Distribution Of Clades Research Articles

Possible European Origin of Circulating Varicella Zoster Virus Strains.

Varicella zoster virus (VZV) is the causative agent of chickenpox and shingles. The geographic distribution of VZV clades was taken as evidence that VZV migrated out of Africa with human populations. We show that extant VZV strains most likely originated in Europe and not in Africa. Europe was also identified as the ancestral location for most internal nodes of the VZV phylogeny, including the ancestor of clade 5 strains. We also show that strains from clades 1, 2, 3, and 5 derived a major proportion of their ancestry from each of 4 ancestral populations. Conversely, viruses from other clades displayed variable levels of admixture. Some low-level admixture was also observed for clade 5 genomes, but only for non-African viruses. This pattern indicates that the clade 5 VZV strains do not represent recent introductions from Africa due to migratory fluxes. These data have also relevance for the definition and classification of VZV clades.

Integrating historical biogeography and environmental niche evolution to understand the geographic distributionof Datureae.

The distributions of plant clades are shaped by abiotic and biotic factors as well as historical aspects such as center of origin. Dispersals between distant areas may lead to niche evolution when lineages are established in new environments. Alternatively, dispersing lineages may exhibit niche conservatism, moving between areas with similar environmental conditions. Here we test these contrasting hypotheses in the Datureae clade (Solanaceae). We used maximum likelihood methods to estimate the ancestral range of Datureae along with the history of biogeographic events. We then characterized the niche of each taxon using climatic and soil variables and tested for shifts in environmental niche optima. Finally, we examined how these shifts relate to the niche breadth of taxa and clades within Datureae and the degree of overlap between them. Datureae originated in the Andes and subsequently expanded its range to North America and non-Andean regions of South America. The ancestral niche, and that of most Datura and Trompettia species, is dry, while Brugmansia species likely shifted toward a more mesic environment. Nonetheless, most Datureae present moderate to high overlap in niche breadth today. The expansion of Datureae into North America was associated with niche conservatism, with dispersal into similarly dry areas as occupied by the ancestral lineage. Subsequent niche evolution, including the apparent shift to a mesic niche in Brugmansia, diversified the range of habitats occupied by species in the tribe Datureae but also led to significant niche overlap among the three genera.

Phylogeographic patterns and conservation implications of the endangered Chinese giant salamander.

Understanding genetic diversity patterns of endangered species is an important premise for biodiversity conservation. The critically endangered salamander Andrias davidianus, endemic to central and southern mainland in China, has suffered from sharp range and population size declines over the past three decades. However, the levels and patterns of genetic diversity of A. davidianus populations in wild remain poorly understood. Herein, we explore the levels and phylogeographic patterns of genetic diversity of wild‐caught A. davidianus using larvae and adult collection with the aid of sequence variation in (a) the mitochondrial DNA (mtDNA) fragments (n = 320 individuals; 33 localities), (b) 19 whole mtDNA genomes, and (c) nuclear recombinase activating gene 2 (RAG2; n = 88 individuals; 19 localities). Phylogenetic analyses based on mtDNA datasets uncovered seven divergent mitochondrial clades (A–G), which likely originated in association with the uplifting of mountains during the Late Miocene, specific habitat requirements, barriers including mountains and drainages and lower dispersal ability. The distributions of clades were geographic partitioned and confined in neighboring regions. Furthermore, we discovered some mountains, rivers, and provinces harbored more than one clades. RAG2 analyses revealed no obvious geographic patterns among the five alleles detected. Our study depicts a relatively intact distribution map of A. davidianus clades in natural species range and provides important knowledge that can be used to improve monitoring programs and develop a conservation strategy for this critically endangered organism.

