references.bib

@article{knuth84,
  author = {Knuth, Donald E.},
  title = {Literate Programming},
  year = {1984},
  issue_date = {May 1984},
  publisher = {Oxford University Press, Inc.},
  address = {USA},
  volume = {27},
  number = {2},
  issn = {0010-4620},
  url = {https://doi.org/10.1093/comjnl/27.2.97},
  doi = {10.1093/comjnl/27.2.97},
  journal = {Comput. J.},
  month = may,
  pages = {97–111},
  numpages = {15}
}


@article{gruber2018,
	title = {{DARTR} : {An} {R} package to facilitate analysis of {SNP} data generated from reduced representation genome sequencing},
	volume = {18},
	issn = {1755098X},
	shorttitle = {{\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12745},
	doi = {10.1111/1755-0998.12745},
	abstract = {Although vast technological advances have been made and genetic software packages are growing in number, it is not a trivial task to analyse SNP data. We announce a new R package, DARTR, enabling the analysis of single nucleotide polymorphism data for population genomic and phylogenomic applications. DARTR provides user-friendly functions for data quality control and marker selection, and permits rigorous evaluations of conformation to Hardy–Weinberg equilibrium, gametic-phase disequilibrium and neutrality. The package reports standard descriptive statistics, permits exploration of patterns in the data through principal components analysis and conducts standard F-statistics, as well as basic phylogenetic analyses, population assignment, isolation by distance and exports data to a variety of commonly used downstream applications (e.g., NEWHYBRIDS, FASTSTRUCTURE and phylogeny applications) outside of the R environment. The package serves two main purposes: first, a user-friendly approach to lower the hurdle to analyse such data—therefore, the package comes with a detailed tutorial targeted to the R beginner to allow data analysis without requiring deep knowledge of R. Second, we use a single, well-established format—genlight from the ADEGENET package—as input for all our functions to avoid data reformatting. By strictly using the genlight format, we hope to facilitate this format as the de facto standard of future software developments and hence reduce the format jungle of genetic data sets. The DARTR package is available via the R CRAN network and GitHub.},
	language = {en},
	number = {3},
	urldate = {2023-05-11},
	journal = {Molecular Ecology Resources},
	author = {Gruber, Bernd and Unmack, Peter J. and Berry, Oliver F. and Georges, Arthur},
	month = may,
	year = {2018},
	pages = {691--699},
	file = {Gruber et al. - 2018 - dartrspan.pdf:C\:\\Users\\ejstr\\Zotero\\storage\\FG86QHIZ\\Gruber et al. - 2018 - dartrspan.pdf:application/pdf},
}

@article{mijangos2022,
	title = {{dartR} v2: {An} accessible genetic analysis platform for conservation, ecology and agriculture},
	volume = {13},
	copyright = {© 2022 The Authors. Methods in Ecology and Evolution published by John Wiley \& Sons Ltd on behalf of British Ecological Society.},
	issn = {2041-210X},
	shorttitle = {{dartR} v2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13918},
	doi = {10.1111/2041-210X.13918},
	abstract = {Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.},
	language = {en},
	number = {10},
	urldate = {2024-02-27},
	journal = {Methods in Ecology and Evolution},
	author = {Mijangos, Jose Luis and Gruber, Bernd and Berry, Oliver and Pacioni, Carlo and Georges, Arthur},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13918},
	keywords = {conservation genetics, DArT, next-generation sequencing, R, single nucleotide polymorphism},
	pages = {2150--2158},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\2P77JRCR\\Mijangos et al. - 2022 - dartR v2 An accessible genetic analysis platform .pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\4P8G6HMC\\2041-210X.html:text/html},
}

  Mijangos, J. L., Gruber, B., Berry, O., Pacioni,
  C., & Georges, A. (2022). dartR v2: An accessible
  genetic analysis platform for conservation, ecology
  and agriculture. Methods in Ecology and Evolution,
  (early access).
  https://doi.org/10.1111/2041-210X.13918

 @Article{jombart2015,
    title = {adegenet 1.3-1: new tools for the analysis of genome-wide SNP data},
    journal = {Bioinformatics},
    year = {2011},
    author = {T. Jombart and I. Ahmed},
    doi = {10.1093/bioinformatics/btr521}
}


@article{robledo2023,
	title = {Easy-to-use {R} functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment},
	year = {2023},
	volume = {0},
	copyright = {© 2023 The Authors. Molecular Ecology Resources published by John Wiley \& Sons Ltd.},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13844},
	doi = {10.1111/1755-0998.13844},
	abstract = {Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8\% accuracy and sex-linked loci with an average accuracy of 87.8\%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7\% of sex-linked loci. This led to (i) overestimation of population FIS by up to 24\%, and the number of private alleles by up to 8\%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring 11\% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation\_genomics).},
	language = {en},
	number = {n/a},
	urldate = {2024-02-28},
	journal = {Molecular Ecology Resources},
	author = {Robledo-Ruiz, Diana A. and Austin, Lana and Amos, J. Nevil and Castrejón-Figueroa, Jesús and Harley, Daniel K. P. and Magrath, Michael J. L. and Sunnucks, Paul and Pavlova, Alexandra},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13844},
	keywords = {bioinformatic filtering, COLONY, molecular sexing, multilocus contigs, sex chromosomes, sex-linked loci},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\WLYECV3W\\Robledo-Ruiz et al. - Easy-to-use R functions to separate reduced-repres.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\VEFNJPAT\\1755-0998.html:text/html},
}



