Evolutionary forces shaping genomic islands of population differentiation in humans

Background Levels of differentiation among populations depend both on demographic and selective factors: genetic drift and local adaptation increase population differentiation, which is eroded by gene flow and balancing selection. We describe here the genomic distribution and the properties of genomic regions with unusually high and low levels of population differentiation in humans to assess the influence of selective and neutral processes on human genetic structure. Methods Individual SNPs of the Human Genome Diversity Panel (HGDP) showing significantly high or low levels of population differentiation were detected under a hierarchical-island model (HIM). A Hidden Markov Model allowed us to detect genomic regions or islands of high or low population differentiation. Results Under the HIM, only 1.5% of all SNPs are significant at the 1% level, but their genomic spatial distribution is significantly non-random. We find evidence that local adaptation shaped high-differentiation islands, as they are enriched for non-synonymous SNPs and overlap with previously identified candidate regions for positive selection. Moreover there is a negative relationship between the size of islands and recombination rate, which is stronger for islands overlapping with genes. Gene ontology analysis supports the role of diet as a major selective pressure in those highly differentiated islands. Low-differentiation islands are also enriched for non-synonymous SNPs, and contain an overly high proportion of genes belonging to the 'Oncogenesis' biological process. Conclusions Even though selection seems to be acting in shaping islands of high population differentiation, neutral demographic processes might have promoted the appearance of some genomic islands since i) as much as 20% of islands are in non-genic regions ii) these non-genic islands are on average two times shorter than genic islands, suggesting a more rapid erosion by recombination, and iii) most loci are strongly differentiated between Africans and non-Africans, a result consistent with known human demographic history.

Towards a spatial understanding of trade-offs in sustainable development: A meso-scale analysis of the nexus between land use, poverty, and environment in the Lao PDR

In land systems, equitably managing trade-offs between planetary boundaries and human development needs represents a grand challenge in sustainability oriented initiatives. Informing such initiatives requires knowledge about the nexus between land use, poverty, and environment. This paper presents results from Lao PDR, where we combined nationwide spatial data on land use types and the environmental state of landscapes with village-level poverty indicators. Our analysis reveals two general but contrasting trends. First, landscapes with paddy or permanent agriculture allow a greater number of people to live in less poverty but come at the price of a decrease in natural vegetation cover. Second, people practising extensive swidden agriculture and living in intact environments are often better off than people in degraded paddy or permanent agriculture. As poverty rates within different landscape types vary more than between landscape types, we cannot stipulate a land use–poverty–environment nexus. However, the distinct spatial patterns or configurations of these rates point to other important factors at play. Drawing on ethnicity as a proximate factor for endogenous development potentials and accessibility as a proximate factor for external influences, we further explore these linkages. Ethnicity is strongly related to poverty in all land use types almost independently of accessibility, implying that social distance outweighs geographic or physical distance. In turn, accessibility, almost a precondition for poverty alleviation, is mainly beneficial to ethnic majority groups and people living in paddy or permanent agriculture. These groups are able to translate improved accessibility into poverty alleviation. Our results show that the concurrence of external influences with local—highly contextual—development potentials is key to shaping outcomes of the land use–poverty–environment nexus. By addressing such leverage points, these findings help guide more effective development interventions. At the same time, they point to the need in land change science to better integrate the understanding of place-based land indicators with process-based drivers of land use change.

A legacy of human-induced ecosystem changes: spatial processes drive the taxonomic and functional diversities of testate amoebae in Sphagnum peatlands of the Galápagos

