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Fig. 24 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)

Fig. 24. (Most likely ancestral ranges for lineages of the subgenus Melanobombus von Dalla Torre, 1880. reconstructed with DIVALIKE+J (BioGeoBEARS) using the short-distance dispersal (no jumps) model in Fig. 23, the estimate of species phylogeny in Fig. 22, and with B. nobilis representing the outgroup (not shown). Letters represent the area units defined in Table 5 and in Fig. 23: letter combinations in grey below terminals show species' current distributions; letter combinations above the nodes show the most likely reconstructions for ancestral distributions (with four selected dispersal events numbered), with the probabilities of these solutions for these ancestors shown below the nodes. Species groups discussed in the text are labelled in circles: rp = rufipes-group; fs = festivus-group; rf = rufofasciatus- group; tg = tanguticus-group; la = lapidarius-group; si = sichelii-group; and ke = keriensis-group. Inset map shows sequenced samples for the species groups (blue = the rufipes-group and festivus-group; green = the rufofasciatus-group; yellow = the tanguticus-group and lapidarius-group; orange = the sichelii-group; and red = the keriensis-group) with arrows showing the four numbered dispersal events.

Figs 14‒16 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)

Figs 14‒16. Maps of sequenced samples as in Figs 12–13. 14. The tanguticus-group and the lapidarius- group. 15. The sichelii-group. 16. The keriensis-group.

Figs 181‒189 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)

Figs 181‒189. Morphology of the male genitalia for species of the subgenus Melanobombus von Dalla Torre, 1880 from the dorsal aspect, anterior at the bottom of the image, posterior at the top. 181. Bombus eximius Smith, 1852, China-Guangxi. 182. B. rufipes Lepeletier, 1835, IndonesiaJava. 183. B. festivus Smith, 1861, Nepal. 184. B. simillimus Smith, 1852, India-Himachal Pradesh. 185. B. miniatus Bingham, 1897, Bhutan. 186. B. eurythorax Wang, 1982 stat. rev., India-Kashmir. 187. B. prshewalskyi Morawitz, 1880 stat. rev., China-Sichuan. 188. B. rufofasciatus Smith, 1852, IndiaKashmir. 189. B. richardsiellus (Tkalců, 1968), Burma (left volsella distal part missing). Scale bars = 1 mm.

Figs 64–102 in Widespread polytypic species or complexes of local species? Revising bumblebees of the subgenus Melanobombus world-wide (Hymenoptera, Apidae, Bombus)

Figs 64–102. Simplified diagrams for the colour patterns of the hair on the dorsum for the species from the integrative analysis. The dorsum is divided into regions, each of which shows only the predominant or most apparent colour for that region using a simplified colour palette, with olive indicating a mixture of black and yellow hair, and grey indicating a mixture of black and white hair. The rufofasciatus-group. 64. Queen, China-Yunnan. 65. Queen, China-Sichuan. 66. Worker, China-Xizang. 67. Worker, ChinaXizang. 68. Worker, China-Gansu. 69. Male, China-Yunnan. 70. Male, China-Xizang. 71. Queen, IndiaKashmir. 72. Queen, India-Kashmir. 73. Queen, Pakistan. 74. Worker, India-Kashmir. 75. Worker, IndiaKashmir. 76. Male, Pakistan. 77. Male, India-Kashmir. 78. Queen, Burma. 79. Worker, Burma. 80. Worker, China-Xizang. 81. Worker, China-Xizang. 82. Male, Burma. 83. Queen, China-Sichuan. 84. Worker, China-Sichuan. 85. Worker, China-Sichuan. 86. Worker, China-Sichuan. 87. Worker, China-Sichuan. 88. Worker, China-Xizang. 89. Male, China-Sichuan. 90. Male, China-Sichuan. 91. Queen, China-Beijing. 92. Queen, China-Beijing. 93. Worker, China-Shanxi. 94. Worker, China-Beijing. 95. Worker, ChinaBeijing. 96. Male, China-Beijing. 97. Male, China-Beijing. 98. Queen, China-Taiwan. 99. Worker, ChinaTaiwan. 100. Worker, China-Taiwan. 101. Worker, China-Taiwan. 102. Male, China-Taiwan.