@article{jaya_population_2022,
	title = {Population genomics and sexual signals support reproductive character displacement in {Uperoleia} ({Anura}: {Myobatrachidae}) in a contact zone},
	volume = {31},
	copyright = {© 2022 The Authors. Molecular Ecology published by John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	shorttitle = {Population genomics and sexual signals support reproductive character displacement in {Uperoleia} ({Anura}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16597},
	doi = {10.1111/mec.16597},
	abstract = {When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which probably reduces attractiveness to females. Integrating population genomic data, mitochondrial sequencing, morphology and behavioural approaches provides an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.},
	language = {en},
	number = {17},
	urldate = {2024-03-05},
	journal = {Molecular Ecology},
	author = {Jaya, Frederick R. and Tanner, Jessie C. and Whitehead, Michael R. and Doughty, Paul and Keogh, J. Scott and Moritz, Craig C. and Catullo, Renee A.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16597},
	keywords = {mitochondrial genome, range expansion, reproductive interference, speciation, unidirectional hybridization},
	pages = {4527--4543},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\U97TNTSH\\Jaya et al. - 2022 - Population genomics and sexual signals support rep.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\WZ3UY8JY\\mec.html:text/html},
}


  @Article{archer2016,
  title = "strataG: An R package for manipulating, summarizing and analysing population genetic data",
  year = "2016",
  author = "F. Archer, P. Adams, B. Schneiders", 
  journal = "Molecular Ecology Resources",
  doi = "10.1111/1755-0998.12559",
  url = "https://github.com/ericarcher/strataG"
  }
  
  @Article{petkova2016,
  author    = {Petkova, Desislava and Novembre, John and Stephens, Matthew},
  title     = {Visualizing spatial population structure with estimated effective migration surfaces},
  journal   = {Nature Genetics},
  volume    = {48},
  number    = {1},
  pages     = {94--100},
  year      = {2016},
  doi       = {10.1038/ng.3464},
  publisher = {Nature Publishing Group}
}

  
  @article{lynch2019,
	title = {Inference of {Historical} {Population}-{Size} {Changes} with {Allele}-{Frequency} {Data}},
	volume = {10},
	issn = {2160-1836},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945023/},
	doi = {10.1534/g3.119.400854},
	abstract = {With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex.},
	number = {1},
	urldate = {2024-03-03},
	journal = {G3: Genes{\textbar}Genomes{\textbar}Genetics},
	author = {Lynch, Michael and Haubold, Bernhard and Pfaffelhuber, Peter and Maruki, Takahiro},
	month = nov,
	year = {2019},
	pmid = {31699776},
	pmcid = {PMC6945023},
	pages = {211--223},
	file = {PubMed Central Full Text PDF:C\:\\Users\\s425824\\Zotero\\storage\\C8UZEY67\\Lynch et al. - 2019 - Inference of Historical Population-Size Changes wi.pdf:application/pdf},
}



@article{liu2020,
	title = {Stairway {Plot} 2: demographic history inference with folded {SNP} frequency spectra},
	volume = {21},
	shorttitle = {Stairway {Plot} 2},
	doi = {10.1186/s13059-020-02196-9},
	abstract = {Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms.},
	journal = {Genome Biology},
	author = {Liu, Xiaoming and Fu, Yun-Xin},
	month = nov,
	year = {2020},
	file = {Liu_Fu_2020_Genome Biology_Stairway Plot 2.pdf:C\:\\Users\\s425824\\Zotero\\storage\\2DZNMTBS\\Liu_Fu_2020_Genome Biology_Stairway Plot 2.pdf:application/pdf},
}


@article{santiago2020,
  author    = {Santiago, E. and Novo, I. and Pardiñas, A.F. and Saura, M. and Wang, J. and Caballero, A.},
  title     = {Recent demographic history inferred by high-resolution analysis of linkage disequilibrium},
  journal   = {Molecular Biology and Evolution},
  volume    = {37},
  number    = {12},
  pages     = {3642--3653},
  year      = {2020},
  doi       = {10.1093/molbev/msaa174},
  pmid      = {32642779}
}

@article{devloodelva_rivers_2023,
	title = {From rivers to ocean basins: {The} role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator},
	volume = {13},
	issn = {2045-7758},
	shorttitle = {From rivers to ocean basins},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944188/},
	doi = {10.1002/ece3.9837},
	abstract = {The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA‐capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo‐Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo‐West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land‐bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population‐level impacts of this harvest., In this study, 922 putative Bull Sharks were obtained from 19 locations for the first global assessment of population structure of this cosmopolitan coastal species. Nuclear DNA identified distinct populations in each ocean basin, with distinct island populations in Japan and Fiji. While nuclear DNA indicated that the Indo‐West Pacific is well‐connected, mitochondrial DNA—only inherited from the mother—showed that females return to the same locations for breeding.},
	number = {2},
	urldate = {2024-03-06},
	journal = {Ecology and Evolution},
	author = {Devloo‐Delva, Floriaan and Burridge, Christopher P. and Kyne, Peter M. and Brunnschweiler, Juerg M. and Chapman, Demian D. and Charvet, Patricia and Chen, Xiao and Cliff, Geremy and Daly, Ryan and Drymon, J. Marcus and Espinoza, Mario and Fernando, Daniel and Barcia, Laura Garcia and Glaus, Kerstin and González‐Garza, Blanca I. and Grant, Michael I. and Gunasekera, Rasanthi M. and Hernandez, Sebastian and Hyodo, Susumu and Jabado, Rima W. and Jaquemet, Sébastien and Johnson, Grant and Ketchum, James T. and Magalon, Hélène and Marthick, James R. and Mollen, Frederik H. and Mona, Stefano and Naylor, Gavin J. P. and Nevill, John E. G. and Phillips, Nicole M. and Pillans, Richard D. and Postaire, Bautisse D. and Smoothey, Amy F. and Tachihara, Katsunori and Tillet, Bree J. and Valerio‐Vargas, Jorge A. and Feutry, Pierre},
	month = feb,
	year = {2023},
	pmid = {36844667},
	pmcid = {PMC9944188},
	pages = {e9837},
	file = {PubMed Central Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\LE9CDLTG\\Devloo‐Delva et al. - 2023 - From rivers to ocean basins The role of ocean bar.pdf:application/pdf},
}


