Sea surface temperature, rather than land mass or geographic distance, may drive genetic differentiation in a species complex of highly dispersive seabirds

Torres, Lucas; Pante, Eric; González‐Solís, Jacob; Viricel, Amélia; Ribout, Cécile; Zino, Francis; MacKin, Will; Precheur, Carine; Tourmetz, Julie; Calabrese, Licia; Militão, Teresa; Zango, Laura; Shirihai, Hadoram; Bretagnolle, Vincent

doi:10.1002/ece3.8180

Cited by 6 publications

(21 citation statements)

References 130 publications

(166 reference statements)

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“…2.1. DNA extraction, PCR amplification and sequencing of mitochondrial and numt loci Our dataset is an extension of a companion study [30], in which blood samples from a total of 228 individuals were obtained from Puffinus lheminieri and P. bailloni shearwaters, totalling 13 different royalsocietypublishing.org/journal/rsos R. Soc. Open Sci.…”

Section: Methodsmentioning

confidence: 99%

“…Digestion of linear DNA is an efficient way of removing numts when only orthologous mtDNA is desired [30] but has the drawback of requiring a substantial amount of DNA (starting with 1 µg of gDNA usually resulted in trace amounts of circular mtDNA post-exonuclease digestion). If mtDNA is fragmented, it will be digested as nuclear DNA.…”

Section: Avoiding the Coamplification Of Numtsmentioning

confidence: 99%

“…They found that primer specificity does not correlate with lower numt coamplification, numt age or background noise in Sanger sequencing of PCR products (ambiguities). Our study originally started using primers designed specifically for the Puffinus genus, based on publicly available sequences [30]; this strategy did not prevent us from hitting numts. Likewise, Deane [73] used copy-specific primers to amplify the CR and found ambiguities nevertheless.…”

Section: Avoiding the Coamplification Of Numtsmentioning

confidence: 99%

“…In this study, we use the petrel species complex Puffinus lherminieri, in which all three problems occur simultaneously [23,30], as a worst-case scenario to investigate the effects of amalgamating mitochondrial loci and their paralogues when attempting to estimate genetic diversity, divergence and differentiation within and among populations. Numts corresponding to several mitochondrial loci were recently detected in this group [30]. Moreover, this species is one of the many Procellariiformes that show a duplicated region in the mitochondrial genome [19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

“…Our first aim consisted of evaluating the impact of these multiple copies on population-level statistics routinely used in genetic analyses, while our second aim consisted of evaluating to which extent numts affect the evolutionary scenarios obtained from mitochondrial sequences. We chose to target cytochrome-b ( mt-cytb ) because this mitochondrial gene is informative at the phylogeographic scale in this group of shearwaters [30] and has been a marker of choice for many seabird species (e.g. electronic supplementary material, table S1).…”

Section: Introductionmentioning

confidence: 99%

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Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

2022

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Mitochondrial DNA (mtDNA) translocated into the nuclear genome (numt), when co-analysed with genuine mtDNA, could plague phylogeographic studies. To evaluate numt-related biases in population genetics parameters in birds, which are prone to accumulating numts, we targeted the mitochondrial mt-cytb gene. We looked at 13 populations of Audubon's shearwater ( Puffinus lherminieri ), including five mitochondrial lineages. mt-cytb homologue and paralogue (numt) sequences were determined by Sanger sequencing with and without prior exonuclease digestion of nuclear DNA. Numts formed monophyletic clades corresponding to three of the five mitochondrial lineages tested (the remaining two forming a paraphyletic group). Nineteen percent of numt alleles fell outside of their expected mitochondrial clade, a pattern consistent with multiple translocation events, incomplete lineage sorting (ILS), and/or introgression. When co-analysing mt-cytb paralogues and homologues, excluding individuals with ambiguities underestimates genetic diversity (4%) and differentiation (11%) among least-sampled populations. Removing ambiguous sites drops the proportion of inter-lineage genetic variance by 63%. While co-analysing numts with mitochondrial sequences can lead to severe bias and information loss in bird phylogeographic studies, the separate analysis of genuine mitochondrial loci and their nuclear paralogues can shed light on numt molecular evolution, as well as evolutionary processes such as ILS and introgression.