Aim Our aims were to compare the composition of testate amoeba (TA) communities from Santa Cruz Island, Galápagos Archipelago, which are likely in existence only as a result of anthropogenic habitat transformation, with similar naturally occurring communities from northern and southern continental peatlands. Additionally, we aimed at assessing the importance of niche-based and dispersal-based processes in determining community composition and taxonomic and functional diversity. Location The humid highlands of the central island of Santa Cruz, Galápagos Archipelago. Methods We survey the alpha, beta and gamma taxonomic and functional diversities of TA, and the changes in functional traits along a gradient of wet to dry habitats. We compare the TA community composition, abundance and frequency recorded in the insular peatlands with that recorded in continental peatlands of Northern and Southern Hemispheres. We use generalized linear models to determine how environmental conditions influence taxonomic and functional diversity as well as the mean values of functional traits within communities. We finally apply variance partitioning to assess the relative importance of niche- and dispersal-based processes in determining community composition. Results TA communities in Santa Cruz Island were different from their Northern Hemisphere and South American counterparts with most genera considered as characteristic for Northern Hemisphere and South American Sphagnum peatlands missing or very rare in the Galápagos. Functional traits were most correlated with elevation and site topography and alpha functional diversity to the type of material sampled and site topography. Community composition was more strongly correlated with spatial variables than with environmental ones. Main conclusions TA communities of the Sphagnum peatlands of Santa Cruz Island and the mechanisms shaping these communities contrast with Northern Hemisphere and South American peatlands. Soil moisture was not a strong predictor of community composition most likely because rainfall and clouds provide sufficient moisture. Dispersal limitation was more important than environmental filtering because of the isolation of the insular peatlands from continental ones and the young ecological history of these ecosystems.

Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners

1. The spatial distribution of individual plants within a population and the population’s genetic structure are determined by several factors, like dispersal, reproduction mode or biotic interactions. The role of interspecific interactions in shaping the spatial genetic structure of plant populations remains largely unknown. 2. Species with a common evolutionary history are known to interact more closely with each other than unrelated species due to the greater number of traits they share. We hypothesize that plant interactions may shape the fine genetic structure of closely related congeners. 3. We used spatial statistics (georeferenced design) and molecular techniques (ISSR markers) to understand how two closely related congeners, Thymus vulgaris (widespread species) and T. loscosii (narrow endemic) interact at the local scale. Specific cover, number of individuals of both study species and several community attributes were measured in a 10 × 10 m plot. 4. Both species showed similar levels of genetic variation, but differed in their spatial genetic structure. Thymus vulgaris showed spatial aggregation but no spatial genetic structure, while T. loscosii showed spatial genetic structure (positive genetic autocorrelation) at short distances. The spatial pattern of T. vulgaris’ cover showed significant dissociation with that of T. loscosii. The same was true between the spatial patterns of the cover of T. vulgaris and the abundance of T. loscosii and between the abundance of each species. Most importantly, we found a correlation between the genetic structure of T. loscosii and the abundance of T. vulgaris: T. loscosii plants were genetically more similar when they were surrounded by a similar number of T. vulgaris plants. 5. Synthesis. Our results reveal spatially complex genetic structures of both congeners at small spatial scales. The negative association among the spatial patterns of the two species and the genetic structure found for T. loscosii in relation to the abundance of T. vulgaris indicate that competition between the two species may account for the presence of adapted ecotypes of T. loscosii to the abundance of a competing congeneric species. This suggests that the presence and abundance of close congeners can influence the genetic spatial structure of plant species at fine scales.

Assembly processes of invertebrate communities in springs across different spatial scales

