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dryad36/100

SNP genotype dataset from brown and anadromous trout

Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed the high-confidence assignment of known-origin individuals to the region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long-distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.

opencc-zeroJul 2024View details →

zenodo36/100

Anadromous Waters Cataloging and Fish Inventories in Subbasins of the Koyukuk and Kobuk Rivers - 2022

Synopsis During the summers and falls of 2022 and 2023, staff from the Alaska Department of Fish and Game (ADF&G), Division of Sport Fish, Alaska Freshwater Fish Inventory (AFFI) program, will conduct a rapid, systematic inventory of anadromous fish distribution and associated aquatic and riparian habitat in select drainages of the Kanuti River and upper Kobuk River. AFFI program staff will identify and select target streams most likely to fill gaps in coverage of the State of Alaska's Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes (AWC); for each water body in which anadromous fish are observed, nominations to the AWC will be submitted. Introduction In Alaska, habitats that support migrating, spawning, or rearing anadromous fish are protected under state, federal, and local administrative jurisdictions. Alaska Statute (AS) 16.05.871 (the Anadromous Fish Act) is a keystone statutory protection for freshwater habitats of anadromous fish in Alaska, requiring the ADF&G to "specify the various rivers, lakes, and streams or parts of them" of the state that are important to the spawning, rearing, or migration of anadromous fish. The resulting product is known as the Anadromous Waters Catalog (AWC) and Atlas which are adopted as regulation under 5 AAC 95.011. Under the Anadromous Fish Act, activities and uses conducted in or otherwise affecting water bodies specified in the AWC require a permit from the ADF&G Habitat Section. Many other federal, state, and local government policies specify additional protections for anadromous fish habitat in Alaska. Like the ADF&G Habitat Section, these agencies apply protections only to those water bodies where anadromous fish use is explicitly documented, typically by reference to the AWC. It is important that water bodies used by anadromous fish are listed in the AWC because only listed water bodies are afforded protection. To be listed in the AWC, water bodies must have site-specific, drect, unambiguous observations of anadromous fish by a qualified observer.  The various anadromous fish habitat management tools in Alaska are predicated on explicit knowledge of the distribution of individual anadromous fish species and life stages. However, Alaska has over 3,000 streams totaling over a half a million kilometers (km) in length, > three million lakes, and > 10,000 km of coastline. These represent critical habitats for many fish species and the communities that depend upon them. But in the vastness of Alaska, only a fraction of extant anadromous fish freshwater habitats has been documented. The AWC currently lists nearly 20,000 streams, rivers, or lakes around the state, which have been specified as being important for the spawning, rearing, or migration of anadromous fish. Based on current areas surveyed, this number likely represents a small proportion of the streams, rivers, and lakes used by anadromous species. Until these habitats are inventoried, they will not be protected under Alaska’s Anadromous Fish Act.  The long-term goal of the AFFI program is to complete a statewide baseline inventory of fish assemblages and associated aquatic and riparian habitats. Knowing foundational aspects of biology, such as where and when anadromous fishes (and resident species) use habitats in Alaska, is crucial to respond to natural disturbances, manage fisheries, mitigate (or approve, deny, or plan) development, and understand regional ecology. However, due to the remoteness and multitudes of Alaska’s waterbodies, much remains to be learned about basic information of fishes in the state. This foundational knowledge is especially critical to areas such as western and interior Alaska (e.g., waters draining the Brooks Range), where subsistence and commercial fisheries for chum, Chinook, and sockeye salmon (and anadromous whitefishes and Dolly Varden) exist among ongoing and planned development (e.g., mining, road building) in addition to intensifying effects of climate change (permafrost thawing, hydrological changes). The proposed Ambler Road, a 340-km long road to assist mining development, would connect the Dalton Highway to the mining district north of the community of Kobuk by crossing several tributaries of the Koyukuk and Kobuk rivers.  