@article{nikolic_stepping_2023,
	title = {Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark {Prionace} glauca},
	volume = {32},
	copyright = {© 2022 The Authors. Molecular Ecology published by John Wiley \& Sons Ltd.},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.16822},
	doi = {10.1111/mec.16822},
	abstract = {The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible archetype of the “grey zone of population differentiation,” coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific RAD method (DArTseq), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-west Pacific samples (Southern population). Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested divergence between Northern and Southern populations occurred about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. Given that the management plans of the blue shark (targeted or bycatch) fisheries currently assume panmictic regional stocks, we strongly recommend that the results presented here be considered in future stock assessments and conservation strategies.},
	language = {en},
	number = {5},
	urldate = {2024-03-06},
	journal = {Molecular Ecology},
	author = {Nikolic, Natacha and Devloo-Delva, Floriaan and Bailleul, Diane and Noskova, Ekaterina and Rougeux, Clément and Delord, Chrystelle and Borsa, Philippe and Liautard-Haag, Cathy and Hassan, Mohamad and Marie, Amandine D. and Feutry, Pierre and Grewe, Peter and Davies, Campbell and Farley, Jessica and Fernando, Daniel and Biton-Porsmoguer, Sebastian and Poisson, François and Parker, Denham and Leone, Agostino and Aulich, Jorden and Lansdell, Matt and Marsac, Francis and Arnaud-Haond, Sophie},
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16822},
	keywords = {blue shark, bycatch, genome scans, pelagic, population genetics, SNPs, stock differentiation and assessment},
	pages = {1000--1019},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\SJ4K2LPV\\Nikolic et al. - 2023 - Stepping up to genome scan allows stock differenti.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\5MHC6PML\\mec.html:text/html},
}


@article{sopniewski_estimates_2024,
	title = {Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong},
	issn = {1755-0998},
	doi = {10.1111/1755-0998.13947},
	abstract = {Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.},
	language = {eng},
	journal = {Molecular Ecology Resources},
	author = {Sopniewski, Jarrod and Catullo, Renee A.},
	month = mar,
	year = {2024},
	pmid = {38433491},
	keywords = {DArT-seq, genetic conservation, heterozygosity, population genomics, single nucleotide polymorphisms, tri-allelic site},
	pages = {e13947},
}







@article{sherwin_information_2017,
	title = {Information {Theory} {Broadens} the {Spectrum} of {Molecular} {Ecology} and {Evolution}},
	volume = {32},
	issn = {0169-5347},
	url = {https://www.sciencedirect.com/science/article/pii/S0169534717302550},
	doi = {10.1016/j.tree.2017.09.012},
	abstract = {Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance.},
	number = {12},
	urldate = {2024-03-07},
	journal = {Trends in Ecology \& Evolution},
	author = {Sherwin, W. B. and Chao, A. and Jost, L. and Smouse, P. E.},
	month = dec,
	year = {2017},
	keywords = {diversity profile, entropy, gene expression, linkage disequilibrium, selection, Shannon},
	pages = {948--963},
	file = {ScienceDirect Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\2E2SSPDG\\S0169534717302550.html:text/html},
}

@article{sherwin_information_2021,
	title = {Information theory broadens the spectrum of molecular ecology and evolution: ({Trends} in {Ecology} and {Evolution} 32:12, p:948–963, 2017)},
	volume = {36},
	issn = {0169-5347},
	shorttitle = {Information theory broadens the spectrum of molecular ecology and evolution},
	url = {https://www.sciencedirect.com/science/article/pii/S0169534721001968},
	doi = {10.1016/j.tree.2021.07.005},
	number = {10},
	urldate = {2024-03-07},
	journal = {Trends in Ecology \& Evolution},
	author = {Sherwin, W. B. and Chao, A. and Jost, L. and Smouse, P. E.},
	month = oct,
	year = {2021},
	keywords = {diversity-profile, entropy, gene-expression, linkage-disequilibrium, selection, Shannon},
	pages = {955--956},
	file = {Full Text:C\:\\Users\\ejstr\\Zotero\\storage\\EL42RUYR\\Sherwin et al. - 2021 - Information theory broadens the spectrum of molecu.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\MTNLTGWL\\S0169534721001968.html:text/html},
}

