Colonization Events Research Articles

A framework for quantifying deviations from dynamic equilibrium theory

AbstractAimIn an age of increased anthropogenic changes, it is crucially important to understand how and why ecological communities change. Community assembly is governed by colonization and extinction processes, and the simplest model describing it is dynamic equilibrium (DE), which assumes that communities are shaped solely by stochastic colonization and extinction events. Deviations from this model can point to the role of species life histories, niches or human stressors acting on communities. Despite its potential to serve as a null model for community dynamics, there is currently no accepted methodology for identifying and measuring such deviations.InnovationHere we propose a new, easily applicable methodology for testing and quantifying deviations of empirically observed time series of community dynamics from the predictions and assumptions of the classical DE model, in which assemblages of independent species undergo stochastic colonization–extinction dynamics with constant rates. The methodology consists of a novel randomization‐based null model to generate synthetic time series (PARIS) and a set of statistics that quantify and test how different facets of community dynamics deviate from DE. These statistics are designed to test the assumptions of the theory, namely species independence and constancy of colonization and extinction rates, and the predictions of the theory regarding the magnitude of changes in species richness and composition.Main conclusionsTested against simulated data and a case study, the proposed methodology is shown to have good statistical properties: acceptable type I error rates, good statistical power and robustness against errors in the data. We discuss alternative methods and present guidelines for practical use of the methodology, hoping it will enhance the applicability of DE as a reference for studying changes in ecological communities.

How did the toad get over the sea to Skye? Tracing the colonisation of Scottish inshore islands by common toads (Bufo bufo)

Processes of island colonisation have long been of interest to biologists. Colonisation events themselves are rarely observed, but the processes involved may be inferred using genetic approaches. We investigated possible means of island colonisation by common toads (Bufo bufo) in western Scotland (the Isle of Skye and five neighbouring small islands), using evidence derived from nuclear microsatellites and mitochondrial (mt) DNA. Levels of microsatellite allelic richness for populations on Skye were high and comparable to adjacent mainland populations, but lower for populations on small islands. Pairwise measures of genetic distances between populations and a clustering algorithm were both suggestive of frequent gene flow between Skye and the mainland. For small islands the levels of genetic differentiation were higher, implying stronger isolation and no evidence for inbreeding. The distribution of mtDNA haplotypes broadly mirrored the genetic structure revealed by microsatellites. Reconciled with existing palaeoclimatological evidence, since the last glaciation, our findings rule out the possibility that the B. bufo populations stem from glacial refugia, or that recent anthropogenic transfer of toads is responsible for their current distribution. The most parsimonious explanation of our data is that the studied inshore islands have been repeatedly colonised via rafting from the mainland or neighbouring islands. This may give us insights into the processes likely to take place when ice sheets retreat poleward as a result of climate change. It also has implications for the colonisation of both native and invasive non-native species, and hence the biosecurity of island refugia.

Phylogeny identifies multiple colonisation events and Miocene aridification as drivers of South Asian bulbul (Passeriformes: Pycnonotidae) diversification

Phylogeny identifies multiple colonisation events and Miocene aridification as drivers of South Asian bulbul (Passeriformes: Pycnonotidae) diversification

New fossil discoveries illustrate the diversity of past terrestrial ecosystems in New Caledonia

New Caledonia was, until recently, considered an old continental island harbouring a rich biota with outstanding Gondwanan relicts. However, deep marine sedimentation and tectonic evidence suggest complete submergence of the island during the latest Cretaceous to the Paleocene. Molecular phylogenies provide evidence for some deeply-diverging clades that may predate the Eocene and abundant post-Oligocene colonisation events. Extinction and colonization biases, as well as survival of some groups in refuges on neighbouring paleo-islands, may have obscured biogeographic trends over long time scales. Fossil data are therefore crucial for understanding the history of the New Caledonian biota, but occurrences are sparse and have received only limited attention. Here we describe five exceptional fossil assemblages that provide important new insights into New Caledonia’s terrestrial paleobiota from three key time intervals: prior to the submersion of the island, following re-emergence, and prior to Pleistocene climatic shifts. These will be of major importance for elucidating changes in New Caledonia’s floristic composition over time.

