Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby <i>Gobiosoma bosc</i>

Milá, Borja; Tassell, James L. Van; Calderón, Jatziri A.; Rüber, Lukas; Zardoya, Rafael

doi:10.1002/ece3.3161

Cited by 28 publications

(40 citation statements)

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“…different thresholds for missing sites (0.75, 0.50, 0.25 and 0.05). These filters resulted in 20 datasets (electronic supplementary material, table S4), of which six were further selected according to the amount of missing data (9-46%), number of individuals present, number of SNPs(15 112 -42 406), and number of populations(8)(9)(10)(11)(12)(13)(14)(15). Additional details on molecular protocols for de novo assembly of RAD loci are given in the electronic supplementary material.…”

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confidence: 99%

Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Pedraza-Marrón

Silva²,

Deeds

et al. 2019

Proc. R. Soc. B.

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Species delimitation is a major quest in biology and is essential for adequate management of the organismal diversity. A challenging example comprises the fish species of red snappers in the Western Atlantic. Red snappers have been traditionally recognized as two separate species based on morphology: Lutjanus campechanus (northern red snapper) and L. purpureus (southern red snapper). Recent genetic studies using mitochondrial markers, however, failed to delineate these nominal species, leading to the current lumping of the northern and southern populations into a single species ( L. campechanus ). This decision carries broad implications for conservation and management as red snappers have been commercially over-exploited across the Western Atlantic and are currently listed as vulnerable. To address this conflict, we examine genome-wide data collected throughout the range of the two species. Population genomics, phylogenetic and coalescent analyses favour the existence of two independent evolutionary lineages, a result that confirms the morphology-based delimitation scenario in agreement with conventional taxonomy. Despite finding evidence of introgression in geographically neighbouring populations in northern South America, our genomic analyses strongly support isolation and differentiation of these species, suggesting that the northern and southern red snappers should be treated as distinct taxonomic entities.

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confidence: 99%

Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Pedraza-Marrón

Silva²,

Deeds

et al. 2019

Proc. R. Soc. B.

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“…In fact, Atlantic populations of G. bosc demonstrated less noticeable differentiation among geographically spaced locations than within the Gulf of Mexico (i.e., Atlantic locations were separated by fewer sequence changes than were Gulf locations). For example, in the Gulf, geographic differentiation was much more apparent with a considerable break at Apalachicola Bay, sub-dividing the Florida panhandle in two (Mila et al 2017). In the Atlantic, it may be that the Gulf Stream is playing a role in the greater genetic connectivity (albeit still subregionally differentiated) that was detected among Atlantic populations compared to the Gulf of Mexico populations.…”

Section: Biogeography Of Us Populationsmentioning

confidence: 99%

“…Kohn & Clements 2011) like G. bosc. However, a recent study on the population genetics of naked gobies (Mila et al 2017) has provided some understanding of the large-scale phylogeographic differences throughout much of the species' range. This investigation found that G. bosc is strongly structured based on geography, particularly between Gulf vs Atlantic populations, but within those major regions, gobies are further subdivided into subclades based upon geography (e.g., East and West of the Apalachicola River along the Florida panhandle), due to biogeographic breaks that inhibit gene flow.…”

Section: Introductionmentioning

confidence: 99%

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Peer Review #1 of "Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries (v0.1)"

2018

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Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically-important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (~3 ppt to ~ 18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from Genbank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries. Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work. Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population. Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and

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“…Atlantic Florida, Gulf Florida, Louisiana, Mississippi, and Texas (Mila et al 2017). An 237 additional 9 sequences came from a study by Van Tassell et al (2015): 5 of these were from a 238 non-native population (Germany) and 4 were from the USA (Florida and the Gulf of Mexico)…”

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Peer Review #2 of "Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries (v0.1)"

2018

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Many species of fish produce larvae that undergo a prolonged dispersal phase. However, evidence from a number of recent studies on demersal fishes suggests that the dispersal of propagules may not be strongly correlated with gene flow. Instead, other factors like larval behavior and the availability of preferred settlement habitat may be more important to maintaining population structure. We used an ecologically-important benthic fish species, Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and gene flow along a salinity gradient (~3 ppt to ~ 18 ppt) in two North Carolina estuaries. G. bosc is an abundant and geographically widespread species that requires complex but patchy microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence data from Genbank to determine how North Carolina populations fit into the larger biogeographic understanding of this species. In North Carolina, we found a significant amount of gene flow within and between estuaries.Our analysis also showed high predicted genetic diversity based upon a large number of rare haplotypes found within many of our sampled populations. Moreover, we detected a number of new haplotypes in North Carolina that had not yet been observed in prior work.Sampling along a salinity gradient did not reveal any significant positive or negative correlations between salinity and genetic diversity, nor the proportion of singleton haplotypes, with the exception of a positive correlation between salinity standard deviation and genetic diversity. We also found evidence that an introduced European population of naked gobies may have originated from an Atlantic source population.Altogether, this system offers a compelling way to evaluate whether factors other than dispersal per se mediate recruitment in an estuarine-dependent species of fish with a larval dispersal phase. It also demonstrates the importance of exploring both smaller and larger scale population structure in marine organisms to better understand local and behavior and the availability of preferred settlement habitat may be more important to 47 maintaining population structure. We used an ecologically-important benthic fish species, 48Gobiosoma bosc (naked goby), to investigate local and regional scale population structure and 49 gene flow along a salinity gradient (~3 ppt to ~ 18 ppt) in two North Carolina estuaries. G. bosc 50 is an abundant and geographically widespread species that requires complex but patchy 51 microhabitat (e.g. oyster reefs, rubble, woody debris) for reproduction and refuge. We sequenced 52 155 fish from 10 sites, using a common barcoding gene (COI). We also included recent sequence

show abstract

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc

Cited by 28 publications

References 72 publications

Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation

Peer Review #1 of "Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries (v0.1)"

Peer Review #2 of "Distribution and population structure in the naked goby Gobiosoma bosc (Perciformes: Gobiidae) along a salinity gradient in two western Atlantic estuaries (v0.1)"

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