1
|
Petersma FT, Thomas L, Harris D, Bradley D, Papastamatiou YP. Age is not just a number: How incorrect ageing impacts close-kin mark-recapture estimates of population size. Ecol Evol 2024; 14:e11352. [PMID: 38840589 PMCID: PMC11150428 DOI: 10.1002/ece3.11352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 06/07/2024] Open
Abstract
Population size is a key parameter for the conservation of animal species. Close-kin mark-recapture (CKMR) relies on the observed frequency and type of kinship among individuals sampled from the population to estimate population size. Knowledge of the age of the individuals, or a surrogate thereof, is essential for inference with acceptable precision. One common approach, particularly in fish studies, is to measure animal length and infer age using an assumed age-length relationship (a 'growth curve'). We used simulation to test the effect of misspecifying the length measurement error and the growth curve on population size estimation. Simulated populations represented two fictional shark species, one with a relatively simple life history and the other with a more complex life history based on the grey reef shark (Carcharhinus amblyrhynchos). We estimated sex-specific adult abundance, which we assumed to be constant in time. We observed small median biases in these estimates ranging from 1.35% to 2.79% when specifying the correct measurement error standard deviation and growth curve. CI coverage was adequate whenever the growth curve was correctly specified. Introducing error via misspecified growth curves resulted in changes in the magnitude of the estimated adult population, where underestimating age negatively biased the abundance estimates. Over- and underestimating the standard deviation of length measurement error did not introduce a bias and had negligible effect on the variance in the estimates. Our findings show that assuming an incorrect standard deviation of length measurement error has little effect on estimation, but having an accurate growth curve is crucial for CKMR whenever ageing is based on length measurements. If ageing could be biased, researchers should be cautious when interpreting CKMR results and consider the potential biases arising from inaccurate age inference.
Collapse
Affiliation(s)
- Felix T. Petersma
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Len Thomas
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Danielle Harris
- Centre for Research into Environmental and Ecological ModellingUniversity of St AndrewsSt AndrewsUK
| | - Darcy Bradley
- Bren School of Environmental Science & ManagementUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Yannis P. Papastamatiou
- Department of Biological Sciences, Institute of EnvironmentFlorida International UniversityNorth MiamiFloridaUSA
| |
Collapse
|
2
|
Sévêque A, Lonsinger RC, Waits LP, Brzeski KE, Komoroske LM, Ott-Conn CN, Mayhew SL, Norton DC, Petroelje TR, Swenson JD, Morin DJ. Sources of bias in applying close-kin mark-recapture to terrestrial game species with different life histories. Ecology 2024; 105:e4244. [PMID: 38272487 DOI: 10.1002/ecy.4244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/18/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
Close-kin mark-recapture (CKMR) is a method analogous to traditional mark-recapture but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used to identify related individuals in one or more sampling occasions, which enables the opportunistic use of samples from harvested wildlife. To apply the method accurately, it is important to build appropriate CKMR models that do not violate assumptions linked to the species' and population's biology and sampling methods. In this study, we evaluated the implications of fitting overly simplistic CKMR models to populations with complex reproductive success dynamics or selective sampling. We used forward-in-time, individual-based simulations to evaluate the accuracy and precision of CKMR abundance and survival estimates in species with different longevities, mating systems, and sampling strategies. Simulated populations approximated a range of life histories among game species of North America with lethal sampling to evaluate the potential of using harvested samples to estimate population size. Our simulations show that CKMR can yield nontrivial biases in both survival and abundance estimates, unless influential life history traits and selective sampling are explicitly accounted for in the modeling framework. The number of kin pairs observed in the sample, in combination with the type of kinship used in the model (parent-offspring pairs and/or half-sibling pairs), can affect the precision and/or accuracy of the estimates. CKMR is a promising method that will likely see an increasing number of applications in the field as costs of genetic analysis continue to decline. Our work highlights the importance of applying population-specific CKMR models that consider relevant demographic parameters, individual covariates, and the protocol through which individuals were sampled.
