Draft Feasibility Report with Integrated Environmental Assessment Harlow Island HREP. Appendix F Habitat Evaluation and Quantification

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1 Appendix F Habitat Evaluation and Quantification

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3 UPPER MISSISSIPPI RIVER RESTORATION SYSTEM FEASIBILITY REPORT WITH INTEGRATED ENVIRONMENTAL ASSESSMENT HARLOW ISLAND HABITAT REHABILIATION AND ENHANCEMENT PROJECT MIDDLE MISSISSIPPI RIVER MILES THROUGH JEFFERSON COUNTY, MISSOURI APPENDIX F HABITAT EVALUATION AND QUANTIFICATION

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5 TABLE OF CONTENTS INTRODUCTION... 1 HABITAT EVALUATION METHODOLOGY Quantity Component Quality Component... 3 ASSUMPTIONS General Assumptions... 5 Feature Specific Assumptions... 6 RESULTS Total Habitat Benefits REFERENCES SUB-APPENDIX REGENERATION CALCULATIONS LIST OF TABLES Table 1. Team that Participated in the Habitat Benefits Analysis for the 1 Table 2. Aquatic and Wildlife Evaluation Species Selected for Analysis 2 Table 3. Alternative and Feature Combinations 7 Table 13. Future Without Project and Future With Project Benefit Evalutation Results for All Alternatives 13 Table 5. Benefit Evaluation Results for Alternative 1 14 Table 6. Benefit Evaluation Results for Alternative 2 15 Table 7. Benefit Evaluation Results for Alternative 3 16 Table 8. Benefit Evaluation Results for Alternative 4 17 Table 9. Benefit Evaluation Results for Alternative 5 18 Table 10. Benefit Evaluation Results for Alternative 6 19 Table 11. Benefit Evaluation Results for Alternative 7 20 Table 12. Benefit Evaluation Results for Alternative 8 21 Table 13. Benefit Evaluation Results for Alternative 7B 22 Table 14. Benefit Evaluation Results for Alternative 7C 23 i

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7 INTRODUCTION This appendix provides the documentation of the habitat evaluation and quantification process that was conducted to evaluate the benefits of various habitat features for the Harlow Island Habitat Rehabilitation and Enhancement Project (HREP). Active participants included biologists from the St. Louis District Corps of Engineers and the U.S. Fish and Wildlife Service (Clarence Cannon National Wildlife Refuge, Two Rivers National Wildlife Refuge, Middle Mississippi River National Wildlife Refuge, and Southern Illinois Ecological Services Office) included in Table 1. Table 1. Team that Participated in the Habitat Benefits Analysis for the Team Member Specialty Affiliation John Hartleb Wildlife Refuge Specialist USFWS Ken Dalrymple Wildlife Biologist USFWS Ben McGuire Wildlife Biologist USACE Kat McCain Ecologist USACE Donovan Henry Fisheries Biologist USFWS Matt Mangan Fish and Wildlife Biologist USFWS Shane Simmons Fisheries Biologist USACE Jason Wilson Refuge Manager USFWS The purpose of the habitat benefits evaluation is to evaluate and quantify, to the extent possible, environmental benefits of alternative plans for the aquatic and floodplain habitat improvements within the study area. Quantification is needed in the project planning process to evaluate benefits of project measures because traditional benefit/cost evaluation is not applicable. To determine environmental restoration project benefits, models have been developed to quantify habitat benefits of project measures for selected species. We used both wildlife and fisheries-based models to evaluate the effects of project measures on habitat at Harlow Island. This was done because wildlife and aquatic habitats would be affected by some or all of the proposed measures. For evaluation, we followed the USFWS Habitat Evaluation Procedures Handbook (USFWS 1980). When assessing habitat types we used the Habitat Suitability Index (HSI) Models, developed by the USFWS. HSI models are widely accepted by local agencies and have become the certified method for habitat evaluation in the Corps. The team selected the species habitat models because the species utilize the current or are anticipated to use the future habitat at Harlow Island, and they represented different guilds from different taxonomic families. Table 2 summarizes the species selected and the applicable habitat type. Table 3 summarizes what project measures corresponded to what habitat model used in the evaluation. HSI species included smallmouth buffalo, bullfrog, and fox squirrel for the backwater excavation, wetland construction, and area protected by the sediment deflection berm, respectfully. The smallmouth buffalo, in the family Catostomidae, is an important commercial fish in the Mississippi River drainage basin. This species occurs in deep, flowing water, as well as sloughs, oxbow lakes and other backwaters for resting, spawning, and rearing. They feed on organisms in the substrate of large rivers and backwater lakes. The bullfrog, in the family Ranidae, is an important amphibian species that inhabits permanent bodies of standing or slow-moving water in wetlands throughout the Mississippi River drainage USACE Habitat Evaluation and Quantification Appendix F F-1