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Section: Methodsmentioning

confidence: 99%

Section: Avoiding the Coamplification Of Numtsmentioning

confidence: 99%

Section: Avoiding the Coamplification Of Numtsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

2022

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Genetic–environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet (Cerorhinca monocerata) breeding colonies

Graham,

Hipfner,

Wellband

et al. 2024

Ecology and Evolution

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Animals are strongly connected to the environments they live in and may become adapted to local environments. Examining genetic–environment associations of key indicator species, like seabirds, provides greater insights into the forces that drive evolution in marine systems. Here we examined a RADseq dataset of 19,213 SNPs for 99 rhinoceros auklets (Cerorhinca monocerata) from five western Pacific and 10 eastern Pacific breeding colonies. We used partial redundancy analyses to identify candidate adaptive loci and to quantify the effects of environmental variation on population genetic structure. We identified 262 candidate adaptive loci, which accounted for 3.0% of the observed genetic variation among western Pacific and eastern Pacific breeding colonies. Genetic variation was more strongly associated with pH and maximum current velocity, than maximum sea surface temperature. Genetic–environment associations explain genetic differences between western and eastern Pacific populations; however, genetic variation within the western and eastern Pacific Ocean populations appears to follow a pattern of isolation‐by‐distance. This study represents a first to quantify the relationship between environmental and genetic variation for this widely distributed marine species and provides greater insights into the evolutionary forces that act on marine species.

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Isolation and characterization of 50 microsatellite loci for two shearwater species, Ardenna pacifica and Puffinus bailloni

et al. 2022

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BackgroundShearwaters (order Procellariiformes) are an excellent study system to investigate the genetic consequences of the co-called "seabird paradox", as they are able to disperse long distances but many species exhibit natal and breeding philopatry. However, few microsatellite markers are currently available for these taxa, hampering genetic inferences. Methods and resultsIn this study, 25 novel microsatellite loci were isolated and characterized for each of two distantly related shearwater species: the wedge-tailed shearwater (Ardenna pacifica) and the tropical shearwater (Puffinus bailloni). Polymorphism tests were performed for a total of 91 A. pacifica individuals sampled at Reunion and Round Island, and 48 P. bailloni individuals from Reunion and Europa Island, in the western Indian Ocean. The analyses revealed 23 polymorphic loci for A. pacifica, with the number of alleles per locus (Na) ranging from 2 to 8 (mean = 3.957 ± 0.364). Nineteen polymorphic loci were found for P. bailloni, with Na varying from two to five (mean = 3.053 ± 0.247). The observed heterozygosity (Ho) was relatively low for the two species, with Ho ranging from 0.022 to 0.725 (mean = 0.326 ± 0.044) for A. pacifica and from 0.021 to 0.688 (mean = 0.271 ± 0.051) for P. bailloni, but comparable to the estimates available for other Puffinus species.Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site. ConclusionsThe new microsatellite loci provide a valuable tool for further population genetic studies, and will allow for design of effective conservation and management plans for A. pacifica, P. bailloni and other closelyrelated species.

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Sea surface temperature, rather than land mass or geographic distance, may drive genetic differentiation in a species complex of highly dispersive seabirds

Cited by 6 publications

References 130 publications

Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

Translocation of mitochondrial DNA into the nuclear genome blurs phylogeographic and conservation genetic studies in seabirds

Genetic–environment associations explain genetic differentiation and variation between western and eastern North Pacific rhinoceros auklet (Cerorhinca monocerata) breeding colonies

Isolation and characterization of 50 microsatellite loci for two shearwater species, Ardenna pacifica and Puffinus bailloni

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