Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.
Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS:Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%).CONCLUSIONS: High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.
The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.
Aim Islands are often hotspots of endemism due to their isolation, making colonization a rare event and hence facilitating allopatric speciation. Dispersal usually occurs between nearby locations according to a stepping‐stone model. We aimed to reconstruct colonization and speciation processes in an endemic‐rich system of land‐based islands that does not seem to follow the obvious stepping‐stone model of dispersal. Location Five land‐based habitat archipelagos of limestone outcrops in the floodplain of the Kinabatangan River in Sabah, Malaysian Borneo. Methods We studied the phylogeography of three species complexes of endemic land snails, using multiple genetic markers. We calculated genetic distances between populations, applied beast2 to reconstruct phylogenies for each taxon and subsequently reconstructed ancestral ranges using ‘BioGeoBEARS’. Results We found spatial‐genetic structure among nearby locations to be highly pronounced for each taxon. Genetic correlation was present at small spatial scales only and disappeared at distances of 5 km and above. Most archipelagos have been colonized from within the region multiple times over the past three million years, in 78% of the cases as a result of long‐distance dispersal (LDD) or dispersal from non‐adjacent limestone outcrops. The flow of the main geographical feature within the region, the Kinabatangan River, did not play a role. Main conclusions Phylogeographic structure in these Bornean land snails has only partly been determined by small‐scale dispersal, where it leads to isolation‐by‐distance, but mostly by LDD. Our results demonstrate that island endemic taxa only very locally follow a simple stepping‐stone model, whilst dispersal to non‐adjacent islands and especially LDD, is most important. This leads to the formation of highly localized, isolated “endemic populations” forming the onset of a complex radiation of endemic species.
The Bornean representatives of the genus Georissa (Hydrocenidae) have small, dextral, conical, calcareous shells consisting of ca. three teleoconch whorls. Our recent study on the Georissa of Malaysian Borneo has revealed high intra- and inter-specific variation in the “scaly” group (a group of species with striking scale-like surface sculpture). The present study on the “non-scaly” Georissa is the continuation of the species revision for the genus. The “non-scaly” species are also diverse in shell sculptures. This informal group comprises Georissa with subtle spiral and/or radial sculpture. The combination of detailed conchological assessment and molecular analyses provides clear distinctions for each of the species. Conchological, molecular, and biogeographic details are presented for 16 species of “non-scaly” Georissa. Three of these are new to science, namely Georissacorrugatasp. n., Georissainsulaesp. n., and Georissatrusmadisp. n.
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.
The subtribe Anthroherponina form an iconic group of obligate cave beetles, typical representatives of the Dinaric subterranean fauna, which is considered to be the richest in the world. Phylogenetic studies within this subtribe are scarce and based only on morphological characters, which, due to troglomorphic convergence, are frequently unreliable. Moreover, morphological stasis and morphological polymorphism make classification of taxa difficult. To test if characters that have traditionally been accepted as informative for Anthroherponina classification are indeed reliable, we evaluated the monophyly of the most speciesrich genus of this subtribe -Anthroherpon Reitter, 1889. Our study, based on a molecular phylogenetic analysis of fragments of the 18S, 28S, and COI (both 5' and 3' end) loci revealed that the genus Anthroherpon as conventionally defined is polyphyletic. To resolve this polyphyly, we defined one new additional genus, Graciliella n. gen., for which we then examined the intrageneric diversity using molecular and morphometric approaches. Molecular phylogenetic analysis of two COI mitochondrial gene fragments revealed the presence of four species inside Graciliella n. gen., including two new species, which we here describe as G. kosovaci n. sp. and G. ozimeci n. sp. To analyze interspecific morphological differences within Graciliella we performed a discriminant analysis based on 40 linear morphometric measurements. The results showed that differences between species and subspecies inside Graciliella, however subtle they may seem, are measurable and reproducible. All species of the genus are briefly diagnosed, an identification key is proposed and a distribution map of all taxa of Graciliella is provided.
Herbivore diets are often generalistic, and communities of herbivores tend to share much of their diets. In the tropical lowlands of Malaysian Borneo, tens of different noncarnivorous land snail species are able to coexist in communities on limestone outcrops. We tried to answer the question whether diet differentiation plays a role in their coexistence. We show, with a large metabarcoding study of the plant diet from gut contents of 658 individual snails (from 26 species, with a focus on three of the most common species in the region), that the different snail species indeed share much of their plant diet, but that mean diet richness varies strongly among species (up to 15.3×). These differences are mostly explained by snail size, with larger snails having wider diets. Furthermore, phylogenetic analyses of the plant diet by individual snails showed signs of clustering in c. 28% of the individuals, possibly suggesting phylogenetic specialization, although such clustering was weak when diets were considered by species. We discuss how observed trends in diet richness and diet clustering could also be explained by random feeding, with larger species simply eating more or less specifically, and by other, noncompetitive interactions, such as snails avoiding desiccation. Our study shows how to efficiently put the power of metabarcoding to work in unravelling the complex community processes commonly encountered in tropical ecosystems and is thus of substantial relevance to both community ecologists and conservationists.
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