Il presente lavoro ha lo scopo di comprendere i processi sottesi ai pattern di coesistenza tra le specie di invertebrati sorgentizi, distinguendo tra dinamiche stocastiche e deterministiche. Le sorgenti sono ecosistemi complessi e alcune loro caratteristiche (ad esempio l’insularità, la stabilità termica, la struttura ecotonale “a mosaico”, la frequente presenza di specie rare ed endemiche, o l’elevata diversità in taxa) le rendono laboratori naturali utili allo studio dei processi ecologici, tra cui i processi di assembly. Al fine di studiare queste dinamiche è necessario un approccio multi-scala, per questo motivi sono state prese in considerazione tre scale spaziali. A scala locale è stato compiuto un campionamento stagionale su sette sorgenti (quattro temporanee e tre permanenti) del Monte Prinzera, un affioramento ofiolitico vicino alla città di Parma. In questa area sono stati valutati l’efficacia e l’impatto ambientale di diversi metodi di campionamento e sono stati analizzati i drivers ecologici che influenzano le comunità. A scala più ampia sono state campionate per due volte 15 sorgenti della regione Emilia Romagna, al fine di identificare il ruolo della dispersione e la possibile presenza di un effetto di niche-filtering. A scala continentale sono state raccolte informazioni di letteratura riguardanti sorgenti dell’area Paleartica occidentale, e sono stati studiati i pattern biogeografici e l’influenza dei fattori climatici sulle comunità. Sono stati presi in considerazione differenti taxa di invertebrati (macroinvertebrati, ostracodi, acari acquatici e copepodi), scegliendo tra quelli che si prestavano meglio allo studio dei diversi processi in base alle loro caratteristiche biologiche e all’approfondimento tassonomico raggiungibile. I campionamenti biologici in sorgente sono caratterizzati da diversi problemi metodologici e possono causare impatti sugli ambienti. In questo lavoro sono stati paragonati due diversi metodi: l’utilizzo del retino con un approccio multi-habitat proporzionale e l’uso combinato di trappole e lavaggio di campioni di vegetazione. Il retino fornisce dati più accurati e completi, ma anche significativi disturbi sulle componenti biotiche e abiotiche delle sorgenti. Questo metodo è quindi raccomandato solo se il campionamento ha come scopo un’approfondita analisi della biodiversità. D’altra parte l’uso delle trappole e il lavaggio della vegetazione sono metodi affidabili che presentano minori impatti sull’ecosistema, quindi sono adatti a studi ecologici finalizzati all’analisi della struttura delle comunità. Questo lavoro ha confermato che i processi niche-based sono determinanti nello strutturare le comunità di ambienti sorgentizi, e che i driver ambientali spiegano una rilevante percentuale della variabilità delle comunità. Infatti le comunità di invertebrati del Monte Prinzera sono influenzate da fattori legati al chimismo delle acque, alla composizione e all’eterogeneità dell’habitat, all’idroperiodo e alle fluttuazioni della portata. Le sorgenti permanenti mostrano variazioni stagionali per quanto riguarda le concentrazioni dei principali ioni, mentre la conduttività, il pH e la temperatura dell’acqua sono più stabili. È probabile che sia la stabilità termica di questi ambienti a spiegare l’assenza di variazioni stagionali nella struttura delle comunità di macroinvertebrati. L’azione di niche-filtering delle sorgenti è stata analizzata tramite lo studio della diversità funzionale delle comunità di ostracodi dell’Emilia-Romagna. Le sorgenti ospitano più del 50% del pool di specie regionale, e numerose specie sono state rinvenute esclusivamente in questi habitat. Questo è il primo studio che analizza la diversità funzionale degli ostracodi, è stato quindi necessario stilare una lista di tratti funzionali. Analizzando il pool di specie regionale, la diversità funzionale nelle sorgenti non è significativamente diversa da quella misurata in comunità assemblate in maniera casuale. Le sorgenti non limitano quindi la diversità funzionale tra specie coesistenti, ma si può concludere che, data la soddisfazione delle esigenze ecologiche delle diverse specie, i processi di assembly in sorgente potrebbero essere influenzati da fattori stocastici come la dispersione, la speciazione e le estinzioni locali. In aggiunta, tutte le comunità studiate presentano pattern spaziali riconoscibili, rivelando una limitazione della dispersione tra le sorgenti, almeno per alcuni taxa. Il caratteristico isolamento delle sorgenti potrebbe essere la causa di questa limitazione, influenzando maggiormente i taxa a dispersione passiva rispetto a quelli a dispersione attiva. In ogni caso nelle comunità emiliano-romagnole i fattori spaziali spiegano solo una ridotta percentuale della variabilità biologica totale, mentre tutte le comunità risultano influenzate maggiormente dalle variabili ambientali. Il controllo ambientale è quindi prevalente rispetto a quello attuato dai fattori spaziali. Questo risultato dimostra che, nonostante le dinamiche stocastiche siano importanti in tutte le comunità studiate, a questa scala spaziale i fattori deterministici ricoprono un ruolo prevalente. I processi stocastici diventano più influenti invece nei climi aridi, dove il disturbo collegato ai frequenti eventi di disseccamento delle sorgenti provoca una dinamica source-sink tra le diverse comunità. Si è infatti notato che la variabilità spiegata dai fattori ambientali diminuisce all’aumentare dell’aridità del clima. Disturbi frequenti potrebbero provocare estinzioni locali seguite da ricolonizzazioni di specie provenienti dai siti vicini, riducendo la corrispondenza tra gli organismi e le loro richieste ambientali e quindi diminuendo la quantità di variabilità spiegata dai fattori ambientali. Si può quindi concludere che processi deterministici e stocastici non si escludono mutualmente, ma contribuiscono contemporaneamente a strutturare le comunità di invertebrati sorgentizi. Infine, a scala continentale, le comunità di ostracodi sorgentizi mostrano chiari pattern biogeografici e sono organizzate lungo gradienti ambientali principalmente collegati altitudine, latitudine, temperatura dell’acqua e conducibilità. Anche la tipologia di sorgente (elocrena, reocrena o limnocrena) è influente sulla composizione delle comunità. La presenza di specie rare ed endemiche inoltre caratterizza specifiche regioni geografiche.