Collapse
Affiliation(s)
- Anthony Sévêque
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
| | - Robert C Lonsinger
- U.S. Geological Survey, Oklahoma Cooperative Fish and Wildlife Research Unit, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Caitlin N Ott-Conn
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Sarah L Mayhew
- Wildlife Division, Michigan Department of Natural Resources, Lansing, Michigan, USA
| | - D Cody Norton
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - Tyler R Petroelje
- Wildlife Division, Michigan Department of Natural Resources, Marquette, Michigan, USA
| | - John D Swenson
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Dana J Morin
- Department of Wildlife, Fisheries and Aquaculture, Forest and Wildlife Research Center, Mississippi State University, Mississippi State, Mississippi, USA
| |
Collapse
|
3
|
Rosenbaum SW, May SA, Shedd KR, Cunningham CJ, Peterson RL, Elliot BW, McPhee MV. Reliability of trans-generational genetic mark-recapture (tGMR) for enumerating Pacific salmon. Evol Appl 2024; 17:e13647. [PMID: 38333554 PMCID: PMC10848877 DOI: 10.1111/eva.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
As Pacific salmon (Oncorhynchus spp.) decline across much of their range, it is imperative to further develop minimally invasive tools to quantify population abundance. One such advancement, trans-generational genetic mark-recapture (tGMR), uses parentage analysis to estimate the size of wild populations. Our study examined the precision and accuracy of tGMR through a comparison to a traditional mark-recapture estimate for Chilkat River Chinook salmon (O. tshawytscha) in Southeast Alaska. We examined how adult sampling location and timing impact tGMR by comparing estimates derived using samples collected in the lower river mainstem to those using samples obtained in upriver spawning tributaries. Results indicated that tGMR estimates using a representative sample of mainstem adults were most concordant with, and 3% more precise than, the traditional mark-recapture estimate for this stock. Importantly, the timing and location of adult sampling were found to impact abundance estimates, depending on what proportion of the population dies or moves to unsampled areas between downriver and upriver sampling events. Additionally, we identified potential sources of bias in tGMR arising from violations of key assumptions using a novel individual-based modeling framework, parameterized with empirical values from the Chilkat River. Simulations demonstrated that increased reproductive success and sampling selectivity of older, larger individuals, introduced negative bias into tGMR estimates. Our individual-based model offers a customizable and accessible method to identify and quantify these biases in tGMR applications (https://github.com/swrosenbaum/tGMR_simulations). We underscore the critical role of system-specific sampling design considerations in ensuring the precision and accuracy of tGMR projects. This study validates tGMR as a potentially useful tool for improved population enumeration in semelparous species.
Collapse
Affiliation(s)
- Samuel W. Rosenbaum
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | - Samuel A. May
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | | | - Curry J. Cunningham
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| | | | | | - Megan V. McPhee
- College of Fisheries and Ocean SciencesUniversity of Alaska FairbanksJuneauAlaskaUSA
| |
Collapse
|
4
|
Marcy‐Quay B, Wilson CC, Osborne CA, Marsden JE. Optimization of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout ( Salvelinus namaycush). Ecol Evol 2023; 13:e10020. [PMID: 37082322 PMCID: PMC10111404 DOI: 10.1002/ece3.10020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Kinship-based methods of population assessment such as close-kin mark-recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing-based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next-generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously-published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 μL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known-origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent-offspring, half-sibling, and largely-unrelated pairs. Our results indicate that sequencing-based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between-population F ST, and kinship-based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources.
Collapse
Affiliation(s)
- Benjamin Marcy‐Quay
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| | - Chris C. Wilson
- Ontario Ministry of Natural Resources and ForestryTrent UniversityPeterboroughOntarioCanada
| | | | - J. Ellen Marsden
- Rubenstein Ecosystem Science LaboratoryUniversity of VermontBurlingtonVermontUSA
| |
Collapse
|
5
|
Chen C, Zhou B, Lin J, Gong Q, Xu F, Li Z, Huang Y. Liver Transcriptome Analysis Reveals Energy Regulation and Functional Impairment of Onychostoma sima During Starvation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:247-258. [PMID: 36790593 DOI: 10.1007/s10126-023-10201-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 05/06/2023]
Abstract
Releasing juvenile fish into resource-depleted waters is regarded as an effective way to restore fishery resources. However, during this stage, released fish are most vulnerable to long-term food deprivation due to environmental changes and low adaptability. Therefore, research regarding the energy regulation of fish under starvation stress is crucial to the optimization of release strategies. In this study, we performed a transcriptome analysis of the liver of Onychostoma sima subjected to starvation for 14 days. The results showed that, under long-term starvation, the liver regulated glucose homeostasis by activating the gluconeogenesis pathway. Meanwhile, the fatty acid metabolism pathway was activated to supply acetyl-coA to the TCA cycle, thus increasing mitochondrial ATP production and maintaining the balance of energy metabolism. Nevertheless, the activation of energy metabolism could not completely compensate for the role of exogenous nutrients, as evidenced by the downregulation of many genes involved in antioxidant defenses (e.g., cat, gpx3, mgst1, and mgst2) and immune response (e.g., c3, cd22, trnfrsf14, and a2ml). In summary, our data reveal the effects of long-term starvation on the energy metabolism and defensive regulation of starved juvenile fish, and these findings will provide important reference for the optimization of artificial release.
