Colonization Events Research Articles

Disentangling fine‐ and large‐scale colonization processes in metapopulation dynamics: a case study on a threatened epiphytic bryophyte

Understanding the colonization process of species living in a dynamic fragmented habitat is essential to assess their persistence. In the metapopulation theory, the colonization of a species can be quantified using the turnover of occupancy in habitat patches. However, this approach is often limited by the feasible size of surveyed areas. Because many species are capable of long‐distance dispersal, such areas often constitute open systems undergoing colonization of propagules coming from outside, the ‘background deposition'. We focus on disentangling background deposition from local colonization among surveyed patches when analyzing turnover. We consider two spatial scales: 1) focal areas where all patches are monitored over time; 2) a larger extent, encompassing the focal areas, over which the distribution of the target species is quantified with a coarse spatial grain. Our key idea is to use the regional connectivity of focal areas within the larger scale as a covariate when analyzing colonization events within focal areas. A positive effect of regional connectivity on the colonization probability of patches may indicate background deposition. We applied this approach to the epiphytic bryophyte Dicranum viride in a managed temperate deciduous forest, considering phorophyte trees as patches, forest stands as focal areas and the whole forest as the larger scale. We combined a fine‐grained turnover survey of occupied trees within three forest stands (~ 3 ha) with a coarse‐grained snapshot of D. viride distribution over the forest (~ 15 000 ha). Regional connectivity came out as the most significant factor, with a strong positive effect on colonization probability within stands. However, it was attributed to sources in the immediate vicinity of focal stands, suggesting a short‐ranged colonization process occurring across stands' borders rather than long‐distance background deposition. Our results thus call for maintaining a stepping‐stone of habitat across the forest through time to improve D. viride persistence.

Refugia within refugium of Geranium yesoense varieties: a follow-up study using chloroplast genome sequencing data of specimens from Mt. Asama, Japan

Abstract Recent phylogeographical studies have revealed that refugia sometimes retain high levels of genetic heterogeneity due to multiple colonization events, a phenomenon defined as ‘refugia within refugium’. In previous research, we reported a complex genetic structure within the Geranium yesoense complex, an alpine plant found in an interglacial refugium at high elevation in Central Japan, probably resulting from multiple colonization and hybridization events. However, we were unable to evaluate instances of introgression due to limited sample size. In the present study, we performed additional chloroplast genome sequencing, along with Sanger sequencing of selected chloroplast DNA regions, to elucidate the phylogenetic relationships among the refugial populations. The chloroplast genome sequence of a sample from Mt. Asama (an important refugium) was nested within the northern lineage (i.e. var. yesoense and var. pseudopratense), and haplotypes from Mt. Asama and Mt. Ibuki were also grouped with those of the northern lineage. Although our previous study suggested hybridization events between northern and southern lineages (i.e. var. nipponicum) at Mt. Asama, haplotypes from the southern lineage were not detected at range margins. This suggests that directional introgression occurred in these regions. Overall, our results further support that genetic heterogeneity within these refugia was amplified by recolonization and hybridization during past climate oscillations.

A simple genetic method to distinguish mule deer and bighorn sheep fecal pellets and its application to detecting bighorn sheep colonization events in California

Bighorn sheep (Ovis canadensis) habitat frequently is geographically discontinuous and the metapopulation model fits this species well. Consequently, extinction-colonization dynamics are important and need to be monitored. Much of the conservation history of bighorn sheep, however, was based on a theory that natural colonization is not part of the biology of this species. That theory is not supported by a growing body of evidence that natural colonization of vacant habitat does occur in this species. Here I present a simple PCR test that distinguishes bighorn sheep fecal pellets from those of mule deer (Odocoileus hemionus) as a useful tool in documenting bighorn sheep occupancy where mule deer are present. I include examples from California of applications of this method to investigate potential colonization events.

