The centromere represents a single region in most eukaryotic chromosomes. However, several plant and animal lineages assemble holocentromeres along the entire chromosome length. Here, we compare genome organization and evolution as a function of centromere type by assembling chromosome-scale holocentric genomes with repeat-based holocentromeres from three beak-sedge (Rhynchospora pubera, R. breviuscula, and R. tenuis) and their closest monocentric relative, Juncus effusus. We demonstrate that transition to holocentricity affected 3D genome architecture by redefining genomic compartments, while distributing centromere function to thousands of repeat-based centromere units genome-wide. We uncover a complex genome organization in R. pubera that hides its unexpected octoploidy and describe a marked reduction in chromosome number for R. tenuis, which has only two chromosomes. We show that chromosome fusions, facilitated by repeat-based holocentromeres, promoted karyotype evolution and diploidization. Our study thus sheds light on several important aspects of genome architecture and evolution influenced by centromere organization.

• Keywords
• Rhynchospora, centromere, dysploidy, genome regulation, holocentric chromosomes, spatial genome organization, transposable elements, whole-genome duplication,
• MeSH
• Centromere * genetics   MeSH
• Karyotype MeSH
• Evolution, Molecular MeSH
• Plants genetics   MeSH
• Cyperaceae * genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Rapidly radiated groups are usually accompanied by unclear lineage and taxa delineation, which complicates their better understanding in terms of biodiversity, evolutionary processes, and taxonomic treatment. The most species-rich orchid subtribe, Pleurothallidinae, exemplifies an extremely diverse group with a complex evolutionary history associated with Andean orography. Here we combined multi-loci phylogeny reconstruction (HybSeq), genome-wide traits (inferred by flow cytometry), spatial analyses, and biogeography to investigate the evolutionary intricacy of one clade of Pleurothallidinae orchids. To achieve deep insights, we performed multiple species tree reconstruction approaches with the implementation of custom scripts to reveal sources of topological discrepancies and alternative evolutionary scenarios. The phylogeny clearly resolves the delimitation of the main evolutionary lineages corresponding to the accepted genera, with the exception of the genus Specklinia, which is divided into three distinct monophyletic lineages whose taxonomic treatment is proposed. Genome-wide characters (especially genome size) show an association with precipitation seasonality in a geographical context, and partial endoreplication, a unique character of orchids, is geographically restricted to the Andes, Central America, and the Caribbean. Specifically, the Andean region exemplifies the prevalence of bigger genome size and higher GC content, resulting from a higher proportion of species with partial endoreplication. The Andean origin of the clade was also revealed by biogeographic analysis. Our comprehensive approach has provided deep insights into the evolution of this clade and may be a useful tool for unraveling the intricate evolutionary history of similarly complex lineages.

• Keywords
• Andes, GC content, HybSeq, Pleurothallidinae, endoreplication, evolution, genome size, spatial analysis,
• MeSH
• Biological Evolution * MeSH
• Genome Size MeSH
• Phylogeny * MeSH
• Genome, Plant * genetics   MeSH
• Evolution, Molecular MeSH
• Orchidaceae * genetics   classification   MeSH
• Publication type
• Journal Article MeSH

The study of mating systems, defined as the distribution of who mates with whom and how often in a sexually reproducing population, forms a core pillar of evolution research due to their effects on many evolutionary phenomena. Historically, the "mating system" has either been used to refer to the rate of self-fertilization or to the formation of mating pairs between individuals of distinct sexes. Consequently, these two types of mating systems have tended to be studied separately rather than jointly. This separation often means that mating systems are not necessarily researched in a coherent manner that might apply to different types of organisms (e.g., plants versus animals, or hermaphrodites versus dioecious species), even if similar mechanisms may drive the evolution of self-fertilization and mating pair formation. Here, we review the evolution of both plant and animal mating systems, highlighting where similar concepts underlie both these fields and also where differing mechanisms are at play. We particularly focus on the effects of inbreeding, but also discuss the influence of spatial dynamics on mating-system evolution. We end with a synthesis of these different ideas and propose ideas for which concepts can be considered together to move towards a more cohesive approach to studying mating-system evolution.

• Keywords
• Baker’s law, inbreeding, mating system, polygyny, self-fertilization, spatial evolution, transmission advantage,
• MeSH
• Biological Evolution * MeSH
• Plant Physiological Phenomena * MeSH
• Plants * genetics   MeSH
• Reproduction MeSH
• Self-Fertilization MeSH
• Sexual Behavior, Animal * MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Review MeSH

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalisation analyses, historical biogeography and ancestral state estimations. Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae. Smaller families display unique and often divergent evolutionary trajectories. The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.

• Keywords
• biogeography, evolution, evolutionary transitions, grasslands, grass‐like plants, savannas, spatial phylogenetics,
• MeSH
• Biological Evolution MeSH
• Ecosystem * MeSH
• Phylogeny MeSH
• Poaceae * MeSH
• Publication type
• Journal Article MeSH

Animal eyes can vary in complexity ranging from a single photoreceptor cell shaded by a pigment cell to elaborate arrays of these basic units, which allow image formation in compound eyes of insects or camera-type eyes of vertebrates. The evolution of the eye requires involvement of several distinct components-photoreceptors, screening pigment and genes orchestrating their proper temporal and spatial organization. Analysis of particular genetic and biochemical components shows that many evolutionary processes have participated in eye evolution. Multiple examples of co-option of crystallins, Galpha protein subunits and screening pigments contrast with the conserved role of opsins and a set of transcription factors governing eye development in distantly related animal phyla. The direct regulation of essential photoreceptor genes by these factors suggests that this regulatory relationship might have been already established in the ancestral photoreceptor cell.

