bibliography.bib

@ARTICLE{Cooke2020-qv,
  title    = "Genomic signatures in the coral holobiont reveal host adaptations
              driven by Holocene climate change and reef specific symbionts",
  author   = "Cooke, Ira and Ying, Hua and For{\^e}t, Sylvain and Bongaerts,
              Pim and Strugnell, Jan M and Simakov, Oleg and Zhang, Jia and
              Field, Matt A and Rodriguez-Lanetty, Mauricio and Bell, Sara C
              and Bourne, David G and van Oppen, Madeleine Jh and Ragan, Mark A
              and Miller, David J",
  abstract = "Genetic signatures caused by demographic and adaptive processes
              during past climatic shifts can inform predictions of species'
              responses to anthropogenic climate change. To identify these
              signatures in Acropora tenuis, a reef-building coral threatened
              by global warming, we first assembled the genome from long reads
              and then used shallow whole-genome resequencing of 150 colonies
              from the central inshore Great Barrier Reef to inform population
              genomic analyses. We identify population structure in the host
              that reflects a Pleistocene split, whereas photosymbiont
              differences between reefs most likely reflect contemporary
              (Holocene) conditions. Signatures of selection in the host were
              associated with genes linked to diverse processes including
              osmotic regulation, skeletal development, and the establishment
              and maintenance of symbiosis. Our results suggest that adaptation
              to post-glacial climate change in A. tenuis has involved
              selection on many genes, while differences in symbiont
              specificity between reefs appear to be unrelated to host
              population structure.",
  journal  = "Sci Adv",
  volume   =  6,
  number   =  48,
  month    =  nov,
  year     =  2020,
  language = "en"
}


@ARTICLE{Excoffier1992-pe,
  title    = "Analysis of molecular variance inferred from metric distances
              among {DNA} haplotypes: application to human mitochondrial {DNA}
              restriction data",
  author   = "Excoffier, L and Smouse, P E and Quattro, J M",
  abstract = "We present here a framework for the study of molecular variation
              within a single species. Information on DNA haplotype divergence
              is incorporated into an analysis of variance format, derived from
              a matrix of squared-distances among all pairs of haplotypes. This
              analysis of molecular variance (AMOVA) produces estimates of
              variance components and F-statistic analogs, designated here as
              phi-statistics, reflecting the correlation of haplotypic
              diversity at different levels of hierarchical subdivision. The
              method is flexible enough to accommodate several alternative
              input matrices, corresponding to different types of molecular
              data, as well as different types of evolutionary assumptions,
              without modifying the basic structure of the analysis. The
              significance of the variance components and phi-statistics is
              tested using a permutational approach, eliminating the normality
              assumption that is conventional for analysis of variance but
              inappropriate for molecular data. Application of AMOVA to human
              mitochondrial DNA haplotype data shows that population
              subdivisions are better resolved when some measure of molecular
              differences among haplotypes is introduced into the analysis. At
              the intraspecific level, however, the additional information
              provided by knowing the exact phylogenetic relations among
              haplotypes or by a nonlinear translation of restriction-site
              change into nucleotide diversity does not significantly modify
              the inferred population genetic structure. Monte Carlo studies
              show that site sampling does not fundamentally affect the
              significance of the molecular variance components. The AMOVA
              treatment is easily extended in several different directions and
              it constitutes a coherent and flexible framework for the
              statistical analysis of molecular data.",
  journal  = "Genetics",
  volume   =  131,
  number   =  2,
  pages    = "479--491",
  month    =  jun,
  year     =  1992,
  language = "en"
}


@ARTICLE{Waples2019-kn,
  title    = "Allele frequency-free inference of close familial relationships
              from genotypes or low-depth sequencing data",
  author   = "Waples, Ryan K and Albrechtsen, Anders and Moltke, Ida",
  abstract = "Knowledge of how individuals are related is important in many
              areas of research, and numerous methods for inferring pairwise
              relatedness from genetic data have been developed. However, the
              majority of these methods were not developed for situations where
              data are limited. Specifically, most methods rely on the
              availability of population allele frequencies, the relative
              genomic position of variants and accurate genotype data. But in
              studies of non-model organisms or ancient samples, such data are
              not always available. Motivated by this, we present a new method
              for pairwise relatedness inference, which requires neither allele
              frequency information nor information on genomic position.
              Furthermore, it can be applied not only to accurate genotype data
              but also to low-depth sequencing data from which genotypes cannot
              be accurately called. We evaluate it using data from a range of
              human populations and show that it can be used to infer close
              familial relationships with a similar accuracy as a widely used
              method that relies on population allele frequencies.
              Additionally, we show that our method is robust to SNP
              ascertainment and applicable to low-depth sequencing data
              generated using different strategies, including resequencing and
              RADseq, which is important for application to a diverse range of
              populations and species.",
  journal  = "Mol. Ecol.",
  volume   =  28,
  number   =  1,
  pages    = "35--48",
  month    =  jan,
  year     =  2019,
  keywords = "IBD; NGS; ascertainment bias; identity by descent; low-depth;
              non-model; relatedness",
  language = "en"
}