@article{sherwin_bray-curtis_2022,
	title = {Bray-{Curtis} ({AFD}) differentiation in molecular ecology: {Forecasting}, an adjustment ({AA}), and comparative performance in selection detection},
	volume = {12},
	copyright = {© 2022 The Author. Ecology and Evolution published by John Wiley \& Sons Ltd.},
	issn = {2045-7758},
	shorttitle = {Bray-{Curtis} ({AFD}) differentiation in molecular ecology},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.9176},
	doi = {10.1002/ece3.9176},
	abstract = {Geographic genetic differentiation measures are used for purposes such as assessing genetic diversity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray-Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD). Critically, BCAFD is expected to be partially independent of the commonly used Hill “Q-profile” measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within-population (alpha) variation, undesirable for a between-population (beta) measure. The first dependency is derived from similarity to GST and FST. The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data-filtering or by a modified statistic AA or “Adjusted AFD”. The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions—which is shown in this article for AA, for equilibrium, and nonequilibrium, for the commonly used data type of single-nucleotide-polymorphisms (SNPs) in two locations. Thus, AA can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of AA and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that AA is in one of the best such pairwise criteria. For any application, using AA, rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.},
	language = {en},
	number = {9},
	urldate = {2024-03-07},
	journal = {Ecology and Evolution},
	author = {Sherwin, W. B.},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.9176},
	keywords = {adaptation, allele frequency difference, biodiversity, genetic differentiation, mutual information, outlier loci},
	pages = {e9176},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\G8U39HA3\\Sherwin - 2022 - Bray-Curtis (AFD) differentiation in molecular eco.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\9CIYB4TG\\ece3.html:text/html},
}

@article{oreilly_predicting_2020,
	title = {Predicting {Shannon}’s information for genes in finite populations: new uses for old equations},
	volume = {12},
	issn = {1877-7260},
	shorttitle = {Predicting {Shannon}’s information for genes in finite populations},
	url = {https://doi.org/10.1007/s12686-018-1079-z},
	doi = {10.1007/s12686-018-1079-z},
	abstract = {This study provides predictive equations for Shannon’s information in a finite population, which are intuitive and simple enough to see wide scale use in molecular ecology and population genetics. A comprehensive profile of genetic diversity contains three complementary components: numbers of allelic types, Shannon’s information and heterozygosity. Currently heterozygosity has greater resources than Shannon’s information, such as more predictive models and integration into more mainstream genetics software. However, Shannon’s information has several advantages over heterozygosity as a measure of genetic diversity, so it is important to develop Shannon’s information as a new tool for molecular ecology. Past efforts at making forecasts for Shannon’s information in specific molecular ecology scenarios mostly dealt with expectations for Shannon’s information at genetic equilibrium, but dynamic forecasts are also vital. In particular, we must be able to predict loss of genetic diversity when dealing with finite populations, because they risk losing genetic variability, which can have an adverse effect on their survival. We present equations for predicting loss of genetic diversity measured by Shannon’s information. We also provide statistical justification for these models by assessing their fit to data derived from simulations and managed, replicated laboratory populations. The predictive models will enhance the usefulness of Shannon’s information as a measure of genetic diversity; they will also be useful in pest control and conservation.},
	language = {en},
	number = {2},
	urldate = {2024-03-07},
	journal = {Conservation Genetics Resources},
	author = {O’Reilly, G. D. and Jabot, F. and Gunn, M. R. and Sherwin, W. B.},
	month = jun,
	year = {2020},
	keywords = {Conservation genetics, Entropy, Isolated populations, Population genetics, Simulations, Small populations},
	pages = {245--255},
}



@article{farquharson_restoring_2022,
	title = {Restoring faith in conservation action: {Maintaining} wild genetic diversity through the {Tasmanian} devil insurance program},
	volume = {25},
	issn = {2589-0042},
	shorttitle = {Restoring faith in conservation action},
	doi = {10.1016/j.isci.2022.104474},
	abstract = {Conservation breeding programs aim to maintain 90\% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species' range (64,519 km2). Populations have declined by 80\% since 1996 due to a contagious cancer, devil facial tumor disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for "resistance" alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012 and 2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.},
	language = {eng},
	number = {7},
	journal = {iScience},
	author = {Farquharson, Katherine A. and McLennan, Elspeth A. and Cheng, Yuanyuan and Alexander, Lauren and Fox, Samantha and Lee, Andrew V. and Belov, Katherine and Hogg, Carolyn J.},
	month = jul,
	year = {2022},
	pmid = {35754729},
	pmcid = {PMC9218385},
	keywords = {Animals, Genetics, Zoology},
	pages = {104474},
	file = {Full Text:C\:\\Users\\ejstr\\Zotero\\storage\\QWL2SJIP\\Farquharson et al. - 2022 - Restoring faith in conservation action Maintainin.pdf:application/pdf},
}



@article{dobry_widespread_2023,
	title = {Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, {Varanus} acanthurus ({Varanidae})},
	volume = {31},
	issn = {1573-6849},
	url = {https://doi.org/10.1007/s10577-023-09715-x},
	doi = {10.1007/s10577-023-09715-x},
	abstract = {Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.},
	language = {en},
	number = {1},
	urldate = {2024-03-08},
	journal = {Chromosome Research},
	author = {Dobry, Jason and Wapstra, Erik and Stringer, Emily J. and Gruber, Bernd and Deakin, Janine E. and Ezaz, Tariq},
	month = feb,
	year = {2023},
	keywords = {Adaptation, Chromosomics, Cytogenetics, Drift, Population genetics, Speciation},
	pages = {9},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\BCYT48L3\\Dobry et al. - 2023 - Widespread chromosomal rearrangements preceded gen.pdf:application/pdf},
}

