Rapid Radiation Research Articles

Terebra steering in chalcidoid wasps

Various chalcidoid wasps can actively steer their terebra (= ovipositor shaft) in diverse directions, despite the lack of terebral intrinsic musculature. To investigate the mechanisms of these bending and rotational movements, we combined microscopical and microtomographical techniques, together with videography, to analyse the musculoskeletal ovipositor system of the ectoparasitoid pteromalid wasp Lariophagus distinguendus (Förster, 1841) and the employment of its terebra during oviposition. The ovipositor consists of three pairs of valvulae, two pairs of valvifers and the female T9 (9th abdominal tergum). The paired 1st and the 2nd valvulae are interlocked via the olistheter system, which allows the three parts to slide longitudinally relative to each other, and form the terebra. The various ovipositor movements are actuated by a set of nine paired muscles, three of which (i.e. 1st valvifer-genital membrane muscle, ventral 2nd valvifer-venom gland reservoir muscle, T9-genital membrane muscle) are described here for the first time in chalcidoids. The anterior and posterior 2nd valvifer-2nd valvula muscles are adapted in function. (1) In the active probing position, they enable the wasps to pull the base of each of the longitudinally split and asymmetrically overlapping halves of the 2nd valvula that are fused at the apex dorsally, thus enabling lateral bending of the terebra. Concurrently, the 1st valvulae can be pro- and retracted regardless of this bending. (2) These muscles can also rotate the 2nd valvula and therefore the whole terebra at the basal articulation, allowing bending in various directions. The position of the terebra is anchored at the puncture site in hard substrates (in which drilling is extremely energy- and time-consuming). A freely steerable terebra increases the chance of contacting a potential host within a concealed cavity. The evolution of the ability actively to steer the terebra can be considered a key innovation that has putatively contributed to the acquisition of new hosts to a parasitoid’s host range. Such shifts in host exploitation, each followed by rapid radiations, have probably aided the evolutionary success of Chalcidoidea (with more than 500,000 species estimated).

Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers.

Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately and may have unique and even conflicting evolutionary histories. Phylogenetic reconstructions from these discrete genomes can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance (i.e. discordant evolutionary histories between the nuclear and mitochondrial genomes) has been widely documented, but its causes are often considered idiosyncratic and inscrutable. We show that a case of mitonuclear discordance in Todiramphus kingfishers can be explained by extensive genome-wide incomplete lineage sorting (ILS), likely a result of the explosive diversification history of this genus. For these kingfishers, quartet frequencies reveal that the nuclear genome is dominated by discordant topologies, with none of the internal branches in our consensus nuclear tree recovered in >50% of genome-wide gene trees. Meanwhile, a lack of inter-species shared ancestry, non-significant pairwise tests for gene flow, and little evidence for meaningful migration edges between species, leads to the conclusion that gene flow cannot explain the mitonuclear discordance we observe. This lack of evidence for gene flow combined with evidence for extensive genome-wide gene tree discordance, a hallmark of ILS, leads us to conclude that the mitonuclear discordance we observe likely results from ILS, specifically deep coalescence of the mitochondrial genome. Based on this case study, we hypothesize that similar demographic histories in other 'great speciator' taxa across the Indo-Pacific likely predispose these groups to high levels of ILS and high likelihoods of mitonuclear discordance.

Plastome phylogenomics reveals an early Pliocene North- and Central America colonization by long-distance dispersal from South America of a highly diverse bromeliad lineage.

