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FIGURE 7 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 7. Photos of live specimens of Hemidactylus boavistensis boavistensis (top left, A–C) versus H. b. chevalieri (top right, D–F), and H. bouvieri (bottom left, G–I) versus H. nicolauensis (bottom right, J–L). All photos by PG, GK, RV and PAC. A) Adult female from 1 km E of Sal Rei, Boavista (PGe.1479); B) adult male from 3 km E of Sal Rei, Boavista (PGe.1485); C) subadult female from 1 km E of Sal Rei, Boavista (PGe.1481); D) adult from 1 km SE Santa Maria, Sal (PGe.1499); E) adult from Buracona, Sal (PGe.1507); F) adult from 1 km ESE Santa Maria, Sal (PGe.1500); G) adult from Chã do Castelo, Raso (H28; PGe.1476); H) adult from Praia Grande, Calhau, São Vicente (Hrv3); I) adult from Lombo de Diogo, Santo Antão (Hrv1); J) adult female from Cachaço, São Nicolau (H06; BEV.T5651); K) adult female from Cachaço, São Nicolau (H07; BEV.T5652); L) adult female from Ribeira Funda, São Nicolau (UCV2018/004, paratype).
FIGURE 1 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 1. Location of the study area and samples. Map of the Cabo Verde Islands showing the geographical location (latitudes and longitudes) and altitudes of the islands and the origins of the Hemidactylus samples included in the morphological (X) and genetic (+) analyses (Geographic Coordinate System, Datum WGS 84). Island and taxa colours match the colours used in the network analyses. No specimens were found on Maio.
FIGURE 4 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 4. Scale details of the holotype of Hemidactylus nicolauensis (SMF 86992). A) Finger lamella; B) toe lamella; C) mid-dorsum scales; D) mid-venter scales; E) nasal scales; F) ventral tail scales. Scale bar = 1 mm.
FIGURE 3 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 3. General and head views of the holotype of Hemidactylus nicolauensis (SMF 86992) from Cabo Verde. A) dorsal general view; B) ventral general view; C) right view of head; D) left view of head; E) dorsal view of head; F) ventral view of head. Scale bar = 5 mm in A and B, 1 mm in C to F.
FIGURE 5 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 5. Phylogenetic tree with integrative taxonomy results. Relationships in endemic Cabo Verde Hemidactylus and their relatives based on a maximum-likelihood analysis of a 2524 base pairs (bp) concatenated alignment composed of two mitochondrial (669 bp of cyt b and approximately 380 bp of 12S rRNA) and two nuclear (668 bp of MC1R and 804 bp of RAG2) gene sequences. Black circles on top of nodes indicate bootstrap support for ML and Bayesian posterior probability values. Lines of evidence (in light grey): (1) Mitochondrial DNA (independent cyt b parsimony networks with a connection limit of 95%); (2) Nuclear DNA (absence of shared haplotypes in MC1R) and; (3) Morphology (detection of any diagnostic morphological character). Integration approaches (in red) from the most conservative to the most inflationist: ITC stands for an integration by total congruence (all lines of evidence should be congruent), IPC stands for integration by partial congruence which have been presently retained in this study (at least two lines of evidence are necessary); IC stands for an integration by cumulation (one line of evidence is sufficient). Species are represented in red bars, and for the IPC protocol, subspecies are represented within those bars in yellow. For fuller locality data and GenBank accession numbers see Table 1.
FIGURE 6 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 6. Pairwise genetic distances. Distribution of K2P distances of the concatenated dataset using the four markers between all pairs of samples for samples belonging to different species based on current taxonomy (black), to the same species based on current taxonomy (pale grey), and between samples of São Nicolau and other islands (dark grey).
FIGURE 2 in A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde
FIGURE 2. Parsimony networks corresponding to cyt b (mtDNA), and MC1R (nDNA) sequence variation. Lines represent mutational steps, circles haplotypes and dots unsampled haplotypes. The size of circles is proportional to the number of individuals. Samples from the same geographic location are similarly coloured. For correspondences of sample and location codes see Table 1.
Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six nuclear loci and complete sampling for all known species. We use a time-calibrated Bayesian estimate of phylogeny and model-testing approach to biogeographic inference to infer ancestral areas and probable means of diversification. These analyses identify Sanguirana as an additional clade for which the biogeographic 'Out-of-Palawan' biogeographic scenario is unambiguously preferred. This study lends additional support to recent work suggesting that a substantial portion of Philippine vertebrate megadiversity originated via colonization of the archipelago from the Palawan microcontinent, with subsequent invasion of oceanic islands (e.g., range expansion over Huxley's Modification of Wallace's Line), numerous instances of overwater dispersal, and geographic radiation across the archipelago.