• MeSH
• Photoreceptor Cells, Invertebrate physiology   MeSH
• Evolution, Molecular * MeSH
• Ocular Physiological Phenomena genetics   MeSH
• Eye Proteins genetics   MeSH
• Retinal Pigments genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Eye Proteins MeSH
• Retinal Pigments MeSH

On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.

• Keywords
• Gemmatimonadota, gene order, genome evolution, genome organization, strand bias,
• MeSH
• Bacteria genetics   classification   MeSH
• Chromosomes, Bacterial * genetics   MeSH
• DNA, Bacterial genetics   MeSH
• Genome, Bacterial MeSH
• Evolution, Molecular * MeSH
• Gene Transfer, Horizontal MeSH
• DNA Replication * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• DNA, Bacterial MeSH

The structure of ecological networks reflects the evolutionary history of their biotic components, and their dynamics are strongly driven by ecoevolutionary processes. Here, we present an appraisal of recent relevant research, in which the pervasive role of evolution within ecological networks is manifest. Although evolutionary processes are most evident at macroevolutionary scales, they are also important drivers of local network structure and dynamics. We propose components of a blueprint for further research, emphasising process-based models, experimental evolution, and phenotypic variation, across a range of distinct spatial and temporal scales. Evolutionary dimensions are required to advance our understanding of foundational properties of community assembly and to enhance our capability of predicting how networks will respond to impending changes.

• Keywords
• adaptive network, ecoevolution, ecophylogenetics, metacommunity, microevolution, phylogeny,
• MeSH
• Biological Evolution * MeSH
• Ecosystem * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

Tropical forests are notable for their high species diversity, even on small spatial scales, and right-skewed species and size abundance distributions. The role of individual species as drivers of the spatial organization of diversity in these forests has been explained by several hypotheses and processes, for example, stochastic dilution, negative density dependence, or gap dynamics. These processes leave a signature in spatial distribution of small trees, particularly in the vicinity of large trees, likely having stronger effects on their neighbors. We are exploring species diversity patterns within the framework of various diversity-generating hypotheses using individual species-area relationships. We used the data from three tropical forest plots (Wanang-Papua New Guinea, Barro Colorado Island-Panama, and Sinharaja-Sri Lanka) and included also the saplings (DBH ≥ 1 cm). Resulting cross-size patterns of species richness and evenness reflect the dynamics of saplings affected by the distribution of large trees. When all individuals with DBH ≥1 cm are included, ~50% of all tree species from the 25- or 50-ha plot can be found within 35 m radius of an individual tree. For all trees, 72%-78% of species were identified as species richness accumulators, having more species present in their surroundings than expected by null models. This pattern was driven by small trees as the analysis of DBH >10 cm trees showed much lower proportion of accumulators, 14%-65% of species identified as richness repellers and had low richness of surrounding small trees. Only 11%-26% of species had lower species evenness than was expected by null models. High proportions of species richness accumulators were probably due to gap dynamics and support Janzen-Connell hypothesis driven by competition or top-down control by pathogens and herbivores. Observed species diversity patterns show the importance of including small tree size classes in analyses of the spatial organization of diversity.

• Keywords
• individual species–area relationship, null model, spatial pattern, species diversity, species evenness, tropical forest,
• Publication type
• Journal Article MeSH

Birds' beaks play a key role in foraging, and most research on their size and shape has focused on this function. Recent findings suggest that beaks may also be important for thermoregulation, and this may drive morphological evolution as predicted by Allen's rule. However, the role of thermoregulation in the evolution of beak size across species remains largely unexplored. In particular, it remains unclear whether the need for retaining heat in the winter or dissipating heat in the summer plays the greater role in selection for beak size. Comparative studies are needed to evaluate the relative importance of these functions in beak size evolution. We addressed this question in a clade of birds exhibiting wide variation in their climatic niche: the Australasian honeyeaters and allies (Meliphagoidea). Across 158 species, we compared species' climatic conditions extracted from their ranges to beak size measurements in a combined spatial-phylogenetic framework. We found that winter minimum temperature was positively correlated with beak size, while summer maximum temperature was not. This suggests that while diet and foraging behavior may drive evolutionary changes in beak shape, changes in beak size can also be explained by the beak's role in thermoregulation, and winter heat retention in particular.

• Keywords
• Allen's rule *, Meliphagoidea *, beak size *, thermoregulation *,
• MeSH
• Biological Evolution * MeSH
• Phylogeny MeSH
• Cold Temperature MeSH
• Body Temperature Regulation * MeSH
• Beak anatomy & histology   MeSH
• Songbirds anatomy & histology   physiology   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH

The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barriers. Spatial expansion of the currently most widespread "albipes" mtDNA clade was followed by population fragmentation, lineage sorting and again by hybridization and mtDNA introgression. Comparison of this genetic structure to other Ethiopian endemic taxa highlight the geographical areas of special conservation concern, where more detailed biodiversity studies should be carried out to prevent many endemic taxa from going extinct even before they are recognized.

• Keywords
• Ecological speciation, Ethiopian highlands, Great Rift Valley, Mitochondrial introgression, Rodentia, Stenocephalemys,
• MeSH
• Cytochromes b chemistry   classification   genetics   MeSH
• Ecosystem MeSH
• Phylogeny MeSH
• Haplotypes MeSH
• Hybridization, Genetic MeSH
• Karyotype MeSH
• DNA, Mitochondrial chemistry   isolation & purification   metabolism   MeSH
• Evolution, Molecular * MeSH
• Murinae anatomy & histology   classification   genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Geographicals
• Ethiopia MeSH
• Names of Substances
• Cytochromes b MeSH
• DNA, Mitochondrial MeSH