The Koyukuk and Kobuk rivers are both critical watersheds to local communities for subsistence harvests in addition to supporting regional communities through commercial fisheries in Kotzebue Sound or the Yukon River drainage. Summer chum salmon are the biggest contributor to Koyukuk River basin harvests, with the Koyukuk River being the largest single contributor to the summer chum salmon run in the Yukon River drainage. Chum salmon are the largest contributor to commercial and subsistence harvests in Kotzebue Sound and the Kobuk River. However, all species of Pacific salmon are harvested to some degree by these areas’ commercial and subsistence fisheries. The various communities, resources, fisheries, and land uses allow for multiple stewardship roles in this region, including those performed by native communities, native corporations, private enterprises, the National Park Service (NPS), the Bureau of Land Management (BLM), and the U.S. Fish & Wildlife Service (USFWS). Accordingly, accurately depicting the distributions and timing of fish species in the AWC can simultaneously inform responsible decisions and support the needs (or goals) of stakeholders across a landscape. However, despite cultural, ecological, and economic interest in this region, the upper Kobuk and Koyukuk rivers (and Ambler Road corridor) had not been investigated for anadromous and freshwater fishes at a landscape level prior to 2018. Prior to 2018, there was minimal data available on fish species assemblage and habitat use, generally limited to a few main waterbodies across the region. In 2017, an NPS wildlife biologist alerted ADF&G staff in the AWC and AFFI programs that GPS-collared grizzly bears had been observed eating salmon in streams that were not currently documented in the AWC. This represents a significant ecological link between marine and inland Alaska ecosystems, and presented an opportunity for AFFI biologists to use this knowledge to inform and plan a landscape-scale AFFI investigation which began in the summer of 2018.  When ADF&G habitat biologists surveyed the upper Kobuk and Koyukuk river systems in 2018 and 2019, they found numerous previously unlisted waters that support anadromous and resident fishes. These efforts added 972 km of stream to the AWC among 68 different waterbodies, notably for (in order of highest to lowest contribution of added AWC length): chum salmon, Chinook salmon, sockeye salmon, pink salmon, and Dolly Varden. However, these efforts were plagued by several days of work lost to mechanical issues with helicopters, leaving large areas and potentially important fish habitat unexplored and undocumented. Accordingly, ADF&G staff will return through this project to fill in remaining knowledge gaps of this region.  From July 25-August 2, 2022, one 2-person crew (plus helicopter pilot) will sample fish communities using AFFI protocols in selected tributaries of the Kanuti River watershed and middle Koyukuk River. Sampling target survey sites will include backpack electrofishing wadeable smaller headwater streams and raft-mounted electrofishing un-wadeable medium-sized streams. This timing will maximize the ability to detect juvenile and spawning or migrating Chinook salmon as well as spawning or migrating summer chum salmon. Then, from August 25-September 2, 2022, one 2-person crew (plus helicopter pilot) will sample fish communities using AFFI protocols in selected streams of the Kobuk River basin. This timing is to maximize encounters of spawning and migrating chum salmon but could also include coho salmon. In 2023, crews based in Kiana and the Kobuk River sampled fishes from August 20-September 1. 3.      Locations: Sampling will be performed in select drainages of the Koyukuk and Kobuk rivers with a base camp in Bettles, AK (66.91938, -151.52536) for the Koyukuk River basin field season and a base camp in Kobuk (66.90218, -156.87492) for the Kobuk River basin field season. The approximate region would include an area bounded to the west by the community of Kiana (66.96914, -160.44455) and to the east by the Dalton Highway (67.15459, -150.35730), e.g., 66.864255, -156.87492 (e.g., Pick River: 66.618510, -156.724571 ).  Objectives ·         I    Increase documented anadromous fish habitats in the AWC within the study area. Record aquatic habitat characteristics (including riparian zone) at each sampling          location. II.                