Data from: Biogeography in a continental island: population structure of the relict endemic centipede Craterostigmus tasmanianus (Chilopoda, Craterostigmomorpha) in Tasmania using 16S rRNA and COI
We used 16S ribosomal RNA (rRNA) and cytochrome c oxidase subunit I (COI) sequence data to investigate the population structure in the centipede Craterostigmus tasmanianus Pocock, 1902 (Chilopoda: Craterostigmomorpha: Craterostigmidae) and to look for possible barriers to gene flow on the island of Tasmania, where C. tasmanianus is a widespread endemic. We first confirmed a molecular diagnostic character in 28S rRNA separating Tasmanian Craterostigmus from its sister species Craterostigmus crabilli (Edgecombe and Giribet 2008) in New Zealand and found no shared polymorphism in this marker for the 2 species. In Tasmania, analysis of molecular variance analysis showed little variation at the 16S rRNA and COI loci within populations (6% and 13%, respectively), but substantial variation (56% and 48%, respectively) among populations divided geographically into groups. We found no clear evidence of isolation by distance using a Mantel test. Bayesian clustering and gene network analysis both group the C. tasmanianus populations in patterns which are broadly concordant with previously known biogeographical divisions within Tasmania, but we did not find that genetic distance varied in a simple way across cluster boundaries. The coarse-scale geographical sampling on which this study was based should be followed in the future by sampling at a finer spatial scale and to investigate genetic structure within clusters and across cluster boundaries.
Data from: Ecological explanations to island gigantism: dietary niche divergence, predation and size in an endemic lizard
Although rapid evolution of body size on islands has long been known, the ecological mechanisms behind this island phenomenon remain poorly understood. Diet is an important selective pressure for morphological divergence. Here we investigate if selection for novel diets has contributed to the multiple independent cases of island gigantism in the Skyros wall lizard (Podarcis gaigeae) and if diet, predation, or both factors best explain island gigantism. We combined data on body size, shape, bite force, and realized and available diets to address this. Several lines of evidence suggest that diet has contributed to the island gigantism. The larger islet lizards have relatively wider heads and higher bite performance in relation to mainland lizards than would be expected from size differences alone. The proportions of consumed and available hard prey are higher on islets than mainland localities, and lizard body size is significantly correlated with the proportion of hard prey. Furthermore, the main axis of divergence in head shape is significantly correlated with dietary divergence. Finally, a model with only diet and one including diet and predation regime explain body size divergence equally well. Our results suggest that diet is an important ecological factor behind insular body size divergence, but could be consistent with an additional role for predation.
Data from: Forest fragmentation genetics in a formerly widespread island endemic tree: Vateriopsis seychellarum (Dipterocarpaceae)
Habitat fragmentation and changed land use have seriously reduced population size in many tropical forest tree species. Formerly widespread species with limited gene flow may be particularly vulnerable to the negative genetic effects of forest fragmentation and small population size. Vateriopsis seychellarum (Dipterocarpaceae) is a formerly widespread canopy tree of the Seychelles, but is now reduced to 132 adult individuals distributed in eleven sites. Using ten microsatellite loci, a genetic inventory of all adult trees and a sample of 317 progeny, we demonstrate that despite its restricted range, overall genetic diversity was relatively high (HE: 0.56). The juvenile cohort, however, had significantly lower allelic richness (adults RS: 3.91; juveniles RS: 2.83) and observed heterozygosity than adult trees (adults HO: 0.62; juveniles HO: 0.48). Rare alleles were fewer and kinship between individuals was stronger in juveniles. Significant fine-scale spatial genetic structure was observed in remnant adults, and parentage analysis indicated that more than 90% of sampled progeny disperse <25 m and pollen dispersed <50 m. The molecular data confirmed that two populations were derived entirely from self-fertilized offspring from a single surviving mother tree. These populations produce viable offspring. Despite this extreme genetic bottleneck, self-compatibility may provide V. seychellarum with some resistance to the genetic consequences of habitat fragmentation, at least in the short term. We discuss our findings in the context of other rare and threatened dipterocarp species which are vulnerable to mis-management of genetic resources and population fragmentation.