Why is fruit colour so variable? Phylogenetic analyses reveal relationships between fruit‐colour evolution, biogeography and diversification

AbstractAimAre different fruit colours related to large‐scale patterns of dispersal, distribution and diversification? Here, we investigate this question for the first time, using phylogenetic approaches in the tribe Gaultherieae (Ericaceae). We test relationships between fruit colour and (a) biogeographic dispersal, (b) elevational and latitudinal species distributions and (c) rates of diversification.LocationGlobal.Time periodRecent to 30 million years ago.Major taxa studiedThe plant tribe Gaultherieae in the family Ericaceae (blueberries and relatives).MethodsWe estimated a new time‐calibrated phylogeny for Gaultherieae. Data on fruit colours and geographic distributions for each species were compiled from published sources and field observations. Using phylogenetic methods, we estimated major dispersal events across the tree and the most likely fruit colour associated with each dispersal event, and tested whether dispersal between major biogeographic regions was equally likely for different fruit colours, and whether dispersal distances were larger for certain colours. We then tested the relationships between fruit colours and geographic variables (latitude, elevation) and diversification rates.ResultsLarge‐scale dispersal events were significantly associated with red‐fruited lineages, even though red‐fruited species were relatively uncommon. Further, different fruit colours were associated with different elevations and latitudes (e.g. red at lower elevations, violet at lower latitudes, white at higher elevations). Violet colour was related to increased diversification rates, leading to more violet‐fruited species globally.Main conclusionsOverall, we show that different fruit colours can significantly impact the large‐scale dispersal, distribution and diversification of plant clades. Furthermore, the interplay between biogeography and fruit‐colour evolution seems to generate “taxon cycles” in fruit colour that may drive variation in fruit colour over macroevolutionary time‐scales.

Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses.

SummaryMetal‐sulfides are wide‐spread in marine benthic habitats. At deep‐sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene‐based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate‐reducing Nitrospirae and sulfide‐oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr‐clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide‐oxidizers potentially facilitating metal‐sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.

Contribution to the phylogeography of the nose-horned viper (Vipera ammodytes, Linnaeus, 1758) in the Central Balkan Peninsula

Seven genetic clades have been recognized within the species Vipera ammodytes (nose-horned viper); however, the precise phylogenetic position of many Balkan populations is unknown. We used Bayesian analysis of the mtDNA sequences from the 16S rRNA mtDNA gene obtained from 47 individuals (26 novel samples sequenced in this study and 21 sequences available from GenBank). Our results show that sampled nose-horned vipers from localities in Serbia are clustered within three clades: the northeastern (23 individuals), the northwestern (two individuals) and the southeastern (one individual). Results revealed an overlapping distribution of the northeastern and the northwestern clades in two populations. We have revealed that the northeastern clade extends further south than previously suggested, to the Ohrid/Prespa lakes in North Macedonia. Our findings contribute to the knowledge of the genetic diversity of this species in Serbia and help to clarify the geographical distributions of mtDNA-defined clades. [Projects of the Serbian Ministry of Education, Science and Technological Development, Grant no. 173025 and Grant no. TR37009]

Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host.

Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green® real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease.

Historical biogeography reveals new independent evolutionary lineages in the Pantosteus plebeius-nebuliferus species-group (Actinopterygii: Catostomidae)

BackgroundThe Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North Mexico. The geological history of this region is considered an important factor in explaining the evolutionary history of low vagility animals like freshwaters fishes. The aim of this study was to examine the phylogenetic relationships and describe the evolutionary history of the species-group. We hypothesized that the genetic structure and distribution of the main clades of Pantosteus plebeius-nebuliferus are associated with the geological history of Northern Mexico. To this end, we obtained DNA sequences of mitochondrial and nuclear genes and performed phylogenetic and phylogeographic analyses. Divergence time estimation and ancestral area reconstruction were also carried out to propose a biogeographical hypothesis, and species boundaries within the species-group were also tested.ResultsWe identified four clades within the Pantosteus plebeius-nebuliferus species-group in both markers. Divergence ranged from 5.9% to 9.2% for cytb and 0.1% to 0.9% for GHI. We observed significant genetic structure and no shared haplotypes between clades. We estimated that the clades diverged during the last 5.1 Myr, with a biogeographic scenario suggesting eight vicariant and four dispersal events through the historic range of the species-group. We found that the best species-delimitation model is when four species are assumed, which correspond to the main clades. We identified nine evolutionary significance units (ESUs), pertinent to the conservation of the group, each representing populations present in distinct drainage basins.ConclusionsThe evolutionary history of the Pantosteus plebeius-nebuliferus species-group is characterized by vicariant post-dispersal processes, linked to geological changes in the Sierra Madre Occidental and central Northern Mexico since the Pliocene. This is congruent with biogeographic patterns described for other co-distributed fish species. We propose a new phylogenetic hypothesis for the species-group, clarifying the taxonomy of this evolutionarily complex group. Our results suggest that the species-group consists of at least four clades with independent evolutionary histories, two of which may represent new undescribed species. Our identification of ESUs provides a basis upon which conservation measures can be developed for the species-group.

Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective.

Widespread fish clades that occur mainly or exclusively in fresh water represent a key target of biogeographical investigation due to limited potential for crossing marine barriers. Timescales for the origin and diversification of these groups are crucial tests of vicariant scenarios in which continental break-ups shaped modern geographic distributions. Evolutionary chronologies are commonly estimated through node-based palaeontological calibration of molecular phylogenies, but this approach ignores most of the temporal information encoded in the known fossil record of a given taxon. Here, we review the fossil record of freshwater fish clades with a distribution encompassing disjunct landmasses in the southern hemisphere. Palaeontologically derived temporal and geographic data were used to infer the plausible biogeographic processes that shaped the distribution of these clades. For seven extant clades with a relatively well-known fossil record, we used the stratigraphic distribution of their fossils to estimate confidence intervals on their times of origin. To do this, we employed a Bayesian framework that considers non-uniform preservation potential of freshwater fish fossils through time, as well as uncertainty in the absolute age of fossil horizons. We provide the following estimates for the origin times of these clades: Lepidosireniformes [125-95million years ago (Ma)]; total-group Osteoglossomorpha (207-167Ma); Characiformes (120-95Ma; a younger estimate of 97-75Ma when controversial Cenomanian fossils are excluded); Galaxiidae (235-21Ma); Cyprinodontiformes (80-67Ma); Channidae (79-43Ma); Percichthyidae (127-69Ma). These dates are mostly congruent with published molecular timetree estimates, despite the use of semi-independent data. Our reassessment of the biogeographic history of southern hemisphere freshwater fishes shows that long-distance dispersals and regional extinctions can confound and erode pre-existing vicariance-driven patterns. It is probable that disjunct distributions in many extant groups result from complex biogeographic processes that took place during the Late Cretaceous and Cenozoic. Although long-distance dispersals likely shaped the distributions of several freshwater fish clades, their exact mechanisms and their impact on broader macroevolutionary and ecological dynamics are still unclear and require further investigation.

The Distribution of Different Clades of Seneca Valley Viruses in Guangdong Province, China.

Seneca Valley virus (SVV), a newly determined etiological agent of vesicular disease in swine, causes porcine idiopathic disease and occasional acute death in piglets. Recently, an increased number of SVV infection cases have been reported in the United States (US) and China, resulting in significant economic losses to the swine industry. The first identification of SVV in China was reported in Guangdong Province, a major swine producing province. The cases of SVV were continuously reported in Guangdong in 2015 and 2016. However, the spread of SVV in Guangdong in 2017 remains unknown. In this study, we determined two new SVV strains, CH-GD-2017-1 and CH-GD-2017-2, from Guangdong. The genetic analysis suggested that the two Guangdong strains showed different characteristics to previous Guangdong strains. They showed lower nucleotide similarity with strains isolated in 2015 and 2016, and were more similar to the US strains. Phylogenetic analyses indicated that the new strains were clustered in a different clade with previous Guangdong strains. We found 28 mutated amino acids in the new strains, compared with the first Guangdong strain, SVV CH-01-2015. In the geographic analysis, we found that the US and China reported more SVV cases than other countries, and most of the SVV cases were reported in east and central China-of which, Guangdong Province is one of the major epidemic regions. In conclusion, our findings indicate that SVV continued to spread in Guangdong Province in 2017, and two different clades of SVVs have emerged in this region.

