3.1. Gas Concentrations and Gas Transfer Velocities
 The partial pressure of CO2 averaged >1,500 μatmos (n = 981) for all samples, with approximately 95% of samples having pCO2 in excess of atmospheric equilibrium. Samples having near or less than atmospheric pCO2 were mostly located in the Upper Yukon region, in streams receiving meltwater directly from ice and snowfields (Figure 2a). Excess CO2 (Cw − Ca) averaged 68 μmol L−1 across the YRB and was highly positively skewed (γ = 5.6), meaning that there were relatively few very high values. Excess CO2 was much greater in the tributaries, averaging 100 μmol L−1, as compared with the main stem Yukon River, 40 μmol L−1 (Figures 3a and 3b) (two-tailed t-test on log-transformed data,df = 979, t = 15.8, P < 0.0001).
Figure 3. Medians and quartiles (boxes), 90 percent confidence intervals (whiskers), and ranges of measured values of excess (a and b) CO2 and (c and d) CH4 (micromoles C L−1); and (e and f) CO2 exchange velocity kCO2 (m d−1) for the Upper, Middle and Lower Yukon River basin main stem and tributaries.
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 River pCH4 averaged 8.4 μatmos (n = 947) and all samples were supersaturated with CH4 respective to the atmosphere (Figure 2b). Excess CH4 averaged 0.37 μmol L−1 and was also positively skewed (γ = 9.5). Similar to CO2, excess CH4 was significantly greater in the tributaries, 0.6 μmol L−1, than in the main stem Yukon River, 0.2 μmol L−1 (Figures 3c and 3d) (two-tailed t-test on log-transformed data,df = 945, t = 6.4, P < 0.0001).
 Mean kCO2 was greater in the tributaries, 5.2 m d−1, than in the main stem Yukon River, 3.1 m d−1 (Figures 2c, 3e, and 3f) (two-tailed t-test on log-transformed values,t = 3.4, P < 0.001). The data had slightly positive skew (γ = 2.1 and 1.2 in the main stem and tributaries, respectively). Other studies from the boreal region report widely ranging k600 values for streams and rivers, from 1–3 m d−1 [Aufdenkampe et al., 2011] to 6–15 m d−1 [Humborg et al., 2010]. Our gas exchange velocities, expressed as k600, fall within this range, 7.6 m d−1 in the tributaries and 4.9 m d−1 in the main stem Yukon River and were similar to the average k estimated for streams of like order in the contiguous USA [Butman and Raymond, 2011]. Humborg et al.  calculated k600 based on water discharge and stream slope [O'Conner and Dobbins, 1958] resulting in lower k values at high stream discharge for their observation locations. Our sample locations were generally on larger rivers having greater average discharge and smaller measured k600 than the Swedish streams, which is consistent with the model used by Humborg et al. .
 One-way ANOVAs were performed on log-transformed river concentration data, defined as log C = ln(100 + C). Calculations of excess CO2 confirmed the validity of our a priori decision to divide the basin into three subbasins, the Upper Yukon, Middle Yukon, and Lower Yukon (Figure 3). The three subbasins differed significantly from each other in both the main stem (F = 68, P < 0.0001, LSD P < 0.05 for all levels) and the tributaries (F = 32, P < 0.0001, LSD P < 0.05 for all levels). Excess CO2 generally increased in the main stem Yukon River from upstream to downstream (Figure 2a). Excess CO2 in the tributaries was greatest in the Middle Yukon region (Figure 2b).
 The data for excess CH4 and kCH4were not normally distributed after being parsed into subbasins, even after several different attempts at transformation. So, one-way ANOVA statistics would not necessarily be instructive to test for differences among the regions for those values. Nevertheless, we used the six a priori categories originally proposed for basin-wide extrapolation because differences were found for excess CO2 among the regions and because differences were apparent between the Yukon River and its tributaries.