@article{dobry_fixed_2023,
	title = {Fixed {Allele} {Differences} {Associated} {With} the {Centromere} {Reveal} {Chromosome} {Morphology} and {Rearrangements} in a {Reptile} ({Varanus} acanthurus {BOULENGER})},
	volume = {40},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msad124},
	doi = {10.1093/molbev/msad124},
	abstract = {Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multiplatform next-generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa; however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (Varanus acanthurus BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the V. acanthurus complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support de novo chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterized by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken, and the platypus. We demonstrated that the synteny of genes in Reptilia remains conserved despite centromere repositioning across these taxa.},
	number = {6},
	urldate = {2024-03-08},
	journal = {Molecular Biology and Evolution},
	author = {Dobry, Jason and Zhu, Zexian and Zhou, Qi and Wapstra, Erik and Deakin, Janine E and Ezaz, Tariq},
	month = jun,
	year = {2023},
	pages = {msad124},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\JV79RSI6\\Dobry et al. - 2023 - Fixed Allele Differences Associated With the Centr.pdf:application/pdf},
}

@article{fukuda2024,
	title = {Natal origin and dispersal of problem saltwater crocodiles in the {Darwin} {Harbor}, {Australia}},
	volume = {88},
	copyright = {© 2023 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.},
	issn = {1937-2817},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jwmg.22525},
	doi = {10.1002/jwmg.22525},
	abstract = {Management programs that successfully recovered wild saltwater crocodile (Crocodylus porosus) populations in the Northern Territory of Australia did so with an expanding commitment to maintaining public safety. One aspect of the program is the ongoing removal of resident and immigrant crocodiles within Darwin Harbor (since 1979), the main urban center. We determined the likely sources of crocodiles caught as problem animals between 2015–2017 by comparing recently developed methods for population assignment. Depending on the assignment model used, we estimated that between 30\% and 50\% of crocodiles in Darwin Harbor originated from the Adelaide and Mary rivers, and the Kakadu region east of Darwin, and between 20\% and 30\% of crocodiles originated from the Finniss, Reynolds, and Daly rivers southwest of Darwin. Saltwater crocodiles occur at particularly high densities in these catchments. The remainder came from a mixture of different sources across the Northern Territory. The most common animals captured were immature (150–180 cm) males that have traveled 100–200 km. We did not identify any relationships between the distance from the inferred origin to Darwin Harbor and the size and sex of the crocodiles, or the year of capture. The targeted removal of crocodiles from specific sites such as Darwin Harbor, near where most people live, improves public safety in the highest risk areas, without compromising abundant source populations in most areas.},
	language = {en},
	number = {2},
	urldate = {2024-03-09},
	journal = {The Journal of Wildlife Management},
	author = {Fukuda, Yusuke and Moritz, Craig and FitzSimmons, Nancy N. and Jang, Namchul and Webb, Grahame and Lindner, Garry and Campbell, Hamish and Christian, Keith and Leeder, Steven and Banks, Sam},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/jwmg.22525},
	keywords = {Crocodylus porosus, dispersal, estuarine crocodile, genetics, human–crocodile conflict, natal origin, population assignment, SNP},
	pages = {e22525},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\645K8G6X\\Fukuda et al. - 2024 - Natal origin and dispersal of problem saltwater cr.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\KKG3YJV9\\jwmg.html:text/html},
}




@article{attard_fish_2022,
	title = {Fish out of water: {Genomic} insights into persistence of rainbowfish populations in the desert},
	volume = {76},
	issn = {1558-5646},
	shorttitle = {Fish out of water},
	doi = {10.1111/evo.14399},
	abstract = {How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.},
	language = {eng},
	number = {1},
	journal = {Evolution; International Journal of Organic Evolution},
	author = {Attard, Catherine R. M. and Sandoval-Castillo, Jonathan and Brauer, Chris J. and Unmack, Peter J. and Schmarr, David and Bernatchez, Louis and Beheregaray, Luciano B.},
	month = jan,
	year = {2022},
	pmid = {34778944},
	keywords = {Adaptation, Physiological, Adaptive resilience, Animals, arid zone, Biological Evolution, climate change, freshwater fish, Genomics, Humans, landscape genomics, metapopulation, Population Density, Water},
	pages = {171--183},
}

@article{batley_whole_2021,
	title = {Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus},
	volume = {30},
	issn = {1365-294X},
	doi = {10.1111/mec.15873},
	abstract = {Wildlife species are challenged by various infectious diseases that act as important demographic drivers of populations and have become a great conservation concern particularly under growing environmental changes. The new era of whole genome sequencing provides new opportunities and avenues to explore the role of genetic variants in the plasticity of immune responses, particularly in non-model systems. Cetacean morbillivirus (CeMV) has emerged as a major viral threat to cetacean populations worldwide, contributing to the death of thousands of individuals of multiple dolphin and whale species. To understand the genomic basis of immune responses to CeMV, we generated and analysed whole genomes of 53 Indo-Pacific bottlenose dolphins (Tursiops aduncus) exposed to Australia's largest known CeMV-related mortality event that killed at least 50 dolphins from three different species. The genomic data set consisted of 10,168,981 SNPs anchored onto 23 chromosome-length scaffolds and 77 short scaffolds. Whole genome analysis indicated that levels of inbreeding in the dolphin population did not influence the outcome of an individual. Allele frequency estimates between survivors and nonsurvivors of the outbreak revealed 15,769 candidate SNPs, of which 689 were annotated to 295 protein coding genes. These included 50 genes with functions related to innate and adaptive immune responses, and cytokine signalling pathways and genes thought to be involved in immune responses to other morbilliviruses. Our study characterised genomic regions and pathways that may contribute to CeMV immune responses in dolphins. This represents a stride towards clarifying the complex interactions of the cetacean immune system and emphasises the value of whole genome data sets in understanding genetic elements that are essential for species conservation, including disease susceptibility and adaptation.},
	language = {eng},
	number = {23},
	journal = {Molecular Ecology},
	author = {Batley, Kimberley C. and Sandoval-Castillo, Jonathan and Kemper, Catherine M. and Zanardo, Nikki and Tomo, Ikuko and Beheregaray, Luciano B. and Möller, Luciana M.},
	month = dec,
	year = {2021},
	pmid = {33675577},
	keywords = {Animals, Bottle-Nosed Dolphin, Cetacea, cetacean morbillivirus, Communicable Diseases, ecological genomics, immune genes, Immunity, inshore dolphin, Morbillivirus Infections, whole genome sequencing, wildlife disease},
	pages = {6434--6448},
}

