Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

Rincón-Sandoval, Melissa; Betancur‐R, Ricardo; Maldonado‐Ocampo, Javier A.

doi:10.1111/mec.15036

Cited by 35 publications

(33 citation statements)

References 152 publications

(289 reference statements)

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“…Comparing divergence histories (e.g. population sizes, timing of separation and whether and to what degree gene flow is occurring) among multiple diverging lineages in a common geographic framework is a powerful approach to understand both the patterns and the underlying processes of divergence (Campbell, Braile, & Winker, 2016; Peñalba et al, 2019; Rincon‐Sandoval, Betancur‐R, & Maldonado‐Ocampo, 2019; Smith, Harvey, Faircloth, Glenn, & Brumfield, 2014). This comparative approach is most effective in a common molecular framework, when a large number of orthologous markers are used, because orthology facilitates comparability among data sets and direct comparisons of parameters among lineages (Harvey, Smith, Glenn, Faircloth, & Brumfield, 2016; Smith et al., 2014).…”

Section: Methodsmentioning

confidence: 99%

Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

et al. 2020

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Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia.

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Section: Methodsmentioning

confidence: 99%

Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

et al. 2020

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“…However, a handful of genetic markers is not appropriate for inferring fine-scale population structure and genetic differentiation, especially in cryptic species (Struck et al, 2018;Pedraza-Marrón et al, 2019). Recent rapid developments in nextgeneration sequencing (NGS) have provided many extraordinary tools with which to study population divergence (Davey et al, 2011;Xu et al, 2016;Clucas et al, 2018;Friedline et al, 2019;Rincon-Sandoval et al, 2019;Vendrami et al, 2019). The genotyping-by-sequencing (GBS) technique can rapidly generate considerable numbers of genome-wide genetic markers, which has revolutionized the field of ecological and evolutionary genomics (Elshire et al, 2012;Andrews et al, 2016;Hume et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

et al. 2020

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The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

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“…They are relatively easy to align, and a number of software programs have 72 been developed for reading frame-aware alignment (Abascal et al 2010; Ranwez et al 2011, 73 2018), avoiding potential homology errors with UCE flanking regions that are more difficult to 74 align (Edwards et al 2017). Both protein and nucleotide sequences can be used for phylogenetic 75 inference, making them useful for deep (Hughes et al 2018) and shallow phylogenetic scales 76 (Rincon-Sandoval et al 2019). Exon markers are also easy to integrate with both genomic and 77 transcriptomic data, with sequences being produced and archived for a variety of studies from 78 comparative genomics to gene expression analysis that can provide resources for systematists to 79 increase taxon sampling without incurring additional costs.…”

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confidence: 99%

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

Hughes

Ortı́

Saad

et al. 2020

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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

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Comparative phylogeography of trans‐Andean freshwater fishes based on genome‐wide nuclear and mitochondrial markers

Cited by 35 publications

References 152 publications

Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

Divergence, gene flow, and speciation in eight lineages of trans‐Beringian birds

Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China

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

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