8 basin. They are usually found on or near shorelines, but they move short distances to water when water temperatures are warmer than air temperatures, making wetlands with permanent water a critical component for their complete lifecycle. Bullfrogs are considered omnivorous carnivores that can feed on anything that can be captured and swallowed, including: snails, insects, crayfish, fish, frogs, tadpoles, reptiles, and occasionally mammals and birds. The fox squirrel, in the family Sciuridae, is an important game species in eastern North America. This species occurs in a variety of forest types. However, they prefer forest stands with little understory vegetation that are mature hard mast species dominated stands (Allen 1982). In Missouri, fox squirrels were found to consume 52.2% hard mast fruits as a proportion of their overall annual diet (Korschgen 1981). Table 2. Aquatic and Wildlife Evaluation Species Selected for Analysis Species Scientific Name Family Habitat Type AQUATIC Smallmouth Buffalo Ictiobus bubalus Catostomidae Backwater WETLAND Bullfrog Rana catesbeiana Ranidae Semipermanently/permanently flooded wetland FLOODPLAIN FOREST Fox Squirrel Sciurus niger Sciuridae Deciduous Forested Wetland Consistent with guidance from the USACE Ecosystem Planning Center of Expertise, the Agency Technical Review (ATR) Team for the conducted an assessment of the models used for this project. The chosen models, all of which are Corps approved (per EC ) are the fox squirrel (Allen 1982), smallmouth buffalo (Edwards 1982), and bullfrog (Graces 1987). The Habitat Suitability Index (HSI) spreadsheet calculators for each of these models was reviewed by the Ecosystem Restoration Planning Center of Expertise and were approved for regional use (Memorandum for CECW-MVD; 15 September 2016; Enclosure 1) in the UMR. The Corps Model Certification Panel concurred and the spreadsheet calculators were approved for use ( dated 4 October 2016; Enclosure 2). This process evaluated the technical quality and appropriateness of the models utilized. HABITAT EVALUATION METHODOLOGY The HSI models evaluate the quality and quantity of particular habitat for species selected by team members (Table 1). 2.1 Quantity Component Traditionally, the Corps has used the quantity and quality of habitat jointly, in the form of habitat units, to measure benefits provided by ecosystem restoration projects. The quantity proportion is often measured as area (acres of habitat, landform, etc.); in some systems, it is measured as length (feet of stream bank). The evaluation conducted for this study area uses acres, delineated by polygons, to represent the quantity. Polygons were created using InRoads Select Series 2 software and overlaid in ArcGIS 10 software. The area associated with each proposed measure must have a clear definition for use as guidance in estimating the area component of the ecosystem output model, and must be applied consistently to all actions evaluated. Quantities of each feature varied depending on those features in each alternative. Habitat was evaluated in the location in which each feature would be placed. Table 5 at the end of this report provides the acres proposed for use for reach alternative. Final calculations included determining the acreage of backwater, floodplain forest, and wetland USACE Habitat Evaluation and Quantification Appendix F F-2

9 habitat, using topographical data, management plans, land coverage data files, and aerial photography. Acres equate to the action footprint of each feature was determined for each individual feature (Appendix B1 Civil Engineering). The action footprint is a measurement of the physical footprint of the management measures. For example, the area dredged for the backwater or the surface area covered by the sediment deflection berm. When evaluation of features was conducted, the footprint equals the total of the features with no double-counting of overlap areas addressed my multiple features. Applicability: This evaluation method for each individual project features can quantify with a high degree of certainty specific environmental and biological conditions to accurately evaluate Future With and Future Without conditions. Limitations: This method grossly underestimates the aerial extent of ecological benefits from each specific project feature. For example, the aerial extent of the proposed backwater footprint evaluated does not take into account benefits seen within the immediate area outside of the Project Area boundary as well as throughout the Middle Mississippi River region. It is well documented that restoring habitat of this type increases the primary productivity and has a positive effect across a much larger spatial area than just where the backwater dredging is to occur. 2.2 Quality Component The qualitative component of the analysis is rated on a 0.0 to 1.0 scale, with higher values indicating better habitat for that species. The HSI for a particular habitat type is determined by selecting values that reflect present and future project area conditions from a series of abiotic and biotic metrics. Each value corresponds to a suitability index for each species. Future values are determined using management plans, historical conditions, and best professional judgment. The quantitative component is the number of acres of the habitat being evaluated. From the calculated qualitative and quantitative values, the standard unit of measure, the habitat unit (HU) is calculated using the formula (HSI Acres = HUs). Habitat units are calculated for specific target years to forecast changes in habitat values over the life of the project with- and without-project conditions. When HSI scores are not available for each year of analysis, a formula that requires only target year HSI and area estimates is used (USFWS 1980). This formula is: T 0 Where: HU dt 0 T T 1 T 2 A 1 A 2 H 1 H 2 3 and 6 HU dt ( T 2 A1 H T1 ) = cumulative HU s 1 A2 H 3 2 A2 H 1 A1 H 6 = first target year of time interval = last target year of time interval = area of available habitat at beginning of time interval = area of available habitat at end of time interval = habitat suitability index at the beginning of time interval = habitat suitability index at the beginning of time interval constants derived from integration of HIS x Area for the = interval between any two target years This formula was developed to precisely calculate cumulative HUs when either HSI or area or 2 USACE Habitat Evaluation and Quantification Appendix F F-3

10 both change over a time interval, which is common when dealing with the unevenness found in nature. Habitat Unit gains or losses are annualized by summing the cumulative HUs calculated using the above equation across all target years in the period of analysis and dividing the total (cumulative HU) by the number of years in the life of the project (i.e., 50 years). This results in the Average Annual Habitat Units (AAHUs) (USFWS 1980). The calculation of the HUs and AAHUs were completed in a Microsoft Excel spreadsheet containing the formula above. The benefits of each proposed project feature (net AAHUs) are then determined by subtracting with-project benefits from without-project benefits. The effects of various habitat improvement feature combinations (alternatives) can then be evaluated by comparing the net AAHUs and costs for each alternative considered. In preparation of using the HSI models, the evaluation team conducted site visits and took part in a Value Engineering Study. They also reviewed aerial photography, topographic maps, and preliminary hydrological modeling. During the field evaluation, assumptions were developed regarding existing conditions and projected with-project conditions relative to habitat changes over time and management practices. For the purpose of planning, design, and impact analysis, period of analysis was established as 50 years. To facilitate comparison, target years were established at 0 (existing conditions), 1, 5, 25, and 50 years. Target years of 0 (existing condition), 1, 5, 25, and 50 (future without and future with project conditions) are used to analyze HUs and characterize habitat changes over the estimated period of analysis. Target years of 1 and 5 capture short-term changes following construction completion. While target years 25 and 50 capture ecological changes that would occur over a longer period of time. The period of analysis was determined to be 50 years based on the prediction that some project features (e.g., development of key ecological processes needed to restore ecosystem structure and function) would need a longer period of time to reach maximum benefits; and the accrual of benefits were predicted to level off after 50 years. HSIs and cumulative HUs for each evaluation species were calculated at each of these target years. Corps guidance requires that the team evaluate a suite of features that can be combined in various ways to form project alternatives. The approach used to assess the benefits at Harlow Island looked at benefits of project features and their combinations as alternatives and comparatively evaluated each alternative separately. This process is called the iterations process. To determine the habitat units created by each feature, the habitat (aquatic, wetland, and floodplain forest) affected by the feature would be evaluated using the applicable HSI spreadsheets. This appendix contains HSI summary tables and other data derived from the spreadsheet files not included in this appendix. These spreadsheets are available upon request. Please contact, Benjamin McGuire, , Benjamin.M.McGuire@usace.army.mil if you would like an electronic copy of these files. ASSUMPTIONS 3.1 Habitat Cover Type Assumptions The following assumptions were made when determining existing and future without project conditions for the primary habitat cover types located within the project area: A. Aquatic. Existing environmental and biological specific conditions was obtained during a data collection visit on 25AUG15. Fisheries monitoring data used as a surrogate for missing data at Harlow Island was obtained from USFWS Future With and Without Project data was estimated using best professional judgment of the evaluation team and Hydrology & Hydraulics modeling when applicable. USACE Habitat Evaluation and Quantification Appendix F F-4

