Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds

Obiol, Joan Ferrer; Herranz, José M.; Paris, Josephine R.; Whiting, James R.; Rozas, Julio; Riutort, Marta; González‐Solís, Jacob

doi:10.1016/j.ympev.2022.107671

Cited by 8 publications

(4 citation statements)

References 102 publications

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“…Another issue is that subspecies are often treated as the beginnings of future species, which Patten (2010) argues is incorrect because initial divergence may be reversed by future gene flow. Ferrer Obiol et al (2023) provided evidence that elevation of two puffin subspecies to species status was not justified based on evidence. Historical subspecific designations may also not stand up to more rigorous modern analyses.…”

Section: Manage: At What Level?mentioning

confidence: 99%

Losing the forest for the tree? On the wisdom of subpopulation management

Powell

2023

Zoo Biology

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Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often‐misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.

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Section: Manage: At What Level?mentioning

confidence: 99%

Losing the forest for the tree? On the wisdom of subpopulation management

Powell

2023

Zoo Biology

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“…With the increasing availability of genomic‐scale data, it is now possible to understand the interplay between different evolutionary processes responsible for formation and distribution of biological diversity (Ferrer Obiol et al., 2023). Although whole genomes are now being sequenced at a relatively fast rate and are potentially an ideal source of data for phylogenomic studies, they remain unavailable for many non‐model taxa (Breinholt et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture

Khan,

Joshi,

Espeland

et al. 2023

Molecular Ecology

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The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well‐informed taxonomic delimitations involving parapatric taxa.

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“…An evaluation of nearly 600 bp of COI revealed that approximately 75% of Anastrepha species can successfully be identified using this approach, but it does not discriminate members of the A. fraterculus cryptic complex and some other closely related species of the fraterculus group (Barr et al, 2018; Bartolini et al, 2020). On the other hand, genomic data coupled with multispecies coalescent approaches have provided invaluable information on evolutionary histories of cryptic species complexes in a great variety of animal taxa, such as insects, mammals, reptiles, and birds (Dupuis, Bremer, et al, 2018; Herrera et al, 2022; Obiol et al, 2023; Singhal et al, 2018; Thawornwattana et al, 2018; Zhang et al, 2021), as well as plants, such as ferns and angiosperms (Kinosian et al, 2020; Wu et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Congrains,

Dupuis,

Rodriguez

et al. 2023

Evolutionary Applications

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Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole‐genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome‐scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.

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Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds

Cited by 8 publications

References 102 publications

Losing the forest for the tree? On the wisdom of subpopulation management

Losing the forest for the tree? On the wisdom of subpopulation management

Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

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