Dimitar Dimitrov

University of Bergen | UiB ·  University Museum of Bergen

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 di...

Cryptic species could represent a substantial fraction of biodiversity. However, inconsistent definitions and taxonomic treatment of cryptic species prevent informed estimates of their contribution to biodiversity and impede our understanding of their evolutionary and ecological significance. We propose a conceptual framework that recognizes crypti...

Floristic regions reflect the geographic organization of floras and provide essential tools for biological studies. Previous global floristic regions are generally based on floristic endemism, lacking a phylogenetic consideration that captures floristic evolution. Moreover, the contribution of tectonic dynamics and historical and current climate to...

Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in speci...

Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage...

The rapid diversification and high species richness of flowering plants is regarded as ‘Darwin’s second abominable mystery’. Today the global spatiotemporal pattern of plant diversification remains elusive. Using a newly generated genus-level phylogeny and global distribution data for 14,244 flowering plant genera, we describe the diversification d...

The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. We foun...

Floral symmetry plays an important role in plant-pollinator interactions and may have remarkable impacts on angiosperm diversification. However, spatiotemporal patterns in floral symmetry and drivers of these patterns remain unknown. Here, using newly compiled floral symmetry (actinomorphy versus zygomorphy) data of 279,877 angiosperm species and t...

Floral symmetry plays an important role in plant-pollinator interactions and may have remarkable impacts on angiosperm diversification. However, spatiotemporal patterns in floral symmetry and drivers of these patterns remain unknown. Here, using newly compiled floral symmetry (actinomorphy versus zygomorphy) data of 279,877 angiosperm species and t...

Aim Pollination is an essential stage of angiosperm reproduction, and the mode of pollination plays a major role in driving evolutionary and ecological responses of plants to environmental changes. However, the effects of climate, evolutionary history and floral traits (i.e. plant sexual systems) on pollination mode variation remain unclear. Here,...

Geographic range size of endemic species is the most important indicator of species' vulnerability to extinction and conservation prioritization, yet variation in range size among species and across space has been relatively understudied. We investigated the variations and geographic patterns of the range size of 9898 angiosperm species endemic to...

The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the p...

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, aut...

Aim Climate has been regarded as an important explanation for large‐scale species richness patterns. However, the mechanisms underlying the significant variations in species richness–climate relationships across different clades remain to be tested. We explored how niche conservatism, diversification rates and time for speciation influenced species...

The repeated evolution of phenotypes is ubiquitous in nature and offers some of the clearest evidence of the role of natural selection in evolution. The genomic basis of repeated phenotypic evolution is often complex and can arise from a combination of gene flow, shared ancestral polymorphism and de novo mutation. Here, we investigate the genomic b...

Nesticidae is a small family of spiders with a worldwide distribution that includes 15 genera and 272 described species. Seven genera and 56 species are known from Europe, distributed from the Iberian Peninsula to the Caucasus and the Ural Mountains. Most of these European species are cave dwellers and many of them are troglobites. In this study we...

Aim Woody and herbaceous habits represent one of the most distinct contrasts among angiosperms, and the proportion of woody species in floras (i.e., “woodiness” hereafter) represents a fundamental structural element of plant diversity. Despite its core influence on ecosystem processes, spatio‐temporal patterns in woodiness remain poorly understood....

Editorial on the Research Topic: Temporal and Large-Scale Spatial Patterns of Plant Diversity and Diversification.

Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Her...

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics,...

Magnoliaceae, a primitive group of angiosperms and distinguished ornamental plants with more than 100 species in China, is one of the most threatened plant family in the wild due to logging, habitat loss, over-collection and climate change. To provide a scientific guide of its conservation for policymakers, we explore the diversity patterns of 114...

Spiders (Araneae) have a diverse spectrum of morphologies, behaviours and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, in...

We address the phylogenetic relationships of pimoid spiders (Pimoidae) using a standard target-gene approach with an extensive taxonomic sample, which includes representatives of the four currently recognized pimoid genera, 26 linyphiid genera, a sample of Physoglenidae, Cyatholipidae and one Tetragnathidae species. We test the monophyly of Pimoida...

The effects of contemporary climate, habitat heterogeneity and long-term climate change on species richness are well studied for woody plants in forest ecosystems, but poorly understood for herbaceous plants, especially in alpine–arctic ecosystems. Here, we aim to test if the previously proposed hypothesis based on the richness–environment relation...

