The Classification and Scientific Names of Rainbow and Cutthroat Trouts

Two unambiguous discoveries involving rainbow trout require scientific name changes. First, the rainbow trout has been demonstrated to be the same species as the Kamchatka trout. Second, studies of osteology and biochemistry of trout and salmon show that rainbow and cutthroat trout, and their close relatives, the golden, Mexican golden, Gila, and Apache trouts, are more closely related to Pacific salmons (Oncorhynchus) than to brown trout and Atlantic salmon (Salmo). The different names required by these two discoveries will cause some confusion in communications in which the formal classification is used, so we present evidence to acquaint biologists and managers with the rationale for the changes. The species name of the rainbow trout becomes mykiss, an older Latinized indigenous name of the Kamchatka trout. The generic designation of rainbow and cutthroat trout poses a more subjective problem, involving four possibilities: Salmo, Oncorhynchus, Rhabdofario, and Parasalmo. The balance of evidence indicates to us that the generic name for Pacific trouts and salmons should be Oncorhynchus. We suggest recognition of two divergent sister lineages, (1) Atlantic trout and salmon, and (2) Pacific trouts and salmons, as the genera Salmo and Oncorhynchus, respectively. Alternative generic classifications considered include the following: (a) Enlarge Salmo to include all Atlantic and Pacific trouts and salmons. This would be well supported by morphological and biochemical characters, but would fail to emphasize the distinctions between the Pacific and Atlantic groups. (b) Use a separate generic name, Rhabdofario, for rainbow and cutthroat trout, and their inland relatives. This would be valid, but would fail to recognize the gradation between Pacific trouts and Pacific salmons. (c) Continue to assign Pacific trout to the genus Salmo, separate from Oncorhynchus. This would be stable, but at the expense of evolutionary information in the classification—rainbow and cutthroat trout are on the same branch of evolution as the Pacific salmon. To reflect these biological relationships in the classification of trouts and salmons will contribute to better understanding of their life histories and better predictions for their management.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140998/1/fsh0004.pd

I. SALMONID FISHES FROM MIO-PLIOCENE LAKE SEDIMENTS IN THE WESTERN SNAKE RIVER PLAIN AND THE GREAT BASIN

Salmon are iconic fishes of the North Pacific Rim. The evolution of Pacific salmon, formerly thought to be an ice age phenomenon, is now known to date back at least to the middle Miocene. We report nine lineages of salmons, trouts, and chars from the late Miocene in drainages of the North Pacific in North America. The lacustrine fossil fish assemblage from the Late Miocene Chalk Hills Formation (8.7 to 6.3 Ma), southwest Idaho and southeast Oregon, exhibits the greatest salmonine diversity of any Cenozoic paleontological site known – five lineages.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134040/1/MP 204.pdfDescription of MP 204.pdf : First paper in MP20

Investigating an API for resilient exascale computing.

Increased HPC capability comes with increased complexity, part counts, and fault occurrences. In- creasing the resilience of systems and applications to faults is a critical requirement facing the viability of exascale systems, as the overhead of traditional checkpoint/restart is projected to outweigh its bene ts due to fault rates outpacing I/O bandwidths. As faults occur and propagate throughout hardware and software layers, pervasive noti cation and handling mechanisms are necessary. This report describes an initial investigation of fault types and programming interfaces to mitigate them. Proof-of-concept APIs are presented for the frequent and important cases of memory errors and node failures, and a strategy proposed for lesystem failures. These involve changes to the operating system, runtime, I/O library, and application layers. While a single API for fault handling among hardware and OS and application system-wide remains elusive, the e ort increased our understanding of both the mountainous challenges and the promising trailheads.

Taphonomic bias in fish diversity from cenozoic floodplain environments

The fossil record of Cenozoic floodplain fishes increases from few species in the Paleocene and Eocene to about 5-15 species per locality in the Pliocene and Pleistocene. Modern floodplain habitats usually have more than 5-10 times this many species. The trend could be interpreted as an evolutionary increase, except that there seem to be no ecological or evolutionary reasons to expect ancient floodplains to have fewer species than modern floodplains.The alternate hypothesis is that ecological and fluvial processes destroy most fish bones before they are finally buried. Although floodplain depositional environments trap many fishes, these are subjected to extensive predation and scavenging, thereby reducing the opportunities for bones of small fishes, which make up most of the diversity, to be preserved in the fossil record. Abrasion in bedload probably destroys most small bones that are reworked. Surface collecting methods exaggerate the bias further because fish bones from fluvial rocks are fragmentary, difficult to discover, and difficult to identify. Screen washing for fossils from fine-grained sedimentary lenses should increase the known diversity from floodplain deposits.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27399/1/0000430.pd

