diethoxycarbonyl-1,4-dihydrocollidine)-fed mice are widely used as a model for cholestatic liver disease. We examined the expression of tight junction protein claudin subspecies by immunofluorescent histochemistry in small intestine and kidney tissues of mice fed a DDC diet for 12 weeks. In the small intestine, decreases in claudin-3, claudin-7 and claudin-15 were observed in villous epithelial cells corresponding to the severity of histological changes while leaving the abundance of these claudin subspecies unchanged in crypt cells. Nevertheless, the proliferative activity of intestinal crypt cells measured by immunohistochemistry for Ki-67 decreased in the mice fed the DDC diet compared with that of control mice. These results suggest the possibility that DDC feeding affects the barrier function of villous epithelial cells and thus inhibits the proliferative activity of crypt epithelial cells. On the other hand, in the kidney, remarkable changes were found in the subcellular localization of claudin subspecies in a segment-specific manner, although histological changes of renal epithelial cells were quite minimal. These results indicate that immunohistochemistry for claudin subspecies can serve as a useful tool for detecting minute functional alterations of intestinal and renal epithelial cells.

Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis).

PubMed

Uphyrkina, O; Miquelle, D; Quigley, H; Driscoll, C; O'Brien, S J

2002-01-01

The Far Eastern or Amur leopard (Panthera pardus orientalis) survives today as a tiny relict population of 25-40 individuals in the Russian Far East. The population descends from a 19th-century northeastern Asian subspecies whose range extended over southeastern Russia, the Korean peninsula, and northeastern China. A molecular genetic survey of nuclear microsatellite and mitochondrial DNA (mtDNA) sequence variation validates subspecies distinctiveness but also reveals a markedly reduced level of genetic variation. The amount of genetic diversity measured is the lowest among leopard subspecies and is comparable to the genetically depleted Florida panther and Asiatic lion populations. When considered in the context of nonphysiological perils that threaten small populations (e.g., chance mortality, poaching, climatic extremes, and infectious disease), the genetic and demographic data indicate a critically diminished wild population under severe threat of extinction. An established captive population of P. p. orientalis displays much higher diversity than the wild population sample, but nearly all captive individuals are derived from a history of genetic admixture with the adjacent Chinese subspecies, P. p. japonensis. The conservation management implications of potential restoration/augmentation of the wild population with immigrants from the captive population are discussed.

Evaluation of the eastern (Centrocercus urophasianus urophasianus) and western (Centrocercus urophasianus phaios) subspecies of Sage-grouse using mitochondrial control-region sequence data

USGS Publications Warehouse

Benedict, N.G.; Oyler-McCance, S.J.; Taylor, S.E.; Braun, C.E.

2003-01-01

The status of Sage-grouse (Centrocercus urophasianus) is of increasing concern, as populations throughout its range have contracted as a result of habitat loss and degradation. Historically, Sage-grouse were classified into two subspecies: eastern(C. u. urophasianus) and western Sage-grouse (C. u. phaios) based on slight differences in coloration noted among eight individuals sampled from Washington, Oregon, and California. We sequenced a rapidly evolving portion of the mitochondrial control region in 332 birds from 16 populations. Although our sampling area covers the proposed boundary between the eastern and western subspecies, no genetic evidence to support the delineation of these subspecies was found. However, a population straddling southwestern Nevada and eastern California was found to contain an unusually high proportion of unique haplotypes, consistent with its genetic isolation from other Sage-grouse populations. Of additional interest was the lack of diversity in the two populations sampled from Washington, one of which contained only a single haplotype. We suggest that multiple lines of evidence are valuable for the formulation of conservation strategies and hence the southwestern Nevada/eastern California population merits further morphological, behavioral, and molecular investigation.

The Effect of Debris-Flow Composition on Runout Distance

NASA Astrophysics Data System (ADS)

Haas, T. D.; Braat, L.; Leuven, J.; Lokhorst, I.; Kleinhans, M. G.

2014-12-01

Estimating runout distance is of major importance for the assessment and mitigation of debris-flow hazards. Debris-flow runout distance depends on debris-flow composition and topography, but state-of-the-art runout prediction methods are mainly based on topographical parameters and debris-flow volume, while composition is generally neglected or incorporated in empirical constants. Here we experimentally investigated the effect of debris-flow composition and topography on runout distance. We created the first small-scale experimental debris flows with self-formed levees, distinct lobes and morphology and texture accurately resembling natural debris flows. In general, debris-flow composition had a larger effect on runout distance than topography. Enhancing channel slope and width, outflow plain slope, debris-flow size and water fraction leads to an increase in runout distance. However, runout distance shows an optimum relation with coarse-material and clay fraction. An increase in coarse-material fraction leads to larger runout distances by increased grain collisional forces and more effective levee formation, but too much coarse debris causes a large accumulation of coarse debris at the flow front, enhancing friction and decreasing runout. An increase in clay fraction initially enlarges the volume and viscosity of the interstitial fluid, liquefying the flow and enhancing runout, while a further increase leads to very viscous flows with high yield strength, reducing runout. These results highlight the importance and further need of research on the relation between debris-flow composition and runout distance. Our experiments further provide valuable insight on the effects of debris-flow composition on depositional mechanisms and deposit morphology.

The effect of debris-flow composition on runout distance

NASA Astrophysics Data System (ADS)

de Haas, Tjalling; Braat, Lisanne; Leuven, Jasper; Lokhorst, Ivar; Kleinhans, Maarten

2015-04-01

Estimating runout distance is of major importance for the assessment and mitigation of debris-flow hazards. Debris-flow runout distance depends on debris-flow composition and topography, but state-of-the-art runout prediction methods are mainly based on topographical parameters and debris-flow volume, while composition is generally neglected or incorporated in empirical constants. Here we experimentally investigated the effect of debris-flow composition and topography on runout distance. We created the first small-scale experimental debris flows with self-formed levees, distinct lobes and morphology and texture accurately resembling natural debris flows. In general, the effect of debris-flow composition on runout distance was larger than the effect of topography. Enhancing channel slope and width, outflow plain slope, debris-flow size and water fraction leads to an increase in runout distance. However, runout distance shows an optimum relation with coarse-material and clay fraction. An increase in coarse-material fraction leads to larger runout distances by increased grain collisional forces and more effective levee formation, but too much coarse debris causes a large accumulation of coarse debris at the flow front, enhancing friction and decreasing runout. An increase in clay fraction initially enlarges the volume and viscosity of the interstitial fluid, liquefying the flow and enhancing runout, while a further increase leads to very viscous flows with high yield strength, reducing runout. These results highlight the importance and further need of research on the relation between debris-flow composition and runout distance. Our experiments further provide valuable insight on the effects of debris-flow composition on depositional mechanisms and deposit morphology.

How many species of woolly monkeys inhabit Colombian forests?

PubMed

Botero, Sergio; Rengifo, Laura Y; Bueno, Marta L; Stevenson, Pablo R

2010-12-01

There is a controversy regarding how many species the genus Lagothrix contains, since the Lagothrix lagothricha subspecies have been recently proposed to be actual species. Clarification of species status is of particular importance in the case of L. l. lugens, because it is the most endangered and its distribution is restricted to the Colombian Andes, a highly deforested region. Using cytogenetic and molecular markers, we obtained evidence indicating that the subspecies status is appropriate for the two taxa occurring in this country. We also report high levels of intraspecific variability in the karyotype. We find evidence for a late Pleistocene separation of the subspecies, and we propose it is the limited area of contact between the taxa that allowed for them to partially differentiate. © 2010 Wiley-Liss, Inc.

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

PubMed Central

Ayub, Qasim; Szpak, Michal; Frandsen, Peter; Chen, Yuan; Yngvadottir, Bryndis; Cooper, David N.; de Manuel, Marc; Hernandez-Rodriguez, Jessica; Lobon, Irene; Siegismund, Hans R.; Pagani, Luca; Quail, Michael A.; Hvilsom, Christina; Mudakikwa, Antoine; Eichler, Evan E.; Cranfield, Michael R.; Marques-Bonet, Tomas; Tyler-Smith, Chris; Scally, Aylwyn

2015-01-01

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival. PMID:25859046

Interpopulational and seasonal variation in the chemical signals of the lizard Gallotia galloti.

PubMed

García-Roa, Roberto; Megía-Palma, Rodrigo; Ortega, Jesús; Jara, Manuel; López, Pilar; Martín, José

2017-01-01

Communicative traits are strikingly diverse and may vary among populations of the same species. Within a population, these traits may also display seasonal variation. Chemical signals play a key role in the communication of many taxa. However, we still know far too little about chemical communication in some vertebrate groups. In lizards, only a few studies have examined interpopulational variation in the composition of chemical cues and signals and only one study has explored the seasonal effects. Here we sampled three subspecies of the Tenerife lizards ( Gallotia galloti ) and analyze the lipophilic fraction of their femoral gland secretions to characterize the potential interpopulational variation in the chemical signals. In addition, we assessed whether composition of these secretions differed between the reproductive and the non-reproductive season. We analyzed variations in both the overall chemical profile and the abundance of the two main compounds (cholesterol and vitamin E). Our results show interpopulational and seasonal differences in G. gallotia chemical profiles. These findings are in accordance with the high interpopulational variability of compounds observed in lizard chemical signals and show that their composition is not only shaped by selective factors linked to reproductive season.

Salmonella Prevalence and Antimicrobial Susceptibility from the National Animal Health Monitoring System Sheep 2011 Study.

PubMed

Dargatz, David A; Marshall, Katherine L; Fedorka-Cray, Paula J; Erdman, Matthew M; Kopral, Christine A

2015-12-01

Salmonella is a major cause of foodborne illness and can cause clinical disease in animals. Understanding the on-farm ecology of Salmonella will be helpful in decreasing the risk of foodborne transmission. An objective of this study was to determine the prevalence of Salmonella among fecal samples collected on sheep operations in the United States. Another objective was to compare the use of composite fecal samples with fecal samples collected from individual sheep as a tool for screening sheep flocks for Salmonella. Sheep fecal samples (individual and composite) were collected on operations in 22 states. Salmonella isolates were characterized with regard to species, serotype, and antimicrobial susceptibility profile. Most operations (72.1%) had at least one positive sample and overall 26.9% of samples were positive. The percentage of positive samples varied by animal age class. Composite and individual samples gave similar results. The majority of the isolates (94%) were Salmonella enterica subspecies diarizonae serotype 61:-:1,5,7. Nearly all of the isolates (91.2%) tested for antimicrobial susceptibility were susceptible to all antimicrobials in the panel. The findings suggest that salmonellae typically associated with foodborne disease transmission are infrequently found on sheep operations in the United States.

Complete mitochondrial genomes of the yellow-bellied slider turtle Trachemys scripta scripta and anoxia tolerant red-eared slider Trachemys scripta elegans.

PubMed

Yu, Danna; Fang, Xindong; Storey, Kenneth B; Zhang, Yongpu; Zhang, Jiayong

2016-05-01

The complete mitochondrial genomes of the yellow-bellied slider (Trachemys scripta scripta) and anoxia tolerant red-eared slider (Trachemys scripta elegans) turtles were sequenced to analyze gene arrangement. The complete mt genomes of T. s. scripta and elegans were circular molecules of 16,791 bp and 16,810 bp in length, respectively, and included an A + 1 frameshift insertion in ND3 and ND4L genes. The AT content of the overall base composition of scripta and elegans was 61.2%. Nucleotide sequence divergence of the mt-genome (p distance) between scripta and elegans was 0.4%. A detailed comparison between the mitochondrial genomes of the two subspecies is shown.

Bifidobacterium animalis subspecies lactis modulates the local immune response and glucose uptake in the small intestine of juvenile pigs infected with the parasitic nematode Ascaris suum

USDA-ARS?s Scientific Manuscript database

The probiotic bacteria Bifidobacterium animalis subspecies lactis (Bb12) or a placebo containing vehicle without Bb12 was administered orally to pregnant sows during the last trimester of pregnancy, and to their offspring from birth through the termination of the study three months later. Weaned-pig...

Effect of monensin withdrawal on intake, digestion, and ruminal fermentation parameters by Bos taurus indicus and Bos taurus taurus steers consuming bermudagrass hay

USDA-ARS?s Scientific Manuscript database

Effects of monensin withdrawal and cattle subspecies on the utilization of bermudagrass hay (14.3% CP, 72.3% NDF, and 36.9% ADF) were evaluated using ruminally cannulated steers (5 Bos Taurus indicus [BI] and 5 Bos taurus taurus [BT]). Subspecies were concurrently subjected to a 2-period, 2-treatme...

Effect of monensin inclusion on intake, digestion, and ruminal fermentation parameters by Bos taurus indicus and Bos taurus taurus steers consuming bermudagrass hay

USDA-ARS?s Scientific Manuscript database

Effects of monensin inclusion and cattle subspecies on utilization of bermudagrass hay (13.7% CP, 77.3% NDF, and 38.8% ADF) were evaluated using ruminally cannulated steers (5 Bos taurus indicus [BI] and 5 Bos taurus taurus [BT]; 398 kg BW). Subspecies were concurrently subjected to a 2-period, 2-t...

Narrow hybrid zone between two subspecies of big sagebrush (Artemisia tridentata: Asteraceae): XI. Plant-insect interactions in reciprocal transplant gardens

Treesearch

John H. Graham; E. Durant McArthur; D. Carl Freeman

2001-01-01

Basin big sagebrush (Artemisia tridentata ssp. tridentata) and mountain big sagebrush (A. t. ssp. vaseyana) hybridize in a narrow zone near Salt Creek, Utah. Reciprocal transplant experiments in this hybrid zone demonstrate that hybrids are more fit than either parental subspecies, but only in the hybrid zone. Do hybrids experience greater, or lesser, use by...

Genotyping of Burkholderia mallei: Effective Subspecies Discrimination Using Ribotyping and Repeat Sequences

DTIC Science & Technology

2005-10-01

1 U.S. Army Soldier and Biological Chemical Command Genotyping of Burkholderia mallei : Effective Subspecies Discrimination using Ribotyping and...number. 1. REPORT DATE 01 OCT 2005 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Genotyping of Burkholderia mallei : Effective...34Also can involve physical, chemical or immunological characteristics 3 Edgewood Chemical Biological Center Burkholderia mallei Biology and Pathogenesis

Evaluation of the genetic structure present in natural populations of four subspecies of black cherry (Prunus serotina Ehrh.) from North America using SSR markers

USDA-ARS?s Scientific Manuscript database

Black cherry (Prunus serotina) is a fruit tree native to North America, and almost all parts of this plant have some use. This species is a complex of five subspecies with morphological differences and distinctive habitats. The genetic structure of 18 natural populations of black cherry was evaluate...

Phylogenetic analysis of Haemaphysalis erinacei Pavesi, 1884 (Acari: Ixodidae) from China, Turkey, Italy and Romania.

PubMed

Hornok, Sándor; Wang, Yuanzhi; Otranto, Domenico; Keskin, Adem; Lia, Riccardo Paolo; Kontschán, Jenő; Takács, Nóra; Farkas, Róbert; Sándor, Attila D

2016-12-15

Haemaphysalis erinacei is one of the few ixodid tick species for which valid names of subspecies exist. Despite their disputed taxonomic status in the literature, these subspecies have not yet been compared with molecular methods. The aim of the present study was to investigate the phylogenetic relationships of H. erinacei subspecies, in the context of the first finding of this tick species in Romania. After morphological identification, DNA was extracted from five adults of H. e. taurica (from Romania and Turkey), four adults of H. e. erinacei (from Italy) and 17 adults of H. e. turanica (from China). From these samples fragments of the cytochrome c oxidase subunit 1 (cox1) and 16S rRNA genes were amplified via PCR and sequenced. Results showed that cox1 and 16S rRNA gene sequence divergences between H. e. taurica from Romania and H. e. erinacei from Italy were below 2%. However, the sequence divergences between H. e. taurica from Romania and H. e. turanica from China were high (up to 7.3% difference for the 16S rRNA gene), exceeding the reported level of sequence divergence between closely related tick species. At the same time, two adults of H. e. taurica from Turkey had higher 16S rRNA gene similarity to H. e. turanica from China (up to 97.5%) than to H. e. taurica from Romania (96.3%), but phylogenetically clustered more closely to H. e. taurica than to H. e. turanica. This is the first finding of H. erinacei in Romania, and the first (although preliminary) phylogenetic comparison of H. erinacei subspecies. Phylogenetic analyses did not support that the three H. erinacei subspecies evaluated here are of equal taxonomic rank, because the genetic divergence between H. e. turanica from China and H. e. taurica from Romania exceeded the usual level of sequence divergence between closely related tick species, suggesting that they might represent different species. Therefore, the taxonomic status of the subspecies of H. erinacei needs to be revised based on a larger number of specimens collected throughout its geographical range.

Does the "kamaroma"-plastron pattern morph occur in both Philippine subspecies of the turtle Cuora amboinensis?

USGS Publications Warehouse

Ernst, C.H.; Laemmerzahl, A.F.; Lovich, J.E.

2011-01-01

Two subspecies of the turtle Cuora amboinensis have been reported from the Philippine Islands, C. a. amboinensis and C. a. kamaroma, distinguished primarily by their carapace morphology, and secondarily by their plastron patterns. We assessed the utility of using shell and postorbital-stripe morphology instead of plastron patterns to distinguish these putative taxa. Adult C. amboinensis from the Philippines were examined to determine the extent of occurrence of C. a. kamaroma on the islands. Several morphological carapace characters and one based on the postorbital stripe were found to differ significantly between the subspecies C. a. amboinensis and C. a. kamaroma, and were used to assign turtles to subspecies. Use of these characters often resulted in conflicting subspecific identifications for those previously assigned by their plastron patterns to C. a. kamaroma. This poses important questions. Using the carapace and postorbital-stripe characters, 95.2% of the turtles in the mainland chain of islands were identified as C. a. amboinensis, and only 4.8% as C. a. kamaroma. Surprisingly, most of those assigned to C. a. kamaroma were from the northern islands of Babuyan and Luzon, not from the southern main chain island populations closest to the likely geographic area of invasion by that subspecies. This may be due to the common practice of importation of C. a. kamaroma into these northern islands, especially Luzon, for food. Turtles with kamaroma-like or C. a. amboinensis ?? C. a. kamaroma plastron patterns have been reported from the Sulu Archipelago and Busuanga/Palawan chain, and those specimens we examined from those islands confirmed this. The questions of whether or not C. a. kamaroma actually occurs in the Philippines and, if so, what is its island distribution, cannot be answered at this time. All specimens previously identified as C. a. kamaroma by their plastron-patterns should be re-evaluated, using the significant carapace and postorbital-stripe characters identified by Rummler & Fritz (1991) and in this paper. Philippine Cuora amboinensis cannot be identified to subspecies by their plastron patterns alone. ?? Biological Society of Washington.

A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus.

PubMed

Tan, Joon Liang; Khang, Tsung Fei; Ngeow, Yun Fong; Choo, Siew Woh

2013-12-13

Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification. A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977T. This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus.

PubMed

Grapputo, A; Pilastro, A; Marin, G

1998-09-01

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia, along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by FST and RST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.

Ways to be different: Foraging adaptations that facilitate higher intake rates in a northerly wintering shorebird compared with a low-latitude conspecific

USGS Publications Warehouse

Ruthrauff, Daniel R.; Dekinga, Anne; Gill, Robert E.; van Gils, Jan A.; Piersma, Theunis

2015-01-01

At what phenotypic level do closely related subspecies that live in different environments differ with respect to food detection, ingestion and processing? This question motivated an experimental study on rock sandpipers (Calidris ptilocnemis). The species' nonbreeding range spans 20 deg of latitude, the extremes of which are inhabited by two subspecies: C. p. ptilocnemis that winters primarily in upper Cook Inlet, Alaska (61°N) and C. p. tschuktschorum that overlaps slightly with C. p. ptilocnemis but whose range extends much farther south (∼40°N). In view of the strongly contrasting energetic demands of their distinct nonbreeding distributions, we conducted experiments to assess the behavioral, physiological and sensory aspects of foraging and we used the bivalve Macoma balthica for all trials. C. p. ptilocnemis consumed a wider range of prey sizes, had higher maximum rates of energy intake, processed shell waste at higher maximum rates and handled prey more quickly. Notably, however, the two subspecies did not differ in their abilities to find buried prey. The subspecies were similar in size and had equally sized gizzards, but the more northern ptilocnemis individuals were 10–14% heavier than their same-sex tschuktschorum counterparts. The higher body mass in ptilocnemis probably resulted from hypertrophy of digestive organs (e.g. intestine, liver) related to digestion and nutrient assimilation. Given the previously established equality of the metabolic capacities of the two subspecies, we propose that the high-latitude nonbreeding range of ptilocnemis rock sandpipers is primarily facilitated by digestive (i.e. physiological) aspects of their foraging ecology rather than behavioral or sensory aspects.