@ARTICLE{Bridge2023-mi,
  title    = "A tenuis relationship: traditional taxonomy obscures systematics
              and biogeography of the `Acropora tenuis' (Scleractinia:
              Acroporidae) species complex",
  author   = "Bridge, Tom C L and Cowman, Peter F and Quattrini, Andrea M and
              Bonito, Victor E and Sinniger, Frederic and Harii, Saki and Head,
              Catherine E I and Hung, Julia Y and Halafihi, Tuikolongahau and
              Rongo, Teina and Baird, Andrew H",
  abstract = "Abstract. Molecular phylogenetics has fundamentally altered our
              understanding of the taxonomy, systematics and biogeography of
              corals. Recently developed phylog",
  journal  = "Zool. J. Linn. Soc.",
  year     =  2023
}




@ARTICLE{Abrego2009-nn,
  title    = "Onset of algal endosymbiont specificity varies among closely
              related species of Acropora corals during early ontogeny",
  author   = "Abrego, David and VAN Oppen, Madeleine J H and Willis, Bette L",
  abstract = "Juveniles of a number of corals with horizontal transmission of
              dinoflagellate endosymbionts naturally acquire and maintain
              Symbiodinium types that differ from those found in adult
              populations. However, the duration of this early period of
              symbiont flexibility and successional changes leading to
              dominance by the characteristic adult (homologous) type are
              unknown. To document natural succession of Symbiodinium types
              within juvenile corals, we monitored Symbiodinium communities in
              juveniles of Acropora tenuis and Acropora millepora for 3.5
              years. Juveniles originating from one of three reef populations,
              characterized by differing adult coral-Symbiodinium associations,
              were raised in a common environment. In four out of five cases,
              juveniles became dominated initially by a nonhomologous adult
              type. Changes in Symbiodinium communities associated with A.
              tenuis juveniles led to the establishment of the adult homologous
              association at approximately 3.5 years of age. These changes were
              not linked to the onset of reproductive maturity, but may be
              linked to micro-environmental changes associated with vertical
              growth of juvenile corals. We hypothesize that fine-tuning of
              specificity mechanisms takes place during ontogeny in A. tenuis,
              leading to the eventual establishment of the adult homologous
              association. However, Symbiodinium communities in A. millepora
              juveniles did not change significantly over the 3.5 years,
              potentially reflecting (i) lack of specificity, (ii) more than a
              3.5-year delay in the onset of specificity, or (iii) lack of
              availability of the adult Symbiodinium type. This study
              demonstrates that juvenile corals may survive for extended
              periods of time with nonhomologous Symbiodinium types and that
              closely related species of Acropora differ in the timing of the
              onset of specificity for algal symbionts.",
  journal  = "Mol. Ecol.",
  volume   =  18,
  number   =  16,
  pages    = "3532--3543",
  month    =  aug,
  year     =  2009,
  language = "en"
}


@ARTICLE{Cruickshank2014-jr,
  title    = "Reanalysis suggests that genomic islands of speciation are due to
              reduced diversity, not reduced gene flow",
  author   = "Cruickshank, Tami E and Hahn, Matthew W",
  abstract = "The metaphor of 'genomic islands of speciation' was first used to
              describe heterogeneous differentiation among loci between the
              genomes of closely related species. The biological model proposed
              to explain these differences was that the regions showing high
              levels of differentiation were resistant to gene flow between
              species, while the remainder of the genome was being homogenized
              by gene flow and consequently showed lower levels of
              differentiation. However, the conditions under which such
              differentiation can occur at multiple unlinked loci are
              restrictive; additionally, essentially, all previous analyses
              have been carried out using relative measures of divergence,
              which can be misleading when regions with different levels of
              recombination are compared. Here, we test the model of
              differential gene flow by asking whether absolute divergence is
              also higher in the previously identified 'islands'. Using five
              species pairs for which full sequence data are available, we find
              that absolute measures of divergence are not higher in genomic
              islands. Instead, in all cases examined, we find reduced
              diversity in these regions, a consequence of which is that
              relative measures of divergence are abnormally high. These data
              therefore do not support a model of differential gene flow among
              loci, although islands of relative divergence may represent loci
              involved in local adaptation. Simulations using the program IMa2
              further suggest that inferences of any gene flow may be incorrect
              in many comparisons. We instead present an alternative
              explanation for heterogeneous patterns of differentiation, one in
              which postspeciation selection generates patterns consistent with
              multiple aspects of the data.",
  journal  = "Mol. Ecol.",
  volume   =  23,
  number   =  13,
  pages    = "3133--3157",
  month    =  jul,
  year     =  2014,
  keywords = "F ST; IM; hitchhiking; recombination; sympatric speciation",
  language = "en"
}