Angiosperm sexual systems are fundamental to the evolution and distribution of plant diversity, yet spatiotemporal patterns in angiosperm sexual systems and their drivers remain poorly known. Using data on sexual systems and distributions of 68453 angiosperm species, we present the first global maps of sexual system frequencies and evaluate sexual...

The tea family (Theaceae) has a highly unusual amphi-Pacific disjunct distribution: most extant species in the family are restricted to subtropical evergreen broadleaf forests in East Asia, while a handful of species occur exclusively in the subtropical and tropical Americas. Here we used an approach that integrates the rich fossil evidence of this...

High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze a...

Aim Biodiversity hotspots are widely used as conservation priorities to preserve the tree of life. However, many conservation practices identify biodiversity hotspots without considering phylogenetic diversity (PD), which reflects total evolutionary history and feature diversity of a region. Moreover, conservation planning rarely distinguishes betw...

Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), non-coding region...

Aim The links between taxonomic, functional, and phylogenetic diversity and how these vary geographically are key to understanding how historical and contemporary processes have shaped communities at regional and local scales. Here, we evaluate the links between taxonomic, functional and phylogenetic diversity for the amphibians in the Continental...

Mechanisms underlying species richness patterns remain a central yet controversial issue in biology. Climate has been regarded as a major determinant of species richness. However, the relative influences of different evolutionary processes, (i.e. niche conservatism, diversification rate and time for speciation) on species richness–climate relations...

Aim Sexual systems strongly influence angiosperm evolution and play important roles in community assembly and species responses to climate change. However, geographical variation in proportions of different sexual systems (dioecy, monoecy and hermaphroditism) in response to changes in climate, life‐history traits and evolutionary age remains poorly...

Morphological stasis or the absence of morphological change is a well‐known phenomenon in the paleontological record, yet it is poorly integrated with neontological evidence. Recent evidence suggests that cryptic species complexes may remain morphologically identical due to morphological stasis. Here, we describe a case of long‐term stasis in the S...

Exploring the biogeographic patterns of soil microbial diversity is critical for understanding mechanisms underlying the response of soil processes to climate change. Using top- and subsoils from an ∼1,500-km temperate grassland transect, we find divergent patterns of microbial diversity and its determinants in the topsoil versus the subsoil. Furth...

We address some of the taxonomic and classification changes proposed by Kuntner et al. (in press) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to re-circumscribe araneids and to rank the subfamily Nephilinae is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss...

Biogeographic patterns and drivers of soil microbial diversity have been extensively studied in the past few decades. However, most research has focused on the topsoil while the subsoil is assumed to have similar microbial diversity patterns as the topsoil. Here we compare patterns and drivers of microbial diversity in the top- (0-10 cm) versus sub...

Aim Although the effects of climate on species richness are known, regional processes may lead to different species richness–climate relationships across continents resulting in species richness anomalies, especially for tropical groups. Phylogenetic niche conservatism may also influence species richness–climate relationships of different lineages....

Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular p...

With almost 600 species, the latest molecular phylogeny of pholcid spiders (Eberle et al. 2018, BMC Evolutionary Biology) more than triples the largest previously available molecular phylogeny of the family. At the level of genera, the coverage is high (86%, i.e., 75 of the 87 named genera), and at the level of subfamilies it is complete. The prese...

Aim Understanding the evolution of the latitudinal diversity gradient (i.e. increase in species diversity towards the tropics) is a prominent issue in ecology and biogeography. Disentangling the relative contributions of environment and evolutionary history in shaping this gradient remains a major challenge because their relative importance has bee...

We report for the first time the occurrence of pimoids (Araneoidea, Pimoidae) in Taiwan, describe Putaoa seediq new species, revise the genus diagnosis accordingly, and illustrate for the first time the web architecture of Putaoa based on field photographs. Males of Putaoa species differ from other pimoids in having distinctively large macrosetae o...

Background Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been publis...

We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups....

Woody plants host diverse communities of associated organisms, including woodinhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and net...

Matrix S1. The character matrix used in phylogenetic analyses.

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to...

Despite the increasing rate of systematic research on scarabaeine dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae), their fossil record has remained largely unrevised. In this paper, we review all 33 named scarabaeine fossils and describe two new species from Dominican amber ( Canthochilum alleni sp.n. , Canthochilum philipsivieorum sp.n. ). W...