Understanding the spatial and temporal frameworks of species diversification is fundamental in evolutionary biology. Assessing the geographic origin and dispersal history of highly diverse lineages of rapid diversification can be hindered by the lack of appropriately sampled, resolved, and strongly supported phylogenetic contexts. The use of currently available cost-efficient sequencing strategies allows for the generation of a substantial amount of sequence data for dense taxonomic samplings, which together with well-curated geographic information and biogeographic models allow us to formally test the mode and tempo of dispersal events occurring in quick succession. Here, we assess the spatial and temporal frameworks for the origin and dispersal history of the expanded clade K, a highly diverse Tillandsia subgenus Tillandsia (Bromeliaceae, Poales) lineage hypothesized to have undergone a rapid radiation across the Neotropics. We assembled full plastomes from Hyb-Seq data for a dense taxon sampling of the expanded clade K plus a careful selection of outgroup species and used them to estimate a time- calibrated phylogenetic framework. This dated phylogenetic hypothesis was then used to perform biogeographic model tests and ancestral area reconstructions based on a comprehensive compilation of geographic information. The expanded clade K colonized North and Central America, specifically the Mexican transition zone and the Mesoamerican dominion, by long-distance dispersal from South America at least 4.86 Mya, when most of the Mexican highlands were already formed. Several dispersal events occurred subsequently northward to the southern Nearctic region, eastward to the Caribbean, and southward to the Pacific dominion during the last 2.8 Mya, a period characterized by pronounced climate fluctuations, derived from glacial-interglacial climate oscillations, and substantial volcanic activity, mainly in the Trans-Mexican Volcanic Belt. Our taxon sampling design allowed us to calibrate for the first time several nodes, not only within the expanded clade K focal group but also in other Tillandsioideae lineages. We expect that this dated phylogenetic framework will facilitate future macroevolutionary studies and provide reference age estimates to perform secondary calibrations for other Tillandsioideae lineages.

Genomic data provide a robust phylogeny backbone for Rhodiola L. (Crassulaceae) and reveal extensive reticulate evolution during its rapid radiation

The Tibetan Plateau and adjacent mountain regions (TP; including the Tibetan Plateau, Himalaya, Hengduan Mountains and Mountains of Central Asia) harbor great biodiversity, some lineages on which may have undergone rapid radiations. However, only a few studies have investigated the evolutionary pattern of such diversification in depth using genomic data. In this study, we reconstructed a robust phylogeny backbone of Rhodiola, a lineage that may have undergone rapid radiation in the TP, using Genotyping-by-sequencing data, and conducted a series of gene flow and diversification analyses. The concatenation and coalescent-based methods yield similar tree topologies, and five well-supported clades were revealed. Potential gene flow and introgression events were detected, both between species from different major clades and closely related species, suggesting pervasive hybridization and introgression. An initial rapid and later slowdown of the diversification rate was revealed, indicating niche filling. Molecular dating and correlation analyses showed that the uplift of TP and global cooling in the mid-Miocene might have played an important role in promoting the rapid radiation of Rhodiola. Our work demonstrates that gene flow and introgression might be an important contributor to rapid radiation possibly by quickly reassembling old genetic variation into new combinations.

Phylogeny and diversification of planthoppers (Hemiptera: Fulgoromorpha) based on a comprehensive molecular dataset and large taxon sampling

Our understanding of the evolution of Fulgoromorpha (Insects, Hemiptera) has relied on molecular studies that have only considered either a limited number of taxa where all the families were not represented simultaneously, or a reduced number of genes.The absence of a global analysis comparing all the available data has thus led to significant biases in the analyzes, as evidenced by the incongruence of the results reported for planthopper phylogeny. Here we provide a phylogenetic and dating analysis of the Fulgoromorpha with a large sampling of 531 ingroup taxa, representing about 80% of the currently described suprageneric taxonomic diversity in this group. This study is based on most of the molecular sequences available to date and duly verified, for a set of nuclear and mitochondrial genes from a taxonomic sampling as complete as possible. The most significant results of our study are: (1) the unexpected paraphyly of Delphacidae whose Protodelphacida seem more related to Cixiidae than to other Delphacidae;(2) the group Meenoplidae-Kinnaridae recovered sister to the remaining Fulgoroidea families; (3) the early branching node of Tettigometridae sister of all the other families;(4) the Achilidae-Derbidae clade with Achilidae Plectoderini including Achilixiidae recovered as monophyletic as well as theFulgoridae-Dictyopharidae clade; and (5) the Tropiduchidae placed sister to the other so called ‘higher’ families (sec. Shcherbakov, 2006).Our divergence times analysis, calibrated with a set of duly verified fossils, suggests that the first diversification of planthoppers occurred in the Early Triassic around 240 Mya and those of the superfamilies Delphacoidea and Fulgoroidea in the Middle-Late Triassic around 210 Mya and 230 Mya, respectively. By the end of the Jurassic, all major planthopper lineages were originated, and all families, around 125 Mya, might havebeen driven in their distribution and evolution (in their first subfamilial divisions) by the geographical constraints of the Gondwanan break-up.Rapid evolutionary radiations occurred particularly in Fulgoridae around 125–130 Mya. Our results stress the importance of the good quality of the sequences used in the molecular analyzes and the primordial importance of a large sampling when analyzing the phylogeny of the group.

