A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad

Coscia, Ilaria; McDevitt, Allan D.; King, James J.; Roche, William K.; McLoughlin, Carol; Mariani, Stefano

doi:10.1016/j.ympev.2013.07.029

Cited by 10 publications

(7 citation statements)

References 24 publications

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“…Available sequences of mitochondrial genes' fragments from the 16s, D‐loop, Cytb, COI, and NADH genes were retrieved from GenBank database (Coscia et al, , ; Faria, Weiss, & Alexandrino, , ; Geiger et al, ; Jolly et al, , ; Keskin & Atar, ; Sotelo et al, ) and aligned in Geneious 11.1.4 (Kearse et al, ). The alignment was checked for specifically fixed SNP sites, and 48 primer pairs for polymerase chain reaction (PCR) amplifications were initially designed using the Primer3web version 4.1.0 (Untergasser et al, ).…”

Section: Methodsmentioning

confidence: 99%

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Taillebois¹,

Sabatino

Manicki³

et al. 2019

Evolutionary Applications

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Hybridization dynamics between co‐occurring species in environments where human‐mediated changes take place are important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations' abundance threatens its persistence. The main objective was to evaluate the extent of hybridization and introgression between those interacting species. We developed a set of 77 species‐specific SNP loci that allowed a better resolution than morphological traits as they enabled the detection of hybrids up to the third generation. Variable rates of contemporary hybridization and introgression patterns were detected in 12 studied sites across the French Atlantic coast. Mitochondrial markers revealed a cyto‐nuclear discordance almost invariably involving A. alosa individuals with an A. fallax mitochondrial DNA and provided evidence of historical asymmetric introgression. Overall, contemporary and historical introgression revealed by nuclear and mitochondrial markers strongly suggests that a transfer of genes occurs from A. fallax toward A. alosa genome since at least four generations. Moreover, the outcomes of introgression greatly depend on the catchments where local processes are thought to occur. Undoubtedly, interspecific interaction and gene flow should not be overlooked when considering the management of those species.

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Section: Methodsmentioning

confidence: 99%

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Taillebois¹,

Sabatino

Manicki³

et al. 2019

Evolutionary Applications

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“…In addition, several recent studies have incorporated molecular taxonomy to investigate species‐level differentiation within clupeids (Faria et al , ; Boyadzhieva‐Doychinova et al , ; Czesny et al , ; DiBattista et al , ; Randall & DiBattista, ; Coscia et al , ; Chiesa et al , ), some focusing on the species of Sardinella of the IWP (Ying et al , ; Willette & Santos, ; Thomas et al , ; Willette et al , ). Several recent phylogenetic studies have rejected monophyly for the whole genus, while confirming a monophyletic grouping for each of the subgenera [see Fig.…”

Section: Introductionmentioning

confidence: 99%

Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo‐West Pacific Ocean

Stern

Rinkevich

Goren

2016

Journal of Fish Biology

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To deal with the difficulties of species differentiation and delimitation among the commercially important sardines from the genus Sardinella, an integrative approach was adopted, incorporating traditional taxonomy with four DNA markers (coI, cytb, 16s and nuclear rag2). Combining these methodologies has enabled a thorough re-description of three of the most common species of Sardinella of the Indo-west Pacific Ocean: white sardinella Sardinella albella, fringescale sardinella Sardinella fimbriata and the goldstripe sardinella Sardinella gibbosa, as well as a description of a new species, Gon's sardinella Sardinella goni, from the island of Boracay, Philippines. In addition, extensive widespread sampling of S. gibbosa reveals a significant genetic separation between the populations from the western Indian Ocean and the west Pacific Ocean, despite no supporting morphological differentiation. An updated morphological key of the species of Sardinella of the Indo-west Pacific Ocean is also provided in order to minimize future misidentifications within these economically important taxa. Finally, the genetic and morphological variabilities within and between the investigated species are used to discuss their biogeographical distribution and possible processes of speciation.

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“…killarnensis ), and Greece ( A . macedonica ) and naturally diverged sometimes during the last 30 thousand years after the retreat of the last Pleistocene glaciers (Coscia et al, 2013 ; Faria et al, 2012 ). The phenotypic changes observed in these freshwater shad appear to reflect this difference in divergence time.…”

Section: Introductionmentioning

confidence: 99%

The genetics of adaptation in freshwater Eurasian shad (Alosa)

Sabatino

Pereira

Carneiro

et al. 2022

Ecology and Evolution

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Studying the genetics of phenotypic convergence can yield important insights into adaptive evolution. Here, we conducted a comparative genomic study of four lineages (species and subspecies) of anadromous shad ( Alosa ) that have independently evolved life cycles entirely completed in freshwater. Three naturally diverged ( A . fallax lacustris , A . f . killarnensis , and A . macedonica ), and the fourth ( A . alosa ) was artificially landlocked during the last century. To conduct this analysis, we assembled and annotated a draft of the A . alosa genome and generated whole‐genome sequencing for 16 anadromous and freshwater populations of shad. Widespread evidence for parallel genetic changes in freshwater populations within lineages was found. In freshwater A . alosa , which have only been diverging for tens of generations, this shows that parallel adaptive evolution can rapidly occur. However, parallel genetic changes across lineages were comparatively rare. The degree of genetic parallelism was not strongly related to the number of shared polymorphisms between lineages, thus suggesting that other factors such as divergence among ancestral populations or environmental variation may influence genetic parallelism across these lineages. These overall patterns were exemplified by genetic differentiation involving a paralog of ATPase ‐ α1 that appears to be under selection in just two of the more distantly related lineages studied, A . f . lacustris and A . alosa . Our findings provide insights into the genetic architecture of adaptation and parallel evolution along a continuum of population divergence.

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A species-to-be? The genetic status and colonization history of the critically endangered Killarney shad

Cited by 10 publications

References 24 publications

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Integrative approach revises the frequently misidentified species of Sardinella (Clupeidae) of the Indo‐West Pacific Ocean

The genetics of adaptation in freshwater Eurasian shad (Alosa)

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