The nose is the best niche for detection of experimental pneumococcal colonisation in adults of all ages, using nasal wash

Previous studies have suggested that the pneumococcal niche changes from the nasopharynx to the oral cavity with age. We use an Experimental Human Pneumococcal Challenge model to investigate pneumococcal colonisation in different anatomical niches with age. Healthy adults (n = 112) were intranasally inoculated with Streptococcus pneumoniae serotype 6B (Spn6B) and were categorised as young 18–55 years (n = 57) or older > 55 years (n = 55). Colonisation status (frequency and density) was determined by multiplex qPCR targeting the lytA and cpsA-6A/B genes in both raw and culture-enriched nasal wash and oropharyngeal swab samples collected at 2-, 7- and 14-days post-exposure. For older adults, raw and culture-enriched saliva samples were also assessed. 64% of NW samples and 54% of OPS samples were positive for Spn6B in young adults, compared to 35% of NW samples, 24% of OPS samples and 6% of saliva samples in older adults. Many colonisation events were only detected in culture-enriched samples. Experimental colonisation was detected in 72% of young adults by NW and 63% by OPS. In older adults, this was 51% by NW, 36% by OPS and 9% by saliva. The nose, as assessed by nasal wash, is the best niche for detection of experimental pneumococcal colonisation in both young and older adults.

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus.

The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.

Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.

An Early Oligocene age for the oldest known monkeys and rodents of South America

The Santa Rosa fossil locality in eastern Perú produced the first Paleogene vertebrate fauna from the Amazon Basin, including the oldest known monkeys from South America. This diverse paleofauna was originally assigned an Eocene age based largely on the stage of evolution of the site's caviomorph rodents and marsupials. Here, we present detrital zircon dates that indicate that the maximum composite age of Santa Rosa is 29.6 ± 0.08 Ma (Lower Oligocene), although several zircons from Santa Rosa date to the Upper Oligocene. The first appearance datum for Caviomorpha in South America is purported to be the CTA-27 site in the Contamana region of Perú, which is hypothesized to be ∼41 Ma (Middle Eocene) in age. However, the presence of the same caviomorph species and/or genera at both CTA-27 and at Santa Rosa is now difficult to reconcile with a >11-My age difference. To further test the Middle Eocene age estimate for CTA-27, we ran multiple Bayesian tip-dating analyses of Caviomorpha, treating the ages of all Paleogene species from Perú as unknown. These analyses produced mean age estimates for Santa Rosa that closely approximate the maximum 29.6 ± 0.08 Ma composite date provided by detrital zircons, but predict that CTA-27 is much younger than currently thought (∼30 Ma). We conclude that the ∼41 Ma age proposed for CTA-27 is incorrect, and that there are currently no compelling Eocene records of either rodents or primates in the known fossil record of South America.

Relationship Between Microbial Growth and Hydraulic Properties at the Sub-Pore Scale

Accumulation of microbial biomass and its influence on porous media flow were investigated under saturated flow conditions. Microfluidic experiments were performed with model organisms, and their accumulation was observed in the pore space and on the sub-pore scale. Time-lapse optical imaging revealed different modes of biomass accumulation through primary colonization, secondary growth, and filtration events, showing the formation of preferential flow pathways in the flooding domain as result of the increasing interstitial velocity. Navier–Stokes–Brinkmann flow simulations were performed on the segmented images—a digital-twin approach—considering locally accumulated biomass as impermeable or permeable based on optical biomass density. By comparing simulation results and the experimental responses, it was shown that accumulated biomass can be considered as a permeable medium. The average intra-biomass permeability was determined to be 500 ± 200 mD, which is more than a factor of 10 larger than previously assumed in modeling studies. These findings have substantial consequences: (1) a remaining interstitial permeability, as a result of the observed channel formation and the intra-biomass permeability, and (2) a potential advective nutrient supply, which can be considered more efficient than a purely diffusive supply. The second point may lead to higher metabolic activity and substrate conversion rates which is of particular interest for geobiotechnological applications.

