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  1. Abstract Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractablemore »for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.« less
  2. Abstract

    The Lesser Sundas Archipelago is comprised of two parallel chains of islands that extend between the Asian continental shelf (Sundaland) and Australo‐Papuan continental shelf (Sahul). These islands have served as stepping stones for taxa dispersing between the Asian and Australo‐Papuan biogeographical realms. While the oceanic barriers have prevented many species from colonizing the archipelago, a number of terrestrial vertebrate species have colonized the islands either by rafting/swimming or by human introduction. Here, we examine phylogeographic structure within the Lesser Sundas for three snake, two lizard and two frog species that each has a Sunda Shelf origin. These species are suspected to have recently colonized the archipelago, though all have inhabited the Lesser Sundas for over 100 years. We sequenced mtDNA from 231 samples to test whether there is sufficiently deep genetic structure within any of these taxa to reject human‐mediated introduction. Additionally, we tested for genetic signatures of population expansion consistent with recent introduction and estimated the ages of Lesser Sundas clades, if any exist. Our results show little to no genetic structure between populations on different islands in five species and moderate structure in two species. Nucleotide diversity is low for all species, and the ages of the mostmore »recent common ancestor for species with monophyletic Lesser Sundas lineages date to the Holocene or late Pleistocene. These results support the hypothesis that these species entered the archipelago relatively recently and either naturally colonized or were introduced by humans to most of the larger islands in the archipelago within a short time span.

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  3. Abstract Aim

    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.


    The Indonesian islands of Java, Lombok, Sumbawa, Flores and Lembata.


    Limnonectes dammermaniandL. kadarsani(Family: Dicroglossidae)


    MitochondrialDNAwas 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.


    The mtDNAphylogeny findsL. kadarsaniparaphyletic with respect toL. 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 theL. dammermanimitochondrion intoL. kadarsanion Lombok resulting from an isolated ancient hybridization event ~4 Ma.more »WithinL. 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 thatL. kadarsanirepresents five distinct species.

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