A multivariate spatial analysis of vowel formants in American English

This paper presents the results of a multivariate spatial analysis of 38 vowel formant variables in the language of 402 informants from 236 cities from across the contiguous United States, based on the acoustic data from the Atlas of North American English (Labov, Ash & Boberg, 2006). The results of the analysis both confirm and challenge the results of the Atlas. Most notably, while the analysis identifies similar patterns as the Atlas in the West and the Southeast, the analysis finds that the Midwest and the Northeast are distinct dialect regions that are considerably stronger than the traditional Midland and Northern dialect region indentified in the Atlas. The analysis also finds evidence that a western vowel shift is actively shaping the language of the Western United States.

Defining the role of floating periphyton mats in shaping food-web dynamics in the Florida Everglades

Expansive periphyton mats are a striking characteristic of the Florida Everglades. Floating periphyton mats are home to a diverse macroinvertebrate community dominated by chironomid and ceratopogonid larvae and amphipods that use the mat as both a food resource and refuge from predation. While this periphyton complex functions as a self-organizing system, it also serves as a base for trophic interactions with larger organisms. The purpose of my research was to quantify variation in the macroinvertebrate community inhabiting floating periphyton mats, describe the role of mats in shaping food-web dynamics, and describe how these trophic interactions change with eutrophication. ^ I characterized the macroinvertebrate community inhabiting periphyton through a wet-season by describing spatial variation on scales from 0.2 m to 3 km. Floating periphyton mats contained a diverse macroinvertebrate community, with greater taxonomic richness and higher densities of many taxa than adjacent microhabitats. Macroinvertebrate density increased through the wet season as periphyton mats developed. While some variation was noted among sites, spatial patterns were not observed on smaller scales. I also sampled ten sites representing gradients of hydroperiod and nutrient (P) levels. The density of macroinvertebrates inhabiting periphyton mats increased with increasing P availability; however, short-hydroperiod P-enriched sites had the highest macroinvertebrate density. This pattern suggests a synergistic interaction of top-down and bottom-up effects. In contrast, macroinvertebrate density was lower in benthic floc, where it was negatively correlated with hydroperiod. ^ I used two types of mesocosms (field cages and tanks) to manipulate large consumers (fish and grass shrimp) with inclusion/exclusion cages over an experimental P gradient. In most cases, periphyton mats served as an effective predation refuge. Macroinvertebrates were consumed more frequently in P-enriched treatments, where mats were also heavily grazed. Macroinvertebrate densities decreased with increasing P in benthic floc, but increased with enrichment in periphyton mats until levels were reached that caused disassociation of the mat. ^ This research documents several indirect trophic interactions that can occur in complex habitats, and emphasizes the need to characterize dynamics of all microhabitats to fully describe the dynamics of an ecosystem. ^

Landscape shaping the economy of small coastal villages

Some years ago visitors and natives had a different way of enjoying the landscape of the coastal villages located in Santa Elena Province, in Ecuador. Nowadays natives of those towns are concerned about the emergent tourist industry, which is not just offering lodging but also it is increasing the construction of vacation homes or second homes. This development is showing notorious social and spatial changes in those coastal towns. Since 80's, the real-estate investments in vacation homes have not stopped. In addition, it has been increasing year in year out, to the north of the Province. Nowadays there are not just homes but also luxury complex of buildings attracting more and more seasonal tourists. This real estate growing has been constantly changing the landscape and shaping the economy of those towns. The authorities in this province are aware of those effects citing in the Province's Master Plan of Development the lack of land use policies. This study aims to describe the socioeconomic activity of coastal villages located in Santa Elena Province, which - during many years - have a resource-based economy: agriculture and fishing economy; but during this last years they have been trying to switch it to tourism. The analysis of spatial changes of the landscape and its effects as a consequence of the land use is another goal of this work. Finally, this study describes the quest of new natural tourist attractions that villagers and stakeholders have taken recently. Key words: Nature and society, sociospatial, rural landscape, coastal landscape, tourism.

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species.