The flora on the isolated high African mountains or ‘sky islands’ is remarkable for its peculiar adaptations, local endemism and striking biogeographical connections to remote parts of the world. Ages of the plant lineages and the timing of their radiations have frequently been debated but remain contentious as there are few estimates based on expl...

核苷酸序列是生物体遗传信息的载体, 是现代生物学和生态学的基础数据。随着测序技术的进步, 大量核苷酸序列被提取并存储在公共数据平台中, 其中GenBank (http://www.ncbi.nlm.nih.gov/genbank/)是目前最大的核苷酸序列数据平台之一。截至2015年2月, 该平台收录核苷酸序列总数已超过1.8亿条、覆盖全球超过30万个物种。但如何从如此海量的数据中准确、快速查找并下载所需数据已成为限制基因数据广泛使用的障碍之一。为此, 我们开发了一款可高效、准确下载GenBank数据的生物信息学软件NCBIminer。NCBIminer可根据用户提供的核苷酸序列名称、数据类型、一或多条初始化参考序列, 查找并下载用户指定的多个物种或类群的特定基因序列数据。该软件下载地址为ht...

NCBIminer is freely available, cross-platform and user-friendly software for mining nucleotide sequence data from GenBank. It has several features that enable users to accurately and efficiently download sequences with specific attributes from the GenBank database: 1) it uses a novel search strategy, and can download sequences for distantly related...

Kreft and Jetz’s critique of our recent update of Wallace’s zoogeographical regions disregards the extensive sensitivity analyses we undertook, which demonstrate the robustness of our results to the choice of phylogenetic data and clustering algorithm. Their suggested distinction between “transition zones” and biogeographic regions is worthy of fur...

We analysed seven genetic markers sampled from 165 pholcids and 34 outgroups in order to test and improve the recently revised classification of the family. Our results are based on the largest and most comprehensive set of molecular data so far to study pholcid relationships. The data were analysed using parsimony, maximum-likelihood and Bayesian...

We combine information about the evolutionary history and distributional patterns of the genus Saintpaulia H. Wendl. (Gesneriaceae; 'African violets') to elucidate the factors and processes behind the accumulation of species in tropical montane areas of high biodiversity concentration. We find that high levels of biodiversity in the Eastern Arc Mou...

Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic grou...

Figure S2. Cladogram depicting the highest-likelihood topology for the Ctenohystrica. Circles at nodes represent bootstrap support (circles: black 100-95%, white 95-70%, gray 70-50%). Maximum likekihood tree (lnL=-714749.2). Displayed clade are highlighted using the simplified full ML topology on the left side of the figure. Molecular marker sampli...

Figure S3. Cladogram depicting the highest-likelihood topology for the Octodontoidea. See Additional file 2: Figure S2 for details of the legend. AB = Abrocomidae, CA = Capromyidae.

Figure S4. Cladogram depicting the highest-likelihood topology for the Sciuroidea. See Additional file 2: Figure S2 for details of the legend. AP = Aplodontidae, RA = Ratufinae, SI = Sciurillinae.

Figure S5. Cladogram depicting the highest-likelihood topology for the Xerinae. See Additional file 2: Figure S2 for details of the legend.

Figure S13. Cladogram depicting the highest-likelihood topology for Murinae [part 2]. See Additional file 2: Figure S2 for details of the legend. Mic = Micromys division, Mil = Millardia division, Col = Colomys division, Cre = Cremnomys division, Gol = Golunda, Oen = Oenomys division, Hyb = Hybomys division, Mi = Micaelamys division, Das = Dasymys...

Rodentia accession numbers by gene.

Loci used in each molecular dating analysis (see Material and Methods).

Figure S1. Rodent species level evolutionary tree. Species-level phylogenetic topology based on the highest-likelihood tree inferred from the 11-gene supermatrix, and combined with the taxonomic information of Wilson and Reeder (2005).

Figure S11. Cladogram depicting the highest-likelihood topology for Arvicolinae. See Additional file 2: Figure S2 for details of the legend. Pro = Prometheomyini, Dic = Dicrostonychini, Ond = Ondatrini, Plio = Pliomyini, Arv = Arvicolini, Ell = Ellobiusini, Lag = Lagurini.

ML RaxML topology.