Differences in phenotypic variance between old and young congeneric species on a small island

AbstractAimInsular environments theoretically promote within‐species phenotypic variance, in part but not only because insular species enjoy a lower number of trophic interactions than their mainland counterparts. However, environmental factors apparently confound empirical comparisons between insular and mainland systems. To address this issue, we studied sympatric, congeneric species from the same small island, but that stemmed from separate colonization events. We predicted that the time since the species had colonized the island would correlate positively with the within‐species variance in morphometrics.LocationLifu island, New Caledonia, South Pacific.TaxaZosterops inornatus, Z. minutus, Z. lateralis (Passeriformes).MethodsWe measured seven morphological traits and used principal component analysis to compute axes of variation.ResultsThe within‐species variance in bill size and in feet/tail ratio corrected for body size increased with the estimated time since the species had been on the island. A similar but non‐significant trend existed for body size and bill width.Main ConclusionsThe morphometrics of the three species of Zosterops birds from Lifu supported the hypothesis that insular environments promote within‐species phenotypic variance, and cast a new light on the role of competition in the erosion of phenotypic variance.

Predator recognition learning by northern redbelly dace Chrosomus eos from a small kettle lake with a dynamic predator community

Predation, and the risk of predation, shape the ecology, behavior, and evolution of many species. Small fishes navigate a perilous landscape of risk in the shallow waters of the littoral zone. Moreover, in small lakes, the predator community can be dynamic due to stochastic colonization and extirpation events. These conditions select for the ability by small fish to acquire recognition of novel predators through associative learning. Chemical cues associated with predation events, such as damage-released chemical cues from conspecifics, and the odor of predators, inform prey of the presence of risk, and facilitate acquired recognition of novel predator odor. Deming Lake, MN, is a small meromictic lake with intermittent connections to neighboring lakes in the watershed. Annual sampling of the littoral fish community between the years 2000 and 2023 reveals a history of colonization and extirpation by relatively large-bodied species such as yellow perch Perca flavescens and pumpkinseed sunfish Lepomis gibbosus. Ice cover data, combined with limnological depth profiles of dissolved oxygen, confirm that dissolved oxygen is limiting during the winter and consistent with the hypothesis that extirpation of large-bodied species in Deming Lake is likely due to winter anoxia. These data set the stage for an experimental demonstration of acquired recognition of the odor of allopatric rock bass Ambloplites rupestris by bass-naïve northern redbelly dace Chrosomus eos from Deming Lake. Rock bass have been absent from Deming Lake since at least the year 2000. Predator-recognition learning allows redbelly dace, and many other small-bodied fishes that face variable predator species over ontogenetic, spatial, and temporal scales, a mechanism to adapt quickly to indicators of predation risk.

Tropical forest birds after 20 years of the establishment of a reservoir: Extinction, colonization, and recolonization events

Reservoirs are fundamental for human well-being but can cause landscape changes (e.g., habitat fragmentation and loss), altering biodiversity and ecosystem services. However, we know little about reservoir long-term effects on bird communities of tropical rainforests at different temporal scales. We assessed species richness and composition changes in four consecutive periods in a reservoir area in the Colombian Tropical Andes. After 20 years of monitoring avifauna within the reservoir, we recorded 360 bird species along with 47 local extinction and 184 colonization events. We found that species richness increased by 42% during the first 11 years after reservoir establishment. After that, changes in species bird composition were largely explained by species turnover. Eighty-two percent of the expected species in the region were recorded within the reservoir area. Also, forests surrounding the reservoir are a habitat for several threatened bird species. Bird community changes observed can be explained by secondary succession, changes in vegetation cover (i.e., increase in forest area), the transformation of aquatic ecosystems, forest protection, and restoration programs focused on biodiversity conservation. Long-term systematic bird sampling in tropical forests is key to understanding biodiversity dynamics and the effectiveness of conservation actions.

Genomic Basis of Freshwater Adaptation in the Palaemonid Prawn GenusMacrobrachium: Convergent Evolution Following Multiple Independent Colonization Events.

