Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of ...action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird‐pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co‐adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
see also the Perspective by Carolyn A. Wessinger
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Aim
Ecological niche‐based models (ENM) frequently rely on bioclimatic variables (BioV) to reconstruct biogeographic scenarios for species evolution, ignoring mechanistic relations. We tested if ...climatic predictors relevant to species hydric and thermal physiology better proximate distribution patterns and support location of Pleistocene refugia derived from phylogeographic studies.
Location
The Western Palaearctic.
Taxon
Vipera berus and Zootoca vivipara, two cold‐adapted species.
Methods
We used two sets of variables, that is physiologically meaningful climatic variables (PMV) and BioV, in a multi‐algorithm ENM approach, to compare their ability to predict current and Last Glacial Maximum (LGM) species ranges. We estimated current and LGM permafrost extent to address spatially the cold hardiness dissimilarity between both species.
Results
PMV explained more accurately the current distribution of these two cold‐adapted species and identified the importance of summer temperature and solar radiation that constrain activity in cold habitats. PMV also provide a better insight than BioV predictors on LGM distribution. By including notably, the permafrost extent, PMV‐based models gave parsimonious putative arrangement and validity of refugia for each clade and subclade in accordance with phylogeographic data. Northern refugia were also identified from 48 to 52° N for V. berus and from 50 to 54° N for Z. vivipara.
Main Conclusions
Our hybrid approach based on PMV generated more realistic predictions for both current (biogeographical validation) and past distributions (phylogeographic validation). By combining constraints during the activity period (summer climatic niche) and those inherent to the wintering period (freeze tolerance), we managed to identify glacial refuges in agreement with phylogeographic hypotheses concerning post‐glacial routes and colonization scenarios.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Local adaptation to different environments has the potential to maintain divergence between populations despite recurrent gene flow and is an important driver for generating biological diversity. In ...this study, we investigate the role of adaptation in the maintenance of two parapatric varieties of a forest tree. We used sequence variation of chloroplastic DNA and restriction site‐associated DNA to investigate the genetic structure of two varieties of Castanopsis carlesii in subtropical China and relate it to climatic variation. We used niche reconstruction methods to investigate niche differentiation between the two varieties and to estimate the past distribution of this species. A deep divergence was observed between the two varieties, but evidence of introgression and genetic admixture was detected in two phenotypically and geographically intermediate populations. Niche reconstruction suggests that the distribution of the two varieties was disjunct during periods of global cooling and that the two varieties occupy significantly different niches. The genetic structure was mainly driven by environmental factors, and 13 outlier loci under divergent selection were correlated with climatic variation. These results suggest that the two varieties evolved in allopatry and came back into secondary contact after the last glacial maximum and that they are an evolutionary example of divergence maintained by climatic selection despite recurrent gene flow.
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Aim: During glaciations, the distribution of temperate species inhabiting the Northern Hemisphere generally contracts into southern refugia; and in boreo-alpine species of the Northern Hemisphere, ...expansion from Northern refugia is the general rule. Little is known about the drivers explaining vast distributions of species inhabiting multiple biogeographic regions (major biogeographic regions defined by the European Environmental Agency). Here we investigate the fine-scale phylogeography and evolutionary history of the Eurasian common lizard (Zootoca vivipara), the terrestrial reptile with the world's widest and highest latitudinal distribution, that inhabits multiple biogeographic regions. Location: Eurasia. Methods: We generated the largest molecular dataset to date of Z. vivipara, ran phylogenetic analyses, reconstructed its evolutionary history, determined the location of glacial refuges and reconstructed ancestral biogeographic regions. Results: The phylogenetic analyses revealed a complex evolutionary history, driven by expansions and contractions of the distribution due to glacials and interglacials, and the colonization of new biogeographic regions by all lineages of Z. vivipara. Many glacial refugia were detected, most were located close to the southern limit of the Last Glacial Maximum. Two subclades recolonized large areas covered by permafrost during the last glaciation: namely, Western and Northern Europe and North-Eastern Europe and Asia. Main conclusions: In Z. vivipara, most of the glacial refugia were located in the South of their current distribution. Previous studies suggested the existence of Northern refuges, but the species' inability to overwinter on permafrost and the lack of genetic support suggest that the presence of a refugia in the north of the Alps is unlikely. This species currently inhabits boreo-alpine climates and retracted during previous glaciations into southern refugia, as temperate species. Two clades exhibited enormous geographic expansion that started from two distinct glacial refugia. These phylogeographic patterns were highly congruent with those of Vipera berus. Together they suggest that glacial retraction, the location of the refugia and absence of competition may have promoted the enormous geographic expansion of two clades.
