Topographic change shapes the evolution of biodiversity by influencing both habitat connectivity and habitat diversity as well as abiotic factors like climate. However, its role in creating global ...biodiversity gradients remains poorly characterized because geology, climate and evolutionary data have rarely been integrated across concordant timescales. Here we show that topographic uplift over the last 3 million years explains more spatial variation in the speciation of all mammals and birds than do the direct effects of palaeoclimate change and both present-day elevation and present-day temperature. By contrast, the effects of topographic changes are much smaller than those of present-day temperatures in eroded areas. Together, our results stress that historical geological processes rather than traditionally studied macroecological gradients may ultimately generate much of the world's biodiversity. More broadly, as the Earth's surface continues to rise and fall, topography will remain an important driver of evolutionary change and novelty.
Species richness is distributed unevenly across the tree of life and this may be influenced by the evolution of novel phenotypes that promote diversification. Viviparity has originated ∼150 times in ...vertebrates and is considered to be an adaptation to highly variable environments. Likewise, possessing an annual life cycle is common in plants and insects, where it enables the colonization of seasonal environments, but rare in vertebrates. The extent to which these reproductive life-history traits have enhanced diversification and their relative importance in the process remains unknown. We show that convergent evolution of viviparity causes bursts of diversification in fish. We built a phylogenetic tree for Cyprinodontiformes, an order in which both annualism and viviparity have arisen, and reveal that while both traits have evolved multiple times, only viviparity played a major role in shaping the patterns of diversity. These results demonstrate that changes in reproductive life-history strategy can stimulate diversification.
Species diversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL). This imbalance is particularly conspicuous within angiosperms, but is largely unexplained. ...Seed mass is one trait that may help clarify why some lineages diversify more than others because it confers adaptation to different environments, which can subsequently influence speciation and extinction. The rate at which seed mass changes across the angiosperm phylogeny may also be linked to diversification by increasing reproductive isolation and allowing access to novel ecological niches. However, the magnitude and direction of the association between seed mass and diversification has not been assessed across the angiosperm phylogeny. Here, we show that absolute seed size and the rate of change in seed size are both associated with variation in diversification rates. Based on the largest available angiosperm phylogenetic tree, we found that smaller-seeded plants had higher rates of diversification, possibly due to improved colonisation potential. The rate of phenotypic change in seed size was also strongly positively correlated with speciation rates, providing rare, large-scale evidence that rapid morphological change is associated with species divergence. Our study now reveals that variation in morphological traits and, importantly, the rate at which they evolve can contribute to explaining the extremely uneven distribution of diversity across the ToL.
Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low ...proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8
) recorded for the Canary Islands (12
) and New Zealand (20
). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa.
Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing ...essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies.
In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals.
We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here.
Using a thermal-chemical model for the generic T Tauri disk of D'Alessio and colleagues, we estimate the strength of the fine-structure emission lines of Ne II and Ne III at 12.81 and 15.55 km that ...arise from the warm atmosphere of the disk exposed to hard stellar X-rays. The Ne ions are produced by the absorption of keV X-rays from the K shell of neutral Ne, followed by the Auger ejection of several additional electrons. The recombination of the Ne ions is slow because of weak charge transfer with atomic hydrogen in the case of Ne super(+2) and by essentially no charge transfer for Ne super(+). For a distance of 140 pc, the 12.81 km line of Ne II has a flux 610 super(-14) ergs cm super(-2) s super(-1), which should be observable with the Spitzer Infrared Spectrometer and suitable ground-based instrumentation. The detection of these fine-structure lines would clearly demonstrate the effects of X-rays on the physical and chemical properties of the disks of young stellar objects and provide a diagnostic of the warm gas in protoplanetary disk atmospheres. They would complement the observed H sub(2) and CO emission by probing vertical heights above the molecular transition layer and larger radial distances that include the location of terrestrial and giant planets.
One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical ...relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.
Recent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results in higher rates of speciation in the tropics. Allowing ...for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. These results were consistently retrieved using two other methods to test the association between occupancy of tropical habitats and speciation rates. Our speciation rate estimates were robust to the effects of both undescribed species and missing taxa. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness. Greater ecological opportunity in the temperate zones, stemming from less saturated communities, higher species turnover or greater environmental change, may ultimately explain these results.
Recent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results from higher rates of speciation in the tropics. Using data for over 60,000 flowering plant species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness
Extinction threatens many species yet is predicted by few factors across the plant tree of life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and ...adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates and thus extinction risk where new taxa have small range and population sizes. To test how age, diversification, and range size were correlated with extinction, we analyzed 639 well-sampled genera representing 8,937 species from across the plant ToL. We found a greater proportion of species were threatened by contemporary extinction in younger and faster-diversifying genera. When we directly tested how range size mediated this pattern in two large, well-sampled groups, our results varied. In conifers, potential range size was smaller in older species and was correlated with higher extinction risk. Age on its own had no direct effect on extinction when accounting for its influence on range size. In palm species, age was neither directly nor indirectly correlated with extinction risk. Our results suggest that range size dynamics may explain differing patterns of extinction risk across the ToL, with consequences for biodiversity conservation.
PREMISE
Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships ...with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations.
METHODS
Here we applied target sequence capture with 353 protein‐coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5–10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species.
RESULTS
We obtained approximately 150 kbp of 353 protein‐coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene‐tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation.
CONCLUSIONS
Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.
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