Methods Study area selection The 131,785 square kilometer study area includes subbasins of the Koyukuk and Kobuk rivers. This includes target streams that were not sampled due to logistical constraints in 2018 (e.g., helicopter mechanical troubles leading to multiple lost days of work). Specifically, areas that were not explored include the Kanuti River in the Koyukuk River basin as well as tributaries of the Kobuk River near Walker Lake and the Pick River. This study area is critical to management and potential mitigation of the proposed Ambler Road.  Target stream selection Target stream selection will be initially carried out using the AFFI published method of using GIS to identify previously unsampled (or not rigorously sampled) streams that can be safely accessed and effectively electrofished while maximizing potential additions to the AWC. Based on past AFFI projects, it is estimated that a minimum of 72 headwater and 4 un-wadeable streams could be sampled during efforts in July-August (9 field days) and August-September (9 field days). However, these estimates are contingent upon no weather or logistical problems preventing sampling. The number of headwater streams in the study area will exceed the project’s limited sampling effort capacity; therefore, a subset of mapped streams comprising the longest stream segments not listed in the AWC will be selected as targets. The headwater team will sample four to six headwater streams per day and, when operating, the raft or riverboat team will float and sample one un-wadeable stream per day, including a reach from all mainstem rivers in the study area. Sites will be prioritized according to logistics (i.e., fuel and time needed to reach location) and potential for addition to the AWC. Further, sites within the study area that have the highest potential for habitat degradation will be identified and prioritized after consultation with the ADF&G Habitat Section and federal land managers and biologists. Sampling methods Following ADF&G's AFFI protocols (Giefer and Cathcart 2019), crews will typically use a helicopter to access streams and sample their fish communities during at least 18 days in 2022 and at least 5 days in 2023. Target survey sites will include wadeable headwater streams sampled with a backpack electrofisher and un-wadeable streams (including mainstem rivers) sampled with a raft-mounted electrofisher.   At all target streams, a length of stream (referred to as a reach) standardized by stream width (i.e., 40 or 120 wetted-channel-widths in wadeable and un-wadeable target streams, respectively), will be sampled to include all aquatic habitat types within that reach. Collected fish will be identified to species, tallied, fork length measured, and examined for external abnormalities.  At selected reaches, the fish community will be sampled with standardized methods and effort according to AFFI protocols. Fish will typically be collected by single-pass electrofishing. Electrofishing is the principal fish collection gear because it is recognized as the most comprehensive and effective method for collecting fish in lotic systems. Opportunistic sampling with gillnets (especially for subsistence targeted species that have demonstrated catchability with gillnets), angling, minnow trapping, and other gears will be performed as needed, such as if conditions prohibit safe or effective electrofishing.  Additionally, standard water chemistry, channel morphology, and riparian habitat parameters will be recorded at each sample site. To enhance data quality and completeness and data entry efficiency, all collected data will be entered each day into an integrated database installed on a notebook computer. Onset Hobo temperature data loggers may be deployed at the beginning of the sampling effort in pre-selected reference streams in the study area to document the full range of water temperatures during the field season. III.             Benefits Updated and more comprehensive AWC coverage will be the primary benefit of this project toward sustaining salmon habitat. Only anadromous fish habitat listed in the AWC receives protection under the Anadromous Fish Act and various other policies that provide additional protections to specified anadromous fish habitat. Providing more complete and accessible fish community and habitat information will help ADF&G and other federal, state, and local resource agencies better implement their respective fish habitat management, protection, and research missions. Together, better protection and management of salmon habitat will benefit subsistence salmon fisheries and the communities they sustain by safeguarding critical salmon habitat, thereby ensuring the long-term productivity of habitats and salmon populations. Enhanced communication and partnerships with tribal communities will be established through community outreach prior to and after the field work.