Data from: Islands within islands: two montane paleo-endemic birds impacted by recent anthropogenic fragmentation
Anthropogenic habitat fragmentation of species that live in naturally patchy metapopulations such as mountaintops or sky islands experiences two levels of patchiness. Effects of such multilevel patchiness on species have rarely been examined. Metapopulation theory suggests that patchy habitats could have varied impacts on persistence, dependent on differential migration. It is not known whether montane endemic species, evolutionarily adapted to natural patchiness, are able to disperse between anthropogenic fragments at similar spatial scales as natural patches. We investigated historic and contemporary gene flow between natural and anthropogenic patches across the distribution range of a Western Ghats sky-island-endemic bird species complex. Data from 14 microsatellites for 218 individuals detected major genetic structuring by deep valleys, including one hitherto undescribed barrier. As expected, we found strong effects of historic genetic differentiation across natural patches, but not across anthropogenic fragments. Contrastingly, contemporary differentiation (DPS) was higher relative to historic differentiation (FST) in anthropogenic fragments, despite the species' ability to historically traverse shallow valleys. Simulations of recent isolation resulted in high DPS/FST values, confirming recent isolation in Western Ghats anthropogenic fragments and also suggesting that this ratio can be used to identifying recent fragmentation in the context of historic connectedness. We suggest that in this landscape, in addition to natural patchiness affecting population connectivity, anthropogenic fragmentation additionally impacts connectivity, making anthropogenic fragments akin to islands within natural islands of montane habitat, a pattern that may be recovered in other sky-island systems.
Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates
Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for one mitochondrial gene and five nuclear loci for species of the Gekko mindorensis-G. kikuchii species complex in Southeast Asia. We used maximum likelihood and Bayesian phylogenetic methods and coalescent-based species delimitation analyses to estimate phylogeographic relationships, construct multilocus haplotype networks and test putative species boundaries. Results: Phylogenetic and population genetic analyses suggest that Kikuchi's Gecko may represent a peripheral population of a widespread species distributed from the northern Philippines to Taiwan. However, we identify a discrepancy between inferences of species boundaries resulting from methods based on allele frequencies versus coalescent-based methods that incorporate evolutionary history. Coalescent-based analyses suggest that G. kikuchii may be a distinct evolutionary lineage. Our study underscores the need for coalescent-based methods in conjunction with population genetic approaches for conservation genetic assessments of widespread species. Main conclusions: This study joins a few recent works suggesting that Philippine-derived anomalies in the fauna of Lanyu (and possibly greater Taiwan) are worthy of careful reconsideration. Determining whether each is the result of recent human-mediated introduction or (possibly more ancient) natural dispersal should be the goal of future studies on this seldom-conceived biogeographic relationship. Isolated species endemic to islands on the outer periphery of biogeographic and political regions represent particular conservation challenges. This is especially true if a species occurs on an isolated island that is allied biogeographically with one nation, but politically administered by another.
Data from: A single panmictic population of endemic red crabs, Gecarcoidea natalis, on Christmas Island with high levels of genetic diversity
The red crab, Gecarcoidea natalis, is endemic to Christmas Island in the Indian Ocean and largely responsible for shaping the unique ecosystem found throughout the island's rainforests. However, the introduction and establishment of supercolonies of the highly invasive yellow crazy ant, Anoplolepis gracilipes, has decimated red crab numbers over the last several decades. This poses a significant risk to the future conservation of G. natalis and consequently threatens the integrity of the unique island ecosystem. Here we undertook a population genetic analysis of G. natalis using a combination of 11 microsatellite markers and sequencing of the mitochondrial cytochrome oxidase subunit I gene from samples collected on Christmas Island as well as a single location from North Keeling Island (located approximately 900 km west of Christmas Island). The genetic results indicate that G. natalis is a single panmictic population on Christmas Island, with no spatial genetic structure or restricted gene flow apparent between sampled locations. Further, G. natalis from North Keeling Island are not genetically distinct and are recent immigrants from Christmas Island. The effective population size of G. natalis has likely remained large and stable on Christmas Island throughout its evolutionary history with relatively moderate to high levels of genetic diversity in microsatellite loci and mitochondrial haplotypes assessed in this study. For management purposes G. natalis can be considered a single panmictic population, which should simplify conservation efforts for the genetic management of this iconic island species.
Data from: Spatial and ecological population genetic structures within two island-endemic Aeonium species of different niche width
The Crassulacean genus Aeonium is a well-known example for plant species radiation on oceanic archipelagos. However, while allopatric speciation among islands is documented for this genus, the role of intra-island speciation due to population divergence by topographical isolation or ecological heterogeneity has not yet been addressed. The aim of this study was to investigate intraspecific genetic structures and to identify spatial and ecological drivers of genetic population differentiation on the island scale. We analyzed inter simple sequence repeat variation within two island-endemic Aeonium species of La Palma: one widespread generalist that covers a large variety of different habitat types (Ae. davidbramwellii) and one narrow ecological specialist (Ae. nobile), in order to assess evolutionary potentials on this island. Gene pool differentiation and genetic diversity patterns were associated with major landscape structures in both species, with phylogeographic implications. However, overall levels of genetic differentiation were low. For the generalist species, outlier loci detection and loci–environment correlation approaches indicated moderate signatures of divergent selection pressures linked to temperature and precipitation variables, while the specialist species missed such patterns. Our data point to incipient differentiation among populations, emphasizing that ecological heterogeneity and topographical structuring within the small scales of an island can foster evolutionary processes. Very likely, such processes have contributed to the radiation of Aeonium on the Canary Islands. There is also support for different evolutionary mechanisms between generalist and specialist species.