Phylogeographic study of Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis Rousi) reveals two distinct haplotype groups and multiple microrefugia on the Qinghai-Tibet Plateau

PubMed Central

Wang, Hongfang; Liu, Han; Yang, Mingbo; Bao, Lei; Ge, Jianping

2014-01-01

Historical climate change can shape the genetic pattern of a species. Studies on this phenomenon provide great advantage in predicting the response of species to current and future global climate change. Chinese seabuckthorn (Hippophae rhamnoides subsp. sinensis) is one of the most important cultivated plants in Northwest China. However, the subspecies history and the potential genetic resources within the subspecies range remain unclear. In this study, we utilized two intergenic chloroplast regions to characterize the spatial genetic distribution of the species. We found 19 haplotypes in total, 12 of which were unique to the Chinese seabuckthorn. The populations observed on the Qinghai-Tibet Plateau (QTP) consisted of most of the haplotypes, while in the northeast of the range of the subspecies, an area not on the QTP, only four haplotypes were detected. Our study also revealed two distinct haplotype groups of the subspecies with a sharp transition region located in the south of the Zoige Basin. 89.96% of the genetic variation located between the regions. Mismatch analysis indicated old expansions of these two haplotype groups, approximately around the early stage of Pleistocene. Additional morphological proofs from existing studies and habitat differentiation supported a long independent colonization history among the two regions. Potential adaptation probably occurred but needs more genome and morphology data in future. Chinese seabuckthorn have an older population expansion compared with subspecies in Europe. The lack of large land ice sheets and the heterogeneous landscape of the QTP could have provided extensive microrefugia for Chinese seabuckthorn during the glaciation period. Multiple localities sustaining high-frequency private haplotypes support this hypothesis. Our study gives clear insight into the distribution of genetic resources and the evolutionary history of Chinese seabuckthorn. PMID:25540697

Wintering ecology of sympatric subspecies of Sandhill Crane: Correlations between body size, site fidelity, and movement patterns

USGS Publications Warehouse

Ivey, Gary L.; Dugger, Bruce D.; Herziger, Caroline P.; Casazza, Michael L.; Fleskes, Joseph P.

2015-01-01

Body size is known to correlate with many aspects of life history in birds, and this knowledge can be used to manage and conserve bird species. However, few studies have compared the wintering ecology of sympatric subspecies that vary significantly in body size. We used radiotelemetry to examine the relationship between body size and site fidelity, movements, and home range in 2 subspecies of Sandhill Crane (Grus canadensis) wintering in the Sacramento–San Joaquin Delta of California, USA. Both subspecies showed high interannual return rates to the Delta study area, but Greater Sandhill Cranes (G. c. tabida) showed stronger within-winter fidelity to landscapes in our study region and to roost complexes within landscapes than did Lesser Sandhill Cranes (G. c. canadensis). Foraging flights from roost sites were shorter for G. c. tabida than for G. c. canadensis (1.9 ± 0.01 km vs. 4.5 ± 0.01 km, respectively) and, consequently, the mean size of 95% fixed-kernel winter home ranges was an order of magnitude smaller for G. c. tabida than for G. c. canadensis (1.9 ± 0.4 km2 vs. 21.9 ± 1.9 km2, respectively). Strong site fidelity indicates that conservation planning to manage for adequate food resources around traditional roost sites can be effective for meeting the habitat needs of these cranes, but the scale of conservation efforts should differ by subspecies. Analysis of movement patterns suggests that conservation planners and managers should consider all habitats within 5 km of a known G. c. tabida roost and within 10 km of a G. c. canadensis roost when planning for habitat management, mitigation, acquisition, and easements.

Recent Evolutionary Radiation and Host Plant Specialization in the Xylella fastidiosa Subspecies Native to the United States

PubMed Central

Vickerman, Danel B.; Bromley, Robin E.; Russell, Stephanie A.; Hartman, John R.; Morano, Lisa D.; Stouthamer, Richard

2013-01-01

The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 “non-IHR” isolates, 2 minimally recombinant “intermediate” ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (ρ/θ = 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): “almond,” “peach,” and “oak” types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity. PMID:23354698

Range-Wide Snow Leopard Phylogeography Supports Three Subspecies.

PubMed

Janecka, Jan E; Zhang, Yuguang; Li, Diqiang; Munkhtsog, Bariushaa; Bayaraa, Munkhtsog; Galsandorj, Naranbaatar; Wangchuk, Tshewang R; Karmacharya, Dibesh; Li, Juan; Lu, Zhi; Uulu, Kubanychbek Zhumabai; Gaur, Ajay; Kumar, Satish; Kumar, Kesav; Hussain, Shafqat; Muhammad, Ghulam; Jevit, Matthew; Hacker, Charlotte; Burger, Pamela; Wultsch, Claudia; Janecka, Mary J; Helgen, Kristofer; Murphy, William J; Jackson, Rodney

2017-09-01

The snow leopard, Panthera uncia, is an elusive high-altitude specialist that inhabits vast, inaccessible habitat across Asia. We conducted the first range-wide genetic assessment of snow leopards based on noninvasive scat surveys. Thirty-three microsatellites were genotyped and a total of 683 bp of mitochondrial DNA sequenced in 70 individuals. Snow leopards exhibited low genetic diversity at microsatellites (AN = 5.8, HO = 0.433, HE = 0.568), virtually no mtDNA variation, and underwent a bottleneck in the Holocene (∼8000 years ago) coinciding with increased temperatures, precipitation, and upward treeline shift in the Tibetan Plateau. Multiple analyses supported 3 primary genetic clusters: (1) Northern (the Altai region), (2) Central (core Himalaya and Tibetan Plateau), and (3) Western (Tian Shan, Pamir, trans-Himalaya regions). Accordingly, we recognize 3 subspecies, Panthera uncia irbis (Northern group), Panthera uncia uncia (Western group), and Panthera uncia uncioides (Central group) based upon genetic distinctness, low levels of admixture, unambiguous population assignment, and geographic separation. The patterns of variation were consistent with desert-basin "barrier effects" of the Gobi isolating the northern subspecies (Mongolia), and the trans-Himalaya dividing the central (Qinghai, Tibet, Bhutan, and Nepal) and western subspecies (India, Pakistan, Tajikistan, and Kyrgyzstan). Hierarchical Bayesian clustering analysis revealed additional subdivision into a minimum of 6 proposed management units: western Mongolia, southern Mongolia, Tian Shan, Pamir-Himalaya, Tibet-Himalaya, and Qinghai, with spatial autocorrelation suggesting potential connectivity by dispersing individuals up to ∼400 km. We provide a foundation for global conservation of snow leopard subspecies, and set the stage for in-depth landscape genetics and genomic studies. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Male death resulting from hybridization between subspecies of the gypsy moth, Lymantria dispar

PubMed Central

Higashiura, Y; Yamaguchi, H; Ishihara, M; Ono, N; Tsukagoshi, H; Yokobori, S; Tokishita, S; Yamagata, H; Fukatsu, T

2011-01-01

We explored the origin of all-female broods resulting from male death in a Hokkaido population of Lymantria dispar through genetic crosses based on the earlier experiments done by Goldschmidt and by testing for the presence of endosymbionts that are known to cause male killing in some insect species. The mitochondrial DNA haplotypes of the all-female broods in Hokkaido were different from those of normal Hokkaido females and were the same as those widely distributed in Asia, including Tokyo (TK). Goldschmidt obtained all-female broods through backcrossing, that is, F1 females obtained by a cross between TK females (L. dispar japonica) and Hokkaido males (L. dispar praeterea) mated with Hokkaido males. He also obtained all-male broods by mating Hokkaido females with TK males. Goldschmidt inferred that female- and male-determining factors were weakest in the Hokkaido subspecies and stronger in the Honshu (TK) subspecies. According to his theory, the females of all-female broods mated with Honshu males should produce normal sex-ratio broods, whereas weaker Hokkaido sexes would be expected to disappear in F1 or F2 generations after crossing with the Honshu subspecies. We confirmed both of Goldschmidt's results: in the case of all-female broods mated with Honshu males, normal sex-ratio broods were produced, but we obtained only all-female broods in the Goldschmidt backcross and obtained an all-male brood in the F1 generation of a Hokkaido female crossed with a TK male. We found no endosymbionts in all-female broods by 4,′6-diamidino-2-phenylindole (DAPI) staining. Therefore, the all-female broods observed in L. dispar are caused by some incompatibilities between Honshu and Hokkaido subspecies. PMID:20628417

Recent evolutionary radiation and host plant specialization in the Xylella fastidiosa subspecies native to the United States.

PubMed

Nunney, Leonard; Vickerman, Danel B; Bromley, Robin E; Russell, Stephanie A; Hartman, John R; Morano, Lisa D; Stouthamer, Richard

2013-04-01

The bacterial pathogen, Xylella fastidiosa, infects many plant species in the Americas, making it a good model for investigating the genetics of host adaptation. We used multilocus sequence typing (MLST) to identify isolates of the native U.S. subsp. multiplex that were largely unaffected by intersubspecific homologous recombination (IHR) and to investigate how their evolutionary history influences plant host specialization. We identified 110 "non-IHR" isolates, 2 minimally recombinant "intermediate" ones (including the subspecific type), and 31 with extensive IHR. The non-IHR and intermediate isolates defined 23 sequence types (STs) which we used to identify 22 plant hosts (73% trees) characteristic of the subspecies. Except for almond, subsp. multiplex showed no host overlap with the introduced subspecies (subspecies fastidiosa and sandyi). MLST sequences revealed that subsp. multiplex underwent recent radiation (<25% of subspecies age) which included only limited intrasubspecific recombination (ρ/θ = 0.02); only one isolated lineage (ST50 from ash) was older. A total of 20 of the STs grouped into three loose phylogenetic clusters distinguished by nonoverlapping hosts (excepting purple leaf plum): "almond," "peach," and "oak" types. These host differences were not geographical, since all three types also occurred in California. ST designation was a good indicator of host specialization. ST09, widespread in the southeastern United States, only infected oak species, and all peach isolates were ST10 (from California, Florida, and Georgia). Only ST23 had a broad host range. Hosts of related genotypes were sometimes related, but often host groupings crossed plant family or even order, suggesting that phylogenetically plastic features of hosts affect bacterial pathogenicity.

The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification--implications for forensic purposes.

PubMed

Kitpipit, Thitika; Tobe, Shanan S; Kitchener, Andrew C; Gill, Peter; Linacre, Adrian

2012-03-01

The tiger (Panthera tigris) is currently listed on Appendix I of the Convention on the International Trade in Endangered Species of Wild Fauna and Flora; this affords it the highest level of international protection. To aid in the investigation of alleged illegal trade in tiger body parts and derivatives, molecular approaches have been developed to identify biological material as being of tiger in origin. Some countries also require knowledge of the exact tiger subspecies present in order to prosecute anyone alleged to be trading in tiger products. In this study we aimed to develop and validate a reliable single assay to identify tiger species and subspecies simultaneously; this test is based on identification of single nucleotide polymorphisms (SNPs) within the tiger mitochondrial genome. The mitochondrial DNA sequence from four of the five extant putative tiger subspecies that currently exist in the wild were obtained and combined with DNA sequence data from 492 tiger and 349 other mammalian species available on GenBank. From the sequence data a total of 11 SNP loci were identified as suitable for further analyses. Five SNPs were species-specific for tiger and six amplify one of the tiger subspecies-specific SNPs, three of which were specific to P. t. sumatrae and the other three were specific to P. t. tigris. The multiplex assay was able to reliably identify 15 voucher tiger samples. The sensitivity of the test was 15,000 mitochondrial DNA copies (approximately 0.26 pg), indicating that it will work on trace amounts of tissue, bone or hair samples. This simple test will add to the DNA-based methods currently being used to identify the presence of tiger within mixed samples. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Fred's Flow (Canada) and Murphy Well (Australia): thick komatiitic lava flows with contrasting compositions, emplacement mechanisms and water contents

NASA Astrophysics Data System (ADS)

Siégel, Coralie; Arndt, Nicholas; Barnes, Stephen; Henriot, Anne-Laure; Haenecour, Pierre; Debaille, Vinciane; Mattielli, Nadine

2014-12-01

Two Archaean komatiitic flows, Fred's Flow in Canada and the Murphy Well Flow in Australia, have similar thicknesses (120 and 160 m) but very different compositions and internal structures. Their contrasting differentiation profiles are keys to determine the cooling and crystallization mechanisms that operated during the eruption of Archaean ultramafic lavas. Fred's Flow is the type example of a thick komatiitic basalt flow. It is strongly differentiated and consists of a succession of layers with contrasting textures and compositions. The layering is readily explained by the accumulation of olivine and pyroxene in a lower cumulate layer and by evolution of the liquid composition during downward growth of spinifex-textured rocks within the upper crust. The magmas that erupted to form Fred's Flow had variable compositions, ranging from 12 to 20 wt% MgO, and phenocryst contents from 0 to 20 vol%. The flow was emplaced by two pulses. A first ~20-m-thick pulse was followed by another more voluminous but less magnesian pulse that inflated the flow to its present 120 m thickness. Following the second pulse, the flow crystallized in a closed system and differentiated into cumulates containing 30-38 wt% MgO and a residual gabbroic layer with only 6 wt% MgO. The Murphy Well Flow, in contrast, has a remarkably uniform composition throughout. It comprises a 20-m-thick upper layer of fine-grained dendritic olivine and 2-5 vol% amygdales, a 110-120 m intermediate layer of olivine porphyry and a 20-30 m basal layer of olivine orthocumulate. Throughout the flow, MgO contents vary little, from only 30 to 33 wt%, except for the slightly more magnesian basal layer (38-40 wt%). The uniform composition of the flow and dendritic olivine habits in the upper 20 m point to rapid cooling of a highly magnesian liquid with a composition like that of the bulk of the flow. Under equilibrium conditions, this liquid should have crystallized olivine with the composition Fo94.9, but the most magnesian composition measured by electron microprobe in samples from the flow is Fo92.9. To explain these features, we propose that the parental liquid contained around 32 wt% MgO and 3 wt% H2O. This liquid degassed during the eruption, creating a supercooled liquid that solidified quickly and crystallized olivine with non-equilibrium textures and compositions.

Physico-mechanical and thermal characteristics of commercially available and newly developed dental flowable composites

NASA Astrophysics Data System (ADS)

Kamalak, Hakan; Canbay, C. Aksu; Yiğit, Oktay; Altin, Serdar

2018-03-01

In this study, we investigated the structural stability, thermal conductivity, thermal analysis, materials' homogeneity of newly developed flowable composites. 6 different dental flowable composite resins; Grandio Flow (GF), Charisma Flow (CF), Tetric N Flow (TNF), Clearfil Majesty Flow (CMF),3M Filtek Ultimate Flow (3MFU), Voco Amaris Flow (VFA) were used. Restorations were made in standard teflon molds and the materials were light-cured for 20s in a 6 mm × 2 mm teflon mould. After polymerization, samples were kept in distilled water at 37 °C/24 h .It was found that the composites have multiphase component such as metallic dopant and organic binder. The XRD investigation showed that there was a broad halo in the pattern which indicates the organic section in the composites. The FTIR results indicate the bond structure of the composites. The temperature dependence of the thermal conductivity of the composites were found below to 5 mW/K value depending on the type of the composites, which are low enough for dental application. The micro-hardness of the samples was analyzed and the result was compared.

Effects of debris flow composition on runout, depositional mechanisms, and deposit morphology in laboratory experiments

NASA Astrophysics Data System (ADS)

Haas, Tjalling; Braat, Lisanne; Leuven, Jasper R. F. W.; Lokhorst, Ivar R.; Kleinhans, Maarten G.

2015-09-01

Predicting debris flow runout is of major importance for hazard mitigation. Apart from topography and volume, runout distance and area depends on debris flow composition and rheology, but how is poorly understood. We experimentally investigated effects of composition on debris flow runout, depositional mechanisms, and deposit geometry. The small-scale experimental debris flows were largely similar to natural debris flows in terms of flow behavior, deposit morphology, grain size sorting, channel width-depth ratio, and runout. Deposit geometry (lobe thickness and width) in our experimental debris flows is largely determined by composition, while the effects of initial conditions of topography (i.e., outflow plain slope and channel slope and width) and volume are negligible. We find a clear optimum in the relations of runout with coarse-material fraction and clay fraction. Increasing coarse-material concentration leads to larger runout. However, excess coarse material results in a large accumulation of coarse debris at the flow front and enhances diffusivity, increasing frontal friction and decreasing runout. Increasing clay content initially enhances runout, but too much clay leads to very viscous flows, reducing runout. Runout increases with channel slope and width, outflow plain slope, debris flow volume, and water fraction. These results imply that debris flow runout depends at least as much on composition as on topography. This study improves understanding of the effects of debris flow composition on runout and may aid future debris flow hazard assessments.

Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle.

PubMed

Kudo, Yuko; Oki, Kaihei; Watanabe, Koichi

2012-11-01

Although four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii, the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii. Together, the results of phenotypic characterization, DNA-DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7%) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221(T) (=JCM 17838(T) =DSM 24966(T)).

Dispersal ecology of lodgepole pine (Pinus contorta Dougl.) in its native environment as related to Swedish forestry

USGS Publications Warehouse

Despain, Don G.

2001-01-01

Lodgepole pine (Pinus contorta Dougl.) covers extensive areas of the mountains of western North America. It has evolved into four subspecies, each adapted to slightly different environmental conditions. All are adapted to reproduce following fire. Subspecies latifolia is the most extensive and economically important in North America. Serotiny is common in this subspecies, but trees bearing nonserotinous cones can be found in most stands, sometimes constituting more that 70% of the trees. Cone crops are produced yearly and seed loss to seed predators, insects and diseases are minimal. Germination and establishment occurs across a broad range of conditions allowing lodgepole pine to grow on poor sites as well as highly productive sites. These characteristics give lodgepole pine the ability to be highly invasive in new areas of suitable habitat.

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

PubMed

Xue, Yali; Prado-Martinez, Javier; Sudmant, Peter H; Narasimhan, Vagheesh; Ayub, Qasim; Szpak, Michal; Frandsen, Peter; Chen, Yuan; Yngvadottir, Bryndis; Cooper, David N; de Manuel, Marc; Hernandez-Rodriguez, Jessica; Lobon, Irene; Siegismund, Hans R; Pagani, Luca; Quail, Michael A; Hvilsom, Christina; Mudakikwa, Antoine; Eichler, Evan E; Cranfield, Michael R; Marques-Bonet, Tomas; Tyler-Smith, Chris; Scally, Aylwyn

2015-04-10

Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival. Copyright © 2015, American Association for the Advancement of Science.

Nuclear mtDNA pseudogenes as a source of new variants of mitochondrial genes: A case study of Siberian rubythroat Luscinia calliope (muscicapidae, aves).

PubMed

Spiridonova, L N; Red'kin, Ya A; Valchuk, O P

2016-01-01

First evidence for the presence of copies of mitochondrial cytochrome b gene of the subspecies group Luscinia calliope anadyrensis-L. c. camtschatkensis in the nuclear genome of nominative L. c. calliope was obtained, which indirectly indicates the nuclear origin of the subspecies-specific mitochondrial haplotypes in Siberian rubythroat. This fact clarifies the appearance of mitochondrial haplotypes of eastern subspecies by exchange between the homologous regions of the nuclear and mitochondrial genomes followed by fixation by the founder effect. This is the first study to propose a mechanism of DNA fragment exchange between the nucleus and mitochondria (intergenomic recombination) and to show the role of nuclear copies of mtDNA as a source of new taxon-specific mitochondrial haplotypes, which implies their involvement in the microevolutionary processes and morphogenesis.

Ecology, Epidemiology and Disease Management of Ralstonia syzygii in Indonesia.

PubMed

Safni, Irda; Subandiyah, Siti; Fegan, Mark

2018-01-01

Ralstonia solanacearum species complex phylotype IV strains, which have been primarily isolated from Indonesia, Australia, Japan, Korea, and Malaysia, have undergone recent taxonomic and nomenclatural changes to be placed in the species Ralstonia syzygii . This species contains three subspecies; Ralstonia syzygii subsp. syzygii , a pathogen causing Sumatra disease of clove trees in Indonesia, Ralstonia syzygii subsp. indonesiensis , the causal pathogen of bacterial wilt disease on a wide range of host plants, and Ralstonia syzygii subsp. celebesensis , the causal pathogen of blood disease on Musa spp. In Indonesia, these three subspecies have devastated the cultivation of susceptible host plants which have high economic value. Limited knowledge on the ecology and epidemiology of the diseases has hindered the development of effective control strategies. In this review, we provide insights into the ecology, epidemiology and disease control of these three subspecies of Ralstonia syzygii .

Habitat selection of Northern Saw-whet Owls (Aegolius acadicus brooksi) on the Queen Charlotte Islands, British Columbia

Treesearch

Michael Gill; Richard J. Cannings

1997-01-01

The Northern Saw-whet Owl of the Queen Charlotte Islands, British Columbia is recognized as a distinct subspecies Aegolius acadicus brooksi. Little is known of the biology of this subspecies, and no nests have ever been found. We surveyed for Northern Saw-whet Owls on the Queen Charlotte Islands between 4 May and 28 May, 1996 establishing 10 survey...

Marine mammal subspecies in the age of genetics: Introductory remarks from the Associate Editor and Editor-in-Chief of Marine Mammal Science

Treesearch

Michael K. Schwartz; Daryl J. Boness

2017-01-01

Almost every conservation genetics and evolutionary biology textbook has a section questioning: "What is a species or subspecies?" It has been one of the most discussed, nearly unanswerable questions in all of biology. At issue is how to logically divide a variable that is generally continuous, with some occasional discrete breaks. Answering this question is...

The other way around: probiotic Lactobacillus acidophilus NP51 restrict progression of Mycobacterium avium subspecies paratuberculosis (MAP) infection in Balb/c mice via activiation of CD8 alpha+ immune cell-mediated immunity

USDA-ARS?s Scientific Manuscript database

The objective of this study was to examine the immune-modulating effects of feeding a novel probiotic Lactobacillus acidophilus strain NP51 to specific pathogen-free Balb/c mice challenged with Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne’s disease (JD) in rumi...

The other way around: Probiotic lactobacillus acidophilus NP51 restricts progression of Mycobacterium avium subspecies paratuberculosis (MAP) infection in Balb/c mice through activation of CD8+ T cell-mediated immunity

USDA-ARS?s Scientific Manuscript database

The objective of this study was to examine immune effects of feeding novel probiotic Lactobacillus acidophilus strain NP51 to specific pathogen-free Balb/c mice challenged with Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne’s disease (JD). We hypothesized that fe...

