Genetic divergence of the Sunda ratsnake (Coelognathus subradiatus) across the Lesser Sunda Islands (Squamata: Colubridae)

Reilly, Sean B.; Stubbs, Alexander L.; Karin, Benjamin R.; Arifin, Umilaela; Arida, Evy; Iskandar, Djoko T.; McGuire, Jimmy A.

doi:10.1163/15685381-bja10048

Cited by 4 publications

(4 citation statements)

References 21 publications

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“…Three comparisons recovered nonzero migration values, including (1) between East Flores 2 and Lembata, (2) between Wetar and the Maluku Islands, and (3) between West Flores and Sumbawa. All migration bands exhibit fewer than 0.5 migrants per generation, a threshold that we and others have previously suggested as a species threshold (Shaffer and Thompson, 2007;Reilly et al, 2021). Asymmetric migration is found predominantly from East Flores 2 into Lembata and from Wetar into Maluku (Fig.…”

Section: Gene Flow and Introgressionsupporting

confidence: 52%

“…However, given the tectonic complexity of the archipelago, this model appears to be an oversimplification when applied to taxa that colonized the archipelago early (such as in the late Miocene (∼5.3-12 Ma) before the Banda Arcs and Sumba had become emergent). Indeed, phylogenetically informed biogeographical analyses for several taxa suggest that more complex patterns of dispersal and vicariance are prevalent (Tänzler et al 2016;Gwee et al 2017;Morinaka et al 2017;Pedersen et al 2018;Reilly et al 2019a;Reilly et al, 2021;Reilly et al 2022a;Reilly et al 2022b;Toussaint et al 2020).…”

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confidence: 99%

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Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus:Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

et al. 2022

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Transcriptome Sequencing: RNA was extracted from three Sphenomorphus samples including S. striolatus (Flores, MVZ293137) and S. melanopogon from Sumbawa (MVZ293067) and Lembata (MVZ292954) using the RNEasy Protect Mini Kit (Qiagen) and provided protocol.RNA extractions were evaluated using a BioAnalyzer 2100 RNA Pico chip (Agilent). Sequencing libraries were prepared with half reactions of the TruSeq RNA Library Preparation Kit V2 (Illumina), starting with Poly-A selection for samples with high RIN scores (> 8.0). Ribo-Zero Magnetic Gold (Epicentre) was used for ribosomal RNA removal for a any samples with low RIN scores (< 8.0). After pooling the libraries they were sequenced on an Illumina HiSeq2500 with 100 bp paired-end reads. Transcriptomic sequence data were cleaned following Singhal (2013). The cleaned data were assembled using TRINITY (Grabherr et al., 2011) and annotated using the Anolis carolinensis genome (Ensembl) as a reference using reciprocal BLASTX (Altschul et al., 1997) and EXONERATE (Slater, Birney, 2005). The three annotated transcripts were compared to search for orthologs via BLAST (Altschul et al., 1990). Mitochondrial sequences were then removed and only transcripts with a GC content between 40%-70% were kept to optimize capture efficiency (Bi et al., 2012). Bioinformatics pipelines for transcriptome data processing and annotation are available at https://github.com/CGRL-QB3-UCBerkeley/DenovoTranscriptome.Marker Development: Annotated and filtered contigs from the three transcripts were aligned to identify shared exons. Markers under 300 bp were removed and those greater than 1,000 bp were cut to a maximum length of 1,000 bp. The three sets of transcripts were screened using the REPEATMASKER Web Server (Smit et al., 2015), which masks repetitive elements and low complexity regions. If any of the three transcripts for a gene contained masked sites, that gene was removed from the final marker set. The resulting 5,103 markers were compared to determine the variability of each marker in terms of the number of polymorphic sites. Invariable loci and loci with only a single variable site were discarded, as well as the top 5% of the most variable loci, leaving 3,619 candidate loci. A total of 1,199 loci were randomly chosen from the candidate loci to be integrated into an in-solution probe design for a MYBaits (MYcroarray-now Arbor Biosciences) target enrichment kit. The target size of the combined loci was approximately 1,090,000 bp. The two S. melanopogon transcripts (MVZ293067 and MVZ292954), which were ~1.6% divergent, were used as references for probe design with 3X tiling of 120bp probes across each reference. Pipelines for marker development can be found at https://github.com/CGRL-QB3-UCBerkeley/MarkerDevelopmentPylogenomics.

