An analysis of nucleotide and amino acid variability in the barcode region of cytochrome c oxidase I (cox1) in fishes

The 655 bp cytochrome c oxidase subunit I barcode region of single specimens of 388 species of fishes (four Holocephali, 61 Elasmobranchii and 323 Actinopterygii) was examined. All but two (Urolophus cruciatus and Urolophus sufflavus) showed different cox1 nucleotide sequences (99.5% species discrimination); the two that could not be resolved are suspected to hybridize. Most of the power of cox1 nucleotide sequence analysis for species identification comes from the degenerate nature of the genetic code and the highly variable nature of the third codon position of amino acids. Variation at the third codon position is bimodally distributed, and the more variable mode is dominated by amino acids with four or six codons, while the less variable mode is dominated by amino acids with two codons. The ratio of nonsynonymous to synomymous changes is much less than one, indicating that this gene is subject to strong purifying selection. Consequently, cox1 amino acid sequence diversity is much less than nucleotide sequence diversity and has very poor species resolution power. Fourteen of the 16 amino acid residues recognized as having important functions in the region of cox1 sequenced were completely conserved over all 388 species (and the bovine cox1 sequence), with one fish species varying at one of these sites, and three fish at another site. No significant differences in amino acid conservation were observed between residues in helices, strands and turns. Patterns of nucleotide and amino acid variability were very similar between elasmobranchs and actinopterygians.     

Effects of coalbed natural gas development on fish assemblages in tributary streams of the Powder and Tongue rivers

1. Extraction of coalbed natural gas (CBNG) often results in disposal of large quantities of CBNG product water, which may affect aquatic ecosystems. We evaluated the effects of CBNG development on fish assemblages in tributary streams of the Powder and Tongue rivers. We used treatment and control, impact versus reference sites comparisons, surveys of CBNG product‐water streams and in situ fish survival approaches to determine if CBNG development affected fish assemblages. 2. Several of our results suggested that CBNG development did not affect fish assemblages. Species richness and index of biotic integrity (IBI) scores were similar in streams with and streams without CBNG development, and overall biotic integrity was not related to the number or density of CBNG wells. Fish occurred in one stream that was composed largely or entirely of CBNG product water. Sentinel fish survived in cages at treatment sites where no or few fish were captured, suggesting that factors such as lack of stream connectivity rather than water quality limited fish abundance at these sites. Fish species richness did not differ significantly from 1994 to 2006 in comparisons of CBNG‐developed and undeveloped streams. Biotic integrity declined from 1994 to 2006; however, declines occurred at both impact and reference sites, possibly because of long‐term drought. 3. Some evidence suggested that CBNG development negatively affected fish assemblages, or may do so over time. Specific conductivity was on average higher in treatment streams and was negatively related to biotic integrity. Four IBI species richness metrics were negatively correlated with the number or density of CBNG wells in the catchment above sampling sites. Bicarbonate, one of the primary ions in product water, was significantly higher in developed streams and may have limited abundance of longnose dace (Rhinichthys cataractae). Total dissolved solids, alkalinity, magnesium and sulphate were significantly higher in developed streams. 4. Biological monitoring conducted before the development of CBNG, and continuing through the life of development and reclamation, together with data on the quantity, quality and fate of CBNG product water will allow robust assessment of potential effects of future CBNG development worldwide.     

Body Size Variations in Caribou Ecotypes and Relationships With Demography

ABSTRACT In many vertebrates size is one of the most influential and variable individual characteristics and a strong determinant of reproductive success. Body size is generally density dependent and decreases when intraspecific competition increases. Frequent and long-distance movements increase energy expenditures and, therefore, may also influence body size, particularly in highly mobile species. Caribou (Rangifer tarandus, also known as reindeer) exhibit tremendous variation in size and movements and thus represent an excellent candidate species to test the relationships between body size, population size, and movements. We analyzed body measurements of adult female caribou from 7 herds of the Québec-Labrador Peninsula, Canada, and we related their morphology to population size, movements, and annual ranges. The herds represented 3 ecotypes (migratory, montane, and sedentary). Ecotypes and herds differed in size (length), shape (roundness), and movements. The sedentary ecotype was larger and moved 4 to 7 times less than the migratory ecotype in the 1990s. At the start of a demographic growth period in the early 1960s, migratory caribou from the Rivière-George (hereafter George) herd had longer mandibles than caribou of the sedentary ecotype. Mandible length in the George herd declined in the 1980s after rapid population growth, while individuals performed extensive movements and the herd's annual range increased. Migratory caribou then became shorter than sedentary caribou. After the George herd decline in the 1990s, mandible length increased again near levels of the 1980s. Caribou from the migratory Rivière-aux-Feuilles herd later showed a similar decline in mandible length during a period of population growth, associated with longer movements and increasing annual range. We hypothesize that the density-dependent effect observed on body size might have been exerted through summer habitat degradation and movement variations during herd growth. Our study has 2 important implications for caribou management: the distinctiveness of different populations and ecotypes, and the correlations between population trajectories and changes in body condition and habitat.     