Phylogeography of 912 Cherry Accessions Insight into Independent Origins of Fruiting Cherries and Domestication Footprints of Cultivated Chinese Cherry (Prunus pseudocerasus Lindl.).

The subgenus Cerasus (Rosaceae) contain numerous fruit trees and ornamentals with high economic values. The origin and genetic divergence among various types of fruiting cherries always remain a perplexing issue. We employed three plastom fragments and ITS sequence matrices derived from 912 cherry accessions to elucidate the phylogeographic structure and genetic relationship among fruiting cherries, as well as the origin and domestication of cultivated Chinese cherry. The integration of haplotype genealogies, Approximate Bayesian computation (ABC) approach and estimation of genetic differentiation within and between different groups and lineages has facilitated the resolution of several previously unresolved questions. Firstly, distant phylogenetic relationships between Cerasus and Microcerasus accessions, as indicated by both nuclear and chloroplast data, suggested independent origins and evolution for these two taxa. Moreover, two distinct geographic origin centers (Europe and China) have been confirmed, with significant phylogeographic signals and high genetic differentiation observed between cherries from these regions. This may be attributed to long-term geographic isolation caused by Himalaya-Hengduan Mountains. Our phylogeographic analyses and ABC analysis suggested that cherries inhabiting in China may have undergone multiple hybridization events during the glacial refugia of the eastern edge and southern Himalaya-Hengduan Mountains, followed by rapid radiation throughout their current habitats during interglacial period. The discrepancy between nuclear and chloroplast data may be attributed to hybridization events and incomplete lineage sorting. Furthermore, we speculated that the domesticated Chinese cherries were derived from wild accessions in Longmenshan Fault Zones approximately 2600 years ago. We have also traced the domestication processes and dispersal routes of cultivated Chinese cherries.

Implementation of a machine-learned gas optics parameterization in the ECMWF Integrated Forecasting System: RRTMGP-NN 2.0

Abstract. Radiation schemes are physically important but computationally expensive components of weather and climate models. This has spurred efforts to replace them with a cheap emulator based on neural networks (NNs), obtaining large speed-ups, but at the expense of accuracy, energy conservation and generalization. An alternative approach, which is slower but more robust than full emulation, is to use NNs to predict optical properties but keep the radiative transfer equations. Recently, NNs were developed to replace the RRTMGP (Rapid Radiative Transfer Model for General circulation model applications–Parallel) gas optics scheme and shown to be accurate while improving speed. However, the evaluations were based solely on offline radiation computations. In this paper, we describe the implementation and prognostic evaluation of RRTMGP-NN in the Integrated Forecasting System (IFS) of the European Centre for Medium-Range Weather Forecasts (ECMWF). The new gas optics scheme was incorporated into ecRad, the modular ECMWF radiation scheme. Using two new methods to improve accuracy – a hybrid loss function designed to reduce radiative forcing errors and an early stopping method based on monitoring fluxes and heating rates with respect to a line-by-line benchmark – we train NN models on RRTMGP k distributions with reduced spectral resolutions. Offline evaluation of the new NN gas optics, RRTMGP-NN 2.0, shows a very high level of accuracy for clear-sky fluxes and heating rates. For instance, the RMSE in the shortwave surface downwelling flux is 0.78 W m−2 for RRTMGP and 0.80 W m−2 for RRTMGP-NN in a present-day scenario, while upwelling flux errors are actually smaller for the NN. Because our approach does not affect the treatment of clouds, no additional errors will be introduced for cloudy profiles. RRTMGP-NN closely reproduces radiative forcings for five important greenhouse gases across a wide range of concentrations such as 8×CO2. To assess the impact of different gas optics schemes in the IFS, four 1-year coupled ocean–atmosphere simulations were performed for each configuration. The results show that RRTMGP-NN and RRTMGP produce very similar model climates, with the differences being smaller than those between existing schemes and statistically insignificant for zonal means of single-level quantities such as surface temperature. The use of RRTMGP-NN speeds up ecRad by a factor of 1.5 compared to RRTMGP (the gas optics being almost 3 times faster) and is also faster than the older and less accurate RRTMG, which is used in the current operational cycle of the IFS.

