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The publish‐or‐perish culture in academia has catalysed the development of an unethical publishing system. This system is characterised by the proliferation of journals and publishers—unaffiliated with learned societies or universities—that maintain extremely large revenues and profit margins diverting funds away from the academic community. Early career researchers (ECRs) are particularly vulnerable to the consequences of this publishing system because of intersecting factors, including pressure to pursue high impact publications, rising publication costs and job insecurity. Moving towards a more ethical system requires that scientists advocate for structural change by making career choices that come with risks, many of which disproportionately impact ECRs. We illuminate major issues facing ECRs in Ecology and Evolution under the current publishing system, and propose a portfolio of actions to promote systemic change that can be implemented by ECRs and established researchers. [ABSTRACT FROM AUTHOR]

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about their relative importance and how they interact. Here, we synthesised data from 152 studies that used state‐dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, SSE model results were correlated to data set properties – trees that were larger, older or less well‐sampled tended to yield trait‐dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species' ecology, demography and genetics. [ABSTRACT FROM AUTHOR]

Aim: Pleistocene (2.58 Ma–11.7 ka) climatic fluctuations have shaped intraspecific genetic patterns worldwide; however, their impact on species in many regions remains unknown. In order to determine the impact of Pleistocene climatic fluctuations on the tropical rain forests of western Ecuador, we explored the evolutionary history of the endemic palm Phytelephas aequatorialis. Location: Western Ecuador, north‐western South America. Taxon: Phytelephas aequatorialis (Arecaceae). Methods: One hundred and seventy‐six nuclear genes were sequenced in 91 individuals for phylogenomic and population structure analyses. The time of divergence between identified genetic lineages was estimated using a coalescent phylogenomic analysis. Palaeoecological niche modelling analyses were performed to determine areas of historical climatic suitability since the Last Glacial Maximum (LGM; 22 ka) that potentially acted as forest refugia during the Pleistocene. A Wilcoxon test and Pearson correlations were used to explore how current levels of genetic diversity, in terms of expected heterozygosity (Hs), have been shaped by several palaeoclimatic and geographic factors. Results: Phylogenomic and population structure analyses revealed two main genetic lineages with a north–south distribution, which diverged 1.14 Ma during the Pleistocene. Two potential Pleistocene refugia were identified, one along the Pacific coast of Ecuador and one in the Andean foothills of south‐western Ecuador. The location of these refugia agrees with the spatial location of the two genetic lineages. Within the Andean foothills, Hs was lower for the southern lineage than for the northern lineage. Hs significantly increased with decreasing latitude across the species as a whole. Main conclusions: Pleistocene climatic fluctuations promoted intraspecific divergence in P. aequatorialis within the rain forests of western Ecuador. The Andean foothills of south‐western Ecuador could be an important area for rain forest evolution because they potentially remained climatically suitable throughout the Pleistocene. Lower genetic diversity in the southern lineage, which apparently remained isolated in the Andean foothills during glacial cycles, adds evidence to the presence of a forest refugium in south‐western Ecuador. The geographic pattern in genetic diversity suggests that P. aequatorialis colonized western Ecuador from the north. This study supports the role of Pleistocene climatic fluctuations in promoting intraspecific divergence, and for the first time, we show their impact west of the Andes. [ABSTRACT FROM AUTHOR]

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co‐occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome‐wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth. [ABSTRACT FROM AUTHOR]

The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north–south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north–south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics. [ABSTRACT FROM AUTHOR]

Aim: Different species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured. Location: South America. Taxon: Austrolebias (Cyprinodontiformes). Methods: We sampled 63 individuals from 26 Austrolebias species. Using phylogenetic trees (BEAST2), data on environmental variables at sampling locations and size data, we compare different models for trait evolution (SURFACE, l1OU) of body size and niche traits. We model the historical biogeography of the areas of endemism (BioGeoBEARS) and use both analyses in combination to reconstruct the history of four species assemblages. Results: We present new phylogenetic trees for Austrolebias and use them to show that large size principally arose within a single area driven by a shifted selection optimum for a subset of the species in that area. We suggest that ecological interactions triggered size divergence and that this large‐bodied lineage subsequently spread to two other areas. A second assemblage may have been shaped by adaptation to a new environment without an associated increase in size divergence. A third assemblage, which has the smallest size range and the most recent origin, is phylogenetically clustered, and we found no evidence of environmental filtering. Main conclusions: Assemblage similarity in Austrolebias is the result of contrasting ecological, evolutionary and historical processes. Modelling trait evolution together with historical biogeography can help to disentangle the complex histories of multispecies assemblages. This approach provides context to commonly used tests investigating the role of ecological processes from phylogenetic data and generates new testable hypotheses on the processes that generated trait diversity and assemblage similarity. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Hazelnut is consumed worldwide and is of critical economic importance to the rural communities of Turkey's northern coast. A new disease outbreak has drastically decreased yields across Turkey and climate change is emerging as a new threat to cultivation. Our study is the first to provide a genomic perspective on diversity in this vulnerable crop, which will prove valuable for future breeding efforts. Such research into perennial crops like hazelnut can help to improve farmer livelihoods and ensure the sustainability of crop production in a changing world. SummaryAssessing and describing genetic diversity in crop plants is a crucial first step toward their improvement. The European hazelnut, Corylus avellana L., is one of the most economically important tree nut crops worldwide. It is primarily produced in Turkey where rural communities depend on it for their livelihoods. Despite this, we know little about its domestication history and the genetic diversity it holds.We use double digest restriction‐site associated DNA (ddRAD) sequencing to produce a genome‐wide dataset containing wild and domesticated hazelnut. We uncover patterns of population structure and diversity, determine levels of crop‐wild gene flow, and estimate the relationships among different genetic clusters.We use a dataset of over 60k single nucleotide polymorphisms to find that genetic clusters of cultivars do not reflect their given names and that there is limited evidence for a reduction in genetic diversity in domesticated individuals. We find evidence that hazelnut may have been domesticated more than once and that admixture has likely occurred multiple times between wild and domesticated hazelnut.We provide the first genomic assessment of Turkish hazelnut diversity and suggest that there has not been an extreme bottleneck during the domestication of this crop, leading to cultivars at different stages of domestication. Our study provides a platform for further research that will protect hazelnut from the threats of climate change and an emerging fungal disease. [ABSTRACT FROM AUTHOR]