11 Inherent in best professional judgment are the underlying assumptions, which are described in General Assumptions and Habitat Characteristics. B. Floodplain Forest. Existing forest conditions were obtained through several site visits and data collection visits. In addition, more intensive forest data conditions from inventory and data analysis performed on Wilkinson Island by researchers from the National Great Rivers Research and Education Center (NGRREC 2007) was used as a surrogate for missing data at Harlow Island. Data from NGRREC 2007 represents the only available forestry data within the MMR that can be used as technical data for existing conditions and Future Without Project assumptions. Forest stands on Wilkinson Island similar to existing conditions on Harlow Island were used in the analysis. Inherent in best professional judgment are the underlying assumptions, which are described in General Assumptions and Habitat Characteristics. C. Wetland. Existing wetland conditions were obtained through several site visits and data collection visits with various wetland specialists. Data from these site visits were used for the habitat evaluation. Inherent in best professional judgment are the underlying assumptions, which are described in General Assumptions General Assumptions 1. It was assumed that target years of 0 (existing condition), 1, 5, 25, and 50 (future without and future with Project conditions) are sufficient to analyze AAHUs and characterize habitat changes over the estimated period of analysis. The period of analysis was determined to be 50 years based on the prediction that some Project features (e.g., reforestation leading to mature trees reproducing; development of key ecological processes needed to restore ecosystem structure and function) would need a longer period of time to reach maximum benefits; and the accrual of benefits were predicted to level off after 50 years. 2. For planning purposes, we used existing gage data (Appendix B2 Hydrology and Hydraulic Engineering) to determine that the Project Area is located at or under a 50% chance of annual exceedance elevation of NAVD 88 at RM and at RM Early successional floodplain forest species, consisting of willow (Salix spp.), silver maple (Acer saccharinum), and eastern cottonwood (Populus deltoides), exist throughout approximately 850 acres in the Project Area. 4. Based on hydrologic flow data, throughout the Project Area, it is assumed that the site will continue to be inundated approximately every other year. 5. Throughout the upper third of the Project Area, large amounts of coarse sediment (i.e., sand) exist. It is assumed that Without Project conditions that this type of material would continue to be deposited throughout the Project Area. For With Project conditions, it is assumed that coarse sediment deposition would be greatly reduced throughout the Project Area by the sediment deflection berm. It is also assumed that the sediment deflection berm would allow for sheetflow/backing of water into the Project Area behind the sediment deflection berm for high flow conditions up to a 10% chance of annual exceedance elevation of 399 feet NAVD 88. Thus, allowing for silt/clay soil development, overtime accumulating enough to support hard mast trees. 6. Without the Project, USFWS will continue to manage the Project Area. USFWS will continue to maintain existing infrastructure like access roads and habitats dependent on funding, staffing, and natural disasters. However, it is assumed no substantial increases USACE Habitat Evaluation and Quantification Appendix F F-5

12 to current operation and maintenance budget for the site would occur while efforts to maintain access roads which will take away from habitat management. 7. We assumed that operation of Harlow Island would continue under the current management plans and objectives for at least the life of the HREP. 8. For future with Project conditions, the sediment deflection berm elevation was set at a 10% chance of annual exceedance elevation, 399 feet NAVD Without the Project, fish use of the existing backwater will continue to be restricted in many years by the lack of connectivity with the main channel. 10. The navigation channel will be maintained in its current location. 11. It is anticipated that USFWS would continue to manage Harlow Island under the 2004 Mark Twain National Wildlife Refuge Complex Comprehensive Conservation Plan and Environmental Assessment. 12. For future with project conditions, we assumed that the backwater would decrease slightly over time. Thus we assumed a 10% reduction at year 25 and an additional 10% relative reduction by year 50. Based on the analysis of transect and multi-beam data, overall depth characteristics of MMR backwaters appear to be stable or increasing, although a considerable amount of interannual variability occurs due to shifting sandbar formations in response to changing river stages and flows. Of the 20 side channels for which bathymetric surveys were available for a period spanning at least 15 years, 13 showed an increase in average depth over the period of record and 7 showed a decrease. Likewise, total volume of MMR side channels has increased in the last 15 years. Although the above evaluations exist for naturally occurring side channels, no data exists for constructed backwaters. Therefore a 10% reduction at year 25 and an additional 10% relative reduction at year 50 were used to conservatively estimate benefits and not over-inflate them. 13. For future with project conditions, we assumed that the swale wetlands would decrease slightly over time. Thus we assumed a 10% reduction at year 25 and an additional 10% relative reduction by year The backwater area was analyzed as two areas including the dredged portion and the upper portion that would be scoured over time during high flow events. It is assumed that due to the elevation in which the four structures would be placed and their relation to annual chance of exceedance that a portion (2.00 acres) of the total area (21.09 acre) would be realized one year following construction completion. Similarly, since the area would continue to receive high flow events that would continue to scour the area below each structure, a larger portion (8.00 acres) would be realized 5 years following construction completion. By year 25, the entire acres will have be scoured out by high flow events and conditions would be similar to S1 and S3. Refer to Appendix B2 Hydrology and Hydraulic Engineering) for the calculations used to determine the size of the scoured area and the time taken to be realized. Feature Specific Assumptions The following sections describe each feature as they relate to baseline conditions, future without project conditions, project conditions, and future with project conditions. A summary of alternatives and their associated features can be associated features can be found in Table 3. USACE Habitat Evaluation and Quantification Appendix F F-6