Contrasting patterns of diversification in a bird family (Aves: Gruiformes: Rallidae) are revealed by analysis of geospatial distribution of species and phylogenetic diversity

Geospatial patterns in the distribution of regional biodiversity reflect the composite processes that underpin evolution: speciation, dispersal and extinction. The spatial distribution and phylogeny of a globally widespread and species rich bird family (Rallidae) were used to help assess the role of large‐scale biogeographical processes in diversity and diversification. Here, we examine how different geostatistical diversity metrics enhance our understanding of species distribution by linking occurrence records of rail species to corresponding species level phylogeny. Tropical regions and temperate zones contained a large proportion of rail species richness and phylogenetic diversity whilst small islands in Australian, Oceanian and Oriental regions held the highest weighted and phylogenetic endemism. Our results suggest that habitat connectivity and dispersal were important ecological features in rail evolution and distribution. Spatial isolation was a significant driver of diversification where islands in Oceania were centres of neo‐endemism with recent multiple and independent speciation events and could be considered as nurseries of biodiversity. Palaeo‐endemism was mostly associated with older stable regions, so despite extensive long distance range shifting these areas retain their own ancient and distinct character. Madagascar was the major area of palaeo‐endemism associated with the oldest rail lineages and could be considered a museum of rail diversity. This implies a mixture of processes determine the current distribution and diversity of rail clades with some areas dominated by recent ‘in situ’ speciation while others harbour old diversity with ecological traits that have stood the test of time.

The Neogene Record of Northern South American Native Ungulates

South America was isolated during most of the Cenozoic, and it was home to an endemic fauna. The South American Native Ungulates (SANUs) exhibited high taxonomical, morphological, and ecological diversity and were widely distributed on the continent. However, most SANU fossil records come from high latitudes. This sampling bias challenges the study of their diversity dynamics and biogeography during important tectonic and biotic events, such as the Great American Biotic Interchange, the faunal exchange between North and South America after the formation of the Isthmus of Panama. We describe new SANU remains from the Neogene of the Cocinetas (northern Colombia) and Falcon (northwestern Venezuela) Basins. In the Cocinetas Basin, the middle Miocene fauna of the Castilletes Formation includes Hilarcotherium miyou sp. nov. (Astrapotheriidae), cf. Huilatherium (Leontiniidae), and Lambdaconus cf. L. colombianus (Proterotheriidae). The late Pliocene fauna of the Ware Formation includes a Toxodontinae indet. and the putative oldest record of Camelidae in South America. In the Falcon Basin, the Pliocene/Pleistocene faunas of the Codore and San Gregorio Formations include Falcontoxodon aguilerai gen. et sp. nov. and Proterotheriidae indet. We provide a phylogenetic analysis for Astrapotheriidae and Toxodontidae. The new data document a low-latitude provinciality within some SANU clades (e.g., Astrapotheriidae, Leontiniidae) during the middle Miocene. This contrasts with the wide latitudinal distribution of clades of other mammals recorded in the fauna, including the sparassodont Lycopsis padillai, the sloth Hyperleptus?, and the proterotheriid Lambdaconus cf. L. colombianus. The Pliocene/Pleistocene tropical faunas from northern South America are characterized by the predominance of native taxa despite their proximity to the Isthmus of Panama (fully emerged by that time). Only one North American ungulate herbivore immigrant is present, a cf. Camelidae indet. The Pliocene and early Pleistocene faunas suggest that environmental changes and biotic interactions affected the diversity dynamics and biogeographic patterns of SANUs during the Great American Biotic Interchange.

Lanthanide-Dependent Methanol Dehydrogenases of XoxF4 and XoxF5 Clades Are Differentially Distributed Among Methylotrophic Bacteria and They Reveal Different Biochemical Properties.

