Gene markers for exon capture and phylogenomics in ray‐finned fishes

Jiang, Jiamei; Yuan, Hao; Zheng, Xin; Wang, Qian; Kuang, Tingyun; Li, Jingyan; Liu, Junning; Song, Shuli; Wang, Weicai; Cheng, Fangyuan; Li, Hongjie; Huang, Junman; Li, Chenhong

doi:10.1002/ece3.5026

Cited by 21 publications

(22 citation statements)

References 73 publications

(134 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Popular markers used in fish phylogenomic studies include ultra‐conserved elements (UCEs) (Alfaro et al., 2018; Chakrabarty et al., 2017; Faircloth et al., 2012, 2013, 2020; Friedman et al., 2019; Harrington et al., 2016; Longo et al., 2017; Roxo et al., 2019), exon capture (Arcila et al., 2017; Betancur‐R et al., 2019; Ilves & López‐Fernández, 2014; Ilves et al., 2017; Jiang et al., 2019; Song et al., 2017), and anchored hybrid enrichment (AHE) approaches (Dornburg et al., 2017; Eytan et al., 2015; Irisarri et al., 2018; Lemmon et al., 2012; Stout et al., 2016). Still, most genome‐scale markers targeted for fish phylogenetics have so far been selected based on the comparison of a limited number of model genomes and some threshold of similarity to define them as “single‐copy” (Li et al., 2007).…”

Section: Introductionmentioning

confidence: 99%

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Hughes

Ortı́

Saad

et al. 2020

Molecular Ecology Resources

Self Cite

View full text Add to dashboard Cite

Exon markers have a long history of use in phylogenetics of ray‐finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target‐capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon‐capture sequence data into an existing data matrix of 1,104 exons and 300 ray‐finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target‐capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR‐generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR‐based exon and mitochondrial data.

show abstract

Section: Introductionmentioning

confidence: 99%

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Hughes

Ortı́

Saad

et al. 2020

Molecular Ecology Resources

Self Cite

View full text Add to dashboard Cite

show abstract

“…Phylogenetic inference relies 100 on the analysis of orthologs, but loci implemented so far for analyses were based on the 101 comparison of a limited number of model genomes and some threshold of similarity to define 102 them as "single-copy" (Li et al 2007). A recent study implementing an explicit tree-based 103 filtering method to test for orthology revealed that one third of the 'single-copy' exons >200 bp 104 in length identified by Jiang et al (2019) were affected by paralogy, potentially biasing tree 105 inference (Hughes et al 2018). A set of 1,105 exons free of vertebrate and teleost WGD-derived 106 paralogs identified in this study resolved the phylogeny with confidence for more than 300 107 species of ray-finned fishes.…”

mentioning

confidence: 79%

“…This improvement in laboratory techniques has resulted in a number of studies using sequence 84 capture to target exons for fish phylogenomics ( resources for fishes has allowed for the comparison of a larger number of genomes for probe 88 design , and ultimately eight ray-finned fish genomes were used to identify 89 >17,000 'single-copy' exons (Song et al 2017) using a modification of the reciprocal BLAST 90 approach of Li et al (2007). A subset (4,434) of these were optimized for capture across all ray-91 5 finned fishes (Jiang et al 2019). Other sets of exon probes have been designed to target more 92 specific groups including cichlids (Ilves & López-Fernández 2014), and otophysans (Arcila et al 93 2017).…”

mentioning

confidence: 99%

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Hughes

Ortı́

Saad

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

24Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse 25 clade of vertebrates with more than 35,000 species. As the number of published genomes 26 increases, it has become easier to test exons and other genetic markers for signals of ancient 27 duplication events and filter out paralogs that can mislead phylogenetic analysis. We present 28 seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons 29 explicitly filtered for paralogs using gene trees. These seven probe sets span the diversity of 30 teleost fishes, including four sets that target five hyper-diverse percomorph clades which 31 together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + 32 Pelagiaria combined). We additionally included probes to capture exon markers that have been 33 commonly used in fish phylogenetics, despite some being flagged for paralogs, to facilitate 34 integration of old and new molecular phylogenetic matrices. We tested these probes and merged 35 new exon-capture sequence data into an existing data matrix of 1,105 exons and 300 ray-finned 36 fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data 37 from raw reads to alignments for downstream analysis. We show that loci with known paralogs 38 are at risk of assembling duplicated sequences with target-capture, but we also assembled many 39 useful orthologous sequences. These probe sets are a valuable resource for advancing fish 40 phylogenomics because they can be easily extracted from increasingly available whole genome 41 and transcriptome datasets, and also may be integrated with existing PCR-based exon and 42 mitochondrial datasets. 43 44 Exon markers have played a pivotal role in resolving phylogenetic relationships among ray-46 finned fishes (Li et al. 2007;Near et al. 2012;Betancur-R. et al. 2013;Betancur-R et al. 2017; 47 Hughes et al. 2018;Rabosky et al. 2018). Identification of these exons has typically involved the 48 comparison of a small number of fish model genomes. For example, a suite of 154 single-copy 49 exons conserved enough for PCR amplification was identified by Li et al. (2007). This study 50 used a reciprocal BLAST approach on two genomes, the pufferfish Takifugu rubripes and the 51 zebrafish Danio rerio, with 10 exons initially optimized with PCR primers for sequencing (Li et 52 al. 2007). These exons demonstrated their utility for resolving previously enigmatic relationships 53 among fishes (Li et al. 2008), and were the basis for largescale reappraisals of the ray-finned fish 54

show abstract

“…A suite of 4,434 target loci were developed for ray‐finned fishes by Jiang et al (). Sequences of the 4,434 loci of two clupeiform species, Denticeps clupeoides and Ilisha elongata , collected in our previous experiments were used in designing RNA baits.…”

Section: Methodsmentioning

confidence: 99%

“…The DNA samples were sheared using a Covaris M220 sonica- A suite of 4,434 target loci were developed for ray-finned fishes by Jiang et al (2019). Sequences of the 4,434 loci of two clupeiform F I G U R E 2 Geographic range of each population (circles) and collection sites (dots) at: Lake Dongting (DT), Lake Poyang (PY), Lake Nanyi (NY), Lake Tai (TH), Luan (LA), Lake Chao (CH), Lake Hongze (HZ), Lake Gaoyou (GY), main channels, and estuary area of the Yangtze River at Chongming, Luchao, and Jingjiang (SH) ).…”

Section: Dna Library Preparation Gene Capture and Sequencingmentioning

confidence: 99%

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River

Cheng

Wang

Delser

et al. 2019

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F‐DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.

show abstract

Gene markers for exon capture and phylogenomics in ray‐finned fishes

Cited by 21 publications

References 73 publications

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River

Contact Info

Product

Resources

About