opencc-by-4.0Dec 2019View details →

Code and processed data accompanying "Widespread haploid-biased gene expression enables sperm-level natural selection"

Code and processed data required to reproduce the analysis in "Widespread haploid-biased gene expression enables sperm-level natural selection".

opencc-zeroNov 2020View details →

Data from: Altitude shapes the environmental drivers of large-scale variation in abundance of a widespread mammal species

Habitat quality and heterogeneity directly influence the distribution and abundance of organisms at different spatial scales. Determining the main environmental factors driving the variation in species abundance is crucial to understand the underlying ecological processes and this is especially important for widely distributed species living in contrasting environments. However, the responses to environmental variation are usually described at relatively small spatial scales. Here, we studied the variation in abundance of a widely distributed mustelid, the European badger (Meles meles), across France. We used (1) direct detections of 9,439 dead and living badgers, from 2006 to 2009, to estimate badger relative abundance in 703 small agricultural regions of metropolitan France and (2) a Bayesian modelling approach to identify the main environmental determinants influencing badger abundance. Despite a continuous distribution of badger in France, we found large variation in badger abundance between regions, explained by environmental factors. Among a set of 13 environmental variables, we demonstrated that badger abundance in lowlands (< 400 m a.s.l.) was mostly driven by biotic factors such as potential food resources (earthworm abundance and fruits crops) and forest fragmentation. Conversely, in mountainous areas, abiotic factors (i.e. soil texture and climate) drove the variation in badger relative abundance. These results underline the importance of mapping the abundance of wildlife species based on environmental suitability, and highlight the complexity of drivers influencing species abundance at such large spatial scales. Altitude shaped the environmental drivers (biotic vs. abiotic) that most influenced relative abundance of a widespread species. In the case of badger, such abundance maps are crucial to identify critical areas for species management as this mustelid is a main wild vector of bovine tuberculosis in several countries.

opencc-zeroDec 2020View details →

Data from: Widespread variation in stable isotope trophic position estimates: patterns, causes, and potential consequences

Stable isotope analysis is one of the most widely used techniques to estimate trophic position and provides fundamental insight into the structure and management of ecological communities. To account for the effects of geographic variation in isotope levels, trophic position is typically estimated relative to an isotope "baseline" (i.e., material representing geographic variation) using a methodology such as a formula or statistical analysis. There is, however, remarkable variation in the baselines and methodologies used to estimate trophic position from stable isotopes. The consequences of this lack of standardization are unknown but could result in biased or erroneous conclusions. We conducted a literature review to quantify the variation in baselines and methodologies used to estimate trophic position from stable isotopes. Next, we assessed the consequences of this variation on individual species estimates and food web structure by extracting published trophic positions and applying various baselines and methodologies to existing datasets. We identified ten baselines and eight methodologies, the use of which varied by ecosystem studied. Moreover, we found that different baselines and methodologies yield significantly different trophic position estimates for individual species, as well as different conclusions about food web structure. Authors should avoid biological interpretations of absolute, stand-alone trophic positions (as these are prone to a number of biases). We recommend pairing stable isotope analysis with other techniques for more robust conclusions. Increased sample size may mitigate some of the variation caused by different baselines and methodologies; however, an alarmingly large proportion of studies collected only one sample in at least one trophic group (41% of all reviewed studies). Authors should collect a minimum of five samples per trophic group (but ten for best-practices) from as many trophic groups as possible to increase statistical power and redundancy in comparisons. When sample size is unavoidably constrained, we recommend using compound-specific isotope analysis with a taxon-specific trophic discrimination factor, because it may be more accurate and require fewer samples to maintain appropriate statistical power. Implementing our recommendations will increase the robustness and accuracy of conclusions based on stable isotopes, resulting in better management decisions and a more accurate understanding of ecological communities.