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Reduced‐representation genome sequencing such as RADseq aids the analysis of genomes by reducing the quantity of data, thereby lowering both sequencing costs and computational burdens. RADseq was ...initially designed for studying genetic variation across genomes at the population level, but has also proved to be suitable for interspecific phylogeny reconstruction. RADseq data pose challenges for standard phylogenomic methods, however, due to incomplete coverage of the genome and large amounts of missing data. Alignment‐free methods are both efficient and accurate for phylogenetic reconstructions with whole genomes and are especially practical for nonmodel organisms; nonetheless, alignment‐free methods have not been applied with reduced genome sequencing data. Here, we test a full‐genome assembly‐ and alignment‐free method, AAF, in application to RADseq data and propose two procedures for reads selection to remove reads from restriction sites that were not found in taxa being compared. We validate these methods using both simulations and real data sets. Reads selection improved the accuracy of phylogenetic construction in every simulated scenario and the two real data sets, making AAF as good or better than a comparable alignment‐based method, even though AAF had much lower computational burdens. We also investigated the sources of missing data in RADseq and their effects on phylogeny reconstruction using AAF. The AAF pipeline modified for RADseq or other reduced‐representation sequencing data, phyloRAD, is available on github (https://github.com/fanhuan/phyloRAD).
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Aims
To conserve forest natural heritage, sustainable forest harvesting requires the recovery of plant diversity and ecosystem functions following management. There is a need to clarify the temporal ...dynamics of plant diversity following harvesting, for both even‐aged and uneven‐aged silvicultural systems. To achieve this goal, the temporal dynamics of plant diversity in the herb layer were measured in unmanaged forests (control) and along a chronosequence (<5 years, 15 years and 30 years after harvesting) for even‐aged and uneven‐aged managed forests.
Location
Hardwood forest of southern Quebec, Canada.
Methods
Plant diversity, plant community composition and ecosystem functioning were investigated using metrics exploring richness, evenness and disparity diversity components, and included two scales of diversity partitioning (alpha and beta). Shrub–canopy layer, forest tree species composition and structure, and total forest basal area were also measured.
Results
In both uneven‐aged and even‐aged managed forest stands, we found: (a) a substantial decrease in mean plant phylogenetic diversity compared with unmanaged forest, even 30 years after harvesting (i.e., decrease of 16% and 22%, respectively); and (b) lowest plant alpha‐diversity in the herb layer 15 years after harvesting. Modification of community composition based upon dissimilarity (beta‐diversity) metrics demonstrated more numerous effects of even‐aged management than uneven‐aged management. For forest composition and structure, plant community and plant traits, dissimilarity relative to the unmanaged control was highest 5 years after even‐aged management. Trait‐based communities were more similar to unmanaged forest at the intermediate levels of forest density (i.e., ~20 m2/ha) that were found 5 years after uneven‐aged management.
Conclusions
Forest management clearly affected diversity, community composition and ecosystem functions along the chronosequence, highlighting the strongest effects of more intensive management (i.e., even‐aged) and the need to improve the sustainability of forest management.
We determined the effects of forest harvesting (clear cuts and partial harvests) on plant diversity 5, 15 and 30 years after harvesting, relative to unmanaged old‐growth forest. We found a substantial decrease in mean plant phylogenetic diversity (all periods after harvesting), plant alpha‐diversity (15 years after harvesting) and beta‐diversity of plant traits (5 years after clear‐cutting) in managed forests compared with unmanaged forest.
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BFBNIB, DOBA, FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UILJ, UKNU, UL, UM, UPUK
Transcriptome analysis has important applications in many biological fields. However, assembling a transcriptome without a known reference remains a challenging task requiring algorithmic ...improvements. We present two methods for substantially improving transcriptome de novo assembly. The first method relies on the observation that the use of a single k-mer length by current de novo assemblers is suboptimal to assemble transcriptomes where the sequence coverage of transcripts is highly heterogeneous. We present the Multiple-k method in which various k-mer lengths are used for de novo transcriptome assembly. We demonstrate its good performance by assembling de novo a published next-generation transcriptome sequence data set of Aedes aegypti, using the existing genome to check the accuracy of our method. The second method relies on the use of a reference proteome to improve the de novo assembly. We developed the Scaffolding using Translation Mapping (STM) method that uses mapping against the closest available reference proteome for scaffolding contigs that map onto the same protein. In a controlled experiment using simulated data, we show that the STM method considerably improves the assembly, with few errors. We applied these two methods to assemble the transcriptome of the non-model catfish Loricaria gr. cataphracta. Using the Multiple-k and STM methods, the assembly increases in contiguity and in gene identification, showing that our methods clearly improve quality and can be widely used. The new methods were used to assemble successfully the transcripts of the core set of genes regulating tooth development in vertebrates, while classic de novo assembly failed.