13 Table 3. Alternative and Feature Combinations Description Alternatives Code Description B 7C Reinforce existing levee as SD berm X X X X X X X X X X C1 Fully degrade cross levees X X X X Swales X X X X X X X X X X R1R Ridges X X X X X X X X X X W1 Depressional wetlands X X X X S1 Backwater Channel (Trapezoidal) X X X X X X S5 Backwater Channel (Benched) X X X X Reforestation X X X X X X X X X X 1. Sediment Deflection Berm (). The fox squirrel (Allen 1982) Corps approved (per EC ) HSI model was used to assess the floodplain forest habitat benefits resulting from the construction of the sediment deflection berm. This species was selected because it requires hard mast tree species as a large component of the forest community in which it lives. The following assumptions in applying the fox squirrel HSI model were made: Baseline Condition. The forest community composition is currently a more flood tolerant early successional forest community consisting of silver maple (Acer saccharinum), willow (Salix spp.), and eastern cottonwood (Populus deltoides). Hard mast species such as oaks (Quercus spp.) and pecans (Carya illinoinensis) do not exist within the Project Area. The Project Area lacks tree species diversity and only consists of early successional soft mast species such as cottonwood (Populus deltoides), box elder (Acer negundo), willow (Salix nigra), and silver maple (Acer saccharinum). The forest immature forest community is only 25 years old or less due to the fact that the area was in agricultural production until It is assumed that this forest community would continue to persist without ideal soil conditions and a seed source for hard mast tree species. Future Without Project Conditions: It is assumed that the forest community composition would continue to provide low habitat benefits through lack of natural succession limited by coarse sediment deposition. Coarse sediment deposition during flood events would continue, limiting hard mast species (i.e., nut-producing trees) establishment. Even-aged low species diversity riverfront forest communities (e.g., silver maple and cottonwood) would persist throughout the island, thus also limiting the establishment of hard mast species. The lack of hard mast species would continue to provide little habitat benefits for wildlife. It is well documented that hard mast forest communities provide higher habitat value for small and large mammals, neotropical migrants, migratory waterfowl, etc. Without the Project, it is anticipated that the Project Area would only support successional forest communities due to lacking ideal soil conditions for hard mast tree species establishment as well as a lack of a seed source for hard mast tree species. USACE Habitat Evaluation and Quantification Appendix F F-7

14 Future With Project Conditions. It is assumed that the sediment deflection berm would be constructed to a 10% chance of annual exceedance elevation, 399 feet NAVD 88. Only the portion behind the sediment deflection berm was evaluated. This total area did not include any other features, including the backwater dredging area (S1 or S5 configurations), reforestation areas ( and R1R), levee degrade areas (C1), swale wetlands (), or depressional wetland areas (W1). We assumed that the construction of the sediment deflection berm would block coarse sediment deposition from the Project Area and thus allow for sheetflow/backing into the area evaluated. The increased sheetflow/backing of water into the Project Area during high flow events would allow for water velocity reduction and the increased deposition of fine sediment. The increased fine sediment deposition depth would increase over time allowing for the development of soils more suitable for the establishment and survival of hard mast tree species including oaks (Quercus spp.) and pecans (Carya illinoinensis). It is assumed that the ground elevation throughout the area behind the sediment deflection berm would increase such that hard mast species would not be as limited by flood frequency elevation as described in Heitmeyer 2008, in which restoration of hard mast species are targeted elevations between 50%-20% chance of annual exceedance elevations. The reforestation project features ( and R1R) would ensure that a viable seed sources is available for the regeneration of hard mast tree species when over time, the deposition of fine sediment has accumulated enough to have suitable soils for hard mast tree species. See Sub appendix, Regeneration Calculations for more details. The forest community throughout the project area would transition passively over time through natural recruitment and regeneration to a more hard mast dominated forest community as site conditions improve. The intent would be that the entire area behind the SD berm would support a higher component of hard mast species over time. It is likely that hard mast trees establish over time once seed trees become mature enough to produce seed. However, recruitment dependent upon dispersal by high water events as well as mammals (squirrels, etc.) dispersing. 2. Backwater Excavation (S1). The smallmouth buffalo (Edwards and Twomey 1982) Corps approved (per EC ) HSI model was used to assess the aquatic habitat benefits resulting from the dredging of the backwater. This species was selected because it requires a variety of off channel habitat conditions throughout its life cycle. The following assumptions in applying the smallmouth buffalo HSI model were made: Baseline Conditions. Currently the backwater at Harlow Island is disconnected from the main channel. The bottom depth of the backwater is approximately ft NAVD88, which has about an 18% daily chance of exceedance. Based on aerial imagery, from 1976 to 2015, the area with water present has decreased by 46%. In addition, based on sedimentation data from Remo et al 2018, the backwater will convert to terrestrial habitat in 12.4 years. After high flow events, water is trapped in two small pockets, where as seen elsewhere, dissolved oxygen concentrations and high temperature conditions lead to anoxic conditions in which no fish species can survive. This habitat does not have the ability to serve as valuable spawning habitat or is able to provide refugia for young of the year fish species that typically use this type of habitat. These deteriorated habitat conditions not only limit fish communities but also reduce the amount in which invertebrates, birds, mammals, reptiles and amphibians can utilize the aquatic habitat thereby limiting the overall ecosystem function of the entire Project Area. Future Without Project Conditions. It is anticipated that this lack of connectivity USACE Habitat Evaluation and Quantification Appendix F F-8