Data from: The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp guanchica
Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a tree species (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance
Data from: Diversification rates of the "Old Endemic" murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity
Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists in two speciose clades of Philippine "Old Endemic" murine rodents—Phloeomyini and Chrotomyini—on the relatively old oceanic island of Luzon. Although phylogenetic analyses confirm the independent, non-contemporaneous colonization of Luzon by the ancestors of these two clades, we found no support for arrested diversification in either. Rather, it appears that diversification of both clades resulted from constant-rate processes that were either uniform or favored the secondary colonists (Chrotomyini), depending on the method used. Our results suggest that ecological incumbency has not played an important role in determining lineage diversification among Luzon murines, despite sympatric occurrence by constituent species within each lineage, and a substantial head start for the primary colonists.
Data from: Microhabitat heterogeneity and a non-native avian frugivore drive the population dynamics of an island endemic shrub, Cyrtandra dentata
Understanding of the role of environmental change in the decline of endangered species is critical to designing scale-appropriate restoration plans. For locally endemic rare plants on the brink of extinction, frugivory can drastically reduce local recruitment by dispersing seeds away from geographically isolated populations. Dispersal of seeds away from isolated populations can ultimately lead to population decline. For localized endemic plants, fine-scale changes in microhabitat can further limit population persistence. Evaluating the individual and combined impact of frugivores and microhabitat heterogeneity on the short-term (i.e. transient) and long-term (i.e. asymptotic) dynamics of plants will provide insight into the drivers of species rarity. In this study, we used four years of demographic data to develop matrix projection models for a long-lived shrub, Cyrtandra dentata (H. St. John & Storey) (Gesneriaceae), which is endemic to the island of O'ahu in Hawai'i. Furthermore, we evaluated the individual and combined influence of a non-native frugivorous bird, Leiothrix lutea, and microhabitat heterogeneity on the short-term and long-term C. dentata population dynamics. Frugivory by L. lutea decreased the short-term and long-term population growth rates. However, under the current level of frugivory at the field site the C. dentata population was projected to persist over time. Conversely, the removal of optimum microhabitat for seedling establishment (i.e. rocky gulch walls and boulders in the gulch bottom) reduced the short-term and long-term population growth rates from growing to declining. Survival of mature C. dentata plants had the greatest influence on long-term population dynamics, followed by the growth of seedlings and immature plants. The importance of mature plant survival was even greater when we simulated the combined effect of frugivory and the loss of optimal microhabitat, relative to population dynamics based on field conditions. In the short-term (10 years), however, earlier life stages had the greatest influence on population growth rate. Synthesis and applications. This study emphasizes how important it is to decouple rare plant management strategies in the short versus long-term in order to prioritize restoration actions, particularly when faced with multiple stressors not all of which can be feasibly managed. From an applied conservation perspective, our findings also illustrate that the life stage that, if improved by management, would have the greatest influence on population dynamics is dependent on the timeframe of interest and initial conditions of the population.
Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
Data from: Partial support for the central–marginal hypothesis within a population: reduced genetic diversity but not increased differentiation at the range edge of an island endemic bird
Large-scale population comparisons have contributed to our understanding of the evolution of geographic range limits and species boundaries, as well as the conservation value of populations at range margins. The central–marginal hypothesis (CMH) predicts a decline in genetic diversity and an increase in genetic differentiation toward the periphery of species' ranges due to spatial variation in genetic drift and gene flow. Empirical studies on a diverse array of taxa have demonstrated support for the CMH. However, nearly all such studies come from widely distributed species, and have not considered if the same processes can be scaled down to single populations. Here, we test the CMH on a species composed of a single population: the Island Scrub-Jay (Aphelocoma insularis), endemic to a 250 km2 island. We examined microsatellite data from a quarter of the total population and found that homozygosity increased toward the island's periphery. However, peripheral portions of the island did not exhibit higher genetic differentiation. Simulations revealed that highly localized dispersal and small total population size, but not spatial variation in population density, were critical for generating fine-scale variation in homozygosity. Collectively, these results demonstrate that microevolutionary processes driving spatial variation in genetic diversity among populations can also be important for generating spatial variation in genetic diversity within populations.
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