Lanthanide-dependent alcohol dehydrogenases have recently emerged as environmentally important enzymes, most prominently represented in methylotrophic bacteria. The diversity of these enzymes, their environmental distribution, and their biochemistry, as well as their evolutionary relationships with their calcium-dependent counterparts remain virtually untapped. Here, we make important advances toward understanding lanthanide-dependent methylotrophy by assessing the distribution of XoxF4 and XoxF5 clades of lanthanide methanol dehydrogenases among, respectively, Methylophilaceae and non-Methylophilaceae methylotrophs, and we carry out comparative biochemical characterization of XoxF4 and XoxF5 enzymes, demonstrating differences in their properties, including catalytic efficiencies. We conclude that one subtype of the XoxF4 enzyme, XoxF4-1 is the dominant type in nature while other XoxF4 subtypes appear to be auxiliary, representatives of this clade only found in the Methylophilaceae (Betaproteobacteria). In contrast, we demonstrate that XoxF5 enzymes are widespread among Alpha-, Beta-, and Gammaproteobacteria. We purified and biochemically characterized two XoxF4 enzymes (XoxF4-1 and XoxF4-2), both from Methylotenera mobilis, and one XoxF5 enzyme, from Methylomonas sp., after expressing their His-tagged versions in respective natural hosts. All three enzymes showed broad specificities toward alcohols and aldehydes and strict dependence on lighter lanthanides. However, they revealed differences in their properties in terms of optimal pH for in vitro activity, ammonia dependence, the range of lanthanides that could serve as cofactors, and in kinetic properties. Overall, our data advance the understanding of the biochemistry and environmental distribution of these recently discovered enzymes that appear to be key enzymes in lanthanide-dependent methylotrophy.

Quantitative palaeobiogeographical analysis of South American Neogene Chioninae (Bivalvia: Veneridae)

Chionine bivalves are one of the most important components of Neogene and Recent molluscan faunas in southern South America, but it was not until recently that their phylogenetic relationships has been explored quantitatively. Based on this robust framework, we analyzed the palaeobiogeographical history of the group. The geographic areas used in this analysis were discretized using a multivariate K-means cluster analysis based on the palaeocoordinates of chionine-bearing localities. Statistical comparison of quantitative, event-based biogeography models using likelihood suggests that our data best fits models that include long-distance jump dispersal (+J), with a slight preference for a model that also gives increased weight to vicariance. The ‘Chione’ clade (including the genera Chione, Anomalocardia, and Chionopsis) is mainly a Caribbean and central Eastern Pacific lineage with expansions to California and the southern Western Atlantic coast. The ‘Protothaca’ clade (including Protothaca, Nioche, Austrovenus, and Chionista) is mainly an Eastern Pacific lineage–with a proposed southern South American origin–with occasional dispersals to the western Pacific (Oceania and East Asia). A new alternative dispersal route is proposed across the North Pacific from California and the north Eastern Pacific to East Asia and Oceania, as shown by Austrovenus stutchburyi, Tuangia crassicosta, and Protocallithaca adamsii. The ‘Ameghinomya’ clade (including all Ameghinomya species) is a southern South American lineage–south Eastern Pacific origin–that subsequently dispersed into the southern Western Atlantic. The ‘Protothaca’ and ‘Ameghinomya’ clades show opposite histories, the former being mainly Pacific and the latter mainly Atlantic. The distribution of both clades on both sides of South America may have been allowed by the opening of the Drake Passage Gateway around the Oligocene-Miocene boundary.

Refining the biogeographical scenario of the land snail Cornu aspersum aspersum: Natural spatial expansion and human-mediated dispersal in the Mediterranean basin

The land snail Cornu aspersum aspersum, native to the Mediterranean region, has been the subject of several anatomical and molecular studies leading to recognize two divergent lineages, named “East” and “West” according to their geographical distribution in North Africa. The first biogeographical scenario proposed the role of Oligocene paleogeographic events and Quaternary glacial refugia to explain spatial patterns of genetic variation. The aim of this study was to refine this scenario using molecular and morphometric data from 169 populations sampled across Mediterranean islands and continents. The two previously described lineages no longer correspond to distinct biogeographical entities. Phylogenetic relationships reveal the existence of seven clades, do not support the Tyrrhenian vicariance hypothesis, and suggest that C. a. aspersum most likely originates from North Africa. We found two contrasted patterns with the seven clades defining spatially well-structured populations in the southern Mediterranean whereas one clade is distributed across the basin. High genetic diversities and rates of endemism in North Africa support the role of this region for the diversification of C. a. aspersum. In referring to divergence times previously estimated, we suggest allopatric differentiation due to geological changes of the Atlas system and multiple refugial areas during Pleistocene glaciations. The new biogeographical scenario implies an initial range expansion from North Africa to the Iberian Peninsula and the peri-Tyrrhenian regions through land bridges connections during the Messinian Salinity Crisis and Pleistocene glaciations. Historical events appear to have also structured morphometric variation but recent dispersal events favored the emergence of secondary contacts between clades. Southern Mediterranean clades are limited to their initial distribution and populations of the recent clade would have rapidly recolonized the whole Mediterranean in the Holocene due to greater adaptive potential and the influence of human transportations.