15 would continue into future leading to loss of total backwater length, depth, and aquatic habitat. The backwater habitat is expected to continue to degrade with shallow depths, zero to minimal flow, low dissolved oxygen, less than ideal water temperatures, and little thermal cover. Further, according to USACE, 2015, projections of increased air temperatures, particularly in the summer months, will result in increased water temperatures, which will likely lead to decreased dissolved oxygen levels. Ultimately, the Project Area would not likely support a diversity of native fish assemblages into the future. Future With Project Conditions. With the dredging of the backwater, it was assumed that restoring connectivity of approximately 18.1 acres of the backwater to the main river would improve dissolved oxygen, temperatures, and depths throughout the year for fish and other aquatic life. This would allow aquatic organism access to the aquatic habitat that does not currently exist, providing benefits to the project area as well as the MMR. Hydraulic and Hydrologic modeling was plotted from +28 LWRP which is below a 2-year flood event to show that the average flow rate through the backwater is approximately 0.05 ft/sec. As flow increases, velocities within the backwater increase as well. For example, at a 2-year flood level, the backwater area would have a velocity of approximately 0.10 ft/sec; at a 5-year flood level, 0.60 ft/sec; at a 10-year flood level, 1.90 ft/sec. The proposed backwater would be excavated approximately 23.5 ft deeper than existing channel bottom elevation. The backwater would have water approximate 96% of the time and a depth of at least 5 ft throughout approximately 90% of the time. 3. Backwater Excavation with benches (S5). The smallmouth buffalo (Edwards and Twomey 1982) Corps approved (per EC ) HSI model was used to assess the aquatic habitat benefits resulting from the dredging of the backwater. This species was selected because it requires a variety of off channel habitat conditions throughout its life cycle. The following assumptions in applying the bullfrog HSI model were made: Baseline Conditions. Similar conditions exist as discussed in Backwater Excavation (S1). Future Without Project Conditions. Similar assumptions were made as discussed in Backwater Excavation (S1) Future Without Project Conditions. Future With Project Conditions. Similar assumptions were made as discussed in Backwater Excavation (S1) Future With Project Conditions. However, Backwater Excavation with terraces (S5) includes the addition of creating benches and 19.7 acres total in size. The bathymetric diversity that would be created with the benching in the backwater design would promote plant growth that would allow for improved habitat for fish and macro and microinvertebrates. The increased aquatic depth would provide refugia for a suite of aquatic organisms. 4. Scoured Backwater Habitat (S1(b) and S3(b)) The smallmouth buffalo (Edwards and Twomey 1982) Corps approved (per EC ) HSI model was used to assess the aquatic habitat benefits resulting from the upper portion of the backwater that would be scoured out over time by high flow events. Although S1(b) and S5(b) are part of S1 and S5, respectively, and not a separate project feature described in the main report, they were separated in this appendix because their benefits would not be realized immediately following construction completion as the dredged portion of the backwater USACE Habitat Evaluation and Quantification Appendix F F-9

16 in S1 and S5 would be. This species was selected because it requires a variety of off channel habitat conditions throughout its life cycle. The following assumptions in applying the bullfrog HSI model were made: Baseline Conditions. Similar conditions exist as discussed in Backwater Excavation (S1) and (S5). Future Without Project Conditions. Similar assumptions were made as discussed in Backwater Excavation (S1) and (S5) Future Without Project Conditions. Future With Project Conditions. It is assumed that due to the elevation in which the structures would be placed and their relation to annual chance of exceedance that a portion (2.00 acres) of the total area (21.09 acre) would be realized one year following construction completion. Similarly, since the area would continue to receive high flow events that would continue to scour the area below each structure, a larger portion (8.00 acres) would be realized 5 years following construction completion. By year 25, the entire acres will have be scoured out by high flow events and conditions would be similar to S1 and S5. Refer to Appendix A, Engineering, sub-section Hydrology & Hydraulics for the calculations used to determine the size of the scoured area and the time taken to be realized. 5. Reforestation (). The fox squirrel (Allen 1982) Corps approved (per EC ) HSI model was used to assess the floodplain forest habitat benefits of reforestation on the site. This species was selected because it requires hard mast tree species as a large component of the forest community in which it lives. The following assumptions in applying the fox squirrel HSI model were made: Baseline Condition. Similar site conditions exist as described in feature Sediment Deflection Berm (A3). Future Without Project Condition. Similar Future Without Project assumptions were made as described in feature Sediment Deflection Berm (A2). Future With Project Condition. Similar Future With Project assumptions were made as described in feature Sediment Deflection Berm (A2). However in addition, we assumed that reforestation would not occur without either the Sediment Deflection Berm (A3/A7) because the reforestation would occur on both of these berm designs for approximately acres. It was assumed that the tree plantings would consist of a high density of trees per acre at a 20 foot by 20 foot spacing in order to increase survivability per acre. It was assumed that the reforestation areas would have annual maintenance for the first five years following the initial planting consisting of mowing between the tree planting rows and a spring application of a non-selective and pre-emergent herbicide around the base of the tree to limit competition of woody and non-wood plant competition. This specific maintenance is to be performed in order to encourage more rapid growth over time so that the container trees reach maturity and produce seed more quickly. 6. Depressional Wetland (W1). The bullfrog (Graves and Anderson 1987) Corps approved (per EC ) HSI model was used to assess restored wetland habitat benefits on the site. This species was selected because relies on permanent bodies of standing or slow-moving water in wetlands. The following assumptions in applying the bullfrog HSI model were made: USACE Habitat Evaluation and Quantification Appendix F F-10