Determinism and stochasticity in the spatial–temporal continuum of ecological communities: the case of tropical mountains

Ecological communities are assembled in a spatial–temporal continuum. However, we still have a poor understanding of the relative importance of different mechanisms structuring community composition (i.e. beta‐diversity) in space and time. In this study, we start by introducing a conceptual model that capitalizes upon the core‐occasional species concept to predict that the assembly process in tropical mountains is driven by the deterministic turnover of core species in space via habitat sorting, but the turnover of occasional species through time via stochastic events of colonization and local extinctions. We then propose a general analytical framework that allows assessing these predictions by partitioning the total variance of a species‐by‐site‐by‐time matrix (i.e. total beta‐diversity) among its purely spatial (variation in space independent of time), purely temporal (variation in time independent of space) and spatiotemporal (i.e. variation across different sites across different moments in time) components. Through simulation models, we provided theoretical support that the proposed analytical framework is suitable to test the predictions derived from our conceptual model. We then used this framework to identify general patterns and quantify the relative importance of processes underlying the spatial and temporal organization of ten distinct insect metacommunities along a tropical elevational gradient. As predicted, we found that, across taxa, spatial beta‐diversity was mainly explained by environmental variation alone: a pattern that indicates the spatial turnover of core species. In contrast, temporal beta‐diversity could not be distinguished from the expectation of null models where communities are simply represented by random draws from species pools: a pattern that indicates a temporal turnover of occasional species within communities. Taken together, our findings illustrate how our conceptual model and quantitative framework can articulate a better understanding of community assembly in space and time.

Genomic footprints of Quaternary colonization and population expansion in the Patagonian‐Fuegian region rules out a separate southern refugium in Tierra del Fuego

AbstractAimDuring the glacial phases, the Andean slopes of southern South America were covered by ice sheets, causing the isolation of many species in glacial refugia. This work aimed to test the number and putative location of glacial refugia in southern South America and establish the sources, timing and direction of post‐glacial colonization events.LocationSouthern South America, Patagonia.TaxonOlive mouse (Abrothrix olivacea).MethodsUsing exome capture, we genotyped 7339 SNPs in 172 specimens of A. olivacea collected at 21 localities distributed across the steppe, grasslands, and forests in the Patagonian‐Fuegian region and seven specimens from two other species of Abrothrix. Based on the effective migration rate, principal component analysis, and admixture composition, we first study the population structure of A. olivacea. The source and direction of colonization events were inferred using the directionality index and standard population genetic analyses. To study the role of the glacial phases, we performed a bayesian demographic analysis to infer divergences times and ancestral population sizes.ResultsPopulation genomic analyses based on SNPs of more than 7000 exons identified three Patagonian genetic clusters: Valdivian forests, continental Magellan forests, and a combination of continental open biomes and Tierra del Fuego. The directionality index supports a single source in northwestern forests, in line with a Valdivian forest refugium, from which the post‐glacial colonization may have started. The effective diversity rate, the onset of population expansions and divergence times also support a Valdivian forest refugium and rule out a separate southern refugium in Tierra del Fuego.Main conclusionsOur results support a coastal refugium located in or near the previously proposed Valdivian refugium and reject in situ differentiation in Tierra del Fuego. More in general, our demographical analysis reveals the role of the Last Glacial Maximum in affecting the population dynamics (i.e., contraction and expansion) of A. olivacea and in fostering the geographical diversification of populations.

The Potential of Jenderal Soedirman's Short Film as Learning Media in National Events of the Colonial Period’s Material for Fifth Graders: A Semiotics Analysis

The stories of Jenderal Soedirman, one of the national instrumental figures in seizing Indonesia's independence from the invaders, have been visualized in many films. Films containing events about the struggle for independence need to be studied, understood and remembered so that the values of nationalism are embedded. This film has the potential to be used as a learning media in packaging stories into interesting and meaningful learning for elementary school students. This leads researchers to analyze Jenderal Soedirman’s short film as learning media on the IPS national events of the time colonization of 5th graders of elementary school. This study used a qualitative approach in observing an individual behavior and to describe the data of research’s findings in detail and moderation. The research method used was Roland Barthes’s semiotic analysis that focused on signs and symbols as markers interpreted by denotation, connotation and myth on the film. The data collecting techniques used were observation, student's journal, questionnaires and documentation. Based on research and discussion of semiotic analysis of Jenderal Soedirman’s short film as learning media on three meanings, it is evident that researchers can better understand the hidden meaning contained in the film. The researchers deeply identify the figure of Jenderal Soedirman, the myth believed by the Indonesian freedom people during his struggle and this film potential to be used as a learning media because it increases students’ learning motivation by a score of 3,00 earned in a reasonably good category.

