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47 results for “Diversification shifts”
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
<p>As species richness varies along the tree of life, there is a great interest in identifying factors that affect the rates by which lineages speciate or go extinct. To this end, theoretical biologists have developed a suit of phylogenetic comparative methods that aim to identify where shifts in diversification rates had occurred along a phylogeny and whether they are associated with some traits. Using these methods, numerous studies have predicted that speciation and extinction rates vary across the tree of life. In this study we show that asymmetric rates of sequence evolution rates lead to systematic biases in the inferred phylogeny, which in turn lead to erroneous inferences regarding lineage diversification patterns. The results demonstrate that as the asymmetry in sequence evolution rates increases, so does the tendency to select more complicated models that include the possibility of diversification rate shifts. These results thus suggest that any inference regarding shifts in diversification pattern should be treated with great caution, at least until any biases regarding the molecular substitution rate have been ruled out.</p>
Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America
<p><strong>Aim</strong>: We investigate the biogeographic history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity-dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate on processes governing the species assembly and evolution of the Cerrado savanna.</p> <p><strong>Location</strong>: South American ecoregions south of the Amazon (e.g. Atlantic Forest, Cerrado, Araucaria Forest, Pampas, Central and Southern Andes).</p> <p><strong>Taxon</strong>: Boana pulchella group.</p> <p><strong>Methods</strong>: We built the most complete time-calibrated phylogeny for the group to date. We then reconstructed ancestral ranges using the dispersal-extinction-cladogenesis (DEC) model comparing different dispersal scenarios considering distance, adjacency and ecological similarity among regions. A center-of-origin hypothesis in forest versus open ecoregions was also tested. Using biogeographical stochastic mapping, we additionally estimated the contribution of range shifts across different biomes. Lastly, we evaluated several diversification models, including the effect of time, diversity-dependence and temperature-dependence on speciation and extinction rates.</p> <p><strong>Results</strong>: The Boana pulchella group originated during the Early Miocene (~17.5 MYA) and underwent high speciation rates during the Middle Miocene Climatic Optimum, with a decreasing trend following the Miocene Climatic Transition. We found no support for a single ecoregion acting as a center of origin and diversification; instead, we inferred recurrent range shifts with dispersal among dissimilar adjacent ecoregions. Speciation linearly dependent on paleotemperatures, with either no or very low constant extinction rates, best explained the slowdown diversification pattern.</p> <p><strong>Main Conclusions</strong>: Our results support a species assembly of Cerrado savanna in South America during the Miocene with intermittent interchange with rainforest habitats. Past climate changes impacted the rate new species originated with apparently no impact on extinction. Finally, the repeated habitat shifts among open/dry and forested/humid ecoregions, rather than long-term in-situ diversification in single areas, highlights the very dynamic historical interchange between contrasting habitats in South America, possibly contributing to its high species diversity.</p>
Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
Background: Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g., the bombycid, Arotros Schaus) were misplaced and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth "arms race". Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
Supporting data for Bryłka et al., 2023 Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms.
<p>These are supporting files used in the analysis in Bryłka et al., 2023 "<em>Gene duplication, shifting selection, and functional diversification of silicon transporter proteins in marine and freshwater diatoms". </em> All data newly generated from the Alverson lab.</p> <p> </p>
Data from: Mosaic adaptive peak shifts underlie body shape diversification in Pelagiaria fishes (Acanthomorpha: Percomorpha)
<p>Extreme body elongation in fishes is a major evolutionary transformation that extends the boundaries of morphological diversity and alters aspects of function, behavior, and ecology. Prior studies have identified features of the cranial and axial skeleton that characterize elongate fishes, but a lack of detailed reconstructions of anatomical evolution has limited inferences about factors that underlie major shifts in body shape. In this study, we fit multi-peak adaptive (Ornstein-Uhlenbeck) evolutionary models to species body shape and anatomical dimensions in Pelagiaria, a radiation of open-ocean fishes whose species span a continuum from deep-bodied to highly elongate. We inferred an ancestral fusiform adaptive peak that is retained by several major pelagiarian lineages (e.g., Scombridae) and found robust support for multiple transitions to deep-bodied (in the families Stromateidae, Bramidae, and Caristiidae) and elongate-bodied optima (within Trichiuroidei), including two instances of sequential shifts toward increasingly elongate optima that followed distinct paths of anatomical evolution. Within Trichiuridae, initial increases in head length and vertebral number were followed by changes in head and vertebral shape. Within an elongate-bodied subclade of taxa traditionally identified as 'gempylids', shifts in head and vertebral shape as well as number of precaudal vertebrae preceded an increase in number of caudal vertebrae. Altogether, this mosaic of anatomical peak shifts suggests that body shape transformations were associated with differing selective demands and developmental changes.</p>
Shell colour diversification induced by ecological release: a shift in natural selection after a migration event