Seasonal trends in intrapack aggression of captive wolves (Canis lupus) and wolf-dog crosses: implications for management in mixed-subspecies exhibits.

PubMed

Mehrkam, Lindsay R; Thompson, Roger K R

2015-01-01

Mixed-species exhibits are becoming increasingly common in the captive management of a wide range of species. Systematic evaluations of enclosures consisting of multiple subspecies, however, are relatively infrequent. The aim of this study was to measure seasonal trends in aggressive behaviors within a captive pack of wolves and wolf-dog crosses in a sanctuary setting. The frequency of intrapack social behaviors occurring within scan-sampling intervals was recorded for wolves and wolf-dog crosses during autumn, winter, and spring (2008-2009). Both subspecies displayed distinct seasonal trends in aggression. Wolf-dog crosses exhibited overall higher levels of aggression than wolves, although these instances were mostly noncontact and no significant differences were observed in the relative frequencies of aggressive behaviors between subspecies during any season. These findings suggest that wolves and wolf-dog crosses may be housed successfully given continuous behavioral monitoring, and these findings represent the first empirical account of wolf-dog cross behavior directly compared to wolves. Future studies should be conducted with similar packs to determine if this dynamic is universal. Such research will aid in the development of management and welfare strategies for captive facilities that provide permanent residences for wolves and wolf-dog crosses.

Subspecies status and population genetic structure in Piping Plover (Charadrius melodus)

USGS Publications Warehouse

Miller, M.P.; Haig, S.M.; Gratto-Trevor, C. L.; Mullins, T.D.

2010-01-01

Piping Plover (Charadrius melodus) is a migratory shorebird that is listed as endangered in Canada and the U.S. Great Lakes and as threatened throughout the rest of its breeding and winter range. We undertook a comprehensive molecular-genetic investigation to (1) address subspecific taxonomy, (2) characterize population genetic structure, and (3) infer past bottlenecks and demographic processes in this species. Analyses included individuals from 23 U.S. states and Canadian provinces and were based on mitochondrial DNA sequences (580 base pairs, n = 245) and 8 nuclear microsatellite loci (n = 229). Our findings provide support for separate Atlantic and Interior subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies and should be referred to as C. m. circumcinctus. Population genetic analyses illustrated stronger genetic structure among Atlantic than among Interior birds, which may reflect reduced natal- and breeding-site fidelity of Interior individuals. Furthermore, analyses suggested that Interior birds previously experienced genetic bottlenecks, whereas there was no evidence of such patterns in the Atlantic subspecies. We interpret these results in light of 25 years of range-wide census data. Overall, differences between Interior and Atlantic Piping Plovers may reflect differences in spatiotemporal stability of nesting habitat between regions. ?? 2010 The American Ornithologists' Union.

Emendation of genus Achromobacter and Achromobacter xylosoxidans (Yabuuchi and Yano) and proposal of Achromobacter ruhlandii (Packer and Vishniac) comb. nov., Achromobacter piechaudii (Kiredjian et al.) comb. nov., and Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) comb. nov.

PubMed

Yabuuchi, E; Kawamura, Y; Kosako, Y; Ezaki, T

1998-01-01

Based on the results of GC content determination and 16S rRNA sequence analysis among the type strains of Achromobacter xylosoxidans, 4 Alcaligenes species, 5 Bordetella species, and 12 species of 4 other genera, the separation of genus Achromobacter Yabuuchi and Yano 1981, with the type species Achromobacter xylosoxidans, is confirmed. Alcaligenes ruhlandii (Packer and Vishniac) Aragno and Schlegel 1992 is a distinct species and not a senior synonym of Achromobacter xylosoxidans. Alcaligenes ruhlandii and Alcaligenes piechaudii Kiredjian et al 1986 are transferred to genus Achromobacter. Thus 2 new combinations, Achromobacter ruhlandii (Packer and Vishniac) and Achromobacter piechaudii (Kiredjian et al) are proposed; their type strains are ATCC 15749 and ATCC 43552, respectively. Alcaligenes denitrificans Rüger and Tan 1983 is also transferred to genus Achromobacter and ranked down to the subspecies of Achromobacter xylosoxidans. Thus a new subspecies name, Achromobacter xylosoxidans subsp. denitrificans (Rüger and Tan) is proposed. The type strain of the subspecies is ATCC 15173. This proposal automatically creates type subspecies, Achromobacter xylosoxidans subsp. xylosoxidans, with type strain ATCC 27061. An emended description of genus Achromobacter and of type species Achromobacter xylosoxidans are given.

Phylogeography and population genetic structure of double-crested cormorants (Phalacrocorax auritus)

USGS Publications Warehouse

Mercer, Dacey; Haig, Susan M.; Roby, Daniel D.

2013-01-01

is genetically divergent from other populations in North America (net sequence divergence = 5.85 %;UST for mitochondrial control region = 0.708; FST for microsatellite loci = 0.052). Historical records, contemporary population estimates, and field observations are consistent with recognition of the Alaskan subspecies as distinct and potentially of conservation interest. Our data also indicated the presence of another divergent lineage, associated with the southwestern portion of the species range, as evidenced by highly unique haplotypes sampled in southern California. In contrast, there was little support for recognition of subspecies within the conterminous U.S. and Canada. Rather than genetically distinct regions corresponding to the putative subspecies [P. a. albociliatus (Pacific), P. a. auritus (Interior and North Atlantic), and P. a. floridanus (Southeast)], we observed a distribution of genetic variation consistent with a pattern of isolation by distance. This pattern implies that genetic differences across the range are due to geographic distance, rather than discrete subspecific breaks. Although three of the four traditional subspecies were not genetically distinct, possible demographic separation, habitat differences, and documented declines at some colonies within the regions, suggests that the Pacific and possibly North Atlantic portions of the breeding range may warrant differential consideration from the Interior and Southeast breeding regions.

Comparative Genomic Analyses of Clavibacter michiganensis subsp. insidiosus and Pathogenicity on Medicago truncatula.

PubMed

Lu, You; Ishimaru, Carol A; Glazebrook, Jane; Samac, Deborah A

2018-02-01

Clavibacter michiganensis is the most economically important gram-positive bacterial plant pathogen, with subspecies that cause serious diseases of maize, wheat, tomato, potato, and alfalfa. Much less is known about pathogenesis involving gram-positive plant pathogens than is known for gram-negative bacteria. Comparative genome analyses of C. michiganensis subspecies affecting tomato, potato, and maize have provided insights on pathogenicity. In this study, we identified strains of C. michiganensis subsp. insidiosus with contrasting pathogenicity on three accessions of the model legume Medicago truncatula. We generated complete genome sequences for two strains and compared these to a previously sequenced strain and genome sequences of four other subspecies. The three C. michiganensis subsp. insidiosus strains varied in gene content due to genome rearrangements, most likely facilitated by insertion elements, and plasmid number, which varied from one to three depending on strain. The core C. michiganensis genome consisted of 1,917 genes, with 379 genes unique to C. michiganensis subsp. insidiosus. An operon for synthesis of the extracellular blue pigment indigoidine, enzymes for pectin degradation, and an operon for inositol metabolism are among the unique features. Secreted serine proteases belonging to both the pat-1 and ppa families were present but highly diverged from those in other subspecies.

Genetics Show Current Decline and Pleistocene Expansion in Northern Spotted Owls

USGS Publications Warehouse

Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

2008-01-01

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the U.S. Endangered Species Act. Because of concern for persistence of the subspecies, logging on Federal lands in the U.S. Pacific Northwest was dramatically reduced under the Northwest Forest Plan in 1994. Despite protection of its remaining forest habitat, recent field studies show continued demographic declines of northern spotted owls. One potential threat to northern spotted owls that has not yet been shown is loss of genetic variation from population bottlenecks that can increase inbreeding depression and decrease adaptive potential. Here, we show recent genetic bottlenecks in northern spotted owls using a large genetic dataset (352 individuals from across the subspecies' range and 11 microsatellite loci). The signature of bottlenecks was strongest in Washington State, in agreement with field data. Interestingly, we also found a genetic signature of Pleistocene expansion in the same study areas where recent bottlenecks were shown. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies' persistence. Reduced effective population size (Ne), shown here in addition to field evidence for demographic decline, highlights the increasing vulnerability of this bird to extinction.

Geographical variations of the skull in the red fox Vulpes vulpes on the Japanese Islands: an exception to Bergmann's rule.

PubMed

Oishi, Takuya; Uraguchi, Kohji; Abramov, Alexei V; Masuda, Ryuichi

2010-12-01

In order to clarify the morphological differences between two subspecies of the red fox (Vulpes vulpes) on the Japanese Islands and test the validity of Bergmann's rule, we examined geographical variations in 25 cranial and 24 dental characters in V. v. schrencki from Hokkaido and V. v. japonica from the other main islands of Japan (Honshu, Shikoku, and Kyushu). Many skull measurements, including the male greatest length, condylobasal length, and the length of upper and lower tooth rows, were significantly larger for V. v. japonica than for V. v. schrencki, whereas most tooth measurements, especially the length of molars and premolars, in V. v. schrencki were larger than those in V. v. japonica. Although the two subspecies were morphologically well-differentiated from each other, the results did not support that they have evolved following Bergmann's rule of adaptation to cold climates. Based on consideration of the relatively large differences of their tooth sizes, which are not easily influenced by food abundance, and previous genetic research on the different migration histories of the two subspecies, the morphological differences detected in the present study may have resulted not only from the present ecological differences between the two subspecies, but also from the difference of migration history and evolutionary constraints.

Genetic structure, diversity and subspecies status of Gull-billed Terns (Gelochelidon nilotica) from the United States

USGS Publications Warehouse

Miller, Mark P.; Mullins, Thomas D.; Haig, Susan M.

2013-01-01

Gull-billed Terns (Gelochelidon nilotica) are among the most widespread, yet scarce, Charadriiformes in the world. Two subspecies are recognized in the United States: G. n. aranea breeds along the U.S. Atlantic and Gulf coasts and G. n. vanrossemi breeds in the Salton Sea and San Diego Bay of California. Conservation concerns exist for the species due to its low abundance in the United States and apparent declines in some parts of its North American range. We used nuclear microsatellite markers and mitochondrial DNA sequences to assess genetic diversity and differentiation patterns among Gull-billed Tern populations from Virginia, Texas, and California. We also tested for evidence of population bottlenecks, and evaluated the support our data provide for the North American subspecies. Genetic diversity was highest in Texas and underscored the importance of habitat in that large population. Significant population differentiation existed, but could not be consistently identified using various analytical approaches and suggested that the magnitude of differentiation was low. No evidence for bottlenecks was identified. Our data could not distinguish individuals from different subspecies and therefore do not support the current intraspecific taxonomy. Tenable explanations for many findings are related to the low site tenacity demonstrated by the species.

Rapid evolution of reproductive isolation between incipient outcrossing and selfing Clarkia species.

PubMed

Briscoe Runquist, Ryan D; Chu, Eric; Iverson, Justin L; Kopp, Jason C; Moeller, David A

2014-10-01

A major goal of speciation research is to understand the processes involved in the earliest stages of the evolution of reproductive isolation (RI). One important challenge has been to identify systems where lineages have very recently diverged and opportunities for hybridization are present. We conducted a comprehensive examination of the components of RI across the life cycle of two subspecies of Clarkia xantiana, which diverged recently (ca. 65,000 bp). One subspecies is primarily outcrossing, but self-compatible, whereas the other is primarily selfing. The subspecies co-occur in a zone of sympatry but hybrids are rarely observed. Premating barriers resulted in nearly complete isolation in both subspecies with flowering time and pollinator preference (for the outcrosser over the selfer) as the strongest barriers. We found that the outcrosser had consistently more competitive pollen, facilitating hybridization in one direction, but no evidence for pollen-pistil interactions as an isolating barrier. Surprisingly, postzygotic isolation was detected at the stage of hybrid seed development, but in no subsequent life stages. This crossing barrier was asymmetric with crosses from the selfer to outcrosser most frequently failing. Collectively, the results provide evidence for rapid evolution of multiple premating and postzygotic barriers despite a very recent divergence time. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Fred's Flow (Canada) and Murphy Well (Australia): thick komatiitic lava flows with contrasting compositions, emplacement mechanisms and water contents

NASA Astrophysics Data System (ADS)

Siégel, C.; Arndt, N. T.; Henriot, A.-L.; Barnes, S. J.

2012-04-01

Two Archaean komatiitic flows, Fred's Flow in Canada and the Murphy Well flow in Australia, have similar thicknesses (120 m and 160 m) but very different compositions and internal structures. Fred's Flow is the type example of a thick komatiitic basaltic flow. It is strongly differentiated and consists of a succession of layers with contrasting textures and compositions. The layering is readily explained by the accumulation of olivine and pyroxene in a lower cumulate layer and by evolution of the liquid composition during downward growth of spinifex-textured rocks within the upper crust. A parental liquid was constrained to contain ca. 18 wt% MgO and ca. 5 to 35%vol phenocrysts and it differentiated into cumulates containing 45 wt% MgO and a residual gabbroic layer with only 6 wt% MgO. The Murphy Well flow, in contrast, has a remarkably uniform composition throughout. It comprises two layers, a 20-m-thick upper layer composed of fine-grained dendritic olivine and 2-10% amygdales, a 120-m-thick lower layer of olivine porphyry, and a lowermost 20 m of olivine orthocumulate. Throughout the flow, MgO contents vary little, from only 30 to 34 wt%, except for the slightly more magnesian basal layer (35-40 wt%). The uniform composition and dendritic olivine habits suggest rapid cooling of a highly magnesian liquid with a composition like that of the bulk of the flow. Under equilibrium conditions this liquid should have crystallized olivine with the composition Fo95.5 but the most magnesian composition measured by electron microprobe in samples from the flow is Fo93. To explain these features, we propose that the original liquid was hydrous and contained around 32% MgO. It degassed during eruption creating a supercooled liquid that solidified quickly and crystallized olivine with non-equilibrium compositions. To account for the 60-70vol% olivine throughout the flow requires a combination of degassing and cooling by the evacuation of heat in the escaping fluid.

Patterns of mandibular variation in Pan and Gorilla and implications for African ape taxonomy.

PubMed

Taylor, Andrea B; Groves, Colin P

2003-05-01

Pan and Gorilla taxonomy is currently in a state of flux, with the number of existing species and subspecies of common chimpanzee and gorilla having been recently challenged. While Pan and Gorilla systematics have been evaluated on the basis of craniometric and odontometric data, only a handful of studies have evaluated multivariate craniometric variation within P. troglodytes, and none have evaluated in detail mandibular variation in either P. troglodytes or Gorilla gorilla. In this paper, we examine ontogenetic and adult mandibular variation in Pan and Gorilla. We test the hypothesis that patterns and degrees of mandibular variation in Pan and Gorilla closely correspond to those derived from previous analyses of craniometric variation. We then use these data to address some current issues surrounding Pan and Gorilla taxonomy. Specifically, we evaluate the purported distinctiveness of P.t. verus from the other two subspecies of Pan troglodytes, and the recent proposals to recognize Nigerian gorillas as a distinct subspecies, Gorilla gorilla diehli, and to acknowledge mountain and lowland gorillas as two separate species. Overall, patterns and degrees of multivariate mandibular differentiation parallel those obtained previously for the cranium and dentition. Thus, differences among the three conventionally recognized gorilla subspecies are somewhat greater than among subspecies of common chimpanzees, but differences between P. paniscus and P. troglodytes are greater than those observed between any gorilla subspecies. In this regard, the mandible does not appear to be more variable, or of less taxonomic value, than the face and other parts of the cranium. There are, however, some finer differences in the pattern and degree of morphological differentiation in Pan and Gorilla, both with respect to cranial and dental morphology, and in terms of the application and manner of size adjustment. Mandibular differentiation supports the conventional separation of bonobos from chimpanzees regardless of size adjustment, but size correction alters the relative alignment of taxa. Following size correction, intergroup distances are greatest between P.t. verus and all other groups, but there is considerable overlap amongst chimpanzee subspecies. Amongst gorillas, the greatest separation is between eastern and western gorillas, but adjustment relative to palatal vs. basicranial length results in a greater accuracy of group classification for G.g. gorilla and G.g. graueri, and more equivalent intergroup distances amongst all gorilla groups. We find no multivariate differentiation of the Nigerian gorillas based on mandibular morphology, suggesting that the primary difference between Nigerian and other western lowland gorillas lies in the nuchal region. Though intergroup distances are greatest between P.t. verus and other chimpanzee subspecies, the degree of overlap amongst all three groups does not indicate a markedly greater degree of distinction in mandibular, as opposed to other morphologies. Finally, mandibular differentiation corroborates previous craniodental studies indicating the greatest distinction amongst gorillas is between eastern and western groups. Thus, patterns and degrees of mandibular variation are in agreement with other kinds of data that have been used to diagnose eastern and western gorillas as separate species.

Noninvasive characterization of a flowing multiphase fluid using ultrasonic interferometry

DOEpatents

Sinha, Dipen N.

2003-11-11

An apparatus for noninvasively monitoring the flow and/or the composition of a flowing liquid using ultrasound is described. The position of the resonance peaks for a fluid excited by a swept-frequency ultrasonic signal have been found to change frequency both in response to a change in composition and in response to a change in the flow velocity thereof. Additionally, the distance between successive resonance peaks does not change as a function of flow, but rather in response to a change in composition. Thus, a measurement of both parameters (resonance position and resonance spacing), once calibrated, permits the simultaneous determination of flow rate and composition using the apparatus and method of the present invention.

Non-Invasive Characterization Of A Flowing Multi-Phase Fluid Using Ultrasonic Interferometry

DOEpatents

Sinha, Dipen N.

2005-11-01

An apparatus for noninvasively monitoring the flow and/or the composition of a flowing liquid using ultrasound is described. The position of the resonance peaks for a fluid excited by a swept-frequency ultrasonic signal have been found to change frequency both in response to a change in composition and in response to a change in the flow velocity thereof. Additionally, the distance between successive resonance peaks does not change as a function of flow, but rather in response to a change in composition. Thus, a measurement of both parameters (resonance position and resonance spacing), once calibrated, permits the simultaneous determination of flow rate and composition using the apparatus and method of the present invention.

Noninvasive Characterization Of A Flowing Multiphase Fluid Using Ultrasonic Interferometry

DOEpatents

Sinha, Dipen N.

2005-05-10

An apparatus for noninvasively monitoring the flow and/or the composition of a flowing liquid using ultrasound is described. The position of the resonance peaks for a fluid excited by a swept-frequency ultrasonic signal have been found to change frequency both in response to a change in composition and in response to a change in the flow velocity thereof. Additionally, the distance between successive resonance peaks does not change as a function of flow, but rather in response to a change in composition. Thus, a measurement of both parameters (resonance position and resonance spacing), once calibrated, permits the simultaneous determination of flow rate and composition using the apparatus and method of the present invention.

Noninvasive characterization of a flowing multiphase fluid using ultrasonic interferometry

DOEpatents

Sinha, Dipen N [Los Alamos, NM

2007-06-12

An apparatus for noninvasively monitoring the flow and/or the composition of a flowing liquid using ultrasound is described. The position of the resonance peaks for a fluid excited by a swept-frequency ultrasonic signal have been found to change frequency both in response to a change in composition and in response to a change in the flow velocity thereof. Additionally, the distance between successive resonance peaks does not change as a function of flow, but rather in response to a change in composition. Thus, a measurement of both parameters (resonance position and resonance spacing), once calibrated, permits the simultaneous determination of flow rate and composition using the apparatus and method of the present invention.

Geochemical variations during development of the 5.46 Ma Broadwell Mesa basaltic volcanic field, California

USGS Publications Warehouse

Buesch, David C.

2017-01-01

The 5.46±0.04 Ma Broadwell Mesa basalt and associated basaltic volcanic field in the western Bristol Mountains, California, formed a ~6 km2 volcanic flow field with architecture including numerous lava flows, a ~1.1 km2 lava lake, and a ~0.17 km2 cinder cone. The local number of lava flows varies from one along the margins of the field to as many as 18 that are stacked vertically, onlapped by younger flows, or are laterally adjacent to each other. Geochemical plots of 40 hand samples indicate that all lava flows are basalt and that the field is slightly compositionally zoned. Typically, there is a progressive change in composition in sequentially overlying lava flows, although in some flow sequences, the overlying flow has an “across trend” step in composition, and a few have an “against trend” step in composition. The progressive compositional change indicates that the magmatic composition evolved during the history of the field, and the “across trend” and minor “against trend” steps probably represent periods of crystal fractionation or reinjection of magma during hiatuses in eruptions. The lack of clastic sedimentary rocks or even aeolianite interstratified with the lava flows probably indicates that the Broadwell Mesa volcanic field was short-lived.

DNA barcoding of gypsy moths from China (Lepidoptera: Erebidae) reveals new haplotypes and divergence patterns within gypsy moth subspecies

Treesearch

Fang Chen; Youqing Luo; Melody A. Keena; Ying Wu; Peng Wu; Juan Shi

2015-01-01

The gypsy moth from Asia (two subspecies) is considered a greater threat to North America than European gypsy moth, because of a broader host range and females being capable of flight. Variation within and among gypsy moths from China (nine locations), one of the native countries of Asian gypsy moth, were compared using DNA barcode sequences (658 bp of mtDNA cytochrome...

Genome Sequences for Multiple Clavibacter Strains from Different Subspecies

PubMed Central

Yuan, Xiaoli (Kat)

2017-01-01

ABSTRACT The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a variety of agricultural crops, such as potato, tomato, corn, barley, etc. Here, we report five new genome sequences, those of strains CFIA-Cs3N, CFIA-CsR14, LMG 3663T, LMG 7333T, and ATCC 33566T, from different subspecies of Clavibacter michiganensis. All these genomic data will be used for reclassification and niche-adapted feature comparisons. PMID:28935724

Evaluation of Veterinary-Specific Interpretive Criteria for Susceptibility Testing of Streptococcus equi Subspecies with Trimethoprim-Sulfamethoxazole and Trimethoprim-Sulfadiazine.