3.2. Water Surface Area of Streams and Rivers
 The total stream and river surface area for all of the YRB is approximately 10,269 km2, or 1.2% of the total basin area (Table 1). Of this, 3666 km2 (36%) was attributed to the main stem Yukon River and 6603 km2(64%) was attributed to tributaries. The width of the Yukon River is commonly >1 km in many reaches and many major Yukon River tributaries are also very wide, making Landsat estimates of river surface area very reliable. While accounting for over 80% of the total stream length in the YRB, the sub-pixel tributaries only comprised 5.1% of the total computed surface area. Additionally, the Yukon does not have extensive flood plains that remain flooded for long periods like the Amazon River [Richey et al., 2002] or some other large rivers, so the area of the river remains fairly constant throughout the season.
 A river water surface area of 1.2% of basin area is high relative to the conterminous USA and worldwide, but much lower than the Amazon basin (Table 1). We speculate that the relatively high river water surface area for the YRB is because the river system is unregulated, having extensive river meanders and braided channels, especially in the upstream main stem Yukon River and in tributaries like the Tanana River. This also suggests that current global estimates of river and stream areas for boreal and arctic regions are low. Aufdenkampe et al.  tabulate a range in total stream plus river surface area for the boreal plus arctic of 10,000 −185,000 km2. The YRB has >10,000 km2, yet it comprises only 7.5% of the basin area of the 6 largest rivers discharging to the Arctic Ocean [Holmes et al., 2012], and a much smaller fraction of all northern high latitudes.
3.3. YRB Carbon Dioxide and Methane Emissions
 We used the product of the bootstrapped mean estimates of the excess CO2 or CH4concentration and gas transfer velocities to scale the results of field studies and estimate C gas emissions for the tributaries and main stem Yukon River in the three geographic regions of the YRB. Despite the high positive skewness in our data, we used the mean values for the basin-level extrapolation. The principal assumption in this approach is that the data are spatially representative of actualpCO2 and pCH4. The implication is that exceptionally high pCO2 and pCH4 are rare but quantitatively important to overall basin fluxes. Therefore, the mean is the best estimator of overall areal flux. Average CO2 excess ranged from 16.3 μmol L−1 in the Upper Yukon main stem river to 110.6 μmol L−1 in the Middle Yukon tributaries and kCO2 ranged from 0.3 m d−1 in the Upper Yukon main stem to 5.6 m d−1 in the Lower Yukon tributaries (Table 2). CH4 excess ranged from 0.15 μmol L−1 in the Upper Yukon main stem to 0.69 μmol L−1 in the Lower Yukon tributaries and kCH4 ranged from 0.4 m d−1 in the Upper Yukon main stem to 7.2 m d−1 in the Lower Yukon tributaries (Table 3).
Table 2. Summary of Bootstrapped Values Used for the CO2 Emission Estimate for the Entire Yukon River Basina
|Basin Division||Excess CO2 (μ mol L−1)||Transfer Velocity (m d−1)||Areal CO2 Flux (mmol m−2 d−1)||Stream Surface Area (km2)||Mass Flux (Tg C yr−1)|
|Sum|| || || || || || ||10269||10058–10491||7.68||6.71–9.20|
|Areal C yield (g C m−2 yr−1)|| || || || || || || || ||10.52||9.18–12.52|
Table 3. Summary of Bootstrapped Values Used for the CH4 Emission Estimate for the Entire Yukon River Basina
|Basin Division||Excess CH4 (μ mol L−1)||Transfer Velocity (m d−1)||Areal CH4 Flux (mmol m−2 d−1)||Stream Surface Area (km2)||Mass Flux (Gg C yr−1)|
|Sum|| || || || || || ||10269||10058–10491||55||48–65|
|Areal C yield (g C m−2 yr−1)|| || || || || || || || ||0.056||0.056–0.076|
 River CO2 emissions totaled 7.68 Tg C yr−1 and CH4 emissions totaled 55 Gg C yr−1for the YRB, assuming 200 ice-free days per year (Tables 2 and 3). Although quantitatively small when compared with CO2 emissions, CH4 emissions are important because CH4 is much more radiatively active than CO2, and CH4 emissions are expected to increase considerably with climate warming and permafrost thaw in high latitudes [Wickland et al., 2006]. Although our calculated CH4 emissions represent only 0.7% of the C mass of gas emitted by YRB rivers, they account for about 6.4% of the radiative forcing [Forster et al., 2007]. Normalized to water surface area, the CO2 emissions averaged 750 g C m−2 water yr−1 for all stream and river surfaces, ranging from 14.4 g m−2 yr−1 for the Upper Yukon main stem river to 1320 g m−2 yr−1 for the Lower Yukon tributaries.