@ARTICLE{Malinsky2015-qq,
  title    = "Genomic islands of speciation separate cichlid ecomorphs in an
              East African crater lake",
  author   = "Malinsky, Milan and Challis, Richard J and Tyers, Alexandra M and
              Schiffels, Stephan and Terai, Yohey and Ngatunga, Benjamin P and
              Miska, Eric A and Durbin, Richard and Genner, Martin J and
              Turner, George F",
  abstract = "The genomic causes and effects of divergent ecological selection
              during speciation are still poorly understood. Here we report the
              discovery and detailed characterization of early-stage adaptive
              divergence of two cichlid fish ecomorphs in a small (700 meters
              in diameter) isolated crater lake in Tanzania. The ecomorphs
              differ in depth preference, male breeding color, body shape,
              diet, and trophic morphology. With whole-genome sequences of 146
              fish, we identified 98 clearly demarcated genomic ``islands'' of
              high differentiation and demonstrated the association of
              genotypes across these islands with divergent mate preferences.
              The islands contain candidate adaptive genes enriched for
              functions in sensory perception (including rhodopsin and other
              twilight-vision-associated genes), hormone signaling, and
              morphogenesis. Our study suggests mechanisms and genomic regions
              that may play a role in the closely related mega-radiation of
              Lake Malawi.",
  journal  = "Science",
  volume   =  350,
  number   =  6267,
  pages    = "1493--1498",
  month    =  dec,
  year     =  2015,
  language = "en"
}

@ARTICLE{Turner2005-pj,
  title    = "Genomic islands of speciation in Anopheles gambiae",
  author   = "Turner, Thomas L and Hahn, Matthew W and Nuzhdin, Sergey V",
  abstract = "The African malaria mosquito, Anopheles gambiae sensu stricto (A.
              gambiae), provides a unique opportunity to study the evolution of
              reproductive isolation because it is divided into two sympatric,
              partially isolated subtaxa known as M form and S form. With the
              annotated genome of this species now available, high-throughput
              techniques can be applied to locate and characterize the genomic
              regions contributing to reproductive isolation. In order to
              quantify patterns of differentiation within A. gambiae, we
              hybridized population samples of genomic DNA from each form to
              Affymetrix GeneChip microarrays. We found that three regions,
              together encompassing less than 2.8 Mb, are the only locations
              where the M and S forms are significantly differentiated. Two of
              these regions are adjacent to centromeres, on Chromosomes 2L and
              X, and contain 50 and 12 predicted genes, respectively. Sequenced
              loci in these regions contain fixed differences between forms and
              no shared polymorphisms, while no fixed differences were found at
              nearby control loci. The third region, on Chromosome 2R, contains
              only five predicted genes; fixed differences in this region were
              also verified by direct sequencing. These ``speciation islands''
              remain differentiated despite considerable gene flow, and are
              therefore expected to contain the genes responsible for
              reproductive isolation. Much effort has recently been applied to
              locating the genes and genetic changes responsible for
              reproductive isolation between species. Though much can be
              inferred about speciation by studying taxa that have diverged for
              millions of years, studying differentiation between taxa that are
              in the early stages of isolation will lead to a clearer view of
              the number and size of regions involved in the genetics of
              speciation. Despite appreciable levels of gene flow between the M
              and S forms of A. gambiae, we were able to isolate three small
              regions of differentiation where genes responsible for ecological
              and behavioral isolation are likely to be located. We expect
              reproductive isolation to be due to changes at a small number of
              loci, as these regions together contain only 67 predicted genes.
              Concentrating future mapping experiments on these regions should
              reveal the genes responsible for reproductive isolation between
              forms.",
  journal  = "PLoS Biol.",
  volume   =  3,
  number   =  9,
  pages    = "e285",
  month    =  sep,
  year     =  2005,
  language = "en"
}

@ARTICLE{Turner2010-wn,
  title    = "Population resequencing reveals local adaptation of Arabidopsis
              lyrata to serpentine soils",
  author   = "Turner, Thomas L and Bourne, Elizabeth C and Von Wettberg, Eric J
              and Hu, Tina T and Nuzhdin, Sergey V",
  abstract = "A powerful way to map functional genomic variation and reveal the
              genetic basis of local adaptation is to associate allele
              frequency across the genome with environmental conditions.
              Serpentine soils, characterized by high heavy-metal content and
              low calcium-to-magnesium ratios, are a classic context for
              studying adaptation of plants to local soil conditions. To
              investigate whether Arabidopsis lyrata is locally adapted to
              serpentine soil, and to map the polymorphisms responsible for
              such adaptation, we pooled DNA from individuals from serpentine
              and nonserpentine soils and sequenced each 'gene pool' with the
              Illumina Genome Analyzer. The polymorphisms that are most
              strongly associated with soil type are enriched at heavy-metal
              detoxification and calcium and magnesium transport loci,
              providing numerous candidate mutations for serpentine adaptation.
              Sequencing of three candidate loci in the European subspecies of
              A. lyrata indicates parallel differentiation of the same
              polymorphism at one locus, confirming ecological adaptation, and
              different polymorphisms at two other loci, which may indicate
              convergent evolution.",
  journal  = "Nat. Genet.",
  volume   =  42,
  number   =  3,
  pages    = "260--263",
  month    =  mar,
  year     =  2010,
  language = "en"
}