17 Baseline Conditions. The Project Area was used for agriculture until Prior to FWS acquisition, the land owners altered the landscape to increase agricultural productivity, including draining and filling wetlands. This eliminated semipermanently/permanently flooded wetland sites in the Project Area. Thus emergent aquatic vegetation wetlands do not exist within the Project Area. Semipermanently/permanently flooded wetland sites do not currently exist in the Project Area. Future Without Project Conditions. It is anticipated that conditions would continue to exist in which no semi-permanent and permanent wetland sites with emergent aquatic vegetation within the Project Area. Since many amphibian and reptile species rely on these habitat types, these populations would continue to be limited throughout the Project Area, further contributing to the overall lack of ecosystem diversity. Future With Project Conditions. It is assumed that with the construction of the depressional wetland feature (W1), the presence of semi-permanently and permanently flooded wetland habitat would exist within the constructed features. This feature would create approximately acres of wetland habitat within the Project Area. These features would be approximately 4 feet deep, with the bottom elevation at approximately 386 ft NAVD 88 and a circular shape approximately 80 ft in diameter. This depth would not exceed the depth of clay/silt soils in the locations proposed, which would allow these wetlands to hold water during the growing season, barring drought conditions. These conditions would allow for emergent vegetation to grow around the perimeter of the depressional wetlands, restoring habitat conditions needed by various amphibian and reptile species where cover is needed adjacent to standing water. 7. Cross Levee Degrade (C1). The bullfrog (Graves and Anderson 1987) Corps approved (per EC ) HSI model was used to assess restored wetland habitat benefits on the site. This species was selected because relies on permanent bodies of standing or slow-moving water in wetlands. The following assumptions in applying the bullfrog HSI model were made: Baseline Conditions. Currently, the cross levees bisecting the Project Area limit the backing of water during low magnitude (>2-year and < 5-year) flood events, which limits the amount of fine sediment deposition in the upper portion thereby limiting the effectiveness of the sediment deflection berm. Semipermanently/permanently flooded wetland sites are limited in the Project Area. The Project Area was used for agriculture until Prior to FWS acquisition, the land owners altered the landscape to increase agricultural productivity, including draining and filling wetlands. Thus emergent aquatic vegetation wetlands do not exist within the Project Area as well. Future Without Project Conditions. It is anticipated that conditions would continue to exist in which limited semi-permanent and permanent wetland sites with emergent aquatic vegetation within the Project Area. Since many amphibian and reptile species rely on these habitat types, these populations would continue to be limited throughout the Project Area, further contributing to the overall lack of ecosystem diversity. Future With Project Conditions. It is assumed that with the cross levee degrade (C1), the presence of semi-permanently and permanently flooded wetland habitat would be restored in the footprint where the cross levees have been degraded. USACE Habitat Evaluation and Quantification Appendix F F-11

18 This feature would create approximately acres of wetland habitat within the Project Area. These features would be approximately 4 feet deep, with the bottom elevation at approximately 386 ft NAVD 88. This depth would not exceed the depth of clay/silt soils in the locations proposed, which would allow these wetlands to hold water during the growing season, barring drought conditions. These conditions would allow for emergent vegetation to grow around the perimeter of the wetlands, restoring habitat conditions needed by various amphibian and reptile species where cover is needed adjacent to standing water. 8. Ridge Forest Habitat (R1R5, 20% ACE and R1R10, 10% ACE) The fox squirrel (Allen 1982) Corps approved (per EC ) HSI model was used to assess the floodplain forest habitat benefits of reforestation on the site. This species was selected because it requires hard mast tree species as a large component of the forest community in which it lives. The following assumptions in applying the fox squirrel HSI model were made: Baseline Condition. Similar site conditions exist as described in feature Sediment Deflection Berm (A3) and Reforestation (). Future Without Project Condition. Similar Future Without Project assumptions were made as described in feature Sediment Deflection Berm (A2) and Reforestation (). Future With Project Condition. Similar Future With Project assumptions were made as described in feature Sediment Deflection Berm (A2). The ridges would have a side slope of 1V:4H from existing grade up to approximately a 20% ACE (5-year flood frequency) elevation, from which a shallower slope of 1V:10H will be used up to an elevation matching a 10% ACE (10 year flood frequency) elevation. It was assumed that the ridges would be planted in the same as the Sediment Deflection Berm (A2). R1R5 refers to the 20% ACE areas and R1R10 refers to the 10% ACE areas. The elevations up to a 20% ACE would support a more flood tolerant mix of bottomland hard mast species such as pecan (Carya illinoinensis), overcup oak (Quercus lyrata), and willow oak (Q. phellos) while the elevations between 20% ACE and 10% ACE would be planted with a more intermediate flood tolerant bottomland hard mast species mix compared to the species previously listed, consisting of pin oak (Q. palustris), nuttall oak (Q. nuttalli), and water hickory (C. aquatica), the elevation of a 10% annual chance of exceedance would be planted with a more flood intolerant mix of bottomland hard mast species compared to the two groups previously listed, which would consist of swamp white oak (Q. bicolor), bur oak (Q. macrocarpa), cherrybark oak (Q. pagoda), and shellbark hickory (C. laciniosa). 8. Swale Habitat () The bullfrog (Graves and Anderson 1987) Corps approved (per EC ) HSI model was used to assess restored wetland habitat benefits on the site. This species was selected because relies on permanent bodies of standing or slow-moving water in wetlands. The following assumptions in applying the bullfrog HSI model were made: Baseline Conditions. The Project Area was used for agriculture until Prior to FWS acquisition, the land owners altered the landscape to increase agricultural productivity, including draining and filling wetlands. This reduced eliminated semi-permanently/permanently flooded wetland sites in the Project Area. Thus USACE Habitat Evaluation and Quantification Appendix F F-12