Collapse
Affiliation(s)
- Chunna Chen
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Bo Zhou
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Jue Lin
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Quan Gong
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Fei Xu
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Zhengyi Li
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China
| | - Yingying Huang
- Fishery Institute of the Sichuan Academy of Agricultural Sciences, Sichuan, Chengdu, 611731, China.
| |
Collapse
|
6
|
Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
Collapse
Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| |
Collapse
|
7
|
Delaval A, Bendall V, Hetherington SJ, Skaug HJ, Frost M, Jones CS, Noble LR. Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population. Evol Appl 2023; 16:461-473. [PMID: 36793682 PMCID: PMC9923483 DOI: 10.1111/eva.13474] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/17/2022] [Accepted: 08/09/2022] [Indexed: 11/04/2022] Open
Abstract
Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6291 genome-wide single nucleotide polymorphisms, 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D. batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N e ), and to catch per unit effort estimates from the trammel-net survey. Although each method was characterized by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site fidelity in D. batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.
Collapse
Affiliation(s)
- Aurélien Delaval
- Faculty of Biosciences and Aquaculture Nord University Bodø Norway
| | - Victoria Bendall
- Centre for Environment Fisheries and Aquaculture Science (CEFAS) Lowestoft UK
| | | | - Hans J Skaug
- Department of Mathematics University of Bergen Bergen Norway
| | - Michelle Frost
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | | | - Leslie R Noble
- Faculty of Biosciences and Aquaculture Nord University Bodø Norway.,School of Biological Sciences University of Aberdeen Aberdeen UK
| |
Collapse
|
8
|
Larroque J, Balkenhol N. A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs. PeerJ 2023; 11:e15151. [PMID: 37070094 PMCID: PMC10105560 DOI: 10.7717/peerj.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/09/2023] [Indexed: 04/19/2023] Open
Abstract
Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).
Collapse
Affiliation(s)
- Jeremy Larroque
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| | - Niko Balkenhol
- Wildlife Sciences, University of Goettingen, Goettingen, Germany
| |
Collapse
|
9
|
Patterson TA, Hillary RM, Kyne PM, Pillans RD, Gunasekera RM, Marthick JR, Johnson GJ, Feutry P. Rapid assessment of adult abundance and demographic connectivity from juvenile kin pairs in a critically endangered species. SCIENCE ADVANCES 2022; 8:eadd1679. [PMID: 36542711 PMCID: PMC9770943 DOI: 10.1126/sciadv.add1679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The viability of spatially structured populations depends on the abundance and connectivity between subpopulations of breeding adults. Yet, for many species, both are extremely difficult to assess. The speartooth shark is a critically endangered elasmobranch inhabiting tropical rivers with only three adults ever recorded in Australia. Close-kin mark-recapture models, informed by sibling pairs among 226 juveniles, were developed to estimate adult abundance and connectivity in two Australian river systems. Sixty-eight sibling pairs were found, and adult abundance was estimated at 892 for the Adelaide River and 1128 for the Alligator Rivers. We found strong evidence for female philopatry, with most females returning to the same river to pup. Adelaide River males appear largely philopatric, whereas Alligator Rivers males are highly connected to the Adelaide River. From only 4 years of sampling, our results demonstrate that juvenile-only kin pairs can inform simultaneous estimates of abundance and connectivity in a rare and threatened species.