Fitting the bill: do different winter food resources influence juniper titmouse (Baeolophus ridgwayi) bill morphology?

Divergent adaptive selection is a prominent mechanism influencing patterns of morphological diversity. We used the juniper titmouse [Baeolophus ridgwayi (Richmond, 1902)], a nonmigratory passerine that inhabits woodlands throughout western North America, to investigate variation in bill morphology in relation to diet and geography. We gathered data from museum specimens and used morphometric techniques to determine the relative strength of support for competing hypotheses using information theoretics: (1) differences in bill morphology are predicted by a key winter food resource that each regional population consumes (seeds of different juniper tree species); or (2) bill morphology scales with body size, and both increase along a latitudinal gradient. Juniper species emerged as the variable with the most support explaining variation in bill size, supporting the hypothesis that seed sizes influence bill size, independently of body size. The shape analysis revealed no distinct patterns in bill shape variation, but employed a powerful method for evaluating the strength of support for numerous candidate models. The differences in bill size of juniper titmice across their range are likely to reflect adaptive variation, because bill morphology is highly heritable in birds, juniper titmouse gene flow appears to be relatively low, and there is a clear mechanistic explanation for why bill sizes may differ among the ranges of the three juniper species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 667–679.     

Pollen tube growth and the pollen‐tube pathway of Nymphaea odorata (Nymphaeaceae)

An important aspect of the evolution of carpel closure, or angiospermy, is the relationship between pollen tube growth patterns and internalization of the pollen‐tube pathway. True carpel closure, involving postgenital fusion of inner carpel margins, is inferred to have arisen once within the ancient order Nymphaeales, in the common ancestor of Nymphaeaceae. We studied pollen tube development, from pollination to fertilization, in a natural population of Nymphaea odorata, using hand pollinations and timed flower collections. Pollen germinates in stigmatic secretions within 15 min and pollen tubes enter subdermal transmitting tissue within an hour, following wide intercellular spaces towards the zone of postgenital fusion. At the zone of fusion they turn downwards to grow in narrow spaces between interlocked cells and then wander freely to ovules within ovarian secretions. The pollen‐tube pathway is 2–6 mm long and upper ovules are first penetrated 2.5 h after pollination. Pollen tubes grow at rates of approximately 1 mm/h whether in stigmatic fluid, transmitting tissues or ovarian secretions. Pollen‐tube pathways are structurally diverse across Nymphaeales, yet their pollen tubes have similar morphologies and rapid growth rates. This pattern suggests pollen tube growth innovations preceded and were essential for the evolution of complete carpel closure. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 581–593.     

Two new species of Dunkleosteus Lehman, 1956, from the Ohio Shale Formation (USA,Famennian) and the Kettle Point Formation (Canada,Upper Devonian), and a cladistic analysis of the Eubrachythoraci (Placodermi,Arthrodira)

Two pachyosteomorph arthrodires are described from the Upper Devonian of North America, Dunkleosteus raveri sp. nov. and Dunkleosteus amblyodoratus sp. nov. (from the Appalachian and the Michigan basins, respectively). Dunkleosteus raveri sp. nov. is found stratigraphically below the only other species within the Ohio Shale Formation (Famennian), and is characterized by the retention of a primitive dermal ornamentation, and shares with Dunkleosteus terrelli ( Newberry, 1873 ) the possession of articular facets on the parasphenoid. Dunkleosteus amblyodoratus sp. nov. (Kettle Point Formation, Upper Devonian), known only from incomplete nuchal, paranuchal, and parasphenoid plates, also retains dermal tuberculation, and is characterized by tapering articular facets on the parasphenoid. The current study reviews three North American species of Dunkleosteus (Du. terrelli, Du. raveri sp. nov. , and Du. amblyodoratus sp. nov. ). Formerly, two subgroups were recognized within the Dinichthyidae, the terrelli and herzeri groups, which are shown here to be members of distinct clades. Dinichthys herzeri Newberry, 1868 (the namesake member of the herzeri group) is now the sole member of the family Dinichthyidae comb. nov. , and is assigned to the Aspinothoracidi sensu Miles & Dennis, 1979 . Heintzichthys Whitley, 1933 and Gorgonichthys Claypole, 1892 (additional members of the herzeri group) were previously placed among the aspinothoracid arthrodires. Likewise, Holdenius holdeni Dunkle & Bungart, 1942 (the final member of the herzeri group) and Hadrosteus rapax Gross, 1932 are now placed within the Aspinothoracidi. The remaining taxa, formerly assigned to the Dinichthyidae (i.e. Dunkleosteus Lehman, 1956 ; Eastmanosteus Obruchev, 1964 ; Golshanichthys Lelièvre, Janvier, & Goujet, 1981 ; and Westralichthys Long, 1987 ), are united within the Dunkleosteidae Stensiö, 1963 . © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 159 , 195–222.