Sr isotopic composition of hydroxyapatite from recent and fossil salmon: the record of lifetime migration and diagenesis

By comparing the Sr isotopic composition of migratory fossil salmon, which lived in the ocean but died in continental regions, to the well established marine Sr isotopic record, the age of the continental deposit could be determined with high accuracy. This approach to marine-continental correlation and dating requires (1) that marine-resident salmon bear a marine 87Sr/86Sr value in their bones or teeth, and (2) that the original 87Sr/86Sr value of fossils is not overprinted by diagenesis. The vertebrae of modern, hatchery-reared salmon exhibit Sr isotopic variations indicative of freshwater to marine migration during bone growth. Modern marine 87Sr/86Sr values were preserved in growth layers formed later in life. Marine-phase growth layers in the bones and teeth of the late Miocene migratory salmon, Oncorhynchus rastrosus, were subjected to stepwise selective leaching to separate biogenic hydroxyapatite from diagenetic calcium carbonate and recrystallized hydroxyapatite. Although the procedure yielded leachates with Sr/Ca and Ca/P values characteristic of apatite, the leachates had 87Sr/86Sr values consistently less radiogenic than values for late Miocene seawater ( [superset or implies] 0.7087. The fossils were substantially contaminated by Sr from the hosting clastic sediments. Specimens in continental deposits differed in 87Sr/86Sr value from host sediments by 0.0002 to 0.0200, supporting the conclusion that these salmon were migrants from marine waters. However, because the original Sr isotopic composition of fossil bones and teeth cannot be determined with confidence, archaeological, paleobiological and stratigraphic applications of this technique may be limited.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30230/1/0000624.pd

Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon

The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm

Climate Change and Marine Fish Distributions: Forecasting from Historical Analogy

nalyses of 36 fish and squid species sampled in standardized bottom-trawl surveys of the northwest Atlantic Ocean (1967–present) revealed a continuum of distributional responses associated with seasonal and annual variations in water temperature. Mean and maximum latitude of occurrence of the species were regressed against average surface- and bottom-water temperatures and indices of relative abundance from spring and autumn trawl surveys. Significant (P ≤ 0.05) regression models were fitted for 17 of 36 species from spring and fall survey data. Variations in water temperature were significant in explaining changes in mean latitude of occurrence for 12 of 36 species in both seasons. Maximum latitude distribution responses to interannual differences in water temperatures occurred for pelagic species, including Atlantic mackerel Scomber scombrus and Atlantic herring Clupea harengus. Weighted mean catches of these species shifted poleward by 0.5–0.8 degree of latitude for each 1°C increase in average water temperature, Statistically significant poleward range extensions, associated with warmer water temperatures, occurred for five species in spring surveys and four in fall surveys. Different responses among species to changing thermal regimes of the northwest Atlantic Shelf have important potential consequences for trophic dynamics and fisheries yields of the ecosystem. Species found to be sensitive in distribution to temperature change include primary prey species of some predators that show limited seasonal or annual changes in distribution. Changes in distributional overlaps between some predators and prey therefore are a likely result of shelf warming associated with climate change

Investigating an API for resilient exascale computing.

Increased HPC capability comes with increased complexity, part counts, and fault occurrences. In- creasing the resilience of systems and applications to faults is a critical requirement facing the viability of exascale systems, as the overhead of traditional checkpoint/restart is projected to outweigh its bene ts due to fault rates outpacing I/O bandwidths. As faults occur and propagate throughout hardware and software layers, pervasive noti cation and handling mechanisms are necessary. This report describes an initial investigation of fault types and programming interfaces to mitigate them. Proof-of-concept APIs are presented for the frequent and important cases of memory errors and node failures, and a strategy proposed for lesystem failures. These involve changes to the operating system, runtime, I/O library, and application layers. While a single API for fault handling among hardware and OS and application system-wide remains elusive, the e ort increased our understanding of both the mountainous challenges and the promising trailheads.