PubMed

Sadaka, Carmen; Kanellos, Theo; Guardabassi, Luca; Boucher, Joseph; Watts, Jeffrey L

2017-01-01

Antimicrobial susceptibility test results for trimethoprim-sulfadiazine with Streptococcus equi subspecies are interpreted based on human data for trimethoprim-sulfamethoxazole. The veterinary-specific data generated in this study support a single breakpoint for testing trimethoprim-sulfamethoxazole and/or trimethoprim-sulfadiazine with S. equi This study indicates trimethoprim-sulfamethoxazole as an acceptable surrogate for trimethoprim-sulfadiazine with S. equi. Copyright © 2016 Sadaka et al.

Evaluation of Veterinary-Specific Interpretive Criteria for Susceptibility Testing of Streptococcus equi Subspecies with Trimethoprim-Sulfamethoxazole and Trimethoprim-Sulfadiazine

PubMed Central

Kanellos, Theo; Guardabassi, Luca; Boucher, Joseph

2016-01-01

ABSTRACT Antimicrobial susceptibility test results for trimethoprim-sulfadiazine with Streptococcus equi subspecies are interpreted based on human data for trimethoprim-sulfamethoxazole. The veterinary-specific data generated in this study support a single breakpoint for testing trimethoprim-sulfamethoxazole and/or trimethoprim-sulfadiazine with S. equi. This study indicates trimethoprim-sulfamethoxazole as an acceptable surrogate for trimethoprim-sulfadiazine with S. equi. PMID:27847375

A distinct species, Dodona formosana, detected in the Dodona eugenes species complex: clarification of the taxonomic status of the Punch butterfly in Taiwan

PubMed Central

Wu, Li-Wei; Lin, Wen-Jie; Hsu, Yu-Feng

2018-01-01

Abstract The Tailed Punch, Dodona eugenes, is widely distributed in East Asia with seven subspecies currently recognized. However, two of them, namely ssp. formosana and ssp. esakii found in Taiwan, are hard to distinguish from each other due to ambiguous diagnostic characters. In this study, their taxonomic status is clarified by comparing genitalia characters and phylogenetic relationships based on mitochondrial sequences, COI and COII (total 2211 bps). Our results show that there is no reliable feature to separate these two subspecies. Surprisingly we found that Dodona in Taiwan is more closely related to the Orange Punch, D. egeon, than to other subspecies of D. eugenes. Therefore, the following nomenclatural changes are proposed: Dodona eugenes formosana is revised to specific status as Dodona formosana Matsumura, 1919, stat. rev, and ssp. esakii is sunk to a junior synonym of Dodona formosana syn. n. PMID:29674868

The type-specimens of Caraboidea beetles (Coleoptera, Adephaga) deposited in the collections of the I.I. Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine.

PubMed

Putshkov, Alexander V; Martynov, Alexander V

2017-03-01

A catalogue of type specimens of species and subspecies of caraboid beetles, tiger-beetles here treated as family Cicindelidae, and ground-beetles (Carabidae) of suborder Adephaga deposited in the I.I. Schmalhausen Institute of Zoology NAS of Ukraine is provided. For all type-specimens original photos of each specimen (with label) and label data are given in the original spelling (translated to English if the original label was in Cyrillic alphabet). In some cases data concerning the current status of taxons are discussed. Nominal taxa names are alphabethically listed within each family. Altogether, 372 type specimens of 133 taxa names (species and subspecies) are included in the catalogue: 15 holotypes, 344 paratypes (120 species and subspecies) and 13 specimens (9 taxa) with other type status.

Ecology, Epidemiology and Disease Management of Ralstonia syzygii in Indonesia

PubMed Central

Safni, Irda; Subandiyah, Siti; Fegan, Mark

2018-01-01

Ralstonia solanacearum species complex phylotype IV strains, which have been primarily isolated from Indonesia, Australia, Japan, Korea, and Malaysia, have undergone recent taxonomic and nomenclatural changes to be placed in the species Ralstonia syzygii. This species contains three subspecies; Ralstonia syzygii subsp. syzygii, a pathogen causing Sumatra disease of clove trees in Indonesia, Ralstonia syzygii subsp. indonesiensis, the causal pathogen of bacterial wilt disease on a wide range of host plants, and Ralstonia syzygii subsp. celebesensis, the causal pathogen of blood disease on Musa spp. In Indonesia, these three subspecies have devastated the cultivation of susceptible host plants which have high economic value. Limited knowledge on the ecology and epidemiology of the diseases has hindered the development of effective control strategies. In this review, we provide insights into the ecology, epidemiology and disease control of these three subspecies of Ralstonia syzygii. PMID:29662468

Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean.

PubMed

González, Ana J; Trapiello, Estefanía

2014-05-01

A yellow Gram-reaction-positive bacterium isolated from bean seeds (Phaseolus vulgaris L.) was identified as Clavibacter michiganensis by 16S rRNA gene sequencing. Molecular methods were employed in order to identify the subspecies. Such methods included the amplification of specific sequences by PCR, 16S amplified rDNA restriction analysis (ARDRA), RFLP and multilocus sequence analysis as well as the analysis of biochemical and phenotypic traits including API 50CH and API ZYM results. The results showed that strain LPPA 982T did not represent any known subspecies of C. michiganensis. Pathogenicity tests revealed that the strain is a bean pathogen causing a newly identified bacterial disease that we name bacterial bean leaf yellowing. On the basis of these results, strain LPPA 982T is regarded as representing a novel subspecies for which the name Clavibacter michiganensis subsp. phaseoli subsp. nov. is proposed. The type strain is LPPA 982T (=CECT 8144T=LMG 27667T).

Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses.

PubMed

Li, Xiang; Tambong, James; Yuan, Kat Xiaoli; Chen, Wen; Xu, Huimin; Lévesque, C André; De Boer, Solke H

2018-01-01

Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.

Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses

PubMed Central

Li, Xiang; Tambong, James; Yuan, Kat (Xiaoli); Chen, Wen; Xu, Huimin; Lévesque, C. André; De Boer, Solke H.

2018-01-01

Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA–DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov. PMID:29160202

The indigenous honey bees of Saudi Arabia (Hymenoptera, Apidae, Apis mellifera jemenitica Ruttner): Their natural history and role in beekeeping.

PubMed

Alqarni, Abdulaziz S; Hannan, Mohammed A; Owayss, Ayman A; Engel, Michael S

2011-01-01

Apis mellifera jemenitica Ruttner (= yemenitica auctorum: videEngel 1999) has been used in apiculture throughout the Arabian Peninsula since at least 2000 BC. Existing literature demonstrates that these populations are well adapted for the harsh extremes of the region. Populations of Apis mellifera jemenitica native to Saudi Arabia are far more heat tolerant than the standard races often imported from Europe. Central Saudi Arabia has the highest summer temperatures for the Arabian Peninsula, and it is in this region where only Apis mellifera jemenitica survives, while other subspecies fail to persist. The indigenous race of Saudi Arabia differs from other subspecies in the region in some morphological, biological, and behavioral characteristics. Further taxonomic investigation, as well as molecular studies, is needed in order to confirm whether the Saudi indigenous bee populations represent a race distinct from Apis mellifera jemenitica, or merely an ecotype of this subspecies.

Sequential patterns of essential trace elements composition in Gracilaria verrucosa and its generated products

NASA Astrophysics Data System (ADS)

Izzati, Munifatul; Haryanti, Sri; Parman, Sarjana

2018-05-01

Gracilaria widely known as a source of essential trace elements. However this red seaweeds also has great potential for being developed into commercial products. This study examined the sequential pattern of essential trace elements composition in fresh Gracilaria verrucosa and a selection of its generated products, nemely extracted agar, Gracilaria salt and Gracilaria residue. The sample was collected from a brackish water pond, located in north part Semarang, Central Java. The collected sample was then dried under the sun, and subsequently processed into aformentioned generated products. The Gracilaria salt was obtain by soaking the sun dried Gracilaria overnight in fresh water overnight. The resulted salt solution was then boiled leaving crystal salt. Extracted agar was obtained with alkali agar extraction method. The rest of remaining material was considered as Gracilaria residue. The entire process was repeated 3 times. The compositin of trace elements was examined using ICP-MS Spectrometry. Collected data was then analyzed by ANOVA single factor. Resulting sequential pattern of its essential trace elements composition was compared. A regular table salt was used as controls. Resuts from this study revealed that Gracilaria verrucosa and its all generated products all have similarly patterned the composition of essential trace elements, where Mn>Zn>Cu>Mo. Additionally this pattern is similar to different subspecies of Gracilaria from different location and and different season. However, Gracilaria salt has distinctly different pattern of sequential essential trace elements composition compared to table salt.

Effects of debris-flow composition on runout and erosion

NASA Astrophysics Data System (ADS)

Haas, T. D.; Kleinhans, M. G.

2016-12-01

Predicting debris-flow runout is of major importance for hazard mitigation. Apart from topography and volume, runout depends on debris-flow composition (i.e., particle-size distribution and water content), but how is poorly understood. Moreover, debris flows can grow greatly in size by entrainment of bed material, enhancing their volume and thereby runout and hazardous impact. Debris-flow erosion rates also depend on debris-flow composition, but the relation between the two is largely unexplored. Composition thus strongly affects the dynamics of debris flows. We experimentally investigate the effects of composition on debris-flow runout and erosion. We find a clear optimum in the relations of runout with coarse-material fraction and clay fraction. Increasing coarse material concentration leads to larger runout. However, excess coarse material results in a large accumulation of coarse debris at the flow front and enhances diffusivity, increasing frontal friction and decreasing runout. Increasing clay content initially enhances runout, but too much clay leads to very viscous flows, reducing runout. We further find that debris-flow runout depends at least as much on composition as on topography. In general, erosion depth increases with basal shear stress in our experiments, while there is no correlation with grain collisional stress. There are substantial differences in the scour caused by different types of debris flows. Mean and maximum erosion depths generally become larger with increasing water fraction and grain size and decrease with increasing clay content. However, the erodibility of the very coarse-grained experimental debris flows is unrelated to basal shear stress. This relates to the relatively large influence of grain-collisional stress to the total bed stress in these flows (30-50%). The relative effect of grain-collisional stress is low in the other experimental debris flows (<5%) causing erosion to be largely controlled by basal shear stress. These results show that the erosive behaviour of debris flows may change from basal-shear stress dominated to grain-collisional stress dominated in increasingly coarse-grained debris flows. In short, this study improves our understanding of the effects of debris-flow composition on runout and erosion.

Effect of pyrrolidone-pyroglutamic acid composition on blood flow in rat middle cerebral artery.

PubMed

Semkina, G A; Matsievskii, D D; Mirzoyan, N R

2006-01-01

We compared the effects of a pyrrolidone-pyroglutamic acid composition and nimodipine on blood circulation in the middle cerebral artery in rats. The composition produced a strong effect on blood supply to the brain, stimulated blood flow in the middle cerebral artery (by 60 +/- 9%) and decreased blood pressure (by 25.0 +/- 2.7%). The cerebrovascular effects of this composition differed from those of nimodipine. Nimodipine not only increased middle cerebral artery blood flow, but also decreased cerebral blood flow in the early period after treatment.

Effects of composition of grains of debris flow on its impact force

NASA Astrophysics Data System (ADS)

Tang, jinbo; Hu, Kaiheng; Cui, Peng

2017-04-01

Debris flows compose of solid material with broad size distribution from fine sand to boulders. Impact force imposed by debris flows is a very important issue for protection engineering design and strongly influenced by their grain composition. However, this issue has not been studied in depth and the effects of grain composition not been considered in the calculation of the impact force. In this present study, the small-scale flume experiments with five kinds of compositions of grains for debris flow were carried out to study the effect of the composition of grains of debris flow on its impact force. The results show that the impact force of debris flow increases with the grain size, the hydrodynamic pressure of debris flow is calibrated based on the normalization parameter dmax/d50, in which dmax is the maximum size and d50 is the median size. Furthermore, a log-logistic statistic distribution could be used to describe the distribution of magnitude of impact force of debris flow, where the mean and the variance of the present distribution increase with grain size. This distribution proposed in the present study could be used to the reliability analysis of structures impacted by debris flow.

A new subspecies of Chamaea fasciata (Wrentit) from Oregon (Aves: Timaliinae)

USGS Publications Warehouse

Browning, M. Ralph

1992-01-01

Geographic variation in plumage color of Chamaea fasciata (Wrentit) from northern California and southern Oregon is related to climate. A new subspecies, Chamaea fasciata margra, is described from a disjunct population of southern interior Oregon. Colonization of C. fasciata in interior Oregon was perhaps from birds crossing coniferous forests via isolated balds of Ceonothus. Recent increases of Wrentits in interior Oregon may be in response to habitat alterations (deforestation, fires) and concurrent global warming.

Genome Sequences for Multiple Clavibacter Strains from Different Subspecies.

PubMed

Li, Xiang Sean; Yuan, Xiaoli Kat

2017-09-21

The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a variety of agricultural crops, such as potato, tomato, corn, barley, etc. Here, we report five new genome sequences, those of strains CFIA-Cs3N, CFIA-CsR14, LMG 3663 T , LMG 7333 T , and ATCC 33566 T , from different subspecies of Clavibacter michiganensis All these genomic data will be used for reclassification and niche-adapted feature comparisons. © Crown copyright 2017.

Brant (Branta bernnicla)

USGS Publications Warehouse

Ward, David H.; Derksen, Dirk V.; Reed, A.; Sedinger, J.S.

2013-01-01

The Brant (called Brent Goose in Europe) is a small dark goose that occurs throughout much of the northern hemisphere. In contrast to other goose species, Brant are characterized by their extensive use of native coastal habitats outside the breeding season. Three to four subspecies are recognized (see Systematics), mainly on the basis of plumage characteristics. The two/three North American subspecies are further separated into four subpopulations based on genetics, location of breeding and wintering areas, and migration routes.

Estimating the population size of island loggerhead shrikes on Santa Rosa and Santa Cruz Islands, USA

USGS Publications Warehouse

Stanley, Thomas R.; Teel, Susan; Hall, Linnea S.; Dye, Linda C.; Laughrin, Lyndal L.

2012-01-01

Island loggerhead shrikes (Lanius ludovicianus anthonyi) are an endemic, genetically distinct subspecies of loggerhead shrike on California’s Santa Rosa and Santa Cruz Islands. This subspecies is listed as a Species of Special Concern by the California Department of Fish and Game and has been petitioned for federal listing under the Endangered Species Act. Because of suspected low numbers and the possibility of federal listing, there was an urgent need to rigorously estimate the number of remaining individuals on the Islands. In 2009 and 2010, biologists from the U.S. Geological Survey and the National Park Service surveyed sample units on Santa Rosa and Santa Cruz Islands using a double-observer method with independent observers, where units were selected under a stratified random sampling design. Shrike abundance was estimated to be 169 in 2009 and 240 in 2010 for Santa Rosa Island, and 35 in 2009 and 42 in 2010 for Santa Cruz Island. These numbers, especially for Santa Rosa Island, are higher than previously reported but nevertheless are still low. Rapid vegetation change on both islands due to recent removal of non-native herbivores may threaten the habitat and status of this subspecies. In view of this circumstance and the still-low numbers of shrikes, additional intensive demographic and habitat-use studies are critical for obtaining information vital for the perpetuation of this subspecies.

Comparative Genome Analysis of Campylobacter fetus Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity

PubMed Central

Kienesberger, Sabine; Sprenger, Hanna; Wolfgruber, Stella; Halwachs, Bettina; Thallinger, Gerhard G.; Perez-Perez, Guillermo I.; Blaser, Martin J.; Zechner, Ellen L.; Gorkiewicz, Gregor

2014-01-01

Campylobacter fetus are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. C. fetus subsp. venerealis is highly niche-adapted, mainly infecting the genital tract of cattle. C. fetus subsp. fetus has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of C. fetus subsp. venerealis 84-112 and comparisons to the genome of C. fetus subsp. fetus 82-40. Functional analysis of genes predicted to be involved in C. fetus virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but C. fetus subsp. venerealis has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in C. fetus isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of C. fetus pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to C. fetus pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens. PMID:24416416

The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.

PubMed

Cho, Yong-Joon; Yi, Hana; Chun, Jongsik; Cho, Sang-Nae; Daley, Charles L; Koh, Won-Jung; Shin, Sung Jae

2013-01-01

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms.

PubMed

Gong, Li; Paris, Harry S; Nee, Michael H; Stift, Gertraud; Pachner, Martin; Vollmann, Johann; Lelley, Tamas

2012-03-01

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.

Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S. attenuata) dolphins, from SNP data

PubMed Central

Morin, Phillip A.

2018-01-01

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution. PMID:29765639

Genome Comparison of Candida orthopsilosis Clinical Strains Reveals the Existence of Hybrids between Two Distinct Subspecies

PubMed Central

Pryszcz, Leszek P.; Németh, Tibor; Gácser, Attila; Gabaldón, Toni

2014-01-01

The Candida parapsilosis species complex comprises a group of emerging human pathogens of varying virulence. This complex was recently subdivided into three different species: C. parapsilosis sensu stricto, C. metapsilosis, and C. orthopsilosis. Within the latter, at least two clearly distinct subspecies seem to be present among clinical isolates (Type 1 and Type 2). To gain insight into the genomic differences between these subspecies, we undertook the sequencing of a clinical isolate classified as Type 1 and compared it with the available sequence of a Type 2 clinical strain. Unexpectedly, the analysis of the newly sequenced strain revealed a highly heterozygous genome, which we show to be the consequence of a hybridization event between both identified subspecies. This implicitly suggests that C. orthopsilosis is able to mate, a so-far unanswered question. The resulting hybrid shows a chimeric genome that maintains a similar gene dosage from both parental lineages and displays ongoing loss of heterozygosity. Several of the differences found between the gene content in both strains relate to virulent-related families, with the hybrid strain presenting a higher copy number of genes coding for efflux pumps or secreted lipases. Remarkably, two clinical strains isolated from distant geographical locations (Texas and Singapore) are descendants of the same hybrid line, raising the intriguing possibility of a relationship between the hybridization event and the global spread of a virulent clone. PMID:24747362

Regional differentiation among populations of the Diamondback terrapin (Malaclemys terrapin)

USGS Publications Warehouse

Hart, Kristen M.; Hunter, Margaret E.; King, Tim L.

2014-01-01

The Diamondback terrapin (Malaclemys terrapin) is a brackish-water turtle species whose populations have been fragmented due to anthropogenic activity such as development of coastal habitat and entrapment in commercial blue crab (Callinectes sapidus) fishing gear. Genetic analyses can improve conservation efforts for the long-term protection of the species. We used microsatellite DNA analysis to investigate levels of gene flow among and genetic variability within 21 geographically separate collections of the species distributed from Massachusetts to Texas. Quantified levels of genetic variability (allelic diversity, genotypic frequencies, and heterozygosity) revealed three zones of genetic discontinuity, resulting in four discrete populations: Northeast Atlantic, Coastal Mid-Atlantic, Florida and Texas/Louisiana. The average number of alleles and expected heterozygosity for the four genetic clusters were NA = 6.54 and HE = 0.050, respectively. However, the geographic boundaries of the populations did not correspond to accepted terrapin subspecies limits. Our results illuminate not only the need to sample terrapins in additional sites, specifically in the southeast, but also the necessity for allowing uninterrupted gene flow among population groupings to preserve current levels of genetic diversity.

Morphological and molecular evidence reveals recent hybridization between gorilla taxa.

PubMed

Ackermann, Rebecca Rogers; Bishop, Jacqueline M

2010-01-01

Molecular studies have demonstrated a deep lineage split between the two gorilla species, as well as divisions within these taxa; estimates place this divergence in the mid-Pleistocene, with gene flow continuing until approximately 80,000 years ago. Here, we present analyses of skeletal data indicating the presence of substantial recent gene flow among gorillas at all taxonomic levels: between populations, subspecies, and species. Complementary analyses of DNA sequence variation suggest that low-level migration occurred primarily in a westerly-to-easterly direction. In western gorillas, the locations of hybrid phenotypes map closely to expectations based on population refugia and riverine barrier hypotheses, supporting the presence of significant vicariance-driven structuring and occasional admixture within this taxon. In eastern lowland gorillas, the high frequency of hybrid phenotypes is surprising, suggesting that this region represents a zone of introgression between eastern gorillas and migrants from the west, and underscoring the conservation priority of this critically endangered group. These results highlight the complex nature of evolutionary divergence in this genus, indicate that historical gene flow has played a major role in structuring gorilla diversity, and demonstrate that our understanding of the evolutionary processes responsible for shaping biodiversity can benefit immensely from consideration of morphological and molecular data in conjunction.

Apolipoproteins E and CIII interact to regulate HDL metabolism and coronary heart disease risk

PubMed Central

Morton, Allyson M.; Koch, Manja; Mendivil, Carlos O.; Furtado, Jeremy D.; Tjønneland, Anne; Overvad, Kim; Wang, Liyun; Jensen, Majken K.; Sacks, Frank M.