@ARTICLE{Santodomingo2015-yl,
  title     = "Fossils reveal a high diversity of the staghorn coral genera
               Acropora and Isopora (Scleractinia: Acroporidae) in the Neogene
               of Indonesia",
  author    = "Santodomingo, Nadiezhda and Wallace, Carden C and Johnson,
               Kenneth G",
  abstract  = "Abstract. Although Acropora is the most diverse and abundant
               coral genus on modern Indo-Pacific reefs, there is only limited
               understanding of its evolutionary h",
  journal   = "Zool. J. Linn. Soc.",
  publisher = "Oxford Academic",
  volume    =  175,
  number    =  4,
  pages     = "677--763",
  month     =  nov,
  year      =  2015,
  language  = "en"
}

@ARTICLE{Keightley2018-dh,
  title    = "Inferring the Probability of the Derived vs. the Ancestral
              Allelic State at a Polymorphic Site",
  author   = "Keightley, Peter D and Jackson, Benjamin C",
  abstract = "It is known that the allele ancestral to the variation at a
              polymorphic site cannot be assigned with certainty, and that the
              most frequently used method to assign the ancestral state-maximum
              parsimony-is prone to misinference. Estimates of counts of sites
              that have a certain number of copies of the derived allele in a
              sample (the unfolded site frequency spectrum, uSFS) made by
              parsimony are therefore also biased. We previously developed a
              maximum likelihood method to estimate the uSFS for a focal
              species using information from two outgroups while assuming
              simple models of nucleotide substitution. Here, we extend this
              approach to allow multiple outgroups (implemented for three
              outgroups), potentially any phylogenetic tree topology, and more
              complex models of nucleotide substitution. We find, however, that
              two outgroups and the Kimura two-parameter model are adequate for
              uSFS inference in most cases. We show that using parsimony to
              infer the ancestral state at a specific site seriously breaks
              down in two situations. The first is where the outgroups provide
              no information about the ancestral state of variation in the
              focal species. In this case, nucleotide variation will be
              underestimated if such sites are excluded. The second is where
              the minor allele in the focal species agrees with the allelic
              state of the outgroups. In this situation, parsimony tends to
              overestimate the probability of the major allele being derived,
              because it fails to account for the fact that sites with a high
              frequency of the derived allele tend to be rare. We present a
              method that corrects this deficiency and is capable of providing
              nearly unbiased estimates of ancestral state probabilities on a
              site-by-site basis and the uSFS.",
  journal  = "Genetics",
  volume   =  209,
  number   =  3,
  pages    = "897--906",
  month    =  jul,
  year     =  2018,
  keywords = "ancestral allele; derived allele; misinference; nucleotide
              polymorphism; parsimony; unfolded site frequency spectrum",
  language = "en"
}


@ARTICLE{Albers2020-vl,
  title    = "Dating genomic variants and shared ancestry in population-scale
              sequencing data",
  author   = "Albers, Patrick K and McVean, Gil",
  abstract = "The origin and fate of new mutations within species is the
              fundamental process underlying evolution. However, while much
              attention has been focused on characterizing the presence,
              frequency, and phenotypic impact of genetic variation, the
              evolutionary histories of most variants are largely unexplored.
              We have developed a nonparametric approach for estimating the
              date of origin of genetic variants in large-scale sequencing data
              sets. The accuracy and robustness of the approach is demonstrated
              through simulation. Using data from two publicly available human
              genomic diversity resources, we estimated the age of more than 45
              million single-nucleotide polymorphisms (SNPs) in the human
              genome and release the Atlas of Variant Age as a public online
              database. We characterize the relationship between variant age
              and frequency in different geographical regions and demonstrate
              the value of age information in interpreting variants of
              functional and selective importance. Finally, we use allele age
              estimates to power a rapid approach for inferring the ancestry
              shared between individual genomes and to quantify genealogical
              relationships at different points in the past, as well as to
              describe and explore the evolutionary history of modern human
              populations.",
  journal  = "PLoS Biol.",
  volume   =  18,
  number   =  1,
  pages    = "e3000586",
  month    =  jan,
  year     =  2020,
  language = "en"
}