Adaptation to different salinity environments can enhance morphological and genomic divergence between related aquatic taxa. Species of prawns in the genus Macrobrachium naturally inhabit different osmotic niches and possess distinctive lifecycle traits associated with salinity tolerance. This study was conducted to investigate the patterns of adaptive genomic divergence during freshwater colonization in 34 Macrobrachium species collected from four continents; Australia, Asia, North and South America. Genotyping-by-sequencing (GBS) technique identified 5018 loci containing 82,636 single nucleotide polymorphisms (SNPs) that were used to reconstruct a phylogenomic tree. An additional phylogeny was reconstructed based on 43 candidate genes, previously identified as being potentially associated with freshwater adaptation. Comparison of the two phylogenetic trees revealed contrasting topologies. The GBS tree indicated multiple independent continent-specific invasions into freshwater by Macrobrachium lineages following common marine ancestry, as species with abbreviated larval development (ALD), i.e., species having a full freshwater life history, appeared reciprocally monophyletic within each continent. In contrast, the candidate gene tree showed convergent evolution for all ALD species worldwide, forming a single, well-supported clade. This latter pattern is likely the result of common evolutionary pressures selecting key mutations favored in continental freshwater habitats Results suggest that following multiple independent invasions into continental freshwaters at different evolutionary timescales, Macrobrachium taxa experienced adaptive genomic divergence, and in particular, convergence in the same genomic regions with parallel shifts in specific conserved phenotypic traits, such as evolution of larger eggs with abbreviated larval developmental.

A new freshwater species of Gnorimosphaeroma (Crustacea, Isopoda, Sphaeromatidae) from Chichi-jima Island, Ogasawara Islands, Japan

This study describes Gnorimosphaeroma rivularesp. nov. from a stream on Chichi-jima Island, Ogasawara Islands, Japan. This is the second freshwater species of Gnorimosphaeroma and the third Sphaeromatidae from oceanic islands. Gnorimosphaeroma rivularesp. nov. is morphologically similar to G. boninense Nunomura, 2006, G. naktongense Kwon & Kim, 1987 and G. saijoense Nunomura, 2013. However, G. rivularesp. nov. differs from these species in various morphological features, such as the shape of pleotelson and pereopod 2, relative length of antennule peduncular articles and pleopod 3 rami, number of setae on maxillula and maxilliped, and setation on pereopod 3. Phylogenetic analyses revealed that G. akanense is sister to G. saijoense, and together they are sister to G. hokurikuense. This three taxa clade is sister to G. rivularesp. nov. with G. iriei basal to them all. Our analysis concludes that G. boninense from Haha-jima Island, Ogasawara Islands is only distantly related to G. rivulare and may represent an independent colonization event.

Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis

BackgroundThe microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silicone tubes.ResultsFollowing the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the silicone tube, while the subsequent bacteria-bacteria interactions are the main driver of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early recolonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization.ConclusionsOur results show that early recolonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host ontogeny.-JTs9knfCQzALX-coLcUGoVideo

The trace fossil Thalassinoides paradoxicus Kennedy, 1967 revisited from its type locality (Albian-Cenomanian chalk, SE England)

The trace fossil Thalassinoides includes ichnospecies that have been recognised for a long time and widely used in the interpretation of depositional systems. Despite its broad occurrence, the ichnotaxonomic status of this important ichnogenus is far from being unmistakable, which in turn hampers its application in palaeoenvironmental reconstructions. One of the most common ichnospecies is Thalassinoides paradoxicus, originally described from the Paradoxica Bed of the Lower Chalk in the Hunstanton Cliff in SE England. To demarcate this characteristic form from similar ichnospecies, T. paradoxicus is reexamined and described from its type locality. It is characterised by an ‘irregular, very extensive horizontal burrow network, occurring at several levels, connected by vertical shafts’ (Kennedy), but its morphological variability also includes a range of significant architectural elements as well as burrow portions with a laminated wall, scratches and pellets. A series of colonisation events along omission surfaces can be reconstructed based on the occurrence of several burrow generations. T. paradoxicus is an important constituent of shallow-marine environments and subtle variations in morphology may help to constrain facies interpretations. Based on modern analogues and finds of body fossils within their burrows, decapod crustaceans (foremost callianassid shrimp) are known producers of T. paradoxicus from the Mesozoic onwards, whereas older records can be attributed to other malacostracans but also trilobites.