2018-01-01

BACKGROUND. Subspecies of HDL contain apolipoprotein E (apoE) and/or apoCIII. Both proteins have properties that could affect HDL metabolism. The relation between HDL metabolism and risk of coronary heart disease (CHD) is not well understood. METHODS. Eighteen participants were given a bolus infusion of [D3]L-leucine to label endogenous proteins on HDL. HDL was separated into subspecies containing apoE and/or apoCIII and then into 4 sizes. Metabolic rates for apoA-I in HDL subspecies and sizes were determined by interactive modeling. The concentrations of apoE in HDL that contain or lack apoCIII were measured in a prospective study in Denmark including 1,949 incident CHD cases during 9 years. RESULTS. HDL containing apoE but not apoCIII is disproportionately secreted into the circulation, actively expands while circulating, and is quickly cleared. These are key metabolic steps in reverse cholesterol transport, which may protect against atherosclerosis. ApoCIII on HDL strongly attenuates these metabolic actions of HDL apoE. In the epidemiological study, the relation between HDL apoE concentration and CHD significantly differed depending on whether apoCIII was present. HDL apoE was associated significantly with lower risk of CHD only in the HDL subspecies lacking apoCIII. CONCLUSIONS. ApoE and apoCIII on HDL interact to affect metabolism and CHD. ApoE promotes metabolic steps in reverse cholesterol transport and is associated with lower risk of CHD. ApoCIII, when coexisting with apoE on HDL, abolishes these benefits. Therefore, differences in metabolism of HDL subspecies pertaining to reverse cholesterol transport are reflected in differences in association with CHD. TRIAL REGISTRATION. Clinicaltrials.gov NCT01399632. FUNDING. This work was supported by NIH grant R01HL095964 to FMS and by a grant to the Harvard Clinical and Translational Science Center (8UL1TR0001750) from the National Center for Advancing Translational Science. PMID:29467335

The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.

PubMed

Huang, Jen-Pan; Knowles, L Lacey

2016-07-01

With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla).

PubMed

Harris, Rebecca B; Alström, Per; Ödeen, Anders; Leaché, Adam D

2018-03-01

Generally, genotypes and phenotypes are expected to be spatially congruent; however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Motacilla) are a genus of birds with striking plumage pattern variation across the Old World. Up to 13 subspecies are recognized within a single species, yet previous studies using mitochondrial DNA have supported polyphyletic phylogeographic groups that are inconsistent with subspecies plumage characteristics. In this study, we investigate the link between phenotypes and genotype by taking a phylogenetic approach. We use genome-wide SNPs, nuclear introns, and mitochondrial DNA to estimate population structure, isolation by distance, and species relationships. Together, our genetic sampling includes complete species-level sampling and comprehensive coverage of the three most phenotypically diverse Palearctic species. Our study provides strong evidence for species-level patterns of differentiation, however population-level differentiation is less pronounced. SNPs provide a robust estimate of species-level relationships, which are mostly corroborated by a combined analysis of mtDNA and nuclear introns (the first time-calibrated species tree for the genus). However, the mtDNA tree is strongly incongruent and is considered to misrepresent the species phylogeny. The extant wagtail lineages originated during the Pliocene and the Eurasian lineage underwent rapid diversification during the Pleistocene. Three of four widespread Eurasian species exhibit an east-west divide that contradicts both subspecies taxonomy and phenotypic variation. Indeed, SNPs fail to distinguish between phenotypically distinct subspecies within the M. alba and M. flava complexes, and instead support geographical regions, each of which is home to two or more different looking subspecies. This is a major step towards our understanding of wagtail phylogeny compared to previous analyses of fewer species and considerably less sequence data. Copyright © 2017 Elsevier Inc. All rights reserved.

Phenotypic Divergence among West European Populations of Reed Bunting Emberiza schoeniclus: The Effects of Migratory and Foraging Behaviours

PubMed Central

Neto, Júlio M.; Gordinho, Luís; Belda, Eduardo J.; Marín, Marcial; Monrós, Juan S.; Fearon, Peter; Crates, Ross

2013-01-01

Divergent selection and local adaptation are responsible for many phenotypic differences between populations, potentially leading to speciation through the evolution of reproductive barriers. Here we evaluated the morphometric divergence among west European populations of Reed Bunting in order to determine the extent of local adaptation relative to two important selection pressures often associated with speciation in birds: migration and diet. We show that, as expected by theory, migratory E. s. schoeniclus had longer and more pointed wings and a slightly smaller body mass than the resident subspecies, with the exception of E. s. lusitanica, which despite having rounder wings was the smallest of all subspecies. Tail length, however, did not vary according to the expectation (shorter tails in migrants) probably because it is strongly correlated with wing length and might take longer to evolve. E. s. witherbyi, which feed on insects hiding inside reed stems during the winter, had a very thick, stubby bill. In contrast, northern populations, which feed on seeds, had thinner bills. Despite being much smaller, the southern E. s. lusitanica had a significantly thicker, longer bill than migratory E. s. schoeniclus, whereas birds from the UK population had significantly shorter, thinner bills. Geometric morphometric analyses revealed that the southern subspecies have a more convex culmen than E. s. schoeniclus, and E. s. lusitanica differs from the nominate subspecies in bill shape to a greater extent than in linear bill measurements, especially in males. Birds with a more convex culmen are thought to exert a greater strength at the bill tip, which is in agreement with their feeding technique. Overall, the three subspecies occurring in Western Europe differ in a variety of traits following the patterns predicted from their migratory and foraging behaviours, strongly suggesting that these birds have became locally adapted through natural selection. PMID:23667594

Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum.

PubMed

Zheng, Chenfei; Nie, Liuwang; Wang, Jue; Zhou, Huaxing; Hou, Huazhen; Wang, Hao; Liu, Juanjuan

2013-01-01

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3' end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.

Recombination and Evolution of Duplicate Control Regions in the Mitochondrial Genome of the Asian Big-Headed Turtle, Platysternon megacephalum

PubMed Central

Zheng, Chenfei; Nie, Liuwang; Wang, Jue; Zhou, Huaxing; Hou, Huazhen; Wang, Hao; Liu, Juanjuan

2013-01-01

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3′ end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum. PMID:24367563

Pediatric Neurocritical Care: A Short Survey of Current Perceptions and Practices.

PubMed

Murphy, Sarah A; Bell, Michael J; Clark, Maureen E; Whalen, Michael J; Noviski, Natan

2015-10-01

Although attention to neurologic injuries and illnesses in pediatric critical care is not new, a sub-specialized field of pediatric neurocritical care has only recently been recognized. Pediatric neurocritical care is an emerging area of clinical and investigative focus. Little is known about the prevalence of specialized pediatric neurocritical care services nor about perceptions regarding how it is impacting medical practice. This survey sought to capture perceptions about an emerging area of specialized pediatric neurocritical care among practitioners in intersecting disciplines, including pediatric intensivists, pediatric neurologits and pediatric neurosurgeons. A web-based survey was distributed via email to members of relevant professional societies and groups. Survey responses were analyzed using descriptive statistics. Differences in responses between groups of respondents were analyzed using Chi-squared analysis where appropriate. Specialized clinical PNCC programs were not uncommon among the survey respondents with 20% currently having a PNCC service at their institution. Despite familiarity with this area of sub-specialization among the survey respondents, the survey did not find consensus regarding its value. Overall, 46% of respondents believed that a specialized clinical PNCC service improves the quality of care of critically ill children. Support for PNCC sub-specialization was more common among pediatric neurologists and pediatric neurosurgeons than pediatric intensivists. This survey found support across specialties for creating PNCC training pathways for both pediatric intensivists and pediatric neurologists with an interest in this specialized field. PNCC programs are not uncommon; however, there is not clear agreement on the optimal role or benefit of this area of practice sub-specialization. A broader dialog should be undertaken regarding the emerging practice of pediatric neurocritical care, the potential benefits and drawbacks of this partitioning of neurology and critical care medicine practice, economic and other practical factors, the organization of clinical support services, and the formalization of training and certification pathways for sub-specialization.

Homogeneity of lava flows - Chemical data for historic Mauna Loan eruptions

NASA Technical Reports Server (NTRS)

Rhodes, J. M.

1983-01-01

Chemical analyses of basalts collected from the major historic eruptions of Mauna Loa volcano show that many of the flow fields are remarkably homogeneous in composition. Despite their large size (lengths 9-85 km), large areal extents (13-114 sq km), and various durations of eruption (1-450 days), many of the flow fields have compositional variability that is within, or close to, the analytical error for most elements. The flow fields that are not homogeneous vary mainly in olivine content in an otherwise homogeneous melt. Some are composite flow fields made up of several, apparently homogeneous subunits erupted at different elevations along the active volcanic rifts. Not all volcanoes produce lavas that are homogeneous like those of Mauna Loa. If studies such as this are to be used to evaluate compositional diversity in lavas where there is a lack of sampling control, such as on other planets, it is necessary to understand why some flow units and flow fields are compositionally homogeneous and others are not, and to develop criteria for distinguishing between them.

Spondylodiskitis secondary to Streptococcus equi subspecies zooepidemicus.

PubMed

Bhatia, Ravi; Bhanot, Nitin

2012-01-01

Streptococcus equi subspecies zooepidemicus, traditionally classified under Group C Streptococci, is primarily a veterinary pathogen. Rarely, it may cause infections such as bacteremia, meningitis, endocarditis and pneumonia in humans. Musculoskeletal infections secondary to this pathogen are very uncommon. The authors present the first case of osteomyelitis due to S. zooepidemicus in a farmer who had close contact with a dead horse. The authors review all cases of osteoarticular infections secondary to this microbe, in addition to providing an overview of clinical manifestations, treatment and outcome of this infection.

Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin.

PubMed

Farias, Izeni Pires; Hrbek, Tomas

2008-10-01

We carried out a phylogeograhic and population genetic analysis of fishes of the taxonomically contentious genus Symphysodon from the Amazon basin in order to test hypotheses of relationships among taxonomic units, and potential processes driving diversification within this genus. We sampled 334 individuals of the genus Symphysodon from 24 localities that span the complete geographic distribution of this genus. The sampling scheme included all known phenotypic groups, species and subspecies. Analyses were based on 474 bp of the mitochondrial control region and 1443 bp of the exon 3 of RAG1 gene. We observed 102 mtDNA haplotypes defined by 89 segregating sites, and 5 nuDNA alleles defined by three segregating sites. Maximum-likelihood, Bayesian-inference and statistical parsimony analyses revealed three well defined monophyletic groups. These clades corresponded to the 'green' and 'blue' groups of Symphysodon aequifasciatus, and to a previously morphologically unrecognized clade from the Xingu River drainage. These three clades were nested within a paraphyletic assemblage consisting of the 'brown' group of S. aequifasciatus and of both described subspecies of S. discus, the 'Heckel' and the 'abacaxi' discus. Nuclear allele sharing was observed among groups, but there were significant differences in frequencies. We inferred several processes including past fragmentation among groups, and restricted gene flow with isolation by distance within the paraphyletic 'brown+Heckel+abacaxi' groups, and suggest that differences among the 'blue', 'Heckel' and 'brown' groups are potentially maintained by differences in water chemistry preferences. We further inferred colonization of the western Amazon basin by an ancestor of the 'green' clade. The 'green' group was the only group with a pattern of haplotype distribution consistent of a demographic expansion, and the divergence of this clade from other groups of discus was consistent with recent geologic evidence on the breach of the Purus Arch which separates western Amazon from eastern Amazon. We further hypothesized that the differentiation of the 'Xingu' clade could be due to vicariance events resulting from Pleistocene sea level, and thus Amazon River level fluctuations. We discuss the bearings of our results on the current taxonomy of this group, and on the biological reality of the different forms, subspecies and species of Symphysodon concluding that we are probably observing a process of diversification, and therefore taxonomy will remain contentious.

Species Delimitation and Global Biosecurity

PubMed Central

Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

2012-01-01

Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits might be drawn. In the species cases here, the results clearly indicate that there is a need for more gene sampling to substantiate either the new cohort of species indicated for B. tabaci or to detect the established subspecies taxonomy of L. dispar. Given the ease of use through the Geneious species delimitation plugins, similar analysis of such multi-gene datasets would be easily accommodated. Overall, the tip to root approach described here is recommended where careful consideration of species delimitation is required to support crucial biosecurity decisions based on accurate species identification. PMID:22267902

Crystallization, flow and thermal histories of lunar and terrestrial compositions

NASA Technical Reports Server (NTRS)

Uhlmann, D. R.

1979-01-01

Contents: a kinetic treatment of glass formation; effects of nucleating heterogeneities on glass formation; glass formation under continuous cooling conditions; crystallization statistics; kinetics of crystal nucleation; diffusion controlled crystal growth; crystallization of lunar compositions; crystallization between solidus and liquidus; crystallization on reheating a glass; temperature distributions during crystallization; crystallization of anorthite and anorthite-albite compositions; effect of oxidation state on viscosity; diffusive creep and viscous flow; high temperature flow behavior of glass-forming liquids, a free volume interpretation; viscous flow behavior of lunar compositions; thermal history of orange soil material; breccias formation by viscous sintering; viscous sintering; thermal histories of breccias; solute partitioning and thermal history of lunar rocks; heat flow in impact melts; and thermal histories of olivines.

The indigenous honey bees of Saudi Arabia (Hymenoptera, Apidae, Apis mellifera jemenitica Ruttner): Their natural history and role in beekeeping

PubMed Central

Alqarni, Abdulaziz S.; Hannan, Mohammed A.; Owayss, Ayman A.; Engel, Michael S.

2011-01-01

Abstract Apis mellifera jemenitica Ruttner (= yemenitica auctorum: vide Engel 1999) has been used in apiculture throughout the Arabian Peninsula since at least 2000 BC. Existing literature demonstrates that these populations are well adapted for the harsh extremes of the region. Populations of Apis mellifera jemenitica native to Saudi Arabia are far more heat tolerant than the standard races often imported from Europe. Central Saudi Arabia has the highest summer temperatures for the Arabian Peninsula, and it is in this region where only Apis mellifera jemenitica survives, while other subspecies fail to persist. The indigenous race of Saudi Arabia differs from other subspecies in the region in some morphological, biological, and behavioral characteristics. Further taxonomic investigation, as well as molecular studies, is needed in order to confirm whether the Saudi indigenous bee populations represent a race distinct from Apis mellifera jemenitica, or merely an ecotype of this subspecies. PMID:22140343

Morphological and morphometric analysis of scutella of six species and two subspecies of Triatoma (Hemiptera: Reduviidae) in Mexico.

PubMed

Rivas, Nancy; Sánchez-Cordero, Víctor; Camacho, Alejandro D; Córdoba-Aguilar, Alejandro; Alejandre-Aguilar, Ricardo

2017-12-01

Morphological characters can be used to distinguish the vast majority of triatomine species, but the existence of high levels of phenotypic plasticity and recently diverged species can lead to erroneous determinations. To approach this problem, we analyzed the male and female morphologies of the scutella of Triatoma barberi, T. dimidiata, T. lecticularia, T. mexicana, T. recurva, T. rubida, and two sub-species, T. protracta protracta and T. protracta nahuatlae. Scutellum samples were observed by scanning electron microscopy and subjected to morphological analysis and morphometric investigation using a canonical discriminant analysis. The results revealed differences primarily in central depression shape, posterior process, and vestiture. We observed clear dimension-based differences in scutellum morphometry in all the taxa under study, providing sound evidence for species and subspecies differentiation. On the other hand, there is no difference between sexes in T. lecticularia, T. protracta protracta, and T. protracta nahuatlae. Our methodology can be implemented to differentiate species of the genus Triatoma. © 2017 The Society for Vector Ecology.

Clarifying the Dioscorea buchananii Benth. species complex: a new potentially extinct subspecies for South Africa

PubMed Central

Wilkin, Paul; Muasya, A. Muthama

2015-01-01

Abstract The Dioscorea buchananii complex is shown to comprise three species, one of which is divided into two subspecies, based on morphological data. Two species, Dioscorea rupicola Kunth and Dioscorea multiloba Kunth, are endemic or subendemic to South Africa and of widespread occurrence in KwaZulu Natal. They differ markedly from each other in inflorescence and floral morphology and appear to be ecologically differentiated. The third species, Dioscorea buchananii Benth., is primarily found in southeastern tropical Africa, but a small number of specimens collected in South Africa in the late 19th and early 20th centuries are placed in an endemic subspecies, Dioscorea buchananii subsp. undatiloba (Baker) Wilkin. The latter taxon is a high priority in terms of rediscovery and conservation. Keys, descriptions, supporting information and illustrations are provided and made available online through eMonocot biodiversity informatics tools. Three nomenclatural acts are undertaken: two names are placed in synonymy and a new combination made. PMID:25931973

Winter distribution of willow flycatcher subspecies

USGS Publications Warehouse

Paxton, E.H.; Unitt, P.; Sogge, M.K.; Whitfield, M.; Keim, P.

2011-01-01

Documenting how different regions across a species' breeding and nonbreeding range are linked via migratory movements is the first step in understanding how events in one region can influence events in others and is critical to identifying conservation threats throughout a migratory animal's annual cycle. We combined two studies that evaluated migratory connectivity in the Willow Flycatcher (Empidonax traillii), one using mitochondrial DNA sequences from 172 flycatchers sampled throughout their winter range, and another which examined morphological characteristics of 68 museum specimens collected in the winter range. Our results indicate that the four subspecies occupy distinct but overlapping regions of the winter range. Connectivity between specific breeding and winter grounds appears to be moderate to strong, with distributions that suggest migration patterns of both the chain and leap-frog types connecting the breeding and nonbreeding grounds. The Pacific lowlands of Costa Rica appear to be a key winter location for the endangered Southwestern Willow Flycatcher (E. t. extimus), although other countries in Central America may also be important for the subspecies. ?? The Cooper Ornithological Society 2011.

Acoustic, genetic and morphological variations within the katydid Gampsocleis sedakovii (Orthoptera, Tettigonioidea)

PubMed Central

Zhang, Xue; Wen, Ming; Li, Junjian; Zhu, Hui; Wang, Yinliang; Ren, Bingzhong

2015-01-01

Abstract In an attempt to explain the variation within this species and clarify the subspecies classification, an analysis of the genetic, calling songs, and morphological variations within the species Gampsocleis sedakovii is presented from Inner Mongolia, China. Recordings were compared of the male calling songs and analysis performed of selected acoustic variables. This analysis is combined with sequencing of mtDNA - COI and examination of morphological traits to perform cluster analyses. The trees constructed from different datasets were structurally similar, bisecting the six geographical populations studied. Based on two large branches in the analysis, the species Gampsocleis sedakovii was partitioned into two subspecies, Gampsocleis sedakovii sedakovii (Fischer von Waldheim, 1846) and Gampsocleis sedakovii obscura (Walker, 1869). Comparing all the traits, the individual of Elunchun (ELC) was the intermediate type in this species according to the acoustic, genetic, and morphological characteristics. This study provides evidence for insect acoustic signal divergence and the process of subspeciation. PMID:26692795

The Clavibacter michiganensis subspecies: molecular investigation of gram-positive bacterial plant pathogens.

PubMed

Eichenlaub, Rudolf; Gartemann, Karl-Heinz

2011-01-01

Clavibacter michiganensis subspecies are actinomycete plant pathogens residing mainly in the xylem vessels that infect economically important host plants. In the Clavibacter subspecies michiganensis and sepedonicus, infecting tomato and potato, respectively, essential factors for disease induction are plasmid encoded and loss of the virulence plasmids converts these biotrophic pathogens into endophytes. The genes responsible for successful colonization of the host plant, including evasion/suppression of plant defense reactions, are chromosomally encoded. Several serine proteases seem to be involved in colonization. They are secreted by Clavibacter, but their targets remain unknown. A type 3 secretion system (T3SS) translocating effectors into the plant cells is absent in these gram-positive pathogens. With the development of the modern 'omics technologies for RNA and proteins based on the known genome sequences, a new phase in the investigation of the mechanisms of plant pathogenicity has begun to allow the genome-wide investigation of the Clavibacter-host interaction. Copyright © 2011 by Annual Reviews. All rights reserved.

Speyeria (Lepidoptera: Nymphalidae) Conservation.

PubMed

Sims, Steven R

2017-04-25

Speyeria (Nymphalidae) are a conspicuous component of the North American butterfly fauna. There are approximately 16 species and >100 associated subspecies (or geographical variants). Speyeria are univoltine, occupy a wide range of habitats, overwinter as first instar larvae, and feed only on native violets. Speyeria species have become a model group for studies of evolution, speciation, and conservation. Several species and subspecies are threatened or endangered. The reasons for this vary with the taxa involved, but always involve the degradation or loss of quality habitat for larvae and adults. The impacts of climate change must be considered among the causes for habitat degradation and in the establishment of conservation measures. In addition to increasing the available habitat, conservation efforts should consider maintaining habitat in a seral "disturbed" successional stage that selectively favors the growth of violets and preferred adult nectar sources. A major future challenge will be determining the most effective allocation of conservation resources to those species and subspecies that have the greatest potential to respond favorably to these efforts.

Speyeria (Lepidoptera: Nymphalidae) Conservation

PubMed Central

Sims, Steven R.

2017-01-01

Speyeria (Nymphalidae) are a conspicuous component of the North American butterfly fauna. There are approximately 16 species and >100 associated subspecies (or geographical variants). Speyeria are univoltine, occupy a wide range of habitats, overwinter as first instar larvae, and feed only on native violets. Speyeria species have become a model group for studies of evolution, speciation, and conservation. Several species and subspecies are threatened or endangered. The reasons for this vary with the taxa involved, but always involve the degradation or loss of quality habitat for larvae and adults. The impacts of climate change must be considered among the causes for habitat degradation and in the establishment of conservation measures. In addition to increasing the available habitat, conservation efforts should consider maintaining habitat in a seral “disturbed” successional stage that selectively favors the growth of violets and preferred adult nectar sources. A major future challenge will be determining the most effective allocation of conservation resources to those species and subspecies that have the greatest potential to respond favorably to these efforts. PMID:28441319

The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus).

PubMed

Steiper, Michael E; Wolfe, Nathan D; Karesh, William B; Kilbourn, Annelisa M; Bosi, Edwin J; Ruvolo, Maryellen

2005-03-01

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.

