skip to main content

Title: Recent colonization and expansion through the Lesser Sundas by seven amphibian and reptile species

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 most more » 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.

« less
 ;  ;  ;  ;  ;  
Publication Date:
Journal Name:
Zoologica Scripta
Page Range or eLocation-ID:
p. 614-626
Sponsoring Org:
National Science Foundation
More Like this
  1. 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.

    « less
  2. Abstract

    Aedes aegyptiis among the best‐studied mosquitoes due to its critical role as a vector of human pathogens and ease of laboratory rearing. Until now, this species was thought to have originated in continental Africa, and subsequently colonized much of the world following the establishment of global trade routes. However, populations of this mosquito on the islands in the southwestern Indian Ocean (SWIO), where the species occurs with its nearest relatives referred to as the Aegypti Group, have received little study. We re‐evaluated the evolutionary history ofAe. aegyptiand these relatives, using three data sets: nucleotide sequence data, 18,489 SNPs and 12 microsatellites. We found that: (a) the Aegypti Group diverged 16 MYA (95% HPD: 7–28 MYA) from its nearest African/Asian ancestor; (b) SWIO populations ofAe. aegyptiare basal to continental African populations; (c) after diverging 7 MYA (95% HPD: 4–15 MYA) from its nearest formally described relative (Ae. mascarensis),Ae. aegyptimoved to continental Africa less than 85,000 years ago, where it recently (<1,000 years ago) split into two recognized subspeciesAe. aegypti formosusand a human commensal,Ae. aegypti aegypti; (d) the Madagascar samples form a clade more distant from all otherAe. aegyptithan the named speciesAe. mascarensis, implying that Madagascar may harbour a new cryptic species; and (e) there is evidencemore »of introgression betweenAe. mascarensisandAe. aegyption Réunion, and between the two subspecies elsewhere in the SWIO, a likely consequence of recent introductions of domesticAe. aegypti aegyptifrom Asia.

    « less
  3. Abstract

    Oceanic islands are unique geographic systems that promote local adaptations and allopatric speciation in many of their highly endemic taxa. This is a common case in the Philippine Archipelago, where numerous unrelated taxa on islands have been inferred to have diversified in isolation. However, few cases have been reported in invertebrates especially among parasitic organisms. Here, we tested for biogeographical structure in novel populations of the “generalist kleptoparasitic spider,Argyrodes lanyuensisYoshida, Tso & Severinghaus, 1998 in the Philippines. Results showed that, in addition to Orchid/Lanyu Island, this species has a wide geographic distribution in the Philippine Archipelago. The estimated divergence time of this lineage using the mitochondrial cytochrome oxidase 1 (mt‐CO1) suggests that this species divergedca3.12 MYA, during the Pliocene. Two reciprocal monophyletic clades were elucidated inA. lanyuensis, but with limited differentiation across Pleistocene Aggregate Island Complex (PAIC) boundaries and modern‐day islands. However, in our analyses of morphological variation, we identified two phenotypically differentiated units in males (Orchid Island, Taiwan + Luzon, Philippine PAIC populations vs. Palawan + West Visayan + Mindanao PAIC populations). We infer that this species diverged in the southern portion of the Philippine Archipelago and only recently colonized Orchid Island. Our study provides new information on the extensive distribution ofA. lanyuensisoutside Orchidmore »Island, Taiwan, but we documented a very limited geographically associated genetic variation. Our study points to behavioral phenomena such as foraging behavior as essential contributor to the evolutionary process of species diversification, in contrast to the traditionally invoked geographic drivers of divergence.

    « less
  4. Abstract Aim

    Biogeographical regions (realms) reflect patterns of co‐distributed species (biotas) across space. Their boundaries are set by dispersal barriers and difficulties of establishment in new locations. We extend new methods to assess these two contributions by quantifying the degree to which realms intergrade across geographical space and the contributions of individual species to the delineation of those realms. As our example, we focus on Wallace’s Line, the most enigmatic partitioning of the world’s faunas, where climate is thought to have little effect and the majority of dispersal barriers are short water gaps.



    Time period

    Present day.

    Major taxa studied

    Birds and mammals.


    Terrestrial bird and mammal assemblages were established in 1‐degree map cells using range maps. Assemblage structure was modelled using latent Dirichlet allocation, a continuous clustering method that simultaneously establishes the likely partitioning of species into biotas and the contribution of biotas to each map cell. Phylogenetic trees were used to assess the contribution of deep historical processes. Spatial segregation between biotas was evaluated across time and space in comparison with numerous hard realm boundaries drawn by various workers.


    We demonstrate that the strong turnover between biotas coincides with the north‐western extent of the region not connected to the mainlandmore »during the Pleistocene, although the Philippines contains mixed contributions. At deeper taxonomic levels, Sulawesi and the Philippines shift to primarily Asian affinities, resulting from transgressions of a few Asian‐derived lineages across the line. The partitioning of biotas sometimes produces fragmented regions that reflect habitat. Differences in partitions between birds and mammals reflect differences in dispersal ability.

    Main conclusions

    Permanent water barriers have selected for a dispersive archipelago fauna, excluded by an incumbent continental fauna on the Sunda shelf. Deep history, such as plate movements, is relatively unimportant in setting boundaries. The analysis implies a temporally dynamic interaction between a species’ intrinsic dispersal ability, physiographic barriers, and recent climate change in the genesis of Earth’s biotas.

    « less
  5. Abstract

    Genetic data can help elucidate the dynamics of biological invasions, which are fueled by the constant expansion of international trade. The introduction of European gypsy moth (Lymantria dispar dispar) into North America is a classic example of human‐aided invasion that has caused tremendous damage to North American temperate forests. Recently, the even more destructive Asian gypsy moth (mainlyL. d. asiaticaandL. d. japonica) has been intercepted in North America, mostly transported by cargo ships. To track invasion pathways, we developed a diagnostic panel of 60 DNA loci (55 nuclear and 5 mitochondrial) to characterize worldwide genetic differentiation withinL. disparand its sister speciesL. umbrosa. Hierarchical analyses supported strong differentiation and recovered five geographic groups that correspond to (1) North America, (2) Europe plus North Africa and Middle East, (3) the Urals, Central Asia, and Russian Siberia, (4) continental East Asia, and (5) the Japanese islands. Interestingly,L. umbrosawas grouped withL. d. japonica, and the introduced North American population exhibits remarkable distinctiveness from contemporary European counterparts. Each geographic group, except for North America, shows additional lower‐level structures when analyzed individually, which provided the basis for inference of the origin of invasive specimens. Two assignment approaches consistently identified a coastal area of continental Eastmore »Asia as the major source for Asian invasion during 2014–2015, with Japan being another source. By analyzing simulation and laboratory crosses, we further provided evidence for the occurrence of natural Asian–North American hybrids in the Pacific Northwest, raising concerns for introgression of Asian alleles that may accelerate range expansion of gypsy moth in North America. Our study demonstrates how genetic data contribute to bio‐surveillance of invasive species with results that can inform regulatory management and reduce the frequency of trade‐associated invasions.

    « less