@ARTICLE{Yi2010-br,
  title    = "Sequencing of 50 human exomes reveals adaptation to high altitude",
  author   = "Yi, Xin and Liang, Yu and Huerta-Sanchez, Emilia and Jin, Xin and
              Cuo, Zha Xi Ping and Pool, John E and Xu, Xun and Jiang, Hui and
              Vinckenbosch, Nicolas and Korneliussen, Thorfinn Sand and Zheng,
              Hancheng and Liu, Tao and He, Weiming and Li, Kui and Luo,
              Ruibang and Nie, Xifang and Wu, Honglong and Zhao, Meiru and Cao,
              Hongzhi and Zou, Jing and Shan, Ying and Li, Shuzheng and Yang,
              Qi and {Asan} and Ni, Peixiang and Tian, Geng and Xu, Junming and
              Liu, Xiao and Jiang, Tao and Wu, Renhua and Zhou, Guangyu and
              Tang, Meifang and Qin, Junjie and Wang, Tong and Feng, Shuijian
              and Li, Guohong and {Huasang} and Luosang, Jiangbai and Wang, Wei
              and Chen, Fang and Wang, Yading and Zheng, Xiaoguang and Li, Zhuo
              and Bianba, Zhuoma and Yang, Ge and Wang, Xinping and Tang,
              Shuhui and Gao, Guoyi and Chen, Yong and Luo, Zhen and Gusang,
              Lamu and Cao, Zheng and Zhang, Qinghui and Ouyang, Weihan and
              Ren, Xiaoli and Liang, Huiqing and Zheng, Huisong and Huang, Yebo
              and Li, Jingxiang and Bolund, Lars and Kristiansen, Karsten and
              Li, Yingrui and Zhang, Yong and Zhang, Xiuqing and Li, Ruiqiang
              and Li, Songgang and Yang, Huanming and Nielsen, Rasmus and Wang,
              Jun and Wang, Jian",
  abstract = "Residents of the Tibetan Plateau show heritable adaptations to
              extreme altitude. We sequenced 50 exomes of ethnic Tibetans,
              encompassing coding sequences of 92\% of human genes, with an
              average coverage of 18x per individual. Genes showing
              population-specific allele frequency changes, which represent
              strong candidates for altitude adaptation, were identified. The
              strongest signal of natural selection came from endothelial
              Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription
              factor involved in response to hypoxia. One single-nucleotide
              polymorphism (SNP) at EPAS1 shows a 78\% frequency difference
              between Tibetan and Han samples, representing the fastest allele
              frequency change observed at any human gene to date. This SNP's
              association with erythrocyte abundance supports the role of EPAS1
              in adaptation to hypoxia. Thus, a population genomic survey has
              revealed a functionally important locus in genetic adaptation to
              high altitude.",
  journal  = "Science",
  volume   =  329,
  number   =  5987,
  pages    = "75--78",
  month    =  jul,
  year     =  2010,
  language = "en"
}



@ARTICLE{Shinzato2015-rz,
  title    = "Genome-wide {SNP} analysis explains coral diversity and recovery
              in the Ryukyu Archipelago",
  author   = "Shinzato, Chuya and Mungpakdee, Sutada and Arakaki, Nana and
              Satoh, Noriyuki",
  abstract = "Following a global coral bleaching event in 1998, Acropora corals
              surrounding most of Okinawa island (OI) were devastated, although
              they are now gradually recovering. In contrast, the Kerama
              Islands (KIs) only 30 km west of OI, have continuously hosted a
              great variety of healthy corals. Taking advantage of the decoded
              Acropora digitifera genome and using genome-wide SNP analyses, we
              clarified Acropora population structure in the southern Ryukyu
              Archipelago (sRA). Despite small genetic distances, we identified
              distinct clusters corresponding to specific island groups,
              suggesting infrequent long-distance dispersal within the sRA.
              Although the KIs were believed to supply coral larvae to OI,
              admixture analyses showed that such dispersal is much more
              limited than previously realized, indicating independent recovery
              of OI coral populations and the necessity of local conservation
              efforts for each region. We detected strong historical migration
              from the Yaeyama Islands (YIs) to OI, and suggest that the YIs
              are the original source of OI corals. In addition, migration
              edges to the KIs suggest that they are a historical sink
              population in the sRA, resulting in high diversity. This
              population genomics study provides the highest resolution data to
              date regarding coral population structure and history.",
  journal  = "Sci. Rep.",
  volume   =  5,
  pages    = "18211",
  month    =  dec,
  year     =  2015,
  language = "en"
}