Data from: Leaf photosynthetic, economics and hydraulic traits are decoupled among genotypes of a widespread species of eucalypt grown under ambient and elevated CO2

Leaf economics and hydraulic traits strongly influence photosynthesis. While the level of coordination among these traits can differ between sets of species, leaf functional trait coordination within species remains poorly understood. Furthermore, elevated concentrations of atmospheric CO2 commonly influence the expression of leaf photosynthetic, economics and hydraulic traits in contrasting ways, yet the effect of variable concentrations of atmospheric CO2 on patterns of trait coordination within species remains largely untested. We examined the relationships among key leaf photosynthetic (e.g. net photosynthesis and photosynthetic biochemistry), economics and water-use (e.g. leaf mass per unit area and stomatal conductance) and hydraulic traits (e.g. vein density) in 14 genotypes of Eucalyptus camaldulensis grown in ambient (aCO2) and elevated (eCO2) [CO2]. We examined the level of coordination among leaf traits in aCO2 and then assessed whether growth in eCO2 altered that coordination. We found that leaf traits related to photosynthetic capacity, economics and water-use, and hydraulics were decoupled among genotypes grown in aCO2, yet strong relationships were generally observed among suites of traits within each 'functional group'. Significant responses to growth in eCO2 were observed for most leaf photosynthetic and economics and water-use traits, with the magnitude and direction of the response varying among traits. In contrast, leaf hydraulics traits were unaffected by variable growth CO2. Despite this, growth in eCO2 did not substantially alter patterns of leaf trait coordination observed in aCO2. These results suggest suites of leaf traits associated with photosynthetic capacity, economics and water-use and hydraulics, respectively, can form independent axes of variation among genotypes of a single species, regardless of growth CO2. Although growth in eCO2 did not substantially alter patterns of trait coordination, decoupling of leaf functional traits among genotypes may allow genetically distinct populations to produce novel combinations of traits that may be adaptive in response to changes in their local environment.

opencc-zeroDec 2019View details →

Data from: High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans-Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified and 29 of these haplotypes were restricted to sngle populations. The within-population genetic diversity was high (mean hS = 0.72), and among-population genetic differentiation showed a strong phylogeographic structure (NST = 0.630 > GST = 0.266; P < 0.001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure and potential distribution models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.

opencc-zeroJun 2021View details →

Genotyping by sequencing data of five legume tree species widespread in the rainforests of West and Central Africa

Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread Legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades -congruent across species- cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using ∂a∂I. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding species with long-distance wind dispersal. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.

Data from: Genome-wide association study in Arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of fifteen a priori oil synthesis candidate genes, two (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions.

opencc-zeroDec 2012View details →

Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)

Aim: Widespread species found in disturbed habitats are often expected to be human commensals. In island systems, this association predicts that dispersal will be mediated by humans. We investigated the biogeographical relationships among populations of a widespread tree skink that inhabits coastal forest and human-cultivated plantations in Southeast Asia. We sought to determine whether populations of the emerald tree skink, Lamprolepis smaragdina, dis- persed via mechanisms that were not human-mediated ('natural' dispersal) or whether dispersal was mediated by humans. The latter scenario predicts low levels of genetic differentiation across a species' range, coupled with a genetic signature of recent range expansion. Location: Southeast Asia, the Philippines, Wallacea and the south-western Pacific. Methods: We analysed sequences of mitochondrial DNA from 204 samples collected throughout the range of this species. We use phylogenetic and popu- lation genetic methods to distinguish between predicted geographical patterns of genetic variation that might indicate natural or human-mediated dispersal. Results: In contrast to predictions derived from similar studies of taxonomy and natural history, we found L. smaragdina to be characterized by highly structured and seemingly geographically stable mitochondrial gene lineages. Main conclusions: Our results demonstrate a novel pattern of widespread species distribution, never before observed in vertebrates of the Indo-Australian Archipelago. Although this widespread and highly dispersive species is capable of long-distance dispersal, and has a clear history of over-water dispersal, it exhibits sharp genetic differentiation across its range. Our results suggest that random waif dispersal has been a pervasive ongoing phenomenon throughout the evolutionary history of this species.

