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Leap-frog dispersal and mitochondrial introgression: Phylogenomics and biogeography of Limnonectes fanged frogs in the Lesser Sundas Archipelago of Wallacea
Reilly S.B.a, Stubbs A.L.a, Karin B.R.a, Bi K.a, Arida E., Iskandar D.T.d, McGuire J.A.a
a Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, United States
b Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, United States
c Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
d School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
[vc_row][vc_column][vc_row_inner][vc_column_inner][vc_separator css=”.vc_custom_1624529070653{padding-top: 30px !important;padding-bottom: 30px !important;}”][/vc_column_inner][/vc_row_inner][vc_row_inner layout=”boxed”][vc_column_inner width=”3/4″ css=”.vc_custom_1624695412187{border-right-width: 1px !important;border-right-color: #dddddd !important;border-right-style: solid !important;border-radius: 1px !important;}”][vc_empty_space][megatron_heading title=”Abstract” size=”size-sm” text_align=”text-left”][vc_column_text]© 2019 John Wiley & Sons LtdAim: The Lesser Sunda Islands are situated between the Sunda and Sahul Shelves, with a linear arrangement that has functioned as a two-way filter for taxa dispersing between the Asian and Australo-Papuan biogeographical realms. Distributional patterns of many terrestrial vertebrates suggest a stepping-stone model of island colonization. Here we investigate the timing and sequence of island colonization in Asian-origin fanged frogs from the volcanic Sunda Arc islands with the goal of testing the stepping-stone model of island colonization. Location: The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata. Taxon: Limnonectes dammermani and L. kadarsani (Family: Dicroglossidae). Methods: Mitochondrial DNA was sequenced from 153 frogs to identify major lineages and to select samples for an exon-capture experiment. We designed probes to capture sequence data from 974 exonic loci (1,235,981 bp) from 48 frogs including the outgroup species, L. microdiscus. The resulting data were analysed using phylogenetic, population genetic and biogeographical model testing methods. Results: The mtDNA phylogeny finds L. kadarsani paraphyletic with respect to L. dammermani, with a pectinate topology consistent with the stepping-stone model. Phylogenomic analyses of 974 exons recovered the two species as monophyletic sister taxa that diverged ~7.6 Ma with no detectable contemporary gene flow, suggesting introgression of the L. dammermani mitochondrion into L. kadarsani on Lombok resulting from an isolated ancient hybridization event ~4 Ma. Within L. kadarsani, the Lombok lineage diverged first while the Sumbawa and Lembata lineages are nested within a Flores assemblage composed of two parapatrically distributed lineages meeting in central Flores. Biogeographical model comparison found strict stepping-stone dispersal to be less likely than models involving leap-frog dispersal events. Main conclusions: These results suggest that the currently accepted stepping-stone model of island colonization might not best explain the current patterns of diversity in the archipelago. The high degree of genetic structure, large divergence times, and absent or low levels of migration between lineages suggests that L. kadarsani represents five distinct species.[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Author keywords” size=”size-sm” text_align=”text-left”][vc_column_text][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Indexed keywords” size=”size-sm” text_align=”text-left”][vc_column_text]amphibians,exon-capture,genomics,Indonesia,island biogeography,phylogeography[/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”Funding details” size=”size-sm” text_align=”text-left”][vc_column_text][{‘$’: ‘We thank Umilaela Arifin, Gilang Ramadhan, Jerome Fuchs and Jim and Carol Patton for their help with the field collection of specimens and tissues. We thank Lydia Smith for laboratory support, Daniel Portik for his help with lab work and bioinformatics, Carol Spencer for accessioning of specimens, Michelle Koo for GIS support, and Robert Hall for reviewing the manuscript. S.B.R. thanks his dissertation committee members Rauri Bowie, Rosemary Gillespie, Craig Moritz and David Wake for their help in developing this project. Funding was provided by the Museum of Vertebrate Zoology, the Department of Integrative Biology at UC Berkeley, the National Geographic Society, and the National Science Foundation (#DEB-1258185, DEB-1652988, and DEB-1457845 awarded to JAM). Fieldwork in Indonesia was carried out under research permits issued by LIPI and RISTEK, and UC Berkeley IACUC protocol #R279. This study utilized the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303.’}, {‘$’: ‘Directorate for Biological Sciences, Grant/ Award Number: DEB-1258185; Museum of Vertebrate Zoology; the Department of Integrative Biology at UC Berkeley; the National Geographic Society; the National Science Foundation, Grant/Award Number: #DEB-1258185, DEB-1652988, DEB-1457845’}, {‘$’: ‘We thank Umilaela Arifin, Gilang Ramadhan, Jerome Fuchs and Jim and Carol Patton for their help with the field collection of specimens and tissues. We thank Lydia Smith for laboratory support, Daniel Por-tik for his help with lab work and bioinformatics, Carol Spencer for accessioning of specimens, Michelle Koo for GIS support, and Robert Hall for reviewing the manuscript. S.B.R. thanks his dissertation committee members Rauri Bowie, Rosemary Gillespie, Craig Moritz and David Wake for their help in developing this project. Funding was provided by the Museum of Vertebrate Zoology, the Department of Integrative Biology at UC Berkeley, the National Geographic Society, and the National Science Foundation (#DEB‐1258185, DEB‐1652988, and DEB‐1457845 awarded to JAM). Fieldwork in Indonesia was carried out under research permits issued by LIPI and RISTEK, and UC Berkeley IACUC protocol #R279. This study utilized the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303.’}][/vc_column_text][vc_empty_space][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][vc_empty_space][megatron_heading title=”DOI” size=”size-sm” text_align=”text-left”][vc_column_text]https://doi.org/10.1111/jbi.13526[/vc_column_text][/vc_column_inner][vc_column_inner width=”1/4″][vc_column_text]Widget Plumx[/vc_column_text][/vc_column_inner][/vc_row_inner][/vc_column][/vc_row][vc_row][vc_column][vc_separator css=”.vc_custom_1624528584150{padding-top: 25px !important;padding-bottom: 25px !important;}”][/vc_column][/vc_row]