@article{smith_latitudinal_2020,
	title = {Latitudinal variation in climate-associated genes imperils range edge populations},
	volume = {29},
	issn = {1365-294X},
	doi = {10.1111/mec.15637},
	abstract = {The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates. We generated and integrated information from environmental mapping, phenotypic variation and genome-wide data from across the geographical range of the rainbowfish Melanotaenia duboulayi, an emerging aquatic system for studies of climate change. We detected, after controlling for spatial population structure, strong interactions between genotypes and environment associated with variation in stream flow and temperature. Some of these hydroclimate-associated genes were found to interact within functional protein networks that contain genes of adaptive significance for projected future climates in rainbowfish. Hydroclimatic selection was also associated with variation in phenotypic traits, including traits known to affect fitness of rainbowfish exposed to different flow environments. Consistent with predictions from the "climatic variability hypothesis," populations exposed to extremes of important environmental variables showed stronger adaptive divergence and less variation in climate-associated genes compared to populations at the centre of the environmental gradient. Our findings suggest that populations that evolved at environmental range margins and at geographical range edges may be more vulnerable to changing climates, a finding with implications for predicting adaptive resilience and managing biodiversity under climate change.},
	language = {eng},
	number = {22},
	journal = {Molecular Ecology},
	author = {Smith, Steve and Brauer, Chris J. and Sasaki, Minami and Unmack, Peter J. and Guillot, Gilles and Laporte, Martin and Bernatchez, Louis and Beheregaray, Luciano B.},
	month = nov,
	year = {2020},
	pmid = {32930432},
	keywords = {adaptive resilience, Animals, aquatic biodiversity, climate change, Climate Change, Ecosystem, Fishes, freshwater fish, Genotype, landscape genomics, rainbowfish, Selection, Genetic},
	pages = {4337--4349},
}

@article{brauer_natural_2023,
	title = {Natural hybridization reduces vulnerability to climate change},
	volume = {13},
	copyright = {2023 The Author(s)},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/s41558-022-01585-1},
	doi = {10.1038/s41558-022-01585-1},
	abstract = {Under climate change, species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate-relevant genes. However, hybridization as a source of novel adaptive variation is typically ignored in genomic vulnerability studies. We estimated environmental niche models and genomic vulnerability for closely related species of rainbowfish (Melanotaenia spp.) across an elevational gradient in the Australian Wet Tropics. Hybrid populations between a widespread generalist and several narrow range endemic species exhibited reduced vulnerability to projected climates compared to pure narrow endemics. Overlaps between introgressed and adaptive genomic regions were consistent with a signal of adaptive introgression. Our findings highlight the often-underappreciated conservation value of hybrid populations and indicate that adaptive introgression may contribute to evolutionary rescue of species with narrow environmental ranges.},
	language = {en},
	number = {3},
	urldate = {2024-03-13},
	journal = {Nature Climate Change},
	author = {Brauer, Chris J. and Sandoval-Castillo, Jonathan and Gates, Katie and Hammer, Michael P. and Unmack, Peter J. and Bernatchez, Louis and Beheregaray, Luciano B.},
	month = mar,
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	keywords = {Ecological genetics, Molecular ecology},
	pages = {282--289},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\Y6DZIQ7Q\\Brauer et al. - 2023 - Natural hybridization reduces vulnerability to cli.pdf:application/pdf},
}

@article{grummer_aquatic_2019,
	title = {Aquatic {Landscape} {Genomics} and {Environmental} {Effects} on {Genetic} {Variation}},
	volume = {34},
	issn = {0169-5347},
	url = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(19)30060-6},
	doi = {10.1016/j.tree.2019.02.013},
	language = {English},
	number = {7},
	urldate = {2024-03-13},
	journal = {Trends in Ecology \& Evolution},
	author = {Grummer, Jared A. and Beheregaray, Luciano B. and Bernatchez, Louis and Hand, Brian K. and Luikart, Gordon and Narum, Shawn R. and Taylor, Eric B.},
	month = jul,
	year = {2019},
	pmid = {30904190},
	note = {Publisher: Elsevier},
	keywords = {adaptive capacity, conservation, fragmentation, gene flow, riverscape genetics, seascape},
	pages = {641--654},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\Y3EL46VY\\Grummer et al. - 2019 - Aquatic Landscape Genomics and Environmental Effec.pdf:application/pdf},
}