@ARTICLE{Mao2018, 
year = {2018}, 
title = {{The Roles of Introgression and Climate Change in the Rise to Dominance of Acropora Corals}}, 
author = {Mao, Yafei and Economo, Evan P and Satoh, Noriyuki}, 
journal = {Current Biology}, 
issn = {0960-9822}, 
doi = {10.1016/j.cub.2018.08.061}, 
pmid = {30344117}, 
abstract = {{Reef-building corals provide the structural basis for one of Earth’s most spectacular and diverse—but increasingly threatened—ecosystems. Modern Indo-Pacific reefs are dominated by species of the staghorn coral genus Acropora, but the evolutionary and ecological factors associated with their diversification and rise to dominance are unclear. Recent work on evolutionary radiations has demonstrated the importance of introgression and ecological opportunity in promoting diversification and ecological success. Here, we analyze the genomes of five staghorn coral species to examine the roles of introgression and ecological opportunity in the rise to dominance of Acropora. We found evidence for a history marked by a major introgression event as well as recurrent gene flow across species. In addition, we found that genes with topologies mismatching the species tree are evolving faster, which is suggestive of a role for introgression in spreading adaptive genetic variation. Demographic analysis showed that Acropora lineages profited from climate-driven mass extinctions in the Plio-Pleistocene, indicating that Acropora exploited ecological opportunity opened by a new climatic regime favoring species that could cope with rapid sea-level changes. Collectively, the genomes of reef-building corals have recorded an evolutionary history shaped by introgression and climate change, suggesting that Acropora—among most vulnerable corals to stressors—may be critical for understanding how reefs track the impending rapid sea-level changes of the Anthropocene.}}, 
pages = {3373--3382.e5}, 
number = {21}, 
volume = {28}, 
local-url = {file://localhost/Users/jiaz/Documents/Papers%20Library/Current%20Biology/Mao-The%20Roles%20of%20Introgression%20and%20Climate%20Change%20in%20the%20Rise%20to%20Dominance%20of%20Acropora%20Corals-2018-Current%20Biology.pdf}
}

@ARTICLE{Shinzato2020,
    author = {Shinzato, Chuya and Khalturin, Konstantin and Inoue, Jun and Zayasu, Yuna and Kanda, Miyuki and Kawamitsu, Mayumi and Yoshioka, Yuki and Yamashita, Hiroshi and Suzuki, Go and Satoh, Noriyuki},
    title = "{Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes}",
    journal = {Molecular Biology and Evolution},
    volume = {38},
    number = {1},
    pages = {16-30},
    year = {2020},
    month = {09},
    issn = {0737-4038},
    doi = {10.1093/molbev/msaa216},
    url = {https://doi.org/10.1093/molbev/msaa216},
    eprint = {https://academic.oup.com/mbe/article-pdf/38/1/16/35389303/msaa216.pdf},
}


@ARTICLE{Cowman2020-mo,
  title    = "An enhanced target-enrichment bait set for Hexacorallia provides
              phylogenomic resolution of the staghorn corals (Acroporidae) and
              close relatives",
  author   = "Cowman, Peter F and Quattrini, Andrea M and Bridge, Tom C L and
              Watkins-Colwell, Gregory J and Fadli, Nur and Grinblat, Mila and
              Roberts, T Edward and McFadden, Catherine S and Miller, David J
              and Baird, Andrew H",
  abstract = "Targeted enrichment of genomic DNA can profoundly increase the
              phylogenetic resolution of clades and inform taxonomy. Here, we
              redesign a custom bait set previously developed for the cnidarian
              class Anthozoa to more efficiently target and capture
              ultraconserved elements (UCEs) and exonic loci within the
              subclass Hexacorallia. We test this enhanced bait set (targeting
              2476 loci) on 99 specimens of scleractinian corals spanning both
              the ``complex'' (Acroporidae, Agariciidae) and ``robust''
              (Fungiidae) clades. Focused sampling in the staghorn corals
              (genus Acropora) highlights the ability of sequence capture to
              inform the taxonomy of a clade previously deficient in molecular
              resolution. A mean of 1850 ($\pm$298) loci were captured per
              taxon (955 UCEs, 894 exons), and a 75\% complete concatenated
              alignment of 96 samples included 1792 loci (991 UCE, 801 exons)
              and ~1.87 million base pairs. Maximum likelihood and Bayesian
              analyses recovered robust molecular relationships and revealed
              that species-level relationships within the Acropora are
              incongruent with traditional morphological groupings. Both UCE
              and exon datasets delineated six well-supported clades within
              Acropora. The enhanced bait set will facilitate investigations of
              the evolutionary history of many important groups of reef corals,
              particularly where previous molecular marker development has been
              unsuccessful.",
  journal  = "Mol. Phylogenet. Evol.",
  volume   =  153,
  pages    = "106944",
  month    =  dec,
  year     =  2020,
  keywords = "Exon; Phylogenetics; Scleractinia; Targeted enrichment; UCEs;
              Ultraconserved elements",
  language = "en"
}



@ARTICLE{Meisner2021-um,
  title   = "Detecting Selection in {Low-Coverage} {High-Throughput} Sequencing
             Data using Principal Component Analysis",
  author  = "Meisner, Jonas and Albrechtsen, Anders and Hangh{\o}j, Kristian",
  journal = "bioRXiv",
  year    =  2021
}