 Annual YRB river C gas emissions equaled the 7.8 Tg C yr−1 of dissolved and particulate C exported by the Yukon River to below head of tide during 2001–2005 [Striegl et al., 2007]. This result was somewhat surprising considering the low average water temperature throughout the basin (<10°C) and the fact that soil respiration rates are lower in high latitude ecosystems than in temperate systems [Raich and Schlesinger, 1992], both of which should limit mineralization of organic matter and CO2 production. A first assumption would be that the ratio of Yukon River C gas flux: C lateral flux might be low compared to temperate and tropical systems. Comparison with other river basins having similar data (Table 1) indicates that although this assumption holds true for comparison with the Amazon basin (gas flux: lateral flux = 6.6) [Richey et al., 2002], the 1:1 ratio for the YRB is essentially identical to the ratio for the temperate Mississippi basin (0.9:1.0) [Dubois et al., 2010]. The ratio for Sweden (0.2:1.0) [Humborg et al., 2010] is closer to what we initially expected, and it is likely that many of the small and high elevation watersheds in the YRB behave similarly to the watersheds included in the Swedish C flux estimates.
 Ultimately, CO2 emission from river basins depends on complex interactions among factors that vary geographically, temporally, and perhaps independently of features such as latitude and mean annual temperature. For the Yukon and the Mississippi Rivers, similarity of the ratio of gas flux: lateral flux can be related to the mix of abiotic and biotic processes controlling CO2 emission. Both the Mississippi [Raymond et al., 2008; Dubois et al., 2010] and the Yukon [Striegl et al., 2007; Tank et al., 2012] derive the majority of their DIC from terrestrial carbonate weathering, utilizing soil respiration as a CO2 source for bicarbonate production. The Yukon has additional within stream weathering of glacial carbonate sediments that consume CO2 while also contributing to DIC production [Eberl, 2004; Striegl et al., 2007; Dornblaser and Striegl, 2009]. Weathering sources are sufficient to maintain high DIC concentrations in both rivers and strong upward pCO2 gradients to the atmosphere. However, the percent river water surface area and gas transfer velocities (k) are much greater in the Yukon leading to greater potential for flux. In contrast, the Yukon has ice cover >5 months a year, leaving less time for emissions to occur.
 From a biological perspective, Wickland et al.  report that Yukon River biodegradable DOC is in the range 12–18% of total DOC export, which likely supports <6% of the total CO2emission. Other respiration sources are also likely to be small in the YRB, at least in the river main stem, because of fast currents, low temperatures, lack of pools, and negligible light penetration. Consequently, in-stream biotic processes controlling CO2emission in the Yukon River are small. Conversely, agricultural nutrient loading, slower velocities, warmer temperatures and light penetration in river pools all contribute to in-stream production in the Mississippi, with resultant decreased emission or downward CO2flux into the river during the photoperiod and within-river storage of a fraction of the photosynthate.
 Warming conditions across high latitudes point toward future increases in C gas emissions from the Yukon River system and other high latitude river systems. Bicarbonate yields increase with decreased permafrost coverage across the circumboreal [Tank et al., 2012] and permafrost degradation has been linked to increased base flow and DIC contributions to rivers in the YRB [Striegl et al., 2005; Walvoord and Striegl, 2007]. Additionally, regional hydrologic modeling suggests increased groundwater flow, and potential river migration and redistribution of lakes and other surface water bodies with permafrost degradation [Walvoord et al., 2012]. Any of these changes can directly influence the carbon cycle and CO2 and CH4 emissions from inland waters in boreal and arctic regions.