@article{grummer_aquatic_2019-1,
	title = {Aquatic {Landscape} {Genomics} and {Environmental} {Effects} on {Genetic} {Variation}},
	volume = {34},
	issn = {1872-8383},
	doi = {10.1016/j.tree.2019.02.013},
	abstract = {Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes.},
	language = {eng},
	number = {7},
	journal = {Trends in Ecology \& Evolution},
	author = {Grummer, Jared A. and Beheregaray, Luciano B. and Bernatchez, Louis and Hand, Brian K. and Luikart, Gordon and Narum, Shawn R. and Taylor, Eric B.},
	month = jul,
	year = {2019},
	pmid = {30904190},
	keywords = {adaptive capacity, Animals, Climate, conservation, fragmentation, gene flow, Genetic Variation, Genetics, Population, Genomics, riverscape genetics, seascape, Selection, Genetic},
	pages = {641--654},
}

@article{pratt_seascape_2022,
	title = {Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity},
	volume = {31},
	issn = {1365-294X},
	doi = {10.1111/mec.16389},
	abstract = {Heterogeneous seascapes and strong environmental gradients in coastal waters are expected to influence adaptive divergence, particularly in species with large population sizes where selection is expected to be highly efficient. However, these influences might also extend to species characterized by strong social structure, natal philopatry and small home ranges. We implemented a seascape genomic study to test this hypothesis in Indo-Pacific bottlenose dolphins (Tursiops aduncus) distributed along the environmentally heterogeneous coast of southern Australia. The data sets included oceanographic and environmental variables thought to be good predictors of local adaptation in dolphins and 8081 filtered single nucleotide polymorphisms (SNPs) genotyped for individuals sampled from seven different bioregions. From a neutral perspective, population structure and connectivity of the dolphins were generally influenced by habitat type and social structuring. Genotype-environment association analysis identified 241 candidate adaptive loci and revealed that sea surface temperature and salinity gradients influenced adaptive divergence in these animals at both large- (1000 km) and fine-scales ({\textless}100 km). Enrichment analysis and annotation of candidate genes revealed functions related to sodium-activated ion transport, kidney development, adipogenesis and thermogenesis. The findings of spatial adaptive divergence and inferences of putative physiological adaptations challenge previous suggestions that marine megafauna is most likely to be affected by environmental and climatic changes via indirect, trophic effects. Our work contributes to conservation management of coastal bottlenose dolphins subjected to anthropogenic disturbance and to efforts of clarifying how seascape heterogeneity influences adaptive diversity and evolution in small cetaceans.},
	language = {eng},
	number = {8},
	journal = {Molecular Ecology},
	author = {Pratt, Eleanor A. L. and Beheregaray, Luciano B. and Bilgmann, Kerstin and Zanardo, Nikki and Diaz-Aguirre, Fernando and Brauer, Chris and Sandoval-Castillo, Jonathan and Möller, Luciana M.},
	month = apr,
	year = {2022},
	pmid = {35146819},
	keywords = {adaptive resilience, Animals, Bottle-Nosed Dolphin, cetacean, climate change, Ecosystem, environmental heterogeneity, Genomics, landscape genomics, Salinity, Temperature},
	pages = {2223--2241},
}

@article{sandoval-castillo_seascape_2018,
	title = {Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone ({Haliotis} laevigata), along a longitudinal environmental gradient},
	volume = {27},
	issn = {1365-294X},
	doi = {10.1111/mec.14526},
	abstract = {Populations of broadcast spawning marine organisms often have large sizes and are exposed to reduced genetic drift. Under such scenarios, strong selection associated with spatial environmental heterogeneity is expected to drive localized adaptive divergence, even in the face of connectivity. We tested this hypothesis using a seascape genomics approach in the commercially important greenlip abalone (Haliotis laevigata). We assessed how its population structure has been influenced by environmental heterogeneity along a zonal coastal boundary in southern Australia linked by strong oceanographic connectivity. Our data sets include 9,109 filtered SNPs for 371 abalones from 13 localities and environmental mapping across {\textasciitilde}800 km. Genotype-environment association analyses and outlier tests defined 8,786 putatively neutral and 323 candidate adaptive loci. From a neutral perspective, the species is better represented by a metapopulation with very low differentiation (global FST  = 0.0081) and weak isolation by distance following a stepping-stone model. For the candidate adaptive loci, however, model-based and model-free approaches indicated five divergent population clusters. After controlling for spatial distance, the distribution of putatively adaptive variation was strongly correlated to selection linked to minimum sea surface temperature and oxygen concentration. Around 80 candidates were annotated to genes with functions related to high temperature and/or low oxygen tolerance, including genes that influence the resilience of abalone species found in other biogeographic regions. Our study includes a documented example about the uptake of genomic information in fisheries management and supports the hypothesis of adaptive divergence due to coastal environmental heterogeneity in a connected metapopulation of a broadcast spawner.},
	language = {eng},
	number = {7},
	journal = {Molecular Ecology},
	author = {Sandoval-Castillo, Jonathan and Robinson, Nick A. and Hart, Anthony M. and Strain, Lachlan W. S. and Beheregaray, Luciano B.},
	month = apr,
	year = {2018},
	pmid = {29420852},
	keywords = {Animals, climate change, Cluster Analysis, ddRAD-seq, Discriminant Analysis, ecological genomics, Environment, Fisheries, Genetic Loci, Genetics, Population, Genomics, Genotyping Techniques, Geography, landscape genomics, marine protected areas (MPAs), Molecular Sequence Annotation, Mollusca, Polymorphism, Single Nucleotide, population connectivity, Principal Component Analysis, Regression Analysis, southern Australia},
	pages = {1603--1620},
	file = {Full Text:C\:\\Users\\ejstr\\Zotero\\storage\\6ECNECMV\\Sandoval-Castillo et al. - 2018 - Seascape genomics reveals adaptive divergence in a.pdf:application/pdf},
}