opencc-by-4.0Oct 2024View details →

zenodo36/100

Integrating Local and Traditional Ecological Knowledge into Anadromous Waters Cataloging and Fish Inventories of select drainages of the Tanana and Yukon rivers 2021-2023

***Funded by the Alaska Sustainable Salmon Fund #54007, a part of the Pacific Coastal Salmon Recovery Fund Synopsis During 2021 and 2022, staff from the Alaska Department of Fish and Game (ADF&G), Division of Sport Fish, Alaska Freshwater Fish Inventory (AFFI) program and the Yukon River Drainage Fisheries Association (YRDFA) will collaborate to integrate Local and Traditional Ecological Knowledge (LTK) ethnographic interviews into a rapid systematic inventory of fish communities and associated habitats in select drainages of the lower Tanana River and Upper Yukon River in the area of Tanana and Fairbanks. First, in 2021, LTK surveys in the communities of Tanana, Manley Hot Springs and Nenana will locate important subsistence areas that will be overlain on our GIS-selected target streams to assist in filling gaps in coverage of the State of Alaska's Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes (AWC) in freshwater habitats expected to support anadromous fish populations likely to be impacted by human activities. Then, in 2022, this project will seasonally sample target streams and record observations in the Alaska Freshwater Fish Inventory database (AFFID), nominate water bodies to the AWC when anadromous fish are observed, and provide publicly available data via the AFFID internet mapping service. Anticipated benefits of this project are multiple hundreds of kilometers and/or dozens of water bodies added to the AWC as well as a broader understanding of the importance of this region’s fish species to local human communities. 1.      Introduction In Alaska, habitats that support migrating, spawning, or rearing anadromous fish are protected under multiple administrative jurisdictions, including state, federal, and local habitat protection standards. Alaska Statute (AS) 16.05.871 (the Anadromous Fish Act) is a keystone statutory protection for freshwater habitats of anadromous fish in Alaska, requiring the ADF&G to "specify the various rivers, lakes, and streams or parts of them" of the state that are important to the spawning, rearing, or migration of anadromous fish.  The resulting atlas is known as the Anadromous Waters Catalog (AWC) which is adopted as regulation under 5 AAC 95.011. Under the Anadromous Fish Act, activities and uses conducted in or otherwise affecting water bodies specified in the AWC require permitting from the ADF&G Habitat Section. Many other federal, state, and local government policies specify additional protections for anadromous fish habitat in Alaska. To be listed in the AWC, water bodies must have site-specific, direct, unambiguous observations of anadromous fish by a qualified observer. This is a major reason the AFFI program targets areas with high potential to add water bodies to the AWC. Beginning in spring 2021, YRDFA and AFFI staff will conduct LTK interviews and mapping in the communities of Tanana, Manley Hot Springs, and Nenana. By spring 2022, the LTK contributions will be mapped and added to our site selection criteria prior to field work. Based on seasonality of some fishes in this area, we will establish certain seasonal site locations that are road accessible to determine spatiotemporal patterns in the fish community used by area residents. This will include target streams sampled in June, the main summer season (see following paragraph), and September. From July 10 to August 1, 2022, 4 crews, each with 2 members, will sample fish communities using AFFI protocols in selected streams draining into the Tanana and Yukon rivers within a general area upstream of the Kokrines (a historical settlement downstream of Tanana) and downstream of the city of Fairbanks. Target sites will include wadeable headwater streams and un-wadeable streams. Summer surveys will maximize detection of juvenile and spawning Chinook salmon, juvenile coho salmon, as well as spawning summer chum salmon. More opportunistic seasonal sampling for 5 days, tentatively in late-spring (e.g., early June) and fall (September or October), could enhance the likelihood of detecting multiple life history stages of rearing, migrating, or spawning whitefishes, Chinook salmon, coho salmon, and chum salmon.  Given the size and remoteness of the Yukon and Tanana river drainages, this AFFI proposal is for years 3 and 4 of a multiyear effort to sample the region and provides enough funding to conduct spring, summer, and fall sampling. AFFI staff will pursue additional funding sources to conduct more surveys if possible. Before this proposed study, AKSSF funded AFFI to survey the upper Yukon and Tanana River drainages in 2019 and 2020 (AKSSF projects 44375 and 53013, respectively). For example, 2019 surveys in the upper Yukon and Tanana river drainages documented >40 streams previously unlisted in the AWC for Chinook salmon. 2.      Location(s) Sampling will be done in select drainages of the Yukon and Tanana rivers bounded downstream near the old Yukon River village of Kokrines (N 64.9376, W -154.6944) and upstream to the Tanana River tributary Willow Creek (N 64.6719, W -148.2027). This includes the area and tributaries around the confluence of the Yukon and Tanana rivers (N 65.1682, W -151.9982) between the villages of Tanana and Manley Hot Springs. I.                   Objectives Objective 1: To maximize the spatial increase of documented anadromous fish habitats depicted in the AWC within the study area (sampling a minimum 80 headwater target streams, and 12 un-wadeable target streams) not including repeat sampling of select sites to document seasonal presence of some anadromous species. Objective 2: To use LTK to maximize the spatial increase of documented anadromous fish habitats depicted in the AWC within the study area while also corroborating and verifying the LTK with field surveys. Objective 3:  To record characteristics, using established protocols, of aquatic habitats (including riparian zone) at each sampling location. Objective 4:  To provide the fish distribution and associated aquatic habitat information to State & Federal agencies, participating communities, and the public. II.                