Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

Puritz, Jonathan B.; Addison, Jason A.; Toonen, Robert J.

doi:10.1371/journal.pone.0034241

Cited by 46 publications

(45 citation statements)

References 44 publications

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“…The intron in Glucose-6-Phosphate Isomerase (GPI) was 324 bp long in each species, and sequenced in both the forward and reverse direction. The allelic state of heterozygotes were inferred by matching multiple peak chromatograms to alleles recovered from homozygous individuals, and this approach has been confirmed using next-gen sequencing [35]. All singleton alleles were confirmed by a second amplification and sequencing.…”

Section: Methodsmentioning

confidence: 89%

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

et al. 2012

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Life history plays a critical role in governing microevolutionary processes such as gene flow and adaptation, as well as macroevolutionary processes such speciation. Here, we use multilocus phylogeographic analyses to examine a speciation event involving spectacular life-history differences between sister species of sea stars. Cryptasterina hystera has evolved a suite of derived life-history traits (including internal self-fertilization and brood protection) that differ from its sister species Cryptasterina pentagona, a gonochoric broadcast spawner. We show that these species have only been reproductively isolated for approximately 6000 years (95% highest posterior density of 905-22 628), and that this life-history change may be responsible for dramatic genetic consequences, including low nucleotide diversity, zero heterozygosity and no gene flow. The rapid divergence of these species rules out some mechanisms of isolation such as adaptation to microhabitats in sympatry, or slow divergence by genetic drift during prolonged isolation. We hypothesize that the large phenotypic differences between species relative to the short divergence time suggests that the lifehistory differences observed may be direct responses to disruptive selection between populations. We speculate that local environmental or demographic differences at the southern range margin are possible mechanisms of selection driving one of the fastest known marine speciation events.

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Section: Methodsmentioning

confidence: 89%

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

et al. 2012

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“…In such cases, it is often unclear whether the lack of resolution is a result of power, methodological limitations, or a true lack of any population differentiation (Ryman et al 2006, Lowe and Allendorf 2010, Marko and Hart 2011; Table 2). The emerging field of high-throughput next-generation sequencing shows extreme promise in facilitating broader phylogeographic studies (e.g., Puritz et al 2012), the evolution of mating systems (e.g., Hart 2012), adaptation (e.g., Stapley et al 2010), and has been shown to resolve very recent divergence between marine and freshwater fish populations following an initial colonization event <150 yrs ago (Czesny et al 2012). In the Indo-Pacific region, next-generation sequencing has had a number of interesting applications and an exciting future; this is reviewed in more detail by Willette et al (2014).…”

Section: Discussionmentioning

confidence: 99%

The application of genetics to marine management and conservation: examples from the Indo-Pacific

Heyden¹,

Beger²,

Toonen³

et al. 2014

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ABSTRACT.-Molecular tools and analyses have played pivotal roles in uncovering the processes and patterns of biodiversity in the Indian and Pacific oceans. However, integrating genetic results into management and conservation objectives has been challenging, with few examples that show practical applicability. This review aims to address some of the perceived barriers to an enhanced approach that integrates molecular data into management and conservation goals, by reviewing papers relevant to both conservation and fisheries management in the Indo-Pacific region, particularly with respect to phylogeography, connectivity, and species identification, as well as stock delineation, restoration of depleted wild stocks, mislabeled marine resources and "molecular forensics." We also highlight case studies from each of these areas that illustrate how molecular analyses are relevant to conservation and management in the IndoPacific, spanning a variety of vertebrate and invertebrate species. We discuss the application of genetic data to the design and evaluation of the effectiveness of marine protected area networks, stock delineation, and restoration and the usage of exclusion tests and parentage analyses for fisheries management. We conclude that there is a distinct need for increasing public awareness and ownership of genetically unique lineages and, ultimately, the increased inclusion of genetic research into management policy and conservation. Finally, we make a case for the importance of clear and effective communication for promoting public awareness, public ownership, and for achieving conservation goals within the region.

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“…With the advent of massively parallel "next generation" sequencing it is now possible to generate genomic data and assess phylogeography on scales never before considered (e.g., Puritz et al 2012a). We can now survey entire nuclear, mitochondrial, and chloroplast genomes, and even the expression of genomes (Carstens et al 2012).…”

Section: A Brief Historymentioning

confidence: 99%

Phylogeography unplugged: comparative surveys in the genomic era

Bowen¹,

Shanker²,

Yasuda³

et al. 2014

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ABSTRACT.-In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the IndoPacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional ("unplugged") approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.

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Next-Generation Phylogeography: A Targeted Approach for Multilocus Sequencing of Non-Model Organisms

Cited by 46 publications

References 44 publications

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

Extraordinarily rapid life-history divergence between Cryptasterina sea star species

The application of genetics to marine management and conservation: examples from the Indo-Pacific

Phylogeography unplugged: comparative surveys in the genomic era

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