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Section: Gene Flow and Introgressionsupporting

confidence: 52%

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confidence: 99%

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus:Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

et al. 2022

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“…Initial descriptions of reptile biogeography in the Lesser Sundas were based on patterns of species composition from individual islands (Darlington 1957;Auffenberg 1980;How and Kitchener 1997) and invoked stepping-stone colonization as the process most likely to have created such patterns (Hisheh et al 1998). However, more recent analyses of this fauna (Reilly 2016;Reilly et al 2017Reilly et al , 2019aReilly et al , 2019bReilly et al , 2021Blom et al 2019;Jones et al 2019;) and other fauna (Tänzler et al 2016;Toussaint et al 2020) have shown a wide range of patterns regarding the timing and sequence of island colonization.…”

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Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco)

et al. 2021

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The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9–11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically-distributed non-sister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5–7.5 Ma, with most inter-island colonization events having occurred between 1–3 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five over-water dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries.

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“…Recent molecular studies of southern Wallacean herpetofauna have revealed a wide range of divergence levels and a multitude of biogeographic patterns ranging from recent colonization and expansion through the region without insular species formation (Reilly et al 2017(Reilly et al , 2019bKarin et al 2020;Maryanto et al 2021) to much earlier colonizations that led to extensive species diversification within and between islands (Blom et al 2019;Reilly et al 2019aReilly et al , 2021Reilly et al , 2022. Among early colonizing taxa, a pattern of disconnect between Sunda Arc island populations and populations on Sumba plus the Banda Arc islands has emerged, suggesting that while Sumba is currently closest to Sumbawa and Flores it may have been in a different position in the past (Reilly 2016;Reilly et al 2022).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana)

Reilly

Arifin

Stubbs

et al. 2022

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Frogs in the family Ranidae are diverse in Asia and are thought to have dispersed to the Sahul Shelf approximately 10 million years ago, where they radiated into more than a dozen species. Ranid species in the intervening oceanic islands of Wallacea, such as Hylarana florensis and H. elberti from the Lesser Sundas and H. moluccana from eastern Wallacea, are assumed to belong to the subgenus Papurana, yet this has not been confirmed with molecular data. We analyzed mitochondrial DNA of Hylarana species from five islands spanning the reported ranges of H. florensis and H. elberti and compared them to confirmed Papurana species and closely related subgenera within Hylarana. We find that the Lesser Sunda H. florensis and H. elberti form a clade that is sister to the rest of the Australo-Papuan Papurana assemblage. Species delimitation analyses and divergence time estimates suggest that populations of H. florensis on Lombok may be distinct from those on Flores at the species level. Likewise, populations of H. elberti on Sumba and Timor may be distinct from each other and from those on Wetar, tshe type locality of H. elberti. Samples from Babar Island thought to be members of H. elberti in fact belong to the wide-ranging H. daemeli, which occurs in northern Australia, across New Guinea, and on the neighboring island of Tanimbar. These results suggest that the Lesser Sundas may have served as a stepping-stone for colonization of the Sahul Shelf and that species diversity of Papurana frogs is underestimated in the Lesser Sundas.

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Genetic divergence of the Sunda ratsnake (Coelognathus subradiatus) across the Lesser Sunda Islands (Squamata: Colubridae)

Cited by 4 publications

References 21 publications

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus:Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus:Sphenomorphus) and their colonization of the Lesser Sunda Archipelago

Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco)

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana)

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