@ARTICLE{Alonge2019-yy,
  title    = "{RaGOO}: fast and accurate reference-guided scaffolding of draft
              genomes",
  author   = "Alonge, Michael and Soyk, Sebastian and Ramakrishnan, Srividya
              and Wang, Xingang and Goodwin, Sara and Sedlazeck, Fritz J and
              Lippman, Zachary B and Schatz, Michael C",
  abstract = "We present RaGOO, a reference-guided contig ordering and
              orienting tool that leverages the speed and sensitivity of
              Minimap2 to accurately achieve chromosome-scale assemblies in
              minutes. After the pseudomolecules are constructed, RaGOO
              identifies structural variants, including those spanning
              sequencing gaps. We show that RaGOO accurately orders and orients
              3 de novo tomato genome assemblies, including the widely used M82
              reference cultivar. We then demonstrate the scalability and
              utility of RaGOO with a pan-genome analysis of 103 Arabidopsis
              thaliana accessions by examining the structural variants detected
              in the newly assembled pseudomolecules. RaGOO is available open
              source at https://github.com/malonge/RaGOO .",
  journal  = "Genome Biol.",
  volume   =  20,
  number   =  1,
  pages    = "224",
  month    =  oct,
  year     =  2019,
  keywords = "Genome alignment; Genome assembly; Long-read sequencing;
              Pseudomolecule; Reference-guided; Scaffolding; Tomato",
  language = "en"
}


@ARTICLE{Yi2010-br,
  title    = "Sequencing of 50 human exomes reveals adaptation to high altitude",
  author   = "Yi, Xin and Liang, Yu and Huerta-Sanchez, Emilia and Jin, Xin and
              Cuo, Zha Xi Ping and Pool, John E and Xu, Xun and Jiang, Hui and
              Vinckenbosch, Nicolas and Korneliussen, Thorfinn Sand and Zheng,
              Hancheng and Liu, Tao and He, Weiming and Li, Kui and Luo,
              Ruibang and Nie, Xifang and Wu, Honglong and Zhao, Meiru and Cao,
              Hongzhi and Zou, Jing and Shan, Ying and Li, Shuzheng and Yang,
              Qi and {Asan} and Ni, Peixiang and Tian, Geng and Xu, Junming and
              Liu, Xiao and Jiang, Tao and Wu, Renhua and Zhou, Guangyu and
              Tang, Meifang and Qin, Junjie and Wang, Tong and Feng, Shuijian
              and Li, Guohong and {Huasang} and Luosang, Jiangbai and Wang, Wei
              and Chen, Fang and Wang, Yading and Zheng, Xiaoguang and Li, Zhuo
              and Bianba, Zhuoma and Yang, Ge and Wang, Xinping and Tang,
              Shuhui and Gao, Guoyi and Chen, Yong and Luo, Zhen and Gusang,
              Lamu and Cao, Zheng and Zhang, Qinghui and Ouyang, Weihan and
              Ren, Xiaoli and Liang, Huiqing and Zheng, Huisong and Huang, Yebo
              and Li, Jingxiang and Bolund, Lars and Kristiansen, Karsten and
              Li, Yingrui and Zhang, Yong and Zhang, Xiuqing and Li, Ruiqiang
              and Li, Songgang and Yang, Huanming and Nielsen, Rasmus and Wang,
              Jun and Wang, Jian",
  abstract = "Residents of the Tibetan Plateau show heritable adaptations to
              extreme altitude. We sequenced 50 exomes of ethnic Tibetans,
              encompassing coding sequences of 92\% of human genes, with an
              average coverage of 18x per individual. Genes showing
              population-specific allele frequency changes, which represent
              strong candidates for altitude adaptation, were identified. The
              strongest signal of natural selection came from endothelial
              Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription
              factor involved in response to hypoxia. One single-nucleotide
              polymorphism (SNP) at EPAS1 shows a 78\% frequency difference
              between Tibetan and Han samples, representing the fastest allele
              frequency change observed at any human gene to date. This SNP's
              association with erythrocyte abundance supports the role of EPAS1
              in adaptation to hypoxia. Thus, a population genomic survey has
              revealed a functionally important locus in genetic adaptation to
              high altitude.",
  journal  = "Science",
  volume   =  329,
  number   =  5987,
  pages    = "75--78",
  month    =  jul,
  year     =  2010,
  language = "en"
}