Phylogenomic analyses of the Neotropical Artocarpeae (Moraceae) reveal a history of introgression and support the reinstatement of Acanthinophyllum

This molecular study of the Neotropical Artocarpeae, the closest living allies of the Asia-Pacific breadfruit genus, uses phylogenomic and network analyses to untangle the evolutionary history of this difficult group. Results paint a picture of a rapid radiation, with introgression, incomplete lineage sorting, and lack of gene tree resolution confounding attempts to reconstruct a well-supported bifurcating tree. While coalescent-based species trees were markedly at odds with morphology, multifurcating phylogenetic network analyses recovered multiple histories, with clearer traces of morphological alliances. The sole unambiguous finding is the sister relationship between Clarisia sect. Acanthinophyllum and the rest of the Neotropical Artocarpeae; as a result, the genus Acanthinophyllum is reinstated.

The Role of Introgression During the Radiation of Endemic Fishes Adapted to Living at Extreme Altitudes in the Tibetan Plateau.

Recent genomic analyses of evolutionary radiations suggest that ancient introgression may facilitate rapid diversification and adaptive radiation. The loach genus Triplophysa, a genus with most species endemic to Tibetan Plateau, shows ecological diversity and rapid evolution and represents a potential example of adaptive radiation linked to the uplift of the Tibetan Plateau. Here, we interrogate the complex evolutionary history of Triplophysa fishes through the analysis of whole-genome sequences. By reconstructing the phylogeny of Triplophysa, quantifying introgression across this clade, and simulating speciation and migration processes, we confirm that extensive gene flow events occurred across disparate Triplophysa species. Our results suggest that introgression plays a more substantial role than incomplete lineage sorting in underpinning phylogenetic discordance in Triplophysa. The results also indicate that genomic regions affected by ancient gene flow exhibit characteristics of lower recombination rates and nucleotide diversity and may associate with selection. Simulation analysis of Triplophysa tibetana suggests that the species may have been affected by the Gonghe Movement in the third uplift of the Tibetan Plateau, resulting in founder effects and a subsequent reduction in Ne.

Australia’s hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes

• Inferred a near-complete species-level phylogeny of Australian blind snakes from over 4900 genetic loci. • Added seven previously unsampled Anilios species. • Time-calibrated phylogeny reveals rapid early Miocene radiation of Anilios. • Several paraphyletic groups require taxonomic revision.

From southern Africa and beyond: Historical biogeography of a monocotyledonous bulbous geophyte