Addressing Native Hawaiian historical trauma: Opportunities for increased economic, environmental, and social advancement

Many people view Hawaiʻi as a tropical paradise where people can relax on idyllic beaches. However, for many Native Hawaiians, the Indigenous people of Hawaiʻi, the desire to continue to reside in their homelands has become impossible. Native Hawaiians have lower socio-economic status, home ownership, and educational attainment compared to non-Hawaiians. Simultaneously, Native Hawaiians have higher rates of chronic disease, asthma, and mental health issues, which impact their quality of life. Despite efforts to address these stubborn problems, the gap between the Indigenous Native Hawaiian community and those that settled these islands continue to exist. Native Hawaiian scholars have attributed these persistent challenges to the historical trauma that the community has experienced and continues to experience stemming from the mass trauma events of colonization. Although the community acknowledges the heavy impact that historical trauma has had on Native Hawaiians, many policymakers and individuals in position of authority have expressed a need for evidence of this concept. This project seeks to develop a scale to measure Native Hawaiian historical trauma to support evaluation and advocacy efforts. Moreover, healing Native Hawaiian historical trauma would facilitate increased economic mobility, improved environmental policies, and an enriched social advancement.

Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion

In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein–protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.

A new genus and species of toad from Mount Kenya illuminates East African montane biogeography

Abstract Discoveries of new species can greatly impact our understanding of the biogeography of a region. For example, groups of amphibian lineages restricted to the Afrotemperate forests of Tanzania and Ethiopia are indicative of a shared biogeographical history of this highly discontinuous ecosystem. Curiously, many of these lineages are absent from the geographically intermediate Kenyan highlands. This phylogeographical interval is generally considered to be attributable to the younger, volcanic origins of much of the Kenyan highlands, and thus an amphibian fauna that is derived largely from recent colonization events rather than comprising older relicts. Contrasting with this view, here we report on the discovery of a single specimen of Bufonidae (true toad) from Mount Kenya. The specimen belongs to a species new to science and deserves recognition at the generic level owing to its notable molecular phylogenetic and morphological divergences from other described taxa. It is most closely related to the Tanzanian genera Churamiti and Nectophrynoides. The discovery of this new toad and its association with Afrotemperate species is significant because it links Kenya to the biogeographically more ancient Tanzanian mountains and supports the potential longevity of the Afrotemperate forests in Kenya. Broadly, it highlights that we are still adding major branches to the phylogeny of anurans.

Slowing taxon cycle can explain biodiversity patterns on islands: Insights into the biogeography of the tropical South Pacific from molecular data

AbstractIslands in the tropical Pacific Ocean are renowned for high biodiversity and endemism despite having relatively small landmasses. However, our knowledge of how this biodiversity is formed remains limited. The taxon cycle, where well‐dispersed, earlier colonizers become displaced from coastal to inland habitats by new waves of colonizers, producing isolated, range‐restricted species, has been proposed to explain current biodiversity patterns. Here, we integrate the outcomes of phylogenetic studies in the region to investigate the sources, age, number of colonizations, and diversification of 16 archipelagos in the tropical and subtropical South Pacific. We then evaluate whether the results support the taxon cycle as a plausible mechanism for these observations. We find that most species in the Pacific arrived less than 5 Mya from geographically close sources, suggesting that colonization by new taxa is a frequent and ongoing process. Therefore, our findings are broadly consistent with the theory of the Taxon Cycle, which posits that ongoing colonization results in the gradual displacement of established lineages. Only the oldest archipelagos, New Caledonia and Fiji, do not conform to this trend, having proportionally less recent colonization events, suggesting that the taxon cycle may slow on older islands. This conclusion is further validated by New Caledonia having lower diversification rate estimates than younger islands. We found that diversification rates across archipelagos are negatively correlated with area and age. Therefore, a taxon cycle that slows with island age appears to be a suitable concept for understanding the dynamic nature and biodiversity patterns of the Pacific Islands.