Yaws: 110 years after Castellani's discovery of Treponema pallidum subspecies pertenue.

PubMed

Stamm, Lola V

2015-07-01

Yaws is a neglected infectious disease that affects mostly children and adolescents living in poor, rural communities in humid, tropical areas of Africa, southeast Asia, and the Pacific Islands. The etiological agent of yaws, Treponema pallidum subspecies pertenue (T. pertenue), was discovered by Aldo Castellani in 1905 shortly after Schaudinn and Hoffmann discovered the etiological agent of syphilis, T. pallidum subspecies pallidum. The discovery of T. pertenue enabled the development of animal models and the identification of an effective antibiotic treatment (i.e., penicillin) for yaws. A World Health Organization (WHO) mass treatment campaign from 1952 to 1964 reduced the global burden of yaws by 95%, but failed to eradicate this disease. Today, 110 years after Castellani's discovery of T. pertenue, yaws is again targeted for eradication. Recent advances in the treatment and diagnosis of yaws improve the likelihood of success this time. However, several challenges must be overcome to make the goal of yaws eradication attainable. © The American Society of Tropical Medicine and Hygiene.

Particular Distribution of Enterobacter cloacae Strains Isolated from Urinary Tract Infection within Clonal Complexes.

PubMed

Akbari, Majid; Bakhshi, Bita; Najar Peerayeh, Shahin

2016-01-01

Based on biochemical properties, Enterobacter cloacae represents a large complex of at least 13 variant species, subspecies, and genotypes that progressively identified as the most species causing hospital-acquired infections. The aim of this study was to determine the relevance between phylogenetically related strains within the E. cloacae complex and the frequency of urinary tract infection caused by them. A 268-bp fragment was obtained from hsp60 gene for 50 clinical E. cloacae isolates from urine cultures of inpatients that admitted to six hospitals in Tehran, Iran during December 2012 to November 2013. The 107 nucleotide sequences were analyzed and the evolutionary distances of sequences were computed and neighbor-joining tree was calculated. It showed that all of the genetic clusters have not an equal involvement in pathogenesis of urinary tract infections. Three superior clusters were found, together representing more than two third (80%) of the isolates (cluster VI with 25 members; clusters III and VIII with 9 and 6 members, respectively) and some genetic clusters were absent (IV, X, XII, and xiii), some of which are supposed to be associated with plants and no human infection has been reported. This study, for the first time, reports the unequal contribution of E. cloacae complex subspecies and clusters in urinary tract infections in Iran and together with studies from other countries suggest that the subspecies of E.hormaechei subsp. Oharae is the most prevalent E. cloacae complex subspecies regardless of country under study.

Mitogenomic Phylogenetics of Fin Whales (Balaenoptera physalus spp.): Genetic Evidence for Revision of Subspecies

PubMed Central

Archer, Frederick I.; Morin, Phillip A.; Hancock-Hanser, Brittany L.; Robertson, Kelly M.; Leslie, Matthew S.; Bérubé, Martine; Panigada, Simone; Taylor, Barbara L.

2013-01-01

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using ∼16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species. PMID:23691042

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivas-Ubach, A.; Sardans, J.; Hódar, J. A.

Plants respond locally and systemically to herbivore attack. Most of the research conducted on plant-herbivore relationships at elemental and molecular levels have focused on nutrients or/and certain molecular compounds or specific families of defensive metabolites showing that herbivores tend to select plant individuals or species with higher nutrient concentrations and to avoid those with higher levels of phenolics and terpenes. Unfortunately, the defensive role of phenolics in conifers is still unclear. We performed stoichiometric and metabolomics, local and systemic, analyses in two subspecies of Pinus sylvestris under the herbivorous attack by the caterpillars of the pine processionary moth, an importantmore » pest in the Mediterranean Basin. Herbivorous attack was not associated with any of the elements analyzed. Both pine subspecies responded locally to folivory mainly by increasing the concentrations of various terpenes and phenolics. Systemic responses differed between subspecies and most of the metabolites presented intermediate concentrations between those of the affected parts and unattacked trees. Contrary as usually thought, foliar nutrient concentrations did not show to be a main factor of an alleged plant selection by adult female processionary moths for oviposition. Local increases in phenolics were more associated with antioxidant function for protection against oxidative damage produced by folivory. On the other hand, terpenes were directly related to defense against herbivores. Herbivory attack produced a general systemic shift in pines, including both primary and secondary metabolisms, that was, however, less intense and chemically different from the local responses. Subspecies responded similarly locally but differently to folivory at systemic level.« less

Molecular phylogeny and phylogeography of genus Pseudois (Bovidae, Cetartiodactyla): New insights into the contrasting phylogeographic structure.

PubMed

Tan, Shuai; Wang, Zhihong; Jiang, Lichun; Peng, Rui; Zhang, Tao; Peng, Quekun; Zou, Fangdong

2017-09-01

Blue sheep, Pseudois nayaur , is endemic to the Tibetan Plateau and the surrounding mountains, which are the highest-elevation areas in the world. Classical morphological taxonomy suggests that there are two subspecies in genus Pseudois (Bovidae, Artiodactyla), namely Pseudois nayaur nayaur and Pseudois nayaur szechuanensis . However, the validity and geographic characteristics of these subspecies have never been carefully discussed and analyzed. This may be partially because previous studies have mainly focused on the vague taxonomic status of Pseudois schaeferi (dwarf blue sheep). Thus, there is an urgent need to investigate the evolutionary relationship and taxonomy system of this genus. This study enriches a previous dataset by providing a large number of new samples, based on a total of 225 samples covering almost the entire distribution of blue sheep. Molecular data from cytochrome b and the mitochondrial control region sequences were used to reconstruct the phylogeny of this species. The phylogenetic inferences show that vicariance plays an important role in diversification within this genus. In terms of molecular dating results and biogeographic analyses, the striking biogeographic pattern coincides significantly with major geophysical events. Although the results raise doubt about the present recognized distribution range of blue sheep, they have corroborated the validity of the identified subspecies in genus Pseudois . Meanwhile, these results demonstrate that the two geographically distinct populations, the Helan Mountains and Pamir Plateau populations, have been significantly differentiated from the identified subspecies, a finding that challenges the conventional taxonomy of blue sheep.

Population genetics and evaluation of genetic evidence for subspecies in the Semipalmated Sandpiper (Calidris pusilla)

USGS Publications Warehouse

Miller, Mark P.; Gratto-Trevor, Cheri; Haig, Susan M.; Mizrahi, David S.; Mitchell, Melanie M.; Mullins, Thomas D.

2013-01-01

Semipalmated Sandpipers (Calidris pusilla) are among the most common North American shorebirds. Breeding in Arctic North America, this species displays regional differences in migratory pathways and possesses longitudinal bill length variation. Previous investigations suggested that genetic structure may occur within Semipalmated Sandpipers and that three subspecies corresponding to western, central, and eastern breeding groups exist. In this study, mitochondrial control region sequences and nuclear microsatellite loci were used to analyze DNA of birds (microsatellites: n = 120; mtDNA: n = 114) sampled from seven North American locations. Analyses designed to quantify genetic structure and diversity patterns, evaluate genetic evidence for population size changes, and determine if genetic data support the existence of Semipalmated Sandpiper subspecies were performed. Genetic structure based only on the mtDNA data was observed, whereas the microsatellite loci provided no evidence of genetic differentiation. Differentiation among locations and regions reflected allele frequency differences rather than separate phylogenetic groups, and similar levels of genetic diversity were noted. Combined, the two data sets provided no evidence to support the existence of subspecies and were not useful for determining migratory connectivity between breeding sites and wintering grounds. Birds from western and central groups displayed signatures of population expansions, whereas the eastern group was more consistent with a stable overall population. Results of this analysis suggest that the eastern group was the source of individuals that colonized the central and western regions currently utilized by Semipalmated Sandpipers.

Synopsis of Central Andean Orthalicoid land snails (Gastropoda, Stylommatophora), excluding Bulimulidae.

PubMed

Breure, Abraham S H; Avila, Valentín Mogollón

2016-01-01

A faunal overview is presented of the molluscan families Amphibulimidae, Megaspiridae, Odontostomidae, Orthalicidae, Simpulopsidae in Bolivia, Ecuador, and Peru. These Central Andean countries are known for their biodiverse malacofauna, of which the superfamily Orthalicoidea takes relatively a large share. In this paper the five families containing 103 (sub)species, for which systematic information (original publication, type locality, type depository, summarizing literature) and distributional records are presented. All species are illustrated by photographs of the type material or, if this could not be located, by a reproduction of the original figure. The following new taxon is introduced: Thaumastus (Thaumastus) sumaqwayqu sp. n. Junior subjective synonyms are established for: Plekocheilus (Sparnotion) Pilsbry, 1944 = Plekocheilus (Eudolichotis) Pilsbry, 1896; Scholvienia (Thomsenia) Strebel, 1910 = Scholvienia Strebel, 1910; Sultana (Trachyorthalicus) Strebel, 1909 = Sultana (Metorthalicus) Pilsbry, 1899; Plekocheilus (Eurytus) conspicuus Pilsbry, 1932 = Thaumastus (Thaumastus) hartwegi (Pfeiffer in Philippi, 1846); Zebra gruneri Strebel, 1909 = Orthalicus maracaibensis (Pfeiffer, 1856); Scholvienia jaspidea minor Strebel, 1910 = Scholvienia alutacea (Reeve, 1850); Bulimus bifasciatus unicolor Philippi, 1869 = Scholvienia brephoides (d'Orbigny, 1835). A new status is given to Plekocheilus mcgintyi 'Pilsbry' H.B. Baker, 1963 (subspecies of Bulinus piperitus Sowerby I, 1837); Strophocheilus superstriatus var. prodeflexus Pilsbry, 1895 (subspecies of Bulinus piperitus Sowerby I, 1837); Thaumastus (Quechua) salteri maximus Weyrauch, 1967 (subspecies of Thaumastus (Quechua) olmosensis Zilch, 1954); Pseudoglandina agitata Weyrauch, 1967 (nomen inquirendum). New combinations are: Clathrorthalicus corydon (Crosse, 1869), and Cyclodontina chuquisacana (Marshall, 1930). Lectotypes are now designated for Bulimus incisus Hupé, 1857 and Bulinus piperitus Sowerby I, 1837.

Laminated metal composite formed from low flow stress layers and high flow stress layers using flow constraining elements and making same

DOEpatents

Syn, C.K.; Lesuer, D.R.

1995-07-04

A laminated metal composite of low flow stress layers and high flow stress layers is described which is formed using flow constraining elements, preferably in the shape of rings, individually placed around each of the low flow stress layers while pressure is applied to the stack to bond the layers of the composite together, to thereby restrain the flow of the low flow stress layers from the stack during the bonding. The laminated metal composite of the invention is made by the steps of forming a stack of alternate layers of low flow stress layers and high flow stress layers with each layer of low flow stress material surrounded by an individual flow constraining element, such as a ring, and then applying pressure to the top and bottom surfaces of the resulting stack to bond the dissimilar layers together, for example, by compression rolling the stack. In a preferred embodiment, the individual flow constraining elements surrounding the layers of low flow stress material are formed of a material which may either be the same material as the material comprising the high flow stress layers, or have similar flow stress characteristics to the material comprising the high flow stress layers. Additional sacrificial layers may be added to the top and bottom of the stack to avoid damage to the stack during the bonding step; and these additional layers may then be removed after the bonding step. 5 figs.

Laminated metal composite formed from low flow stress layers and high flow stress layers using flow constraining elements and making same

DOEpatents

Syn, Chol K.; Lesuer, Donald R.

1995-01-01

A laminated metal composite of low flow stress layers and high flow stress layers is described which is formed using flow constraining elements, preferably in the shape of rings, individually placed around each of the low flow stress layers while pressure is applied to the stack to bond the layers of the composite together, to thereby restrain the flow of the low flow stress layers from the stack during the bonding. The laminated metal composite of the invention is made by the steps of forming a stack of alternate layers of low flow stress layers and high flow stress layers with each layer of low flow stress material surrounded by an individual flow constraining element, such as a ring, and then applying pressure to the top and bottom surfaces of the resulting stack to bond the dissimilar layers together, for example, by compression rolling the stack. In a preferred embodiment, the individual flow constraining elements surrounding the layers of low flow stress material are formed of a material which may either be the same material as the material comprising the high flow stress layers, or have similar flow stress characteristics to the material comprising the high flow stress layers. Additional sacrificial layers may be added to the top and bottom of the stack to avoid damage to the stack during the bonding step; and these additional layers may then be removed after the bonding step.

Genetic diversity and population structure of Musa accessions in ex situ conservation

PubMed Central

2013-01-01

Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping. PMID:23497122

Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.

PubMed

Turner, Leslie M; Harr, Bettina

2014-12-09

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows

PubMed Central

Tardiole Kuehne, Bruno; Estrella, Julio Cezar; Nunes, Luiz Henrique; Martins de Oliveira, Edvard; Hideo Nakamura, Luis; Gomes Ferreira, Carlos Henrique; Carlucci Santana, Regina Helena; Reiff-Marganiec, Stephan; Santana, Marcos José

2015-01-01

This paper proposes a system named AWSCS (Automatic Web Service Composition System) to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production. PMID:26068216

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows.

PubMed

Tardiole Kuehne, Bruno; Estrella, Julio Cezar; Nunes, Luiz Henrique; Martins de Oliveira, Edvard; Hideo Nakamura, Luis; Gomes Ferreira, Carlos Henrique; Carlucci Santana, Regina Helena; Reiff-Marganiec, Stephan; Santana, Marcos José

2015-01-01

This paper proposes a system named AWSCS (Automatic Web Service Composition System) to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production.

Composition Pulse Time-Of-Flight Mass Flow Sensor

DOEpatents

Mosier, Bruce P.; Crocker, Robert W.; Harnett, Cindy K. l

2004-01-13

A device for measuring fluid flow rates over a wide range of flow rates (<1 nL/min to >10 .mu.L/min) and at pressures at least as great as 10,000 psi. The invention is particularly adapted for use in microfluidic systems. The device operates by producing compositional variations in the fluid, or pulses, that are subsequently detected downstream from the point of creation to derive a flow rate. Each pulse, comprising a small fluid volume, whose composition is different from the mean composition of the fluid, can be created by electrochemical means, such as by electrolysis of a solvent, electrolysis of a dissolved species, or electrodialysis of a dissolved ionic species. Measurements of the conductivity of the fluid can be used to detect the arrival time of the pulses, from which the fluid flow rate can be determined

T-cell receptor genes in tassel-eared squirrels (Sciurus aberti). I. Genetic polymorphism and divergence in the Abert and Kaibab subspecies.

PubMed

Wettstein, P J; Chakraborty, R; States, J; Ferrari, G

1990-01-01

The role of environmental factors in the evolution and maintenance of diversity of antigen receptor gene families which participate in the immune response in mammals is inadequately understood. In order to elucidate the impact of these factors, we have undertaken the analysis of these gene families in the tassel-eared squirrel (Sciurus aberti) which has been separated into discrete subspecies by geographic barriers and whose food resources can be quantitated for estimating environmental quality. In this communication we describe the initial analysis of the complexity and polymorphism of sequences related to T-cell receptor (Tcr) alpha and beta chain genes in two subspecies, Sciurus aberti aberti (Abert) and Sciurus aberti kaibabensis (Kaibab) which have identical habitats and are separated by the Grand Canyon in Arizona, USA. Genomic blot analysis of 60 Abert and 62 Kaibab individuals collected over a 3-year period was performed with mouse Tcrb and Tcra cDNA probes. Sequences homologous to Tcrb-C, Tcrb-J1, and Tcrb-J2 genes were observed in all individuals from both subspecies; although Tcrb-J1 fragments were monomorphic. Tcrb-C and Tcrb-J2 fragments were polymorphic with both species- and subspecies-specific sequences. A single, monomorphic Tcra-C fragment was observed in addition to multiple Tcra-V fragments homologous to the mouse Tcra-V1 subfamily. Abert samples exhibited greater numbers of Tcra-V1 fragments as well as greater polymorphism than Kaibab samples. Heterozygosity estimates of Tcrb-C and Tcra-V1 sequences were determined for annually collected samples and compared with the yearly estimates of availability of hypogeous fungi, one of the major diet items of tassel-eared squirrels. In the Kaibab annual collections, Tcra-V1 heterozygosity declined with the decline in food resource, whereas heterozygosity of Tcrb-C sequences was inversely related to food resource. Similarly, a reduction in food resource for Abert squirrels in 1985 coincided with an increase in Tcrb-C heterozygosity in the same year. These results suggest that the diversity of gene families which participate in the immune response in mammals may be affected by environmental factors.

Unveiling Current Guanaco Distribution in Chile Based upon Niche Structure of Phylogeographic Lineages: Andean Puna to Subpolar Forests

PubMed Central

González, Benito A.; Samaniego, Horacio; Marín, Juan Carlos; Estades, Cristián F.

2013-01-01

Niche description and differentiation at broad geographic scales have been recent major topics in ecology and evolution. Describing the environmental niche structure of sister taxa with known evolutionary trajectories stands out as a useful exercise in understanding niche requirements. Here we model the environmental niche structure and distribution of the recently resolved phylogeography of guanaco (Lama guanicoe) lineages on the western slope of the southern Andes. Using a maximum entropy framework, field data, and information on climate, topography, human density, and vegetation cover, we identify differences between the two subspecies (L.g.cacsilensis, L.g.guanicoe) and their intermediate-hybrid lineage, that most likely determine the distribution of this species. While aridity seems to be a major factor influencing the distribution at the species-level (annual precipitation <900 mm), we also document important differences in niche specificity for each subspecies, where distribution of Northern lineage is explained mainly by elevation (mean = 3,413 m) and precipitation seasonality (mean = 161 mm), hybrid lineage by annual precipitation (mean = 139 mm), and Southern subspecies by annual precipitation (mean = 553 mm), precipitation seasonality (mean = 21 mm) and grass cover (mean = 8.2%). Among lineages, we detected low levels of niche overlap: I (Similarity Index) = 0.06 and D (Schoener’s Similarity Index) = 0.01; and higher levels when comparing Northern and Southern subspecies with hybrids lineage (I = 0.32-0.10 and D = 0.12-0.03, respectively). This suggests that important ecological and/or evolutionary processes are shaping the niche of guanacos in Chile, producing discrepancies when comparing range distribution at the species-level (81,756 km2) with lineages-level (65,321 km2). The subspecies-specific description of niche structure is provided here based upon detailed spatial distribution of the lineages of guanacos in Chile. Such description provides a scientific tool to further develop large scale plans for habitat conservation and preservation of intraspecific genetic variability for this far ranging South American camelid, which inhabits a diversity of ecoregion types from Andean puna to subpolar forests. PMID:24265726

Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)

PubMed Central

2011-01-01

Background Big sagebrush (Artemisia tridentata) is one of the most widely distributed and ecologically important shrub species in western North America. This species serves as a critical habitat and food resource for many animals and invertebrates. Habitat loss due to a combination of disturbances followed by establishment of invasive plant species is a serious threat to big sagebrush ecosystem sustainability. Lack of genomic data has limited our understanding of the evolutionary history and ecological adaptation in this species. Here, we report on the sequencing of expressed sequence tags (ESTs) and detection of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in subspecies of big sagebrush. Results cDNA of A. tridentata sspp. tridentata and vaseyana were normalized and sequenced using the 454 GS FLX Titanium pyrosequencing technology. Assembly of the reads resulted in 20,357 contig consensus sequences in ssp. tridentata and 20,250 contigs in ssp. vaseyana. A BLASTx search against the non-redundant (NR) protein database using 29,541 consensus sequences obtained from a combined assembly resulted in 21,436 sequences with significant blast alignments (≤ 1e-15). A total of 20,952 SNPs and 119 polymorphic SSRs were detected between the two subspecies. SNPs were validated through various methods including sequence capture. Validation of SNPs in different individuals uncovered a high level of nucleotide variation in EST sequences. EST sequences of a third, tetraploid subspecies (ssp. wyomingensis) obtained by Illumina sequencing were mapped to the consensus sequences of the combined 454 EST assembly. Approximately one-third of the SNPs between sspp. tridentata and vaseyana identified in the combined assembly were also polymorphic within the two geographically distant ssp. wyomingensis samples. Conclusion We have produced a large EST dataset for Artemisia tridentata, which contains a large sample of the big sagebrush leaf transcriptome. SNP mapping among the three subspecies suggest the origin of ssp. wyomingensis via mixed ancestry. A large number of SNP and SSR markers provide the foundation for future research to address questions in big sagebrush evolution, ecological genetics, and conservation using genomic approaches. PMID:21767398

Salmonella isolated from individual reptiles and environmental samples from terraria in private households in Sweden.

PubMed

Wikström, Veronica O; Fernström, Lise-Lotte; Melin, Lennart; Boqvist, Sofia

2014-01-24

This study investigates Salmonella spp. isolated from privately kept reptiles and from environmental samples such as bedding materials or water from the floor of the enclosures (terraria). It also compares isolation of Salmonella using Modified Semisolid Rappaport-Vassiliadis (MSRV) medium or selective enrichment in Rappaport-Vassiliadis-Soya (RVS) pepton broth. Cloacal swabs or swabs from the cloacal area were collected from 63 individual reptiles belonging to 14 households. All reptiles were from different terraria and from 62 of these, environmental samples were also collected. Sampling were done by the reptile owners according to written instructions and sent by mail immediately after sampling. All but three samples were analyzed within 24 h after collection. Colonies suspected for Salmonella were tested for agglutination and serotyped using the White-Kauffmann-Le Minor scheme. The relative sensitivity (se) and specificity (sp) for MSRV compared with RVS, and the agreement coefficient kappa (κ) were calculated. Salmonella was isolated from 50/63 (80%) terraria, either from the reptiles (31/63; 49%) or from bedding material (39/62; 63%). The most common subspecies was Salmonella enterica subspecies enterica followed by S. enterica subspecies diarizonae. In reptiles, the most common S. enterica subspecies enterica serovars were Java (n = 4) and Fluntern (n = 4), compared with the serovars Tennessee (n = 10) and Fluntern (n = 10) in the environmental samples. The exact same set of Salmonella subspecies and serovars were not isolated from the individual reptiles and the environmental samples from any of the households. Isolation using MSRV yielded more Salmonella isolates 61/113 (54%) than enrichment in RVS 57/125 (46%). The se was 97.9% (95% Confidence Interval 93.9-100), the sp 78.5% (95% CI 68.5-88.5) and the κ 0.74, indicating substantial agreement between the tests. Salmonella can be expected to be present in environments where reptiles are kept. This constitutes public health risks and should be considered during handling of the reptiles and during cleaning and disposal of bedding. A combination of different culturing techniques may be used to increase the isolation rate.