19 RESULTS Draft Feasibility Report with Integrated Environmental Assessment emergent aquatic vegetation wetlands do not exist within the Project Area. Future Without Project Conditions. It is anticipated that conditions would continue to exist in which no semi-permanent and permanent wetland sites with emergent aquatic vegetation within the Project Area. Since many amphibian and reptile species rely on these habitat types, these populations would continue to be limited throughout the Project Area, further contributing to the overall lack of ecosystem diversity. Future With Project Conditions. It is assumed that with the construction of the swale wetland feature (), the presence of semi-permanently and permanently flooded wetland habitat would exist within the constructed features. This feature would restore approximately acres of wetland habitat within the Project Area. These features would have a bottom width of approximately 80 ft with gradual 1V:20H side slopes. LiDAR was used to determine lower elevation areas where swales were historically present. These features would be approximately 4 feet deep, with the bottom elevation at approximately 386 ft NAVD 88. This depth would not exceed the depth of clay/silt soils in the locations proposed, which would allow these wetlands to hold water during the growing season, barring drought conditions. These conditions would allow for emergent vegetation to grow around the perimeter of the swale wetlands, restoring habitat conditions needed by various amphibian and reptile species where cover is needed adjacent to standing water. Chapter 4 of the main report, Evaluation of Feasible Project Features and Formulation of Alternatives, describes each potential Project feature in detail. The Project planning team screened out several features and alternatives before this habitat quantification process began. Tables 5-12 displays the summaries of the results of the habitat benefit evaluations respective to the feature evaluated per alternative. 4.1 Total Habitat Benefits Table 13 provides the summary of the total net AAHUs of each considered alternative. Table 4. Future Without Project and Future With Project Benefit Evaluation Results for All Alternatives FWOP Total Net Alternative FWP AAHUs AAHUs AAHUs B C USACE Habitat Evaluation and Quantification Appendix F F-13

20 USACE Habitat Evaluation and Quantification Appendix F F-14

21 Alternative 1 Table 5. Benefit Evaluation Results for Alternative 1 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year TOTAL Species HSI Final Acres Cumlative HU's by target year CUMULATIVE AAHUs Fox Squirrel Bullfrog mallmouth Buffa HU's Existing No Action FWOP A2-1A With Project Existing No Action FWOP S S3-1A With Project S Existing No Action FWOP S1(b) S3-1A With Project S1(b) Existing No Action FWOP A With Project Existing No Action FWOP C C Existing No Action FWOP Existing No Action FWOP W W Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT NET AAHUs/ Feature Total AAHUs/ Alternative 481 USACE Habitat Evaluation and Quantification Appendix F F-15

22 Alternative 2 Table 6. Benefit Evaluation Results for Alternative 2 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S5 S5 S5(b) S5(b) C1 C1 W1 W1 Fox Squirrel Species HSI Final Acres Cumlative HU's by target year Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 482 USACE Habitat Evaluation and Quantification Appendix F F-16

23 Alternative 3 Table 7. Benefit Evaluation Results for Alternative 3 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S1 S1 S1(b) S1(b) C1 C1 Fox Squirrel Species HSI Final Acres Cumlative HU's by target year Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 472 USACE Habitat Evaluation and Quantification Appendix F F-17

24 Alternative 4 Table 8. Benefit Evaluation Results for Alternative 4 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S5 S5 S5(b) S5(b) C1 C1 Fox Squirrel Species HSI Final Acres Cumlative HU's by target year Bullfrog mallmouth Buffa TOTAL CUMULATIVE HU's Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 474 USACE Habitat Evaluation and Quantification Appendix F F-18

25 Alternative 5 Table 9. Benefit Evaluation Results for Alternative 5 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S1 S1 S1(b) S1(b) W1 W1 Fox Squirrel Species HSI Final Acres Cumlative HU's by target year Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 475 USACE Habitat Evaluation and Quantification Appendix F F-19

26 Alternative 6 Table 10. Benefit Evaluation Results for Alternative 6 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year TOTAL Species HSI Final Acres Cumlative HU's by target year CUMULATIVE AAHUs Fox Squirrel Bullfrog mallmouth Buffa HU's Existing No Action FWOP A2-1A With Project Existing No Action FWOP S S3-1A With Project S Existing No Action FWOP S5(b) S3-1A With Project S5(b) Existing No Action FWOP A With Project Existing No Action FWOP W W Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT 0 67 NET AAHUs/ Feature Total AAHUs/ Alternative 477 USACE Habitat Evaluation and Quantification Appendix F F-20

27 Alternative 7 Table 11. Benefit Evaluation Results for Alternative 7 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S1 S1 S1(b) S1(b) Fox Squirrel Species HSI Final Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT Acres Cumlative HU's by target year TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 467 USACE Habitat Evaluation and Quantification Appendix F F-21

28 Alternative 8 Table 12. Benefit Evaluation Results for Alternative 8 Feasibility Report with Integrated Environmental Assessment Measure Number IWR Plan Code Condition Year S5 S5 S5(b) S5(b) Fox Squirrel Species HSI Final Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP S3-1A With Project Existing No Action FWOP A With Project Existing No Action FWOP Existing No Action FWOP Existing No Action FWOP A With Project OUTPUT Acres Cumlative HU's by target year TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 469 USACE Habitat Evaluation and Quantification Appendix F F-22

29 Alternative 7B Table 13. Benefit Evaluation Results for Alternative 7B Feasibility Report with Integrated Environmental Assessment Measure Number S1 S1 S1(b) S1(b) IWR Plan Code Condition Year Fox Squirrel OUTPUT Species HSI Final Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Projec Existing No Action FWOP S3-1A With Projec Existing No Action FWOP S3-1A With Projec Existing No Action FWOP A With Projec Existing No Action FWOP W1-1A With Projec Existing No Action FWOP W1-1A With Projec Existing No Action FWOP A With Projec Acres Cumlative HU's by target year TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 530 USACE Habitat Evaluation and Quantification Appendix F F-23

30 Alternative 7C Feasibility Report with Integrated Environmental Assessment Table 14. Benefit Evaluation Results for Alternative 7C Measure Number IWR Plan Code Condition Year S1 S1 S1(b) S1(b) Fox Squirrel OUTPUT Species HSI Final Bullfrog mallmouth Buffa Existing No Action FWOP A2-1A With Projec Existing No Action FWOP S3-1A With Projec Existing No Action FWOP S3-1A With Projec Existing No Action FWOP A With Projec Existing No Action FWOP W1-1A With Projec Existing No Action FWOP W1-1A With Projec Existing No Action FWOP A With Projec Acres Cumlative HU's by target year TOTAL CUMULATIVE HU's AAHUs NET AAHUs/ Feature Total AAHUs/ Alternative 462 USACE Habitat Evaluation and Quantification Appendix F F-24

