Discordance between phylogenomic methods in Near Eastern mountain newts (Neurergus, Salamandridae)

Molecular Phylogenetics and Evolution, vol. 211, pp. 108386

Abstract

Target enrichment by sequence capture allows researchers to collect genome-wide sequence data, suitable to re-evaluate complex systematic and taxonomic cases. The family Salamandridae is rife with rapid, successive speciation events, introgression and incomplete lineage sorting: factors that complicate the inferring of phylogenetic relationships and species boundaries. Phylogenetic relationships among, and the (sub)species status of, the taxa comprising the newt genus Neurergus are not fully resolved. We perform target enrichment by sequence capture to obtain ca. 7 k nuclear DNA markers, and conduct concatenated analysis with RAxML, gene-tree summary analysis in ASTRAL, and species tree estimation in SNAPPER, and investigate admixture between populations and genetic introgression with ADMIXTURE and Dsuite. We observe discordance between analyses pertaining to the placement of N. crocatus. We consider the placement of N. crocatus as sister to N. derjugini sensu lato in SNAPPER, instead of to N. kaiseri + N. derjugini sensu lato as in RAxML and ASTRAL, to be an artifact of introgression, as backed up by our Dsuite analysis. We show that N. strauchii barani and N. strauchii munzurensis, often treated as distinct species, are deeply nested within N. strauchii sensu stricto and should not be treated as species. Keeping them as subspecies would render the nominotypical subspecies as polyphyletic. Furthermore, we confirm that N. derjugini microspilotus should not be considered a distinct species, but as a subspecies of N. derjugini sensu lato. We consistently recover the northern and southern lineages of N. kaiseri as distinct genetic groups with geographically restricted admixture and recommend that these are treated as two distinct species. Our study highlights the strength of target enrichment by sequence capture in resolving systematic and taxonomic questions in taxa with a history of genetic admixture and introgression.

Authors 15

1. Stephanie Koster corresponding Aachen

   Leiden University · Naturalis Biodiversity Center

   Affiliation as printed

   Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands. Electronic address: sca.koster@outlook.com

   Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands. Electronic address: stephaniekoster222@gmail.com

2. Robin Polanen Aachen

   Leiden University · Naturalis Biodiversity Center

   Affiliation as printed

   Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands

3. Aziz Avcı

   Adnan Menderes University

   Affiliation as printed

   Department of Biology, Faculty of Sciences, Aydın Adnan Menderes University, 09010 Aydın, Türkiye

4. Sergé Bogaerts
   Affiliation as printed

   Strijperstraat 55a NL5595GB Leende, the Netherlands

5. Emin Bozkurt

   Çankırı Karatekin University

   Affiliation as printed

   Department of Veterinary Medicine, Eldivan Health Services Vocational High School, Çankırı Karatekin University, Çankırı, Türkiye

6. Forough Goudarzi

   Shahid Beheshti University

   Affiliation as printed

   Environmental Sciences Research Institute, Shahid Beheshti University, G.C, Tehran, Iran

7. Mahmoud‐Reza Hemami

   Isfahan University of Technology

   Affiliation as printed

   Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran

8. Kurtuluş Olgun

   Adnan Menderes University

   Affiliation as printed

   Department of Biology, Faculty of Sciences, Aydın Adnan Menderes University, 09010 Aydın, Türkiye

9. Frank Pasmans

   Ghent University

   Affiliation as printed

   University of Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine 9820 Merelbeke, Belgium

10. Sebastian Steinfartz

    Leipzig University

    Affiliation as printed

    University of Leipzig, Institute of Biology, Molecular Evolution and Systematics of Animals, Talstrasse 33 04103 Leipzig, Germany

11. Nazan Üzüm

    Adnan Menderes University

    Affiliation as printed

    Department of Biology, Faculty of Sciences, Aydın Adnan Menderes University, 09010 Aydın, Türkiye

12. Manon Chantal de Visser Aachen

    Leiden University · Naturalis Biodiversity Center

    Affiliation as printed

    Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands; Blijdorp Conservation & Science Center, Royal Rotterdam Zoological & Botanical Gardens, P.O. Box 532 3000 AM Rotterdam, the Netherlands

13. James France Aachen

    Leiden University · Naturalis Biodiversity Center

    Affiliation as printed

    Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands

14. Anagnostis Theodoropoulos Aachen

    Leiden University · Naturalis Biodiversity Center

    Affiliation as printed

    Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands

15. Ben Wielstra Aachen

    Leiden University · Naturalis Biodiversity Center

    Affiliation as printed

    Institute of Biology Leiden, Leiden University, P.O. Box 9505 2300 RA Leiden, the Netherlands; Naturalis Biodiversity Center, P.O. Box 9517 2300 RA Leiden, the Netherlands