Salmonella isolated from individual reptiles and environmental samples from terraria in private households in Sweden

PubMed Central

2014-01-01

Background This study investigates Salmonella spp. isolated from privately kept reptiles and from environmental samples such as bedding materials or water from the floor of the enclosures (terraria). It also compares isolation of Salmonella using Modified Semisolid Rappaport-Vassiliadis (MSRV) medium or selective enrichment in Rappaport-Vassiliadis-Soya (RVS) pepton broth. Cloacal swabs or swabs from the cloacal area were collected from 63 individual reptiles belonging to 14 households. All reptiles were from different terraria and from 62 of these, environmental samples were also collected. Sampling were done by the reptile owners according to written instructions and sent by mail immediately after sampling. All but three samples were analyzed within 24 h after collection. Colonies suspected for Salmonella were tested for agglutination and serotyped using the White-Kauffmann-Le Minor scheme. The relative sensitivity (se) and specificity (sp) for MSRV compared with RVS, and the agreement coefficient kappa (κ) were calculated. Results Salmonella was isolated from 50/63 (80%) terraria, either from the reptiles (31/63; 49%) or from bedding material (39/62; 63%). The most common subspecies was Salmonella enterica subspecies enterica followed by S. enterica subspecies diarizonae. In reptiles, the most common S. enterica subspecies enterica serovars were Java (n = 4) and Fluntern (n = 4), compared with the serovars Tennessee (n = 10) and Fluntern (n = 10) in the environmental samples. The exact same set of Salmonella subspecies and serovars were not isolated from the individual reptiles and the environmental samples from any of the households. Isolation using MSRV yielded more Salmonella isolates 61/113 (54%) than enrichment in RVS 57/125 (46%). The se was 97.9% (95% Confidence Interval 93.9-100), the sp 78.5% (95% CI 68.5-88.5) and the κ 0.74, indicating substantial agreement between the tests. Conclusions Salmonella can be expected to be present in environments where reptiles are kept. This constitutes public health risks and should be considered during handling of the reptiles and during cleaning and disposal of bedding. A combination of different culturing techniques may be used to increase the isolation rate. PMID:24461167

Unveiling current Guanaco distribution in chile based upon niche structure of phylogeographic lineages: Andean puna to subpolar forests.

PubMed

González, Benito A; Samaniego, Horacio; Marín, Juan Carlos; Estades, Cristián F

2013-01-01

Niche description and differentiation at broad geographic scales have been recent major topics in ecology and evolution. Describing the environmental niche structure of sister taxa with known evolutionary trajectories stands out as a useful exercise in understanding niche requirements. Here we model the environmental niche structure and distribution of the recently resolved phylogeography of guanaco (Lama guanicoe) lineages on the western slope of the southern Andes. Using a maximum entropy framework, field data, and information on climate, topography, human density, and vegetation cover, we identify differences between the two subspecies (L.g.cacsilensis, L.g.guanicoe) and their intermediate-hybrid lineage, that most likely determine the distribution of this species. While aridity seems to be a major factor influencing the distribution at the species-level (annual precipitation <900 mm), we also document important differences in niche specificity for each subspecies, where distribution of Northern lineage is explained mainly by elevation (mean = 3,413 m) and precipitation seasonality (mean = 161 mm), hybrid lineage by annual precipitation (mean = 139 mm), and Southern subspecies by annual precipitation (mean = 553 mm), precipitation seasonality (mean = 21 mm) and grass cover (mean = 8.2%). Among lineages, we detected low levels of niche overlap: I (Similarity Index) = 0.06 and D (Schoener's Similarity Index) = 0.01; and higher levels when comparing Northern and Southern subspecies with hybrids lineage ( I = 0.32-0.10 and D = 0.12-0.03, respectively). This suggests that important ecological and/or evolutionary processes are shaping the niche of guanacos in Chile, producing discrepancies when comparing range distribution at the species-level (81,756 km(2)) with lineages-level (65,321 km(2)). The subspecies-specific description of niche structure is provided here based upon detailed spatial distribution of the lineages of guanacos in Chile. Such description provides a scientific tool to further develop large scale plans for habitat conservation and preservation of intraspecific genetic variability for this far ranging South American camelid, which inhabits a diversity of ecoregion types from Andean puna to subpolar forests.

Geographic variation and genetic structure in Spotted Owls

USGS Publications Warehouse

Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

2001-01-01

We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

Strong population structure of Schizopygopsis chengi and the origin of S. chengi baoxingensis revealed by mtDNA and microsatellite markers.

PubMed

Liu, Dongqi; Hou, Feixia; Liu, Qin; Zhang, Xiuyue; Yan, Taiming; Song, Zhaobin

2015-02-01

The Tibetan Plateau underwent dramatic geological and climatic changes, which had important implications for genetic divergence and population dynamics of freshwater fish populations. Fluctuations of the ecogeographical environment and major hydrographic formations might have promoted the formation of new subspecies or species. In order to understand the impact of plateau uplift on freshwater fish evolutionary history, we estimated the genetic diversity and population structure in two subspecies of Schizopygopsis chengi (S. c. chengi and S. c. baoxingensis) in upper Yangtze River in Tibetan Plateau area using mitochondrial DNA control region and eight microsatellite markers, which suggested that there was a close genetic relationship. S. chengi showed some significant genetic structure that did not correlate with geographic distance. Bayesian assignment tests indicated that S. chengi samples in the study could be divided into four populations: upstream population, midstream population, tributary population and S. c. baoxingensis population. S. c. chengi and S. c. baoxingensis showed significant genetic divergence. However, phylogenetic analysis, population structure analysis and historical gene flow estimation suggested that there was close genetic relationship between S. c. baoxingensis and the Dawei population which belongs to populations of S. c. chengi. The time that Dawei population suffered from a bottleneck and S. c. baoxingensis underwent population expansion was congruent with the last glacial period on the Tibetan Plateau. The results confirmed the hypothesis that the Dawei River and Baoxing River were once connected, and the Dawei and Baoxing populations originated from a single population, but were isolated into separate populations because of crustal movements and the Baoxing population evolved as S. c. baoxingensis.

The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis.

PubMed

Derakhshani, Hooman; De Buck, Jeroen; Mortier, Rienske; Barkema, Herman W; Krause, Denis O; Khafipour, Ehsan

2016-01-01

Current diagnostic tests for Johne's disease (JD), a chronic granulomatous inflammation of the gastrointestinal tract of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), lack the sensitivity to identify infected animals at early (asymptomatic) stages of the disease. The objective was to determine the pattern of MAP-associated dysbiosis of intestinal microbiota as a potential biomarker for early detection of infected cattle. To that end, genomic DNA was extracted from ileal mucosa and fecal samples collected from 28 MAP-positive and five control calves. High-throughput Illumina sequencing of the V4 hypervariable region of the 16S rRNA gene was used for community profiling of ileal mucosa-associated (MAM) or fecal microbiota. The PERMANOVA analysis of unweighted UniFrac distances revealed distinct clustering of ileal MAM (P = 0.049) and fecal microbiota (P = 0.068) in MAP-infected vs. control cattle. Microbiota profile of MAP-infected animals was further investigated by linear discriminant analysis effective size (LEfSe); several bacterial taxa within the phylum Proteobacteria were overrepresented in ileal MAM of control calves. Moreover, based on reconstructed metagenomes (PICRUSt) of ileal MAM, functional pathways associated with MAP infection were inferred. Enrichment of lysine and histidine metabolism pathways, and underrepresentation of glutathione metabolism and leucine and isoleucine degradation pathways in MAP-infected calves suggested potential contributions of ileal MAM in development of intestinal inflammation. Finally, simultaneous overrepresentation of families Planococcaceae and Paraprevotellaceae, as well as underrepresentation of genera Faecalibacterium and Akkermansia in the fecal microbiota of infected cattle, served as potential biomarker for identifying infected cattle during subclinical stages of JD. Collectively, based on compositional and functional shifts in intestinal microbiota of infected cattle, we inferred that this dynamic network of microorganisms had an active role in intestinal homeostasis.

Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis.

PubMed

Song, Han; Yoo, Young; Hwang, Junghyun; Na, Yun-Cheol; Kim, Heenam Stanley

2016-03-01

Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle. Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear. The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses. We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease. The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Novel Methods of Determining Urinary Calculi Composition: Petrographic Thin Sectioning of Calculi and Nanoscale Flow Cytometry Urinalysis

PubMed Central

Gavin, Carson T; Ali, Sohrab N; Tailly, Thomas; Olvera-Posada, Daniel; Alenezi, Husain; Power, Nicholas E; Hou, Jinqiang; St. Amant, Andre H; Luyt, Leonard G; Wood, Stephen; Wu, Charles; Razvi, Hassan; Leong, Hon S

2016-01-01

Accurate determination of urinary stone composition has significant bearing on understanding pathophysiology, choosing treatment modalities and preventing recurrence. A need exists for improved methods to determine stone composition. Urine of 31 patients with known renal calculi was examined with nanoscale flow cytometry and the calculi collected during surgery subsequently underwent petrographic thin sectioning with polarized and fluorescent microscopy. Fluorescently labeled bisphosphonate probes (Alendronate-fluorescein/Alendronate-Cy5) were developed for nanoscale flow cytometry to enumerate nanocrystals that bound the fluorescent probes. Petrographic sections of stones were also imaged by fluorescent and polarized light microscopy with composition analysis correlated to alendronate +ve nanocrystal counts in corresponding urine samples. Urine samples from patients with Ca2+ and Mg2+ based calculi exhibited the highest alendronate +ve nanocrystal counts, ranging from 100–1000 nm in diameter. This novel urine based assay was in agreement with composition determined by petrographic thin sections with Alendronate probes. In some cases, high alendronate +ve nanocrystal counts indicated a Ca2+ or Mg2+ composition, as confirmed by petrographic analysis, overturning initial spectrophotometric diagnosis of stone composition. The combination of nanoscale flow cytometry and petrographic thin sections offer an alternative means for determining stone composition. Nanoscale flow cytometry of alendronate +ve nanocrystals alone may provide a high-throughput means of evaluating stone burden. PMID:26771074

Sequence Diversity of Pan troglodytes Subspecies and the Impact of WFDC6 Selective Constraints in Reproductive Immunity

PubMed Central

Ferreira, Zélia; Hurle, Belen; Andrés, Aida M.; Kretzschmar, Warren W.; Mullikin, James C.; Cherukuri, Praveen F.; Cruz, Pedro; Gonder, Mary Katherine; Stone, Anne C.; Tishkoff, Sarah; Swanson, Willie J.; Green, Eric D.; Clark, Andrew G.; Seixas, Susana

2013-01-01

Recent efforts have attempted to describe the population structure of common chimpanzee, focusing on four subspecies: Pan troglodytes verus, P. t. ellioti, P. t. troglodytes, and P. t. schweinfurthii. However, few studies have pursued the effects of natural selection in shaping their response to pathogens and reproduction. Whey acidic protein (WAP) four-disulfide core domain (WFDC) genes and neighboring semenogelin (SEMG) genes encode proteins with combined roles in immunity and fertility. They display a strikingly high rate of amino acid replacement (dN/dS), indicative of adaptive pressures during primate evolution. In human populations, three signals of selection at the WFDC locus were described, possibly influencing the proteolytic profile and antimicrobial activities of the male reproductive tract. To evaluate the patterns of genomic variation and selection at the WFDC locus in chimpanzees, we sequenced 17 WFDC genes and 47 autosomal pseudogenes in 68 chimpanzees (15 P. t. troglodytes, 22 P. t. verus, and 31 P. t. ellioti). We found a clear differentiation of P. t. verus and estimated the divergence of P. t. troglodytes and P. t. ellioti subspecies in 0.173 Myr; further, at the WFDC locus we identified a signature of strong selective constraints common to the three subspecies in WFDC6—a recent paralog of the epididymal protease inhibitor EPPIN. Overall, chimpanzees and humans do not display similar footprints of selection across the WFDC locus, possibly due to different selective pressures between the two species related to immune response and reproductive biology. PMID:24356879

Population size of island loggerhead shrikes on Santa Rosa and Santa Cruz Islands

USGS Publications Warehouse

Stanley, Thomas R.; Teel, Susan; Hall, Linnea S.; Dye, Linda C.; Laughrin, Lyndal L.

2012-01-01

Island loggerhead shrikes (Lanius ludovicianus anthonyi) are an endemic, genetically distinct subspecies of loggerhead shrike on California's Santa Rosa, Santa Cruz, and Santa Catalina Islands (USA). This subspecies is listed as a Species of Special Concern by the California Department of Fish and Game and has been petitioned for federal listing under the Endangered Species Act. The combination of suspected low numbers and the possibility of federal listing, prompted us to undertake a study to rigorously estimate the number of remaining individuals on Santa Rosa and Santa Cruz Islands. During the 2009 and 2010 breeding seasons, we surveyed sample units on Santa Rosa and Santa Cruz Islands using a double-observer method with independent observers to estimate joint detection probabilities (p), where we selected units under a stratified random sampling design. We estimated shrike abundance to be 169 in 2009 (p = 0.476) and 240 in 2010 (p = 0.825) for Santa Rosa Island, and 35 in 2009 (p = 0.816) and 42 in 2010 (p = 0.710) for Santa Cruz Island. These numbers, especially for Santa Rosa Island, are higher than previously reported but nevertheless are still low. Rapid vegetation change on both islands due to recent removal of nonnative herbivores may threaten the habitat and status of this subspecies and, therefore, we suggest that intensive demographic and habitat use research be initiated immediately to obtain additional information vital for the management of this subspecies. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Synopsis of Central Andean Orthalicoid land snails (Gastropoda, Stylommatophora), excluding Bulimulidae

PubMed Central

Breure, Abraham S.H.; Avila, Valentín Mogollón

2016-01-01

Abstract A faunal overview is presented of the molluscan families Amphibulimidae, Megaspiridae, Odontostomidae, Orthalicidae, Simpulopsidae in Bolivia, Ecuador, and Peru. These Central Andean countries are known for their biodiverse malacofauna, of which the superfamily Orthalicoidea takes relatively a large share. In this paper the five families containing 103 (sub)species, for which systematic information (original publication, type locality, type depository, summarizing literature) and distributional records are presented. All species are illustrated by photographs of the type material or, if this could not be located, by a reproduction of the original figure. The following new taxon is introduced: Thaumastus (Thaumastus) sumaqwayqu sp. n. Junior subjective synonyms are established for: Plekocheilus (Sparnotion) Pilsbry, 1944 = Plekocheilus (Eudolichotis) Pilsbry, 1896; Scholvienia (Thomsenia) Strebel, 1910 = Scholvienia Strebel, 1910; Sultana (Trachyorthalicus) Strebel, 1909 = Sultana (Metorthalicus) Pilsbry, 1899; Plekocheilus (Eurytus) conspicuus Pilsbry, 1932 = Thaumastus (Thaumastus) hartwegi (Pfeiffer in Philippi, 1846); Zebra gruneri Strebel, 1909 = Orthalicus maracaibensis (Pfeiffer, 1856); Scholvienia jaspidea minor Strebel, 1910 = Scholvienia alutacea (Reeve, 1850); Bulimus bifasciatus unicolor Philippi, 1869 = Scholvienia brephoides (d’Orbigny, 1835). A new status is given to Plekocheilus mcgintyi ‘Pilsbry’ H.B. Baker, 1963 (subspecies of Bulinus piperitus Sowerby I, 1837); Strophocheilus superstriatus var. prodeflexus Pilsbry, 1895 (subspecies of Bulinus piperitus Sowerby I, 1837); Thaumastus (Quechua) salteri maximus Weyrauch, 1967 (subspecies of Thaumastus (Quechua) olmosensis Zilch, 1954); Pseudoglandina agitata Weyrauch, 1967 (nomen inquirendum). New combinations are: Clathrorthalicus corydon (Crosse, 1869), and Cyclodontina chuquisacana (Marshall, 1930). Lectotypes are now designated for Bulimus incisus Hupé, 1857 and Bulinus piperitus Sowerby I, 1837. PMID:27408531

Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

PubMed

Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

2012-10-01

To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

Taxonomic revision of Phascogale tapoatafa (Meyer, 1793) (Dasyuridae; Marsupialia), including descriptions of two new subspecies and confirmation of P. pirata Thomas, 1904 as a ‘Top End’ endemic

USGS Publications Warehouse

Aplin, K. P.; Rhind, S. G.; Ten Have, J.; Chesser, R. Terry

2015-01-01

The Australian Brush-tailed Phascogale (Phascogale tapoatafa sensu lato) has a broad but highly fragmented distribution around the periphery of the Australian continent and all populations are under significant ongoing threat to survival. A new appraisal of morphological and molecular diversity within the group reveals that the population in the ‘Top End’ of the Northern Territory is specifically distinct from all others, including those in the Kimberley region of Western Australia to the west and on Cape York of Queensland to the east. The name P. pirata Thomas, 1904 is available for the ‘Top End’ taxon. Three geographically disjunct populations are distinguished at subspecies level within P. tapoatafa on a suite of external and cranio-dental features; these are found in southeast Australia from South Australia to mid-coastal Queensland (nominotypical tapoatafa), southwest Western Australia (wambenger subsp. nov.), and the Kimberley region of Western Australia (kimberleyensis subsp. nov.). A potential fourth subspecies occurs on Cape York but remains too poorly represented in collections for adequate characterization. Molecular divergence estimates based on partial sequences of the mitochondrial cytochrome b gene indicate that the range disjunction across southern Australia probably dates from the Late Pliocene, with the multiple disjunctions across northern Australia being more recent though almost certainly exceeding 400,000 years. An argument is made for the continued use of the subspecies rank in Australian mammalogy, despite a general lack of consistency in its current application.

The use of Matrix-assisted laser desorption ionization-time of flight mass spectrometry in the identification of Francisella tularensis.

PubMed

Karatuna, Onur; Celebi, Bekir; Can, Simge; Akyar, Isin; Kilic, Selcuk

2016-01-15

Francisella tularensis is the cause of the zoonotic disease tularemia and is classified among highly pathogenic bacteria (HPB) due to its low infection dose and potential for airborne transmission. In the case of HBP, there is a pressing need for rapid, accurate and reliable identification. Phenotypic identification of Francisella species is inappropriate for clinical microbiology laboratories because it is time-consuming, hazardous and subject to variable interpretation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently evaluated as a useful tool for the rapid identification of a variety of microorganisms. In this study, we evaluated the use of MALDI-TOF MS for the rapid identification of Francisella tularensis and differentiation of its subspecies. Using national collection of Francisella isolates from the National Tularemia Reference Laboratory (Public Health Institute of Turkey, Ankara), a total of 75 clinical isolates were investigated by species and subspecies-specific polymerase chain reaction (PCR) test and MALDI-TOF MS. All isolates were originally identified as F. tularensis subsp. holarctica due to RD1 subspecies-specific PCR result. For all isolates MALDI-TOF MS provided results in concordance with subspecies-specific PCR analysis. Although PCR-based methods are effective in identifying Francisella species, they are labor-intensive and take longer periods of time to obtain the results when compared with MALDI-TOF MS. MALDI-TOF MS appeared to be a rapid, reliable and cost-effective identification technique for Francisella spp. Shorter analysis time and low cost make this an appealing new option in microbiology laboratories.

The use of matrix-assisted laser desorption ionization-time of flight mass spectrometry in the identification of Francisella tularensis

PubMed Central

Karatuna, Onur; Çelebi, Bekir; Can, Simge; Akyar, Işın; Kiliç, Selçuk

2016-01-01

Francisella tularensis is the cause of the zoonotic disease tularemia and is classified among highly pathogenic bacteria (HPB) due to its low infection dose and potential for airborne transmission. In the case of HBP, there is a pressing need for rapid, accurate and reliable identification. Phenotypic identification of Francisella species is inappropriate for clinical microbiology laboratories because it is time-consuming, hazardous and subject to variable interpretation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently evaluated as a useful tool for the rapid identification of a variety of microorganisms. In this study, we evaluated the use of MALDI-TOF MS for the rapid identification of Francisella tularensis and differentiation of its subspecies. Using national collection of Francisella isolates from the National Tularemia Reference Laboratory (Public Health Institution of Turkey, Ankara), a total of 75 clinical isolates were investigated by species and subspecies-specific polymerase chain reaction (PCR) test and MALDI-TOF MS. All isolates were originally identified as F. tularensis subsp. holarctica according to region of difference 1 (RD1) subspecies-specific PCR results. For all isolates MALDI-TOF MS provided results in concordance with subspecies-specific PCR analysis. Although PCR-based methods are effective in identifying Francisella species, they are labor-intensive and take longer periods of time to obtain the results when compared with MALDI-TOF MS. MALDI-TOF MS appeared to be a rapid, reliable and cost-effective identification technique for Francisella spp. Shorter analysis time and low cost make this an appealing new option in microbiology laboratories. PMID:26773181

Associations of anthropometry and lifestyle factors with HDL subspecies according to apolipoprotein C-III[S

PubMed Central

Koch, Manja; Furtado, Jeremy D.; Jiang, Gordon Z.; Gray, Brianna E.; Cai, Tianxi; Sacks, Frank; Tjønneland, Anne; Overvad, Kim; Jensen, Majken K.