The Malagasy enigmatic genus Apodocephala (Asteraceae), a new member of the tribe Athroismeae

Apodocephala is a small genus of nine species of shrubs and trees endemic to Madagascar and currently classified in the tribe Astereae (Asteraceae). However, its present tribal position has been questioned, as it lacks some of the salient morphological features of that tribe. This study includes for the first time DNA sequences from Apodocephala (two species including the type of the generic name) to test its phylogenetic position. Phylogenetic analyses based on sequence data from nuclear ribosomal (ETS and ITS) and plastid (ndhF and trnL–trnF) DNA regions, using Bayesian inference and maximum parsimony methods, strongly reject the placement of Apodocephala in the Astereae. Our results, instead, support its position as sister to the Malagasy monospecific genus Lowryanthus within the tribe Athroismeae. Morphological comparison of these sister genera reveal similarities in cypsela morphology, and the inclusion of Apodocephala in the subtribe Lowryanthinae is proposed here. The tribe Athroismeae is now represented by ten genera (Anisochaeta, Anisopappus, Apodocephala, Artemisiopsis, Athroisma, Blepharispermum, Centipeda, Leucoblepharis, Lowryanthus and Symphyllocarpus), six of which occur in Madagascar. The Malagasy Athroismeae occur in all Malagasy terrestrial ecosystems (rainforests, deciduous dry forests, thicket spiny forests and savannas) and are likely the result of multiple independent colonization events mostly from mainland Africa. Citation: Bengtson A., Anderberg A. A. & Razafimandimbison S. G. 2021: The Malagasy enigmatic genus Apodocephala (Asteraceae), a new member of the tribe Athroismeae. – Willdenowia 51: 221–230. Version of record first published online on 10 August 2021 ahead of inclusion in August 2021 issue.

Establishment of Gut Microbiome During Early Life and Its Relationship With Growth in Endangered Crested Ibis (Nipponia nippon).

Gut microbiota during early life could influence host fitness in vertebrates. Studies on how gut microbiota colonize the gut in birds using frequent sampling during early developmental stages and how shifts in microbiota diversity influence host growth are lacking. Here, we examine the microbiome profiles of 151 fecal samples from 14 young crested ibis (Nipponia nippon), an endangered bird species, collected longitudinally across 13 time points during the early stages of development and investigated their correlation with host growth. Gut diversity showed a non-linear change during development, which involved multiple colonization and extinction events, mainly associated with Proteobacteria and Firmicutes. Gut microbiota in young crested ibis became more similar with increasing age. In addition, gut microbiota exhibited a strong temporal structure and two specific developmental stages; the beginning of the latter stage coincided with the introduction of fresh loach, with a considerable increase in the relative abundance of Fusobacteria and several Firmicutes, which may be involved in lipid metabolism. Crested ibis chick growth rate was negatively correlated with gut microbiota diversity and negatively associated with the abundance of Halomonadaceae, Streptococci, Corynebacteriaceae, and Dietziaceae. Our findings highlight the importance of frequent sampling when studying microbiome development during early stages of development of vertebrates. The role of microbial diversity in host growth during the early stages of development of birds warrants further investigations.

Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae).

Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as “Eastern” and “Southern”. These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans‐Mexican Volcanic Belt and Chiapan–Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans‐Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.

Genomic data reveal the biogeographical and demographic history of Ammospiza sparrows in northeast tidal marshes

AbstractAimShaped by climate change and sea‐level rise, tidal salt marshes represent ephemeral systems that are home to only a few species. The dynamic ecological histories of these habitats, however, render it challenging to reconstruct the complete biogeographical histories of their endemic taxa. To better understand the evolutionary history of tidal marsh endemic sparrows, we employ genomic data to evaluate the timing and direction of tidal marsh colonization events and leverage these data to test a series of models describing the biogeographical history of our study taxa.LocationNorth America.TaxonAmmospiza Sparrows.MethodsWe sampled 54 individuals from the Ammospiza clade from freshwater and saltwater habitats. We sequenced whole genomes and generated a dataset containing 21 million SNPs. Detailed phylogenomic analyses were conducted to identify relationships between tidal marsh and freshwater species. These phylogenies were then used to date divergence times and reconstruct the biogeographical history of the clade as well as identify historic signals of introgression.ResultsPhylogenies based on several million SNPs supported well‐resolved clades that correspond to all previous species designations. Demographic modelling within A. nelsoni provided further resolution into the subspecies topology. Phylogenetic and biogeographical reconstructions support a series of saltwater to freshwater colonization events, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time‐scales and some habitat transitions occurring as recently as 5,000 years ago.Main ConclusionsBiogeographical and phylogenomic reconstructions support an original freshwater origin of the Ammospiza sparrows currently inhabiting tidal marshes in North America. We also found strong evidence for a saltwater to freshwater transition in A. n. subvirgatus as opposed to the long hypothesized freshwater origin of this group. We conclude that the increased resolution from genomic data paired with an integrative framework of phylogenomic, demographic and biogeographical reconstructions is important for resolving evolutionary histories in complex and ephemeral environments.