<p><span>Ecological release is often attributed to the rapid adaptive diversification of phenotypic traits. However, it is not well understood how natural selection changes its strength and direction through the process of ecological release. Herein, we demonstrated how shell colour of the Japanese land snail <i>Euhadra peliomphala simodae</i> has diversified via a shift in natural selection due to ecological release after migration from the mainland to an island<i>. </i>This snail's shell colour diversified on the island due to disruptive selection after migration from the mainland. We used trail-camera traps to identify the cause of natural selection on both the mainland and island. We then conducted a mark-recapture experiment while collecting microhabitat use data. In total, we captured and marked around 1700 snails on the mainland, some of which were preyed upon by an unknown predator. The trail-camera traps showed that the predator is the large Japanese field mouse <i>Apodemus speciosus, </i>and the predatory frequency was higher on the mainland than on the island. However, this predation did not correlate with shell colour. Microhabitat use on the island was more extensive than on the mainland, with snails on the island using both ground and arboreal microhabitats. A Bayesian estimation showed that the stabilising selection on shell colour came from factors other than predation. Our results suggest that the course of natural selection was modified due to ecological release after migration from the mainland, explaining one cause of the phenotypic diversification.</span></p>
Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts
<p><span>Despite the vast diversity of phytophagous insects that feed on vascular plants (tracheophytes), insects that feed on bryophytes remain understudied. Agromyzidae, one of the most species-rich phytophagous clades in Diptera, consists mainly of leaf-mining species that feed on tracheophytes. However, a recent discovery of thallus-mining species on liverworts and hornworts within the <em>Liriomyza</em> group of Phytomyzinae provides an opportunity to study host shifts between tracheophytes and bryophytes. This study aimed to explore the origin and diversification of thallus-miners and estimate the pattern and timing of host shifts. Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining agromyzids formed a separate clade, which was sister to a fern pinnule-miner. The diversification of bryophyte-associated agromyzids since the Oligocene involved multiple host shifts across various bryophyte taxa. The diversification of the thallus-mining <em>Phytoliriomyza</em> may have occurred at the same time as the leaf-mining agromyzid flies on herbaceous plants, indicating a dynamic history of interactions between bryophytes and herbivores in angiosperms-dominated ecosystems.</span></p>
Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Data from: Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
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Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts
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Data from: Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum
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Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America
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Data from: Mosaic adaptive peak shifts underlie body shape diversification in Pelagiaria fishes (Acanthomorpha: Percomorpha)
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Shell colour diversification induced by ecological release: a shift in natural selection after a migration event
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Shifting ecosystem connectivity during the Pleistocene drove diversification and gene-flow in a species-complex of Neotropical birds (Tityridae: Pachyramphus)
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Food plant shifts drive the diversification of Sack-bearer moths
<p>Lepidoptera are a highly diverse group of herbivorous insects, however some superfamilies have relatively few species. Two alternative hypotheses for drivers of Lepidoptera diversity are shifts in food plant use or shifts from concealed to external feeding as larvae. Many studies address the former hypothesis, but with bias towards externally feeding taxa. One of the most striking examples of species disparity between sister lineages in Lepidoptera is between the concealed feeding Sack-bearer Moths (Mimallonoidea), which contain about 300 species, and externally feeding Macroheterocera, which have over 74,000 species. We provide the first dated tree of Mimallonidae to understand the diversification dynamics of these moths in order to fill a knowledge gap pertaining to drivers of diversity within an important concealed feeding clade. We find that Mimallonidae is an ancient Lepidoptera lineage that originated in the Cretaceous ca. 105 million years ago and has had a close association with the plant order Myrtales for the past 40 million years. Diversification dynamics are tightly linked with food plant usage in this group. Reliance on Myrtales may have influenced diversification of Mimallonidae because clades that shifted away from the ancestral condition of feeding on Myrtales have the highest speciation rates in the family.</p>
Data from: Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events, and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite co-phylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events, and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
Data from: Shifting barriers and phenotypic diversification by hybridisation
The establishment of hybrid taxa relies on reproductive isolation from the parental forms, typically achieved by ecological differentiation. Here, we present an alternative mechanism, in which shifts in the strength and location of dispersal barriers facilitate diversification by hybridisation. Our case study concerns the highly diverse, stenotopic rock-dwelling cichlids of the African Great Lakes, many of which display geographic colour pattern variation. The littoral habitat of these fish has repeatedly been restructured in the course of ancient lake level fluctuations. Genetic data and an experimental cross support the hybrid origin of a distinct yellow-coloured variant of Tropheus moorii from ancient admixture between two allopatric, red and bluish variants. Deficient assortative mating preferences imply that reproductive isolation continues to be contingent on geographic separation. Linking paleolimnological data with the establishment of the hybrid variant, we sketch a selectively neutral diversification process governed solely by rearrangements of dispersal barriers.
Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9 Ma) or in association with the Eocene–Oligocene transition (33.9 Ma).
Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)
Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results:To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions:Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change.
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