Methods This collaborative project is designed to contribute to the AWC using social and biological methods. Prior to field work, a YRDFA anthropologist and ADF&G staff will contact the Tribal Councils of Tanana, Manley Hot Springs, and Nenana to schedule community meetings (in-person or online, as able) and ethnographic interviews between late spring 2021 and spring 2022. These interviews and mapping activities will establish what is known about the timing and distribution of resident and anadromous fishes and create maps that can be overlain on the AWC with other AFFI site selection criteria to identify streams to sample the following year. The next year, project staff will seek to verify LTK surveys and add to the AWC through seasonal sampling. The proposed study area for 2020 has a road system along the Tanana River which will allow access via truck and boat to certain streams during 5 days each in spring (June) and fall (September). This will likely raise the number of sites this project can sample while avoiding excess helicopter expenses. Additionally, this will allow better seasonal sampling efforts to maximize the ability to document seasonally variable fish distributions such as summer salmon spawning and fall whitefish spawning seasons. Summer sampling will be more expansive and follow ADF&G's AFFI protocols (Giefer and Cathcart 2019) where 4 crews, each with 2 members, will use helicopters to sample fish communities in selected study stream reaches for approximately 21 days in summer of 2022. Target survey sites will include wadeable headwater streams sampled with a backpack electrofisher, and un-wadeable streams sampled with a raft-mounted electrofisher. Sites within the study area that are identified as being anadromous fish rearing from LTK surveys and currently unlisted in the AWC will be prioritized for verification.           Study area selection The long-term goal of the AFFI program is to complete a statewide baseline inventory of fish assemblages and associated aquatic and riparian habitats. At its inception, the AFFI program developed a systematic approach to rank and prioritize Alaska’s 139 subbasin level hydrologic units. At the time of this proposal, the AFFI program has surveyed 81 of the 139 subbasins that were originally prioritized. This project’s 99,099 square kilometer study area includes subbasins of the lower Tanana River between the city Fairbanks and the mouth of the Tanana River, tributaries draining the south side of the Tanana upstream of Fairbanks but west of Clear Creek, and in select subbasins of the Yukon River near the community of Tanana but upstream of Kokrines.  Target stream selection Target stream selection will be performed by integrating LTK survey information with our conventional method of using GIS to identify previously unsampled (or not rigorously sampled) streams that can be safely accessed while maximizing potential additions to the AWC. The number of headwater streams in the study area will exceed the project’s limited sampling effort capacity; therefore, a subset of streams comprising the longest stream segments not listed in the AWC will be selected as targets. The headwater team will sample approximately six to eight headwater streams per day and, when operating, the raft or riverboat team will float and sample one un-wadeable stream per day. Based on past AFFI projects, it is estimated that a minimum of 80 headwater target streams will be sampled, and 12 un-wadeable target streams could be rafted and sampled during the 21 field days (not including the 5 field days in each of June and September).  However, these estimates are contingent upon weather and logistics. Reference sites for seasonal sampling will be prioritized depending on spatial and temporal observations from LTK surveys where we will select road or boat accessible locations to target fishes in spring, summer, and fall. We will seek to access all LTK-identified subbasins for subsistence fishes but they will be prioritized according to logistics (i.e., fuel and time needed to reach location) and potential addition to the AWC. Sampling methods Ideally, the fish community and habitat will be sampled with standardized methods per AFFI protocols. Fish will be collected by single-pass electrofishing standardized by stream width (i.e., 40 or 120 wetted-channel-widths in wadeable and un-wadeable target streams, respectively). Captured fish will be identified, measured, and released. Other gear types (such as beach seines, angling, or minnow traps) may be deployed if conditions prohibit electrofishing. Standard water chemistry, channel morphology, and riparian habitat parameters will be recorded at each sample site in addition to longer-term water temperature or eDNA sampling efforts in reference streams.   III.             Benefits Updated and more comprehensive AWC coverage will be the primary regulatory or fish habitat benefit of this project toward sustaining salmon habitat. Enhanced communication and partnerships with tribal communities will be established through interviews to gather LTK. Based on summer AFFI sampling since 2016, sampling at least 80 headwater target streams and 12 un-wadeable target streams, this project will add many (likely >300) previously unlisted kilometers of salmon habitat among several distinct streams to the AWC. Only anadromous fish habitat listed in the AWC receives protection under the Anadromous Fish Act and various other policies that provide additional protections to specified anadromous fish habitat. Also, providing more complete (e.g., seasonal) and accessible fish community and habitat information will benefit ADF&G, as well as help other federal, state, and local resource agencies better implement their respective fish habitat management, protection, and research missions.  Better protection and management of salmon habitat will benefit salmon fisheries and the communities they sustain by safeguarding critical salmon habitat thereby ensuring the long-term productivity of habitats and salmon populations.