31 REFERENCES Feasibility Report with Integrated Environmental Assessment Allen, A. (1982). Habitat Suitability Index Models: Fox Squirrel. US Department of Interior, Fish and Widlife Services. Edwards, E., & Twomey, K. (1982). Habitat Suitability Index Models: Smallmouth Buffalo. US Department of Interior, Fish and Wildlife Services. Graves, B., & Anderson, S. (1987). Habitat Suitability Index Models: Bullfrog. US Department of Interior, Fish and Wildlife Services. Heitmeyer, M. (2008). An Evaluation of Ecosystem Restoration Options for the Middle Mississippi River Regional Corrido. In Greenbrier Wetland Services Report Advance, MO. Korschgen, L. (1981). Foods for Fox and Gray Squirrels in Missouri. Journal of Wildlife Management, 45(1): Mathias, D., Hardy, T., & Jordan, J. (1996). Aquatic Habitat Appraisal Guide: User's Manual. Instruction Report EL Vicksburg, MS: Waterways Experiment Station, US Army Corps of Engineers. Remo, J., Ryherd, J., Ruffner, C., & Therrell, M. (2018). Temporal and Spatial Patterns of Sedimentation within the Batture Lands of the Middle Mississippi River, USA. Geomorphology 308, USFWS (US Fish and Wildlife Services). (2007). Fisheries Monitoring at Harlow Island, Middle Mississippi River Region 3 Fisheries Data Series Report: FDS USFWS (US Fish and Wildlife Services). (2016, July 15). Habitat Evaluation Procedures (HEP) ESM 102. Retrieved from USACE Habitat Evaluation and Quantification Appendix F F-25

32 Feasibility Report with Integrated Environmental Assessment ENCLOSURE 1 USACE Habitat Evaluation and Quantification Appendix F F-26

33 Feasibility Report with Integrated Environmental Assessment USACE Habitat Evaluation and Quantification Appendix F F-27

34 Feasibility Report with Integrated Environmental Assessment ENCLOSURE 2 USACE Habitat Evaluation and Quantification Appendix F F-28

35 Feasibility Report with Integrated Environmental Assessment SUB-APPENDIX REGENERATION CALCULATIONS Background To achieve a sustainable forest community, i.e., regeneration of desirable species, target basal areas need to be determined. The following calculations are derived from a series of forestry techniques designed to achieve recruitment and regeneration. Mixed bottomland hardwood stands seldom exceed 150 square feet of basal area (BA) per acre and most are between 110 and 130 square feet per acre when mature (Burns 1983). Currently, only one pecan (Carya illinoinensis) is known to exist on Harlow Island. This demonstrates that although pecan does not currently make up a large proportion of the forest community, it is capable of growing with the current soils and hydrology. However, a source of seed is needed throughout the Project Area in order for regeneration to occur. To estimate the capability for hardwood regeneration on Harlow Island, several scenarios can be analyzed to help with the estimation. Applying Two-Age System from Stringer 2006: The two-age system is a viable method for managing hardwood forest communities where longer-lived species are present as well as providing structural components that are lacking in even-aged stands. To achieve this scenario, generally a deferment or shelterwood harvest is performed. The deferment harvest retains a limited basal area of the desirable canopy trees species while allowing the majority of the area to regenerate. This method initially creates a stand that contains scattered or small groups of older trees, which are referred to as reserve trees. The two-age system requires the long-term retention of reserve trees, which serve as the seed source into the future. The reserve trees must be able to maintain themselves into the future, while distribution is carefully determined and managed. When utilizing deferment harvests, reserve tree densities are typically around 30 ft 2 BA/acre. This method can be applied to Harlow Island, where reserve trees are not prevalent. To achieve the presence of reserve trees, tree plantings would serve to provide a seed source for regeneration into the future. Using the above information for the two-age method and the 30 ft 2 BA/acre, estimated tree planting density for the project area can be determined. To achieve 30 ft 2 BA/acre, individual tree densities can be estimated using Table 1, where number of trees per acre by basal area have been calculated, ranging from 612 trees/acre at a 3 in DBH and 9.5 trees/acre at a 24 inches DBH. Typically on UMR reforestation projects, planted trees are a minimum of 5/8 inch basal diameter per planting contract specs (pers. Communication, Robert Cosgriff) and planted at a density of 120 trees/acre. We can infer an average DBH growth over 50 years at 0.5 inches per year, making the planted trees approximately 25 inches DBH. When applying this reserve tree density across the project area to achieve 30 BA/acre the below calculations can be used: 30 BA/acre = 9.5 trees/acre (conservatively) for 24 inch DBH trees 9.5 trees/acre x acres (Project Area) = 8,074 trees 8,074 trees planted 120 trees/ acre (tree planting density) = 67.3 acres The above calculations show that approximately 67.3 acres would need to be planted to achieve 30 BA/acre across the Project Area. This estimation is likely conservative for the minimum of trees needed. The above estimate of 67.3 acres is roughly 8.0% of the total project area behind the sediment deflection berm. The total tree planting acreage for the Tentatively Selected Plan would be 73.2 acres. USACE Sub-Appendix Regeneration Calculations F-29

36 Feasibility Report with Integrated Environmental Assessment Table1. From Countryman and Kemperman References Burns, R. M. (1983). Silvicultural Systems for the Major Forest Types of the United States. In Agriculture Handbook (p. 445). USDA. Countryman, D. W., & Kemperman, J. (2000). Forestry Reference Handbook. Iowa State Univeristy Extension. Stringer, J. W. (2006). Two-Age System and Deferment Harvests (FOR-103). Lexington: University of Kentucky, Cooperative Extension Service. USACE Sub-Appendix Regeneration Calculations F-30