Predicting the spatial expansion of an animal population with presence-only data.

Predictive models can improve the efficiency of wildlife management by guiding actions at the local, landscape and regional scales. In recent decades, a vast range of modelling techniques have been developed to predict species distributions and patterns of population spread. However, data limitations often constrain the precision and biological realism of models, which make them less useful for supporting decision-making. Complex models can also be challenging to evaluate, and the results are often difficult to interpret for wildlife management practitioners. There is therefore a need to develop techniques that are appropriately robust, but also accessible to a range of end users. We developed a hybrid species distribution model that utilises commonly available presence-only distribution data and minimal demographic information to predict the spread of roe deer (Capreolus caprelous) in Great Britain. We take a novel approach to representing the environment in the model by constraining the size of habitat patches to the home-range area of an individual. Population dynamics are then simplified to a set of generic rules describing patch occupancy. The model is constructed and evaluated using data from a populated region (England and Scotland) and applied to predict regional-scale patterns of spread in a novel region (Wales). It is used to forecast the relative timing of colonisation events and identify important areas for targeted surveillance and management. The study demonstrates the utility of presence-only data for predicting the spread of animal species and describes a method of reducing model complexity while retaining important environmental detail and biological realism. Our modelling approach provides a much-needed opportunity for users without specialist expertise in computer coding to leverage limited data and make robust, easily interpretable predictions of spread to inform proactive population management.

Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group

Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 ‘forms’ in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.

Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests.

An open and dry vegetation belt separates Amazonia (AM) and the Atlantic Forest (AF). Evidence from palaeoclimatic and phylogenetic studies suggests past connections between these forests during cycles of increased humidity through the formation of forest corridors. The distinctive northern AF avifauna is known to have affinities both with AM and the southern AF. Still, the extent of how these two regions contributed to the assemblage of this avifauna remains poorly understood. Using historical demographic analyses and comparative phylogeography based on sub-genomic genetic sampling, we assessed how past connections between AM and AF led to shared vicariance and colonization events in four avian AF endemic taxa. Our results supported the occurrence of humid forest corridors promoting the contact between AF and AM populations and suggested two vicariant events and two colonization events from AF to AM. Population divergences were mostly non-synchronous and occurred multiple times during the Pleistocene. Historical gene flow was prevalent across study groups, supporting migration flows after the initial separation between AM and AF - a pattern previously unknown in birds between these regions. Idiosyncratic histories and divergent demographic syndromes suggest that organisms' responses to climate-driven habitat shifts broadly depend on their ecological attributes. This study strengthened our knowledge of past connections between AM and AF and provided demographic scenarios amenable for testing in other groups of co-distributed organisms.

Independent origins or single dispersal? Phylogenetic study supports early Cenozoic origin of three endemic Indo‐Sri Lankan Lygosomine skink genera