Collapse
Affiliation(s)
- Toby A. Patterson
- CSIRO Oceans and Atmosphere, Castray Esplanade, Battery Point, Tasmania 7004, Australia
| | - Richard M. Hillary
- CSIRO Oceans and Atmosphere, Castray Esplanade, Battery Point, Tasmania 7004, Australia
| | - Peter M. Kyne
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory 0909, Australia
| | - Richard D. Pillans
- CSIRO Oceans and Atmosphere, QLD Biosciences Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia
| | | | - James R. Marthick
- Menzies Centre for Population Health, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Grant J. Johnson
- Department of Industry, Tourism, and Trade, Berrimah, Northern Territory 0828, Australia
| | - Pierre Feutry
- CSIRO Oceans and Atmosphere, Castray Esplanade, Battery Point, Tasmania 7004, Australia
| |
Collapse
|
10
|
Akita T. Estimating contemporary migration numbers of adults based on kinship relationships in iteroparous species. Mol Ecol Resour 2022; 22:3006-3017. [PMID: 35789097 DOI: 10.1111/1755-0998.13682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022]
Abstract
This paper describes the development of estimators for the contemporary migration number and rate of adults between two populations in iteroparous species. The proposed estimators are based on known half-sibling (HS) and/or parent-offspring (PO) relationships observed between populations across breeding seasons. The rationale is that HS and PO pairs exhibit information about the occurrence frequency of parental movements during the breeding interval. The proposed method allows for variance in the average number of offspring per parent within and between populations. In addition, coupled with the PO pairs found within the population, the estimators can be obtained using only genetic data. Generally, a sample size representing the square root of the population size is required to obtain meaningful migration information. We describe a detailed evaluation of the performance of the proposed estimators by running an individual-based model, and the results provide guidance regarding sample sizes to ensure the required accuracy and precision. In addition, given that there are few effective methods to estimate adult movement (especially when populations cannot be genetically distinct), we discuss the usefulness of the proposed kinship assignment method in terms of conservation biology and wildlife management.
Collapse
Affiliation(s)
- Tetsuya Akita
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kanagawa, Japan
| |
Collapse
|
11
|
Rosenthal WC, Fennell JM, Mandeville EG, Burckhardt JC, Walters AW, Wagner CE. Hybridization decreases native cutthroat trout reproductive fitness. Mol Ecol 2022; 31:4224-4241. [PMID: 35751487 DOI: 10.1111/mec.16578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/18/2022] [Accepted: 06/08/2022] [Indexed: 11/26/2022]
Abstract
Examining natural selection in wild populations is challenging, but crucial to understanding many ecological and evolutionary processes. Additionally, in hybridizing populations, natural selection may be an important determinant of the eventual outcome of hybridization. We characterized several components of relative fitness in hybridizing populations of Yellowstone cutthroat trout and rainbow trout in an effort to better understand the prolonged persistence of both parental species despite predictions of extirpation. Thousands of genomic loci enabled precise quantification of hybrid status in adult and subsequent juvenile generations; a subset of those data also identified parent-offspring relationships. We used linear models and simulations to assess the effects of ancestry on reproductive output and mate choice decisions. We found a relatively low number of late-stage (F3+) hybrids and an excess of F2 juveniles relative to the adult generation in one location, which suggests the presence of hybrid breakdown decreasing the fitness of F2+ hybrids later in life. Assessments of reproductive output showed that Yellowstone cutthroat trout are more likely to successfully reproduce and produce slightly more offspring than their rainbow trout and hybrid counterparts. Mate choice appeared to be largely random, though we did find statistical support for slight female preference for males of similar ancestry. Together, these results show that native Yellowstone cutthroat trout are able to outperform rainbow trout in terms of reproduction and suggests that management action to exclude rainbow trout from spawning locations may bolster the now-rare Yellowstone cutthroat trout.
Collapse
Affiliation(s)
- William C Rosenthal
- Department of Botany, University of Wyoming, USA.,Program in Ecology and Evolution, University of Wyoming, USA
| | - John M Fennell
- Department of Zoology and Physiology, University of Wyoming, USA.,Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, USA
| | - Elizabeth G Mandeville
- Department of Botany, University of Wyoming, USA.,Program in Ecology and Evolution, University of Wyoming, USA.,Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, USA.,Department of Integrative Biology, University of Guelph, Canada
| | | | - Annika W Walters
- Program in Ecology and Evolution, University of Wyoming, USA.,Department of Zoology and Physiology, University of Wyoming, USA.,Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, USA.,U.S. Geological Survey, USA
| | - Catherine E Wagner
- Department of Botany, University of Wyoming, USA.,Program in Ecology and Evolution, University of Wyoming, USA.,Biodiversity Institute, University of Wyoming, USA
| |
Collapse
|