opencc-by-4.0Oct 2024View details →

zenodo36/100

Supplementary data for: "Emergence of Potential Anadromous Arctic Charr (Salvelinus alpinus) Habitats in the Svalbard Archipelago after the End of the Little Ice Age"

Supplementary data for: “Emergence of Potential Anadromous Arctic Charr (Salvelinus alpinus) Habitats in the Svalbard Archipelago after the End of the Little Ice Age” <a href="https://doi.org/10.1029/2024JG008367">https://doi.org/10.1029/2024JG008367</a>   Abstract: Glaciers in the Svalbard Archipelago are retreating rapidly in response to climate change. The retreat of glaciers leads to alteration of the hydrological and thermal regimes of the freshwater ecosystems. In this delicate context, existing anadromous Arctic charr (Salvelinus alpinus) populations are at severe risk and might disappear from the archipelago. However, the retreat of glaciers also promotes the formation of new lake systems that might be suitable for colonization by anadromous Arctic charr. These systems may provide a substantial opportunity for the establishment of new populations of anadromous charr, potentially buffering the decline in existing systems. To date, there is a lack of information on the number of recently deglaciated lake systems that have emerged since the end of the Little Ice Age (ca. 1920) that might be suitable for charr colonization. Therefore, the goal of this paper is to provide an initial assessment of the number of these lakes. To this end, and in accordance with previously published research, this study assesses whether a recently deglaciated lake system is potentially open to colonization based on gradient, river length, and lake surface area. Depending on the applied threshold (four in total), up to 24 lake systems are classified as potentially open to colonization by anadromous Arctic charr, with Spitsbergen emerging as a colonization hotspot. The findings of this paper might serve as basis for new studies and for implementing proactive management and conservation strategies to protect anadromous charr populations.   Data description:   Recently_Deglaciated_Systems [EPGS: 25833] - Shapefile containing the information of 168 lake systems that emerged between 1936/1938 and 2020 in the Svalbard Archipelago ID: Identification number X: Easting Y: Northing Fall?: Presence of the lake system in fall (with dates when the lake was visible in satellite images) Spring?: Presence of the lake system in spring (with dates when the lake was visible in satellite images) Info: information regarding the type of system (i.e., larger lake surrounded by lakes and ponds or system of multiple lakes and ponds). If blank, lake is considered single.   Analysis [EPGS: 25833] - Shapefile containing the analysis of 125 lake systems with connection to the ocean. ID: Identification number X: Easting Y: Northing Surface (km2): Surface of the connected recently deglaciated lake system (km2) Elevation (m): Elevation of the outlet (m) Length (m): River length (m) Slope (%): Slope of the river (%) SV1: Result of the classification with SV1 SV2: Result of the classification with SV2 HY: Result of the classification with HY NO: Result of the classification with NO

opencc-by-4.0Nov 2024View details →

dryad36/100