@article{brauer_roles_2018,
	title = {On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system},
	volume = {27},
	copyright = {© 2018 John Wiley \& Sons Ltd},
	issn = {1365-294X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14808},
	doi = {10.1111/mec.14808},
	abstract = {Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here, we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray–Darling Basin, Australia. We genotyped 249 rainbowfish at 17,503 high-quality SNP loci and integrated these with models of network connectivity and high-resolution environmental data within a riverscape genomics framework. We tested competing models of gene flow before using multivariate genotype–environment association (GEA) analysis to test for signals of adaptive divergence associated with hydroclimatic variation. Patterns of neutral genetic variation were consistent with expectations based on the stream hierarchy model and M. fluviatilis’ moderate dispersal ability. Models incorporating dendritic network structure suggested that landscape heterogeneity is a more important factor determining connectivity and gene flow than waterway distance. Extending these results, we also introduce a novel approach to controlling for the unique effects of dendritic network structure in GEA analyses of populations of aquatic species. We identified 146 candidate loci potentially underlying a polygenic adaptive response to seasonal fluctuations in stream flow and variation in the relative timing of temperature and precipitation extremes. Our findings underscore an emerging predominant role for seasonal variation in hydroclimatic conditions driving local adaptation and are relevant for informing proactive conservation management.},
	language = {en},
	number = {17},
	urldate = {2024-03-14},
	journal = {Molecular Ecology},
	author = {Brauer, Chris J. and Unmack, Peter J. and Smith, Steve and Bernatchez, Louis and Beheregaray, Luciano B.},
	year = {2018},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14808},
	keywords = {climate change, ddRAD-seq, dendritic networks, landscape genomics, Melanotaenia fluviatilis, Murray-Darling Basin},
	pages = {3484--3497},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\99359NPW\\Brauer et al. - 2018 - On the roles of landscape heterogeneity and enviro.pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\DPQDIG8Z\\mec.html:text/html},
}



@misc{georges_distances_2023,
	title = {Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms ({SNPs})},
	copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
	url = {https://www.biorxiv.org/content/10.1101/2023.03.22.533737v3},
	doi = {10.1101/2023.03.22.533737},
	abstract = {Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci.We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization.Euclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of their underlying models of divergence, population demographic history and linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data that depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should not be used. Careful consideration should be given to which state is scored zero when applying binary distance measures to sequence tag presence-absences (e.g. Jaccard distance).Missing values that arise in the SNP discovery process can cause displacement of affected individuals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Filtering on missing values then imputing those that remain avoids distortion in visual representations. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of individuals (e.g. inclusion of sibs) and lack of independence of both individuals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation.},
	language = {en},
	urldate = {2024-03-15},
	publisher = {bioRxiv},
	author = {Georges, Arthur and Mijangos, Luis and Kilian, Andrzej and Patel, Hardip and Aitkens, Mark and Gruber, Bernd},
	month = dec,
	year = {2023},
	note = {Pages: 2023.03.22.533737
Section: New Results},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\L98VDBMJ\\Georges et al. - 2023 - Distances and their visualization in studies of sp.pdf:application/pdf},
}

@article{battey_space_2020,
	title = {Space is the {Place}: {Effects} of {Continuous} {Spatial} {Structure} on {Analysis} of {Population} {Genetic} {Data}},
	volume = {215},
	issn = {1943-2631},
	shorttitle = {Space is the {Place}},
	url = {https://doi.org/10.1534/genetics.120.303143},
	doi = {10.1534/genetics.120.303143},
	abstract = {Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space. Here, we use simulations of populations living in continuous geography to study the impacts of dispersal and sampling strategy on population genetic summary statistics, demographic inference, and genome-wide association studies (GWAS). We find that most common summary statistics have distributions that differ substantially from those seen in well-mixed populations, especially when Wright’s neighborhood size is \< 100 and sampling is spatially clustered. “Stepping-stone” models reproduce some of these effects, but discretizing the landscape introduces artifacts that in some cases are exacerbated at higher resolutions. The combination of low dispersal and clustered sampling causes demographic inference from the site frequency spectrum to infer more turbulent demographic histories, but averaged results across multiple simulations revealed surprisingly little systematic bias. We also show that the combination of spatially autocorrelated environments and limited dispersal causes GWAS to identify spurious signals of genetic association with purely environmentally determined phenotypes, and that this bias is only partially corrected by regressing out principal components of ancestry. Last, we discuss the relevance of our simulation results for inference from genetic variation in real organisms.},
	number = {1},
	urldate = {2024-03-15},
	journal = {Genetics},
	author = {Battey, C J and Ralph, Peter L and Kern, Andrew D},
	month = may,
	year = {2020},
	pages = {193--214},
	file = {Full Text PDF:C\:\\Users\\ejstr\\Zotero\\storage\\23CPWXPI\\Battey et al. - 2020 - Space is the Place Effects of Continuous Spatial .pdf:application/pdf;Snapshot:C\:\\Users\\ejstr\\Zotero\\storage\\K9SDIJHW\\5930485.html:text/html},
}