Aim
The development of natural habitats into urban land uses has greatly accelerated in the recent past due to human activities. This habitat development disrupts species' natural dispersal processes ...and can lead to both direct and indirect impacts on dispersal. Whether human activities result in restricted or facilitated dispersal may depend on a species' development tolerance; however, this premise has not been tested. We examined the impact of urbanization and road networks on the dispersal of three lizard species in the context of their development tolerance.
Location
Curaçao.
Methods
To quantify species' development tolerance, we modelled three lizard species abundances at sites based on surrounding landscape development. Using microsatellite genotypes, we conducted individual‐based resistance surface analyses and modelled the effect of habitat development on genetic admixture to assess indirect dispersal restriction and facilitation. We explored direct facilitation of dispersal using network analysis of mitochondrial haplotypes.
Results
Phyllodactylus martini, a native gecko species, was the least tolerant of development and experienced indirect dispersal restriction due to roads, according to resistance surface analyses. Anolis lineatus, a native anole species, exhibited a neutral relationship with development. Resistance surfaces and Structure analyses showed that A. lineatus faced indirect dispersal restrictions from roads and developed areas, while mitochondrial haplotype networks suggested they benefited from occasional human‐facilitated long‐distance dispersal events. Hemidactylus mabouia, an introduced gecko species, was the most tolerant of development, and experienced no dispersal restriction, but mitochondrial haplotypes suggest direct long‐distance dispersal facilitation.
Main Conclusions
Our findings highlight development tolerance as a key predictor of dispersal impact for these species and future work should test whether these patterns are upheld in other systems. Understanding how human activities affect species' dispersal will aid in managing introduced species while promoting connectivity for native species navigating dispersal challenges in dynamic landscapes.
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Metabarcoding potentially offers a rapid and cheap method of monitoring biodiversity, but real-world applications are few. We investigated its utility in studying patterns of litter arthropod ...diversity and composition in the tropics. We collected litter arthropods from 35 matched forest-plantation sites across Xishuangbanna, southwestern China. A new primer combination and the MiSeq platform were used to amplify and sequence a wide variety of litter arthropods using simulated and real-world communities. Quality filtered reads were clustered into 3,624 MOTUs at ≥97% similarity and the taxonomy of each MOTU was predicted. We compared diversity and compositional differences between forests and plantations (rubber and tea) for all MOTUs and for eight arthropod groups. We obtained ~100% detection rate after in silico sequencing six mock communities with known arthropod composition. Ordination showed that rubber, tea and forest communities formed distinct clusters. α-diversity declined significantly between forests and adjacent plantations for more arthropod groups in rubber than tea, and diversity of order Orthoptera increased significantly in tea. Turnover was higher in forests than plantations, but patterns differed among groups. Metabarcoding is useful for quantifying diversity patterns of arthropods under different land-uses and the MiSeq platform is effective for arthropod metabarcoding in the tropics.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Amphibian populations have been globally declining since at least 1990. In the temperate forests of eastern North America, vernal pools offer important breeding habitats to many amphibians but are ...usually not considered for forest management because of their small size and temporary status. The effective monitoring and management of amphibians rely on accurate knowledge of their spatiotemporal distributions, which is often expensive to collect due to the amount of fieldwork required. In this study, we tested whether eDNA metabarcoding could identify the same amphibian communities as the traditional inventory protocols. We collected eDNA samples in twelve vernal pools in the spring of 2019 and identified their communities via metabarcoding. At each pool, three traditional amphibian inventory methods were used: call surveys, trapping, and active search surveys. In total, 13 amphibian species were detected, with most of them being detected using both eDNA and the traditional methods. When comparing the results of eDNA with the traditional methods, we found that species ecology and behavior are key factors of its detectability via a specific method. With its higher taxonomical precision and repeatability, eDNA metabarcoding allows for the inventorying of amphibian species living and reproducing in vernal pools and their vicinity with accuracy. As eDNA metabarcoding is inexpensive compared to the traditional methods, we conclude that eDNA sampling should be considered for integration as a standard monitoring tool, after an initial assessment of amphibian diversity.
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