AbstractAimLow taxon sampling and taxonomic uncertainties still obscure our evolutionary knowledge of many taxa, especially widespread lineages across diverse landscapes. Of particular interest are those lineages inhabiting seasonal and arid landscapes, which showcase unique distributional patterns that hint at fascinating histories. Using the most comprehensive sampling to date of a widespread bulbous monocot, we hypothesize two independent dispersals to Madagascar, and that vicariance due to Miocene‐driven aridification contracted a once‐widespread distribution between Africa and Eurasia.LocationSub‐Saharan Africa, Madagascar, Eurasia.TaxonLedebouriinae (Scilloideae, Asparagaceae).MethodsUsing the Angiosperms353 probe set for 195 taxa (86 ingroup taxa), we perform phylogenetic reconstruction using IQ‐Tree, and we infer age estimates using penalized likelihood as implemented in treePL. Capitalizing on our broad geographic sampling, which includes African, Malagasy and Eurasian taxa, we use ‘BioGeoBEARS’ to reconstruct ancestral ranges and investigate the role of vicariance and dispersal.ResultsThe Ledebouriinae originated within the past c. 30 myr in south‐eastern sub‐Saharan Africa, with the major subclades arising soon thereafter. Although long‐distance dispersal cannot be fully ruled out, we argue that vicariance was the major process responsible for the current distribution of Ledebouria in Eurasia. We recover two distinct Ledebouria groups that overlap in eastern Africa but are divided into mostly northern and southern clades with divergent biogeographical histories, each showing an independent dispersal to Madagascar. A similar north–south split is seen in Drimiopsis. Additionally, we recover a complex biogeographic history in the predominantly sub‐Saharan African Ledebouria clade, with rapid radiation at c. 14 mya.Main ConclusionsThe expansion of seasonal rainfall and aridity in sub‐Saharan Africa, coupled with orogenic activity, may have fostered the diversification of the Ledebouriinae and many subclades. Miocene‐driven aridification may have caused fragmentation of a once widespread distribution that led to their occurrence in Eurasia.

Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation.

Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.

Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae)

The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30–24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12–23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.

Molecular evolution and phylogenomic analysis of complete chloroplast genomes of Cotinus (Anacardiaceae).

Cotinus is an oligo-specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced the chloroplast (cp) genomes of all currently recognized taxa of Cotinus, including three species and four varieties. A comparative analysis was performed to investigate their cp genome characteristics and evolution. Furthermore, we inferred the phylogenetic relationships of Cotinus based on whole cp genomes, protein-coding genes, and nuclear ITS data. All cp genomes exhibited a typical quadripartite structure with genome sizes ranging from 158,865 to 160,155 bp. A total of 113-114 genes were identified in the genomes. Seven non-coding and four coding regions were identified as the most divergent hotspots for potential molecular barcodes and phylogenetic markers. Selection pressure analysis showed that there had been positive selection on genes matK and rps8 in the Cotinus cp genomes. Phylogenetic results confirmed that Cotinus is a monophyletic group but the widely distributed species Cotinus coggygria is not monophyletic. The divergence-time analysis suggested that Cotinus underwent an evolutionary divergence from the middle Eocene and rapid adaptive radiation from the middle Miocene. This study revealed new insights into the cp genome evolution and phylogeny of Cotinus and related taxa.

Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa.

Africa has undergone a progressive aridification during the last 20 My that presumably impacted organisms and fostered the evolution of life history adaptations. We test the hypothesis that shift to living in ant nests and feeding on ant brood by larvae of phyto-predaceous Lepidochrysops butterflies was an adaptive response to the aridification of Africa that facilitated the subsequent radiation of butterflies in this genus. Using anchored hybrid enrichment we constructed a time-calibrated phylogeny for Lepidochrysops and its closest, non-parasitic relatives in the Euchrysops section (Poloyommatini). We estimated ancestral areas across the phylogeny with process-based biogeographical models and diversification rates relying on time-variable and clade-heterogeneous birth-death models. The Euchrysops section originated with the emerging Miombo woodlands about 22 million years ago (Mya) and spread to drier biomes as they became available in the late Miocene. The diversification of the non-parasitic lineages decreased as aridification intensified around 10 Mya, culminating in diversity decline. In contrast, the diversification of the phyto-predaceous Lepidochrysops lineage proceeded rapidly from about 6.5 Mya when this unusual life history likely first evolved. The Miombo woodlands were the cradle for diversification of the Euchrysops section, and our findings are consistent with the hypothesis that aridification during the Miocene selected for a phyto-predaceous life history in species of Lepidochrysops, with ant nests likely providing caterpillars a safe refuge from fire and a