AbstractThe Western Ghats‐Sri Lanka biodiversity hotspot is home to three endemic Lygosomine (Reptilia, Scincidae) skink genera—Kaestlea, Ristella and Lankascincus. Phylogenetic reconstructions in the past have suggested a sister relationship between the Western Ghats endemic Ristella and the Sri Lankan endemic Lankascincus, while the placement of Kaestlea has been uncertain. We reconstruct a global, genus‐level, multi‐locus phylogeny of the sub‐family Lygosominae to ask if these endemic genera share an immediate common ancestor, that is, did they arise from a single dispersal event? Furthermore, to understand the possible centres of origin and dispersal routes of these three genera of Indo‐Sri Lankan skinks, we construct a time‐calibrated phylogeny and perform ancestral range evolution. We find that Kaestlea does not share an immediate ancestor with Ristella + Lankascincus. Therefore, their presence in the Indian subcontinent results from two independent colonization events. Both these dispersal events likely occurred during the late Palaeocene‐early Eocene from the Asian landmass. Our molecular dating and ancestral range evolution analyses add further evidence of probable transoceanic dispersal in skinks and early land connections between the Indian subcontinent and Asia. It also reveals that these skinks were some of the earliest lizards to disperse into the Indian subcontinent.

Highly diverse dynamics of Pseudomonas aeruginosa colonization from initial detection in cystic fibrosis patients: A 7-year longitudinal genetic diversity study

In cystic fibrosis (CF), Pseudomonas aeruginosa (Pa) is a major pathogen that can persistently colonize patients. Genetic studies showed a high diversity of Pa, the success of widespread or ‘international’ clones and described epidemic clones in CF and Epidemic High-Risk (ERH) clones. Here, we characterized Pa genetic diversity over time after first colonization in CF patients, with the aim of accurately describing the dynamics of colonization in a context of scarce longitudinal studies including the first isolated Pa strain. Results represent the first genotyping data based on multilocus sequence typing (MLST) available for CF Pa in France. Forty-four CF patients with a first Pa colonization were included; 265 strains collected over 7 years in these patients were genotyped by multiplex rep-PCR, MLST, pulsed-field gel electrophoresis and/or whole genome sequencing. Forty-one sequence types were identified: 4 were unknown, 22 never previously reported for CF patients, and 6 corresponded to widespread clones colonizing 16 patients (36%). Unrelated strains were identified in 41 patients (93%). Twenty-six patients (59%) presented a recurrence during the study period. No specific clones were associated with transient, recurrent or persistent colonization. Our longitudinal study revealed that 9 of the 26 patients with recurrence (35%) harbored strains of different genotypes. Great genetic diversity was observed among initial Pa isolates excluding any cross-transmission. Persistent colonization may appear more complex than expected, imitating persistence, with successive colonization events by unrelated Pa.

Unraveling the complex phylogeographic history of freshwater fishes in Lower Central America: A study of the electric fish Brachyhypopomus occidentalis

Lower Central America (LCA) has a complex biogeographic history shaped by the rise of the Isthmus of Panama and the global climatic oscillations of the Pleistocene. These events have been crucial in structuring biodiversity in LCA, but their consequences for the distribution and partitions of genetic diversity across the region remain to be elucidated. We combined complete mitochondrial genomes and nuclear ultraconserved elements (UCEs) to study the phylogeographic history and population genetic structure of the electric fish Brachyhypopomus occidentalis in LCA. Our results are consistent with the known phylogeographic history of B. occidentalis in LCA, but we update this history in several important ways that help illuminate the phylogeographic history of freshwater fishes in the region. We provide: i) support for three waves of colonization, two of which occurred prior to the final closure of the Panama Isthmus; ii) a more precise understanding of each colonization event, with evidence for a larger footprint of the first event, as well as genetic exchange across the continental divide in subsequent events; and iii) evidence for high levels of previously unrecognized population genetic structure across LCA. This updated model of colonization and diversification of B. occidentalis consists of three waves of dispersal and colonization, which triggered the evolution of geographic breaks in both nuclear and mitochondrial genomes across LCA. These processes are tightly linked to the dynamic uplift of the Isthmus, recent volcanic activity in the region, and the sea-level oscillations of the Pleistocene. These results improve previous phylogeographic inferences regarding the distribution and diversification of freshwater fishes in LCA, and generate testable hypotheses to guide future research exploring the factors shaping biodiversity in the region.