@ARTICLE{Ceballos2018-sx,
  title    = "Runs of homozygosity: windows into population history and trait
              architecture",
  author   = "Ceballos, Francisco C and Joshi, Peter K and Clark, David W and
              Ramsay, Mich{\`e}le and Wilson, James F",
  abstract = "Long runs of homozygosity (ROH) arise when identical haplotypes
              are inherited from each parent and thus a long tract of genotypes
              is homozygous. Cousin marriage or inbreeding gives rise to such
              autozygosity; however, genome-wide data reveal that ROH are
              universally common in human genomes even among outbred
              individuals. The number and length of ROH reflect individual
              demographic history, while the homozygosity burden can be used to
              investigate the genetic architecture of complex disease. We
              discuss how to identify ROH in genome-wide microarray and
              sequence data, their distribution in human populations and their
              application to the understanding of inbreeding depression and
              disease risk.",
  journal  = "Nat. Rev. Genet.",
  volume   =  19,
  number   =  4,
  pages    = "220--234",
  month    =  apr,
  year     =  2018,
  language = "en"
}


@ARTICLE{Smith2018-xt,
  title    = "Estimating Time to the Common Ancestor for a Beneficial Allele",
  author   = "Smith, Joel and Coop, Graham and Stephens, Matthew and Novembre,
              John",
  abstract = "The haplotypes of a beneficial allele carry information about its
              history that can shed light on its age and the putative cause for
              its increase in frequency. Specifically, the signature of an
              allele's age is contained in the pattern of variation that
              mutation and recombination impose on its haplotypic background.
              We provide a method to exploit this pattern and infer the time to
              the common ancestor of a positively selected allele following a
              rapid increase in frequency. We do so using a hidden Markov model
              which leverages the length distribution of the shared ancestral
              haplotype, the accumulation of derived mutations on the ancestral
              background, and the surrounding background haplotype diversity.
              Using simulations, we demonstrate how the inclusion of
              information from both mutation and recombination events increases
              accuracy relative to approaches that only consider a single type
              of event. We also show the behavior of the estimator in cases
              where data do not conform to model assumptions, and provide some
              diagnostics for assessing and improving inference. Using the
              method, we analyze population-specific patterns in the 1000
              Genomes Project data to estimate the timing of adaptation for
              several variants which show evidence of recent selection and
              functional relevance to diet, skin pigmentation, and morphology
              in humans.",
  journal  = "Mol. Biol. Evol.",
  volume   =  35,
  number   =  4,
  pages    = "1003--1017",
  month    =  apr,
  year     =  2018,
  language = "en"
}

@ARTICLE{Voight2006,
  title    = "A Map of Recent Positive Selection in the Human Genome",
  author   = "Voight, Benjamin F AND Kudaravalli, Sridhar AND Wen, Xiaoquan AND Pritchard, Jonathan K",
  abstract = "The identification of signals of very recent positive selection provides information about the adaptation of modern humans to local conditions. We report here on a genome-wide scan for signals of very recent positive selection in favor of variants that have not yet reached fixation. We describe a new analytical method for scanning single nucleotide polymorphism (SNP) data for signals of recent selection, and apply this to data from the International HapMap Project. In all three continental groups we find widespread signals of recent positive selection. Most signals are region-specific, though a significant excess are shared across groups. Contrary to some earlier low resolution studies that suggested a paucity of recent selection in sub-Saharan Africans, we find that by some measures our strongest signals of selection are from the Yoruba population. Finally, since these signals indicate the existence of genetic variants that have substantially different fitnesses, they must indicate loci that are the source of significant phenotypic variation. Though the relevant phenotypes are generally not known, such loci should be of particular interest in mapping studies of complex traits. For this purpose we have developed a set of SNPs that can be used to tag the strongest ∼250 signals of recent selection in each population.",
  journal  = "PLOS Biology",
  volume   =  4,
  number   =  3,
  pages    = "",
  month    =  mar,
  year     =  2006,
  language = "en"
}

@ARTICLE{Dixon2015-xa,
  title    = "{CORAL} {REEFS}. Genomic determinants of coral heat tolerance
              across latitudes",
  author   = "Dixon, Groves B and Davies, Sarah W and Aglyamova, Galina A and
              Meyer, Eli and Bay, Line K and Matz, Mikhail V",
  abstract = "As global warming continues, reef-building corals could avoid
              local population declines through ``genetic rescue'' involving
              exchange of heat-tolerant genotypes across latitudes, but only if
              latitudinal variation in thermal tolerance is heritable. Here, we
              show an up-to-10-fold increase in odds of survival of coral
              larvae under heat stress when their parents come from a warmer
              lower-latitude location. Elevated thermal tolerance was
              associated with heritable differences in expression of oxidative,
              extracellular, transport, and mitochondrial functions that
              indicated a lack of prior stress. Moreover, two genomic regions
              strongly responded to selection for thermal tolerance in
              interlatitudinal crosses. These results demonstrate that
              variation in coral thermal tolerance across latitudes has a
              strong genetic basis and could serve as raw material for natural
              selection.",
  journal  = "Science",
  volume   =  348,
  number   =  6242,
  pages    = "1460--1462",
  month    =  jun,
  year     =  2015,
  language = "en"
}