2017-01-01

The presence of apoC-III on HDL impairs HDL’s inverse association with coronary heart disease (CHD). Little is known about modifiable factors explaining variation in HDL subspecies defined according to apoC-III. The aim was to investigate cross-sectional associations of anthropometry and lifestyle with HDL subspecies in 3,631 participants from the Diet, Cancer, and Health study originally selected for a case-cohort study (36% women; age 50–65 years) who were all free of CHD. Greater adiposity and less activity were associated with higher HDL containing apoC-III and lower HDL lacking apoC-III. Per each 15 cm higher waist circumference, the level of HDL containing apoC-III was 2.8% higher (95% CI: 0.4, 5.3; P = 0.024) and the level of HDL not containing apoC-III was 4.7% lower (95% CI: −6.0, −3.4; P = <0.0001). Associations for physical activity were most robust to multivariable modeling. Each 20 metabolic equivalent task hours per week reported higher physical activity was associated with 0.9% (95% CI: −1.7, −0.1; P = 0.031) lower HDL containing apoC-III and 0.5% higher (95% CI: 0.1, 1.0; P = 0.029) HDL lacking apoC-III. Lower alcohol consumption was associated with lower HDL lacking apoC-III (percent difference per 15 g/day: 1.58 (95% CI: 0.84, 2.32; P = <0.0001). Adiposity and sedentary lifestyle were associated with a less favorable HDL subspecies profile. PMID:28365588

Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages

PubMed Central

Gilbert, Maarten J.; Miller, William G.; Yee, Emma; Zomer, Aldert L.; van der Graaf-van Bloois, Linda; Fitzgerald, Collette; Forbes, Ken J.; Méric, Guillaume; Sheppard, Samuel K.; Wagenaar, Jaap A.; Duim, Birgitta

2016-01-01

Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies. PMID:27333878

Controlled synthesis of germanium nanoparticles by nonthermal plasmas

NASA Astrophysics Data System (ADS)

Ahadi, Amir Mohammad; Hunter, Katharine I.; Kramer, Nicolaas J.; Strunskus, Thomas; Kersten, Holger; Faupel, Franz; Kortshagen, Uwe R.

2016-02-01

The size, composition, and crystallinity of plasma produced nanoparticles are crucial factors for their physical and chemical properties. Here, we investigate the role of the process gas composition, particularly the hydrogen (H2) flow rate, on germanium (Ge) nanoparticles synthesized from a chlorinated precursor by nonthermal plasma. We demonstrate that the gas composition can significantly change the nanoparticle size and also adjust the surface chemistry by altering the dominant reaction mechanisms. A red shift of the Ge-Clx infrared absorptions with increasing H2 flow indicates a weakening of the Ge-Clx bonds at high H2 content. Furthermore, by changing the gas composition, the nanoparticles microstructure can be controlled from mostly amorphous at high hydrogen flow to diamond cubic crystalline at low hydrogen flow.

Investigation of local environments in Nafion-SiO(2) composite membranes used in vanadium redox flow batteries.

PubMed

Vijayakumar, M; Schwenzer, Birgit; Kim, Soowhan; Yang, Zhenguo; Thevuthasan, S; Liu, Jun; Graff, Gordon L; Hu, Jianzhi

2012-04-01

Proton conducting polymer composite membranes are of technological interest in many energy devices such as fuel cells and redox flow batteries. In particular, polymer composite membranes, such as SiO(2) incorporated Nafion membranes, are recently reported as highly promising for the use in redox flow batteries. However, there is conflicting reports regarding the performance of this type of Nafion-SiO(2) composite membrane in the redox flow cell. This paper presents results of the analysis of the Nafion-SiO(2) composite membrane used in a vanadium redox flow battery by nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier Transform Infra Red (FTIR) spectroscopy, and ultraviolet-visible spectroscopy. The XPS study reveals the chemical identity and environment of vanadium cations accumulated at the surface. On the other hand, the (19)F and (29)Si NMR measurement explores the nature of the interaction between the silica particles, Nafion side chains and diffused vanadium cations. The (29)Si NMR shows that the silica particles interact via hydrogen bonds with the sulfonic groups of Nafion and the diffused vanadium cations. Based on these spectroscopic studies, the chemical environment of the silica particles inside the Nafion membrane and their interaction with diffusing vanadium cations during flow cell operations are discussed. This study discusses the origin of performance degradation of the Nafion-SiO(2) composite membrane materials in vanadium redox flow batteries. Copyright © 2011 Elsevier Inc. All rights reserved.

Investigation of Local Environments in Nafion-SiO2 Composite Membranes used in Vanadium Redox Flow Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vijayakumar, M.; Schwenzer, Birgit; Kim, Soowhan

2012-04-01

The proton conducting polymer composite membranes are of technological interest in many energy devices such as fuel cells and redox flow batteries. In particular, the polymer composite membranes such as SiO2 incorporated Nafion membranes are recently reported as highly promising for the redox flow batteries. However, there is conflicting reports regarding the performance of this Nafion-SiO2 composite membrane in the redox flow cell. This paper presents results of the analysis of the Nafion-SiO2 composite membrane used in a vanadium redox flow battery by nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier Transformed Infra Red (FTIR) spectroscopy, and ultravioletmore » visible spectroscopy. The XPS study reveals the chemical identity and environment of vanadium cations accumulated at the surface. On the other hand, the 19F and 29Si NMR measurement explores the nature of the interaction between the silica particles, Nafion side chains and diffused vanadium cations. The 29Si NMR shows that the silica particles interaction via hydrogen bonds to the sulfonic groups of Nafion and diffused vanadium cations. Based on these spectroscopic studies, the chemical environment of the silica particles inside the Nafion membrane and their interaction with diffusing vanadium cations during flow cell operations are discussed. This study discusses the origin of performance degradation of the Nafion-SiO2 composite membrane materials in vanadium redox flow batteries.« less

Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles.

PubMed

Fitzgerald, Collette; Tu, Zheng Chao; Patrick, Mary; Stiles, Tracy; Lawson, Andy J; Santovenia, Monica; Gilbert, Maarten J; van Bergen, Marcel; Joyce, Kevin; Pruckler, Janet; Stroika, Steven; Duim, Birgitta; Miller, William G; Loparev, Vladimir; Sinnige, Jan C; Fields, Patricia I; Tauxe, Robert V; Blaser, Martin J; Wagenaar, Jaap A

2014-09-01

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like strains from humans (n = 8) and reptiles (n = 5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA-DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus. Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus, for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427(T) ( = ATCC BAA-2539(T) = LMG 27499(T)) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus.

Winter distribution of willow flycatcher subspecies (Distribución Invernal de las Subespecies de Empidonax traillii)

USGS Publications Warehouse

Paxton, Eben H.; Unitt, Philip; Sogge, Mark K.; Whitfield, Mary; Keim, Paul

2011-01-01

Documenting how different regions across a species' breeding and nonbreeding range are linked via migratory movements is the first step in understanding how events in one region can influence events in others and is critical to identifying conservation threats throughout a migratory animal's annual cycle. We combined two studies that evaluated migratory connectivity in the Willow Flycatcher (Empidonax traillii), one using mitochondrial DNA sequences from 172 flycatchers sampled throughout their winter range, and another which examined morphological characteristics of 68 museum specimens collected in the winter range. Our results indicate that the four subspecies occupy distinct but overlapping regions of the winter range. Connectivity between specific breeding and winter grounds appears to be moderate to strong, with distributions that suggest migration patterns of both the chain and leap-frog types connecting the breeding and nonbreeding grounds. The Pacific lowlands of Costa Rica appear to be a key winter location for the endangered Southwestern Willow Flycatcher (E. t. extimus), although other countries in Central America may also be important for the subspecies.

Selection of arboreal termitaria for nesting by cooperatively breeding Micronesian Kingfishers Todiramphus cinnamominus reichenbachii

USGS Publications Warehouse

Kesler, Dylan C.; Haig, Susan M.

2005-01-01

Limited nest-site availability appears to be an important factor in the evolution of delayed dispersal and cooperative breeding in some cavity-nesting species. The cooperatively breeding Pohnpei subspecies of Micronesian Kingfisher Todiramphus cinnamominus reichenbachii excavates nest cavities from the nests of arboreal termites Nasutitermes spp., or termitaria. In this first published description of nest-sites for this subspecies, we used surveys, remote sensing and radiotelemetry to evaluate the relationship between nest-site availability and co-operation. Results illustrate that nest termitaria are higher in the forest canopy, larger in volume and occur in areas with more contiguous canopy cover than unused termitaria. Nest termitaria were selected independently of the proximity to forest edges and territory boundaries, and we found no difference in characteristics of termitaria used by cooperative groups and breeding pairs. Logistic regression modelling indicated that termitaria with nest-like characteristics were not limited in abundance, suggesting that neither the prospects of inheriting nesting resources nor limited nest-site abundance are probable explanations for delayed dispersal in the Pohnpei subspecies of Micronesian Kingfisher.

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meincke, Linda; Copeland, A; Lapidus, Alla L.

2012-01-01

Polynucleobacter necessarius subsp. asymbioticus Hahn et al. 2009 is one of currently two subspecies of P. necessarius. While P. necessarius subsp. asymbioticus is a free-living bacterium, the closely related second subspecies, P. necessarius subsp. necessarius is an obligate endosymbiont living in the cytoplasm of freshwater ciliates of the genus Euplotes aediculatus. The two P. necessarius subspecies were the closest thus far reported phylogenetic neighbors that differ in their lifestyle as obligately free-living vs. obligate endosymbiontic, and they are the only members of the genus Polynucleobacter with completely sequenced genomes. The genome-sequenced strain represents a group of closely related strains notmore » distinguishable by 16S rRNA, 16S-23S ITS or glnA sequences, which is persistent in the home habitat of the strain and frequently contributes > 10% of total bacterial numbers in water samples of the habitat. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.« less

Estimating variation in stomatal frequency at intra-individual, intra-site, and inter-taxonomic levels in populations of the Leonardoxa africana (Fabaceae) complex over environmental gradients in Cameroon

NASA Astrophysics Data System (ADS)

Finsinger, Walter; Dos Santos, Thibaut; McKey, Doyle

2013-07-01

Variation of stomatal frequency (stomatal density and stomatal index) includes genetically-based, potentially-adaptive variation, and variation due to phenotypic plasticity, the degree of which may be fundamental to the ability to maintain high water-use efficiency and thus to deal with environmental change. We analysed stomatal frequency and morphology (pore length, pore width) in leaves from several individuals from nine populations of four sub-species of the Leonardoxa africana complex. The dataset represents a hierarchical sampling wherein factors are nested within each level (leaves in individuals, individuals in sites, etc.), allowing estimation of the contribution of different levels to overall variation, using variance-component analysis. SI showed significant variation among sites ("site" is largely confounded with "sub-species"), being highest in the sub-species localized in the highest-elevation site. However, most of the observed variance was accounted for at intra-site and intra-individual levels. This variance could reflect great phenotypic plasticity, presumably in response to highly local variation in micro-environmental conditions.

A revised list of the freshwater mussels (Mollusca: Bivalvia: Unionida) of the United States and Canada

USGS Publications Warehouse

Williams, James D.; Bogan, Arthur E.; Butler, Robert S.; Cummings, Kevin S.; Garner, Jeffrey T.; Harris, John L.; Johnson, Nathan A.; Watters, G. Thomas

2017-01-01

We present a revised list of freshwater mussels (order Unionida, families Margaritiferidae and Unionidae) of the United States and Canada, incorporating changes in nomenclature and systematic taxonomy since publication of the most recent checklist in 1998. We recognize a total of 298 species in 55 genera in the families Margaritiferidae (one genus, five species) and Unionidae (54 genera, 293 species). We propose one change in the Margaritiferidae: the placement of the formerly monotypic genus Cumberlandia in the synonymy of Margaritifera. In the Unionidae, we recognize three new genera, elevate four genera from synonymy, and place three previously recognized genera in synonymy. We recognize for the first time two species (one native and one nonindigenous) in the Asian genus Sinanodonta as occurring in North America. We recognize four new species and one subspecies and elevate 21 species from synonymy. We elevate 10 subspecies to species status and no longer recognize four subspecies. We change common names for five taxa, correct spelling for eight species, and correct the date of publication of original descriptions for four species.

Identification of Staphylococcus spp. using (GTG)₅-PCR fingerprinting.

PubMed

Svec, Pavel; Pantůček, Roman; Petráš, Petr; Sedláček, Ivo; Nováková, Dana

2010-12-01

A group of 212 type and reference strains deposited in the Czech Collection of Microorganisms (Brno, Czech Republic) and covering 41 Staphylococcus species comprising 21 subspecies was characterised using rep-PCR fingerprinting with the (GTG)₅ primer in order to evaluate this method for identification of staphylococci. All strains were typeable using the (GTG)₅ primer and generated PCR products ranging from 200 to 4500 bp. Numerical analysis of the obtained fingerprints revealed (sub)species-specific clustering corresponding with the taxonomic position of analysed strains. Taxonomic position of selected strains representing the (sub)species that were distributed over multiple rep-PCR clusters was verified and confirmed by the partial rpoB gene sequencing. Staphylococcus caprae, Staphylococcus equorum, Staphylococcus sciuri, Staphylococcus piscifermentans, Staphylococcus xylosus, and Staphylococcus saprophyticus revealed heterogeneous fingerprints and each (sub)species was distributed over several clusters. However, representatives of the remaining Staphylococcus spp. were clearly separated in single (sub)species-specific clusters. These results showed rep-PCR with the (GTG)₅ primer as a fast and reliable method applicable for differentiation and straightforward identification of majority of Staphylococcus spp. Copyright © 2010 Elsevier GmbH. All rights reserved.

Highly conductive composites for fuel cell flow field plates and bipolar plates

DOEpatents

Jang, Bor Z; Zhamu, Aruna; Song, Lulu

2014-10-21

This invention provides a fuel cell flow field plate or bipolar plate having flow channels on faces of the plate, comprising an electrically conductive polymer composite. The composite is composed of (A) at least 50% by weight of a conductive filler, comprising at least 5% by weight reinforcement fibers, expanded graphite platelets, graphitic nano-fibers, and/or carbon nano-tubes; (B) polymer matrix material at 1 to 49.9% by weight; and (C) a polymer binder at 0.1 to 10% by weight; wherein the sum of the conductive filler weight %, polymer matrix weight % and polymer binder weight % equals 100% and the bulk electrical conductivity of the flow field or bipolar plate is at least 100 S/cm. The invention also provides a continuous process for cost-effective mass production of the conductive composite-based flow field or bipolar plate.

Rheology of composite solid propellants during motor casting

NASA Technical Reports Server (NTRS)

Rogers, C. J.; Smith, P. L.; Klager, K.

1978-01-01

In a study conducted to evaluate flow parameters of uncured solid composite propellants during motor casting, two motors (1.8M-lb grain wt) were cast with a PBAN propellant exhibiting good flow characteristics in a 260-in. dia solid rocket motor. Attention is given to the effects of propellant compositional and processing variables on apparent viscosity as they pertain to rheological behavior and grain defect formation during casting. It is noted that optimized flow behavior is impaired with solid propellant loading. Non-Newtonian pseudoplastic flow is observed, which is dependent upon applied shear stress and the age of the uncured propellant.

World Checklist of Opiliones species (Arachnida). Part 2: Laniatores – Samooidea, Zalmoxoidea and Grassatores incertae sedis

PubMed Central

Souza, Daniele R.; Pérez-González, Abel

2015-01-01

Abstract Including more than 6500 species, Opiliones is the third most diverse order of Arachnida, after the megadiverse Acari and Araneae. This database is part 2 of 12 of a project containing an intended worldwide checklist of species and subspecies of Opiliones, and it includes the members of the suborder Laniatores, infraorder Grassatores of the superfamilies Samooidea and Zalmoxoidea plus the genera currently not allocated to any family (i.e. Grassatores incertae sedis). In this Part 2, a total of 556 species and subspecies are listed. PMID:26752965

Bi-parentally inherited species-specific markers identify hybridization between rainbow trout and cutthroat trout subspecies

USGS Publications Warehouse

Ostberg, C.O.; Rodriguez, R.J.

2004-01-01

Eight polymerase chain reaction primer sets amplifying bi-parentally inherited species-specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F1 and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.

Effects of temperature on biochemical reactions and drug resistance of virulent and avirulent Aeromonas salmonicida

USGS Publications Warehouse

Hahnel, G.B.; Gould, R.W.

1982-01-01

Incubation temperatures of 11°, 18° and 28° did not substantially affect biochemical reactions of either virulent or avirulent forms of Aeromonas salmonicida subspecies salmonicida. The only change observed, amygdalin fermentation, was positive at 11° and 18° but negative at 28°C. Several isolates utilized sucrose, a characteristic not normally recognized for A. salmonicida subspecies salmonicida.Antimicrobial susceptibility screening indicated resistance to novobiocin increased at the higher incubation temperatures. Standardized drug sensitivity testing procedures and precise zone diameter interpretive standards for bacterial fish pathogens are needed.

Creativity and Flow in Musical Composition: An Empirical Investigation

ERIC Educational Resources Information Center

MacDonald, Raymond; Byrne, Charles; Carlton, Lana

2006-01-01

Although an extensive literature exists on creativity and music, there is a lack of published research investigating possible links between musical creativity and Csikszentmihalyi's concept of flow or optimal experience. This article examines a group composition task to study the relationships between creativity, flow and the quality of the…

Generation of a composite grid for turbine flows and consideration of a numerical scheme

NASA Technical Reports Server (NTRS)

Choo, Y.; Yoon, S.; Reno, C.

1986-01-01

A composite grid was generated for flows in turbines. It consisted of the C-grid (or O-grid) in the immediate vicinity of the blade and the H-grid in the middle of the blade passage between the C-grids and in the upstream region. This new composite grid provides better smoothness, resolution, and orthogonality than any single grid for a typical turbine blade with a large camber and rounded leading and trailing edges. The C-H (or O-H) composite grid has an unusual grid point that is connected to more than four neighboring nodes in two dimensions (more than six neighboring nodes in three dimensions). A finite-volume lower-upper (LU) implicit scheme to be used on this grid poses no problem and requires no special treatment because each interior cell of this composite grid has only four neighboring cells in two dimensions (six cells in three dimensions). The LU implicit scheme was demonstrated to be efficient and robust for external flows in a broad flow regime and can be easily applied to internal flows and extended from two to three dimensions.

Subfossil remains of Pediastrum - a tool to obtain palaeolimnological information parallel to pollen analysis?

NASA Astrophysics Data System (ADS)

Turner, F.; Zhu, L.; Ma, Q.; Peng, P.; Lü, X.

2014-12-01

It has been a long-time goal of palynologists to obtain additionally palaeoenvironmental information by the study of Quaternary non-pollen-palynomorphs (NPPs) in pollen slides. As a group of NPPs, subfossil remains of green algae of the genus Pediastrum (fam. Hydrodictyaceae) are frequently found in lake sediments and withstand the palynological standard preparation methods. Determination of Pediastrum taxa to subspecies level is relatively easy with a standard light microscope. Very few studies, however, have used them as palaeolimnological indicators and the knowledge on recent distribution and ecology of many taxa is limited. Introducing new data from Northwestern Europe and the Tibetan Plateau, we show that analysis of subfossil Pediastrum assemblages can reveal valuable information on limnological and climate parameters. Shifts in taxonomic composition of Pediastrum assemblages from lake sediments in northern Germany are shown to strongly reflect the Northern Atlantic Late Glacial climate oscillations. In contrast to previous studies that recognized trophic state as the main driver of change in Pediastrum species composition, we identify climate shifts and related factors as the major drivers of community change. Water depth and trophic state probably acted as secondary factors only. Ongoing research compares the composition of Pediastrum assemblages in surface sediments of Tibetan lakes to environmental variables. While Pediastrum algae are shown to be a part of phytoplankton communities in freshwater to mesosaline lakes, shifts in species composition along the salinity gradient indicate the possible use of the algae group as palaeobioindicator for past humidity changes on the Tibetan Plateau. Additionally, investigations on the relation between water depth and the Pediastrum species composition in lake Taro Co (4575 m asl.) are presented. Our results suggest this algae group has great potential for enabling environmental inferences.

Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions

PubMed Central

Turner, Leslie M; Harr, Bettina

2014-01-01

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. DOI: http://dx.doi.org/10.7554/eLife.02504.001 PMID:25487987

Culicoides variipennis (Diptera: Ceratopogonidae) complex in California.

PubMed

Holbrook, F R; Tabachnick, W J

1995-07-01

Genetic relationships were examined among 24 collections, representing 23 populations of Culicoides variipennis (Coquillett) using isozyme electrophoresis of 11 protein encoding loci. The populations were collected from alkaline or fresh water larval habitats in California. Distance analysis demonstrated that C. v. occidentalis Wirth and Jones and C. v. sonorensis Wirth and Jones are genetically distinct. All C. v. occidentalis were geographically isolated from each other in highly alkaline or saline larval habitats, whereas C. v. sonorensis populations were collected from artificial freshwater habitats that were polluted with organic wastes. Higher levels of gene flow were found between C. v. sonorensis populations than from C. v. sonorensis populations to nearby C. v. occidentalis populations, indicative of genetic isolation between subspecies. Northern California C. v. sonorensis were genetically distinguishable from southern California C. v. sonorensis. The relationship between this variation and bluetongue disease epidemiology in California is discussed.