The Gray Toad-headed Agama, Phrynocephalus scutellatus, on the Iranian Plateau: The degree of niche overlap depends on the phylogenetic distance

The Gray Toad-headed Agama (Phrynocephalus scutellatus) occurs in Iran, Pakistan and Afghanistan and is represented in Iran by four distinctive genetic clades. We built distribution models for three of these clades (one clade was not included due to a low number of distribution records) using Maximum Entropy Algorithm in order to determine the contribution of ecological factors to the distribution pattern. The degree of spatial niche overlap between every pair of clades were measured using Schoener's D niche overlap metric. The results showed that at species-level climate variables (annual precipitation, annual mean temperature) were the most influential parameters determining the boundaries of the distribution in Iran. Temperature seasonality was found to be the most influential factor in the distribution of both Clade I and Clade II. However, this variable was replaced by the annual mean temperature for Clade VI. Based on the results of Schoener's D metric, Clades I and II had the lowest, and Clades II and VI the highest level of ecological niche overlap. Comparing the result of niche overlap with genetic distance between the clades, it was found that the ecologically least similar clades were those with the longer history of genetic segregation.

Ecological opportunity alters the timing and shape of adaptive radiation.

The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes. Clades that arose following colonization events diversified faster than other clades. Speciation rate shifts were nonrandomly distributed across the phylogeny such that they were disproportionally concentrated around nodes that corresponded with colonization events (i.e., of continents, river basins, or lakes). Young clades tend to expand faster than older clades; however, colonization-associated ecological opportunity accentuated this pattern. There was an interaction between clade age and ecological opportunity that explained the trajectory of clades through phylogenetic space over time. Our results indicate that ecological opportunities afforded by continental and ecosystem-scale colonization events explain the dramatic speciation rate heterogeneity and phylogenetic imbalance that arose during the evolutionary history of cichlid fishes.

Diversification and spatial structuring in the mutualism between Ficus septica and its pollinating wasps in insular South East Asia

BackgroundInterspecific interactions have long been assumed to play an important role in diversification. Mutualistic interactions, such as nursery pollination mutualisms, have been proposed as good candidates for diversification through co-speciation because of their intricate nature. However, little is known about how speciation and diversification proceeds in emblematic nursery pollination systems such as figs and fig wasps. Here, we analyse diversification in connection with spatial structuring in the obligate mutualistic association between Ficus septica and its pollinating wasps throughout the Philippines and Taiwan.ResultsCeratosolen wasps pollinating F. septica are structured into a set of three vicariant black coloured species, and a fourth yellow coloured species whose distribution overlaps with those of the black species. However, two black pollinator species were found to co-occur on Lanyu island. Microsatellite data on F. septica indicates the presence of three gene pools that broadly mirrors the distribution of the three black clades. Moreover, receptive fig odours, the specific message used by pollinating wasps to locate their host tree, varied among locations.ConclusionsF. septica and its black pollinator clades exhibited similar geographic structuring. This could be due originally to geographic barriers leading to isolation, local adaptation, and finally co-structuring. Nevertheless, the co-occurrence of two black pollinator species on Lanyu island suggests that the parapatric distribution of the black clades is now maintained by the inability of migrating individuals of black pollinators to establish populations outside their range. On the other hand, the distribution of the yellow clade strongly suggests an initial case of character displacement followed by subsequent range extension: in our study system, phenotypic or microevolutionary plasticity has allowed the yellow clade to colonise hosts presenting distinct odours. Hence, while variation in receptive fig odours allows specificity in the interaction, this variation does not necessarily lead to coevolutionary plant-insect diversification. Globally, our results evidence evolutionary plasticity in the fig-fig wasp mutualism. This is the first documentation of the presence of two distinct processes in pollinating fig wasp diversification on a host species: the formation of vicariant species and the co-occurrence of other species over large parts of their ranges probably made possible by character displacement.

Geometric morphometrics meets metacommunity ecology: environment and lineage distribution affects spatial variation in shape

Patterns of univariate trait variation across metacommunities are widely explored, as are searches for their underlying causes. Surprisingly, patterns of multivariate shape remain unknown, and the search for drivers of functional traits of communities often neglect the biogeographical distribution of phylogenetic clades. Our aim was to investigate multivariate shape distribution across metacommunities and to determine the main environmental drivers of shape beyond/taking into account the phylogenetic distribution of lineages. We obtained mean skull and mandible shape for 228 species of Neotropical sigmodontine rodents through geometric morphometrics (GM), and then calculated mean shapes for 1° × 1° cells across the Neotropics based on the incidence of sigmodontines. We investigated the effects of lineage distribution on mean trait variation by using phylogenetic fuzzy weighting to calculate principal coordinates of phylogenetic structure (PCPS). Effects of environmental variables on shape variation incorporating phylogenetic composition were realized through redundancy analysis. We found that the different distributions of major lineages throughout the Neotropics were responsible for much of the mean shape variation. The association of landscape features with tribal groupings (Oryzomyini with Amazonia and Phyllotini and Abrotrichini with the Andes) were standouts. Environmental variables and lineage distribution explain the same (i.e. shared) portion of shape variation, suggesting phylogenetic niche conservatism at the metacommunity level. Seasonality in temperature and land cover were the best environmental predictors of mean shape: larger tympanic bullae, incisive foramina, and check teeth are all associated with highly seasonal and less vegetated areas. Our new approach of using GM shape across metacommunities was demonstrably useful in understanding large‐scale biogeographical patterns of shape variation and identifying its underlying causes. The overlap between environmental variables and phylogenetic lineage distribution suggests that a process of niche conservatism is likely: the phenotype–environment correlation is mediated by the differential biogeographical distribution of the main clades.

Phylogenetic and functional structure of climbing plant assemblages in woody patches advancing over Campos grassland

AbstractQuestionAnalysing taxonomic, phylogenetic and functional species distribution across a metacommunity allows understanding of how landscape dynamics may influence forest expansion over grassland. In this context, climbing plants are particularly interesting vegetation components, since they actively prospect the best sunlight position, altering forest structure. We investigated if forest structure differentiation along a patch size/isolation gradient would determine the distribution of phylogenetic clades, dispersal and/or establishment‐related traits in climbing plant assemblages. We hypothesized that taxonomic, phylogenetic and functional species diversities would show a nested pattern along the gradient of increasing vegetation complexity. Furthermore, less mobile diaspores, as well as climbing mechanisms independent of support limitations, and deeper phylogenetic clades characterized by shade‐tolerant species would be associated with more developed and less isolated patches.LocationSubtropical grassland surrounded by Araucaria forest, southern Brazil.MethodWe recorded the composition and abundance of climbing plant species along a gradient of forest patches increasing in size and isolation from the surrounding continuous forest. We performed an analysis of principal coordinates of phylogenetic structure (PCPS) to investigate the distribution of phylogenetic clades across sites, tested its relationship with patch area and isolation using linear models, and for the correlation to species dispersal traits and climbing mechanisms. We employed the treeNODF (Nestedness based on Overlap and Decreasing Fill) method to estimate if there was a phylogenetic, compositional and/or functional nested pattern of the metacommunity structure during forest expansion over grassland.ResultsWe found that species composition distribution was explained by patch size and isolation, but not by phylogeny. Dispersal traits were more structured along the gradient compared to climbing mechanisms. We also found a nested pattern of combined species and phylogenetic/functional diversities, where smaller patches are subsets of larger patches and of continuous forest sites.ConclusionPatch area, isolation and dispersal traits play significant roles in the distribution of climbing plants during the process of forest advance over grassland, independently of phylogenetic relatedness among species. The nested pattern indicated that continuous forest and larger patches provide all the diaspores that colonize the smaller patches in this process, making them important targets for conservation.