Effect of vegetation cover and sediment type on 3D subsurface structure and shear strength in saltmarshes

AbstractThe vulnerability of saltmarshes to lateral erosion at their margin depends on the local biogeomorphological properties of the substrate. In particular, the 3D architecture of pore and root systems is expected to influence shear strength, with repercussions for the wider‐scale stability of saltmarshes. We apply X‐ray computed microtomography (μCT) to visualize and quantify subsurface structures in two UK saltmarshes at Tillingham Farm, Essex (silt/clay rich substrate) and Warton Sands (sand‐rich substrate), with four types of ground cover: bare ground, Spartina spp, Salicornia spp and Puccinellia spp. We extracted μCT structural parameters that characterize pore and root morphologies at each station, and compared them with field measurements of shear strength using a principal component analysis and correlation tests. The 3D volumes show that species‐dependent variations in root structures, plant colonization events and bioturbation activity control the morphology of macropores, while sediment cohesivity determines the structural stability and persistence of these pore structures over time, even after the vegetation has died. Areas of high porosity and high mean pore thickness were correlated to lower values of shear strength, especially at Tillingham Farm, where well‐connected vertical systems of macropores were associated with current or previous colonization by Spartina spp. However, while well‐connected systems of macropores may lower the local deformation threshold of the sediment, they also encourage drainage, promote vegetation growth and reduce the marsh vulnerability to hydrodynamic forces. The highest values of shear strength at both sites were found under Puccinellia spp, and were associated with a high density of mesh‐like root structures that bind the sediment and resist deformation. Future studies of marsh stability should ideally consider time series of vegetation cover, especially in silt/clay‐dominated saltmarshes, in order to consider the potential effect of preserved buried networks of macropores on water circulation, marsh functioning and cliff‐face erosion.

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

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 nonsister 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 overwater 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. [Biogeography; genomics, Indonesia; lizards; phylogeography; reptiles].

Colonizations cause diversification of host preferences: A mechanism explaining increased generalization at range boundaries expanding under climate change.

As species' poleward range limits expand under climate change, generalists are expected to be better colonists than specialists, extending their ranges faster. This effect of specialization on range shifts has been shown, but so has the reverse cause-effect: in a global meta-analysis of butterfly diets, it was range expansions themselves that caused increases in population-level diet breadth. What could drive this unexpected process? We provide a novel behavioral mechanism by showing that, in a butterfly with extensive ecotypic variation, Edith's checkerspot, diet breadths increased after colonization events as diversification of individual host preferences pulled novel hosts into population diets. Subsequently, populations that persisted reverted toward monophagy. We draw together three lines of evidence from long-term studies of 15 independently evolving populations. First, direct observations showed a significant increase in specialization across decades: in recent censuses, eight populations used fewer host genera than in the 1980s while none used more. Second, behavioral preference-testing experiments showed that extinctions and recolonizations at two sites were followed, at first by diversification of heritable preference ranks and increases in diet breadth, and subsequently by homogenization of preferences and contractions of diet breadth. Third, we found a significant negative association in the 1980s between population-level diet breadth and genetic diversity. Populations with fewer mtDNA haplotypes had broader diets, extending to 3-4 host genera, while those with higher haplotype diversity were more specialized. We infer that diet breadth had increased in younger, recently colonized populations. Preference diversification after colonization events, whether caused by (cryptic) host shifts or by release of cryptic genetic variation after population bottlenecks, provides a mechanism for known effects of range shifts on diet specialization. Our results explain how colonizations at expanding range margins have increased population-level diet breadths, and predict that increasing specialization should accompany population persistence as current range edges become range interiors.

Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data.

Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.