Data from: Widespread correlations between climatic niche evolution and species diversification in birds

The adaptability of species' climatic niches can influence the dynamics of colonisation and gene flow across climatic gradients, potentially increasing the likelihood of speciation, or reducing extinction in the face of environmental change. However, previous comparative studies have tested these ideas using geographically, taxonomically and ecologically restricted samples, yielding mixed results, and thus the processes linking climatic niche evolution with diversification remain poorly understood. Focusing on birds, the largest and most widespread class of terrestrial vertebrates, we test whether variation in species diversification among clades is correlated with rates of climatic niche evolution, and the extent to which these patterns are modified by underlying gradients in biogeography and species' ecology. We quantified climatic niches, latitudinal distribution and ecological traits for 7657 (~75%) bird species based on geographical range polygons, and then used Bayesian phylogenetic analyses to test whether niche evolution was related to species richness and rates of diversification across genus and family-level clades. We found that the rate of climatic niche evolution has a positive linear relationship with both species richness and diversification rate at two different taxonomic levels (genus and family). Furthermore, this positive association between labile climatic niches and diversification was detected regardless of variation in clade latitude or key ecological traits. Our findings suggest either that rapid adaptation to unoccupied areas of climatic niche space promotes avian diversification, or that diversification promotes adaptation. Either way, we propose that climatic niche evolution is a fundamental process regulating the link between climate and biodiversity at global scales, irrespective of the geographical and ecological context of speciation and extinction.

opencc-zeroDec 2010View details →

Data from: Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota

Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.

opencc-zeroOct 2019View details →

Populations of a widespread invader and co-occurring native species vary in phenotypic plasticity

Phenotypic plasticity can promote plant invasions and enhance impacts on native species but little is known about variation in plasticity among invader populations compared to native species. Variation in plasticity among invader populations could inform more precise predictions of invader spread and impacts across heterogeneous resource environments. We used a common garden experiment with sun and shade treatments to test for variation in plasticity among 12 populations of an invasive grass, and to determine if the invader exhibited greater plasticity than six native species that co-occur in the Southeast US. Principal component analysis revealed that invader populations from different native ranges consistently varied from each other and native species in traits linked to more favorable phenotypes under resource limitation. Overall, the invader exhibited greater plasticity than native species, as demonstrated by higher plasticity index values for traits such as plant height, leaf mass ratio, and root shoot ratio. Variation in phenotypic plasticity among invader populations suggests the potential for evolution of plasticity, and greater plasticity of invader populations than native species may underlie invader dominance. Differences in plasticity among populations appears to play an important role in predictions of the spread and potentially the impacts of invasive species.

Data from: On the widespread capacity for and functional significance of extreme inbreeding in ferns

Homosporous vascular plants utilize three different mating systems, one of which, gametophytic selfing, is an extreme form of inbreeding only possible in homosporous groups. This mating system results in complete homozygosity in all progeny and has important evolutionary and ecological implications. Ferns are the largest group of homosporous land plants, and the significance of extreme inbreeding for fern evolution has been the subject of debate for decades. We cultured gametophytes in the laboratory and quantified the relative frequencies of sporophyte production from isolated and paired gametophytes, and examined associations between breeding systems and several ecological and evolutionary traits. The majority of fern species studied show a capacity for gametophytic selfing, producing sporophytes from both isolated and paired gametophytes. While we did not follow sporophytes to maturity to investigate potential detrimental effects of homozygosity at later developmental stages, our results suggest that gametophytic selfing may have greater significance for fern evolution and diversification than has previously been realized. We present evidence from the largest study of mating behavior in ferns to date that capacity for extreme inbreeding is prevalent in this lineage, and we discuss its implications and relevance and make recommendations for future studies of fern mating systems.

opencc-zeroDec 2017View details →

Data from: The evolution of fungal substrate specificity in a widespread group of crustose lichens

Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150-200 MYA clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa, and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, "escape" from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.

opennotspecifiedDec 2016View details →

FIGURE 67 in A new widespread European bee species of the genus Dasypoda Latreille (Hymenoptera, Apoidea)

FIGURE 67. Distribution map of Dasypoda morawitzi sp. nov.

opennotspecifiedDec 2012View details →

FIGURE 11 in DNA barcodes reveal that the widespread European tortricid moth Phalonidia manniana (Lepidoptera: Tortricidae) is a mixture of two species

FIGURE 11. Larval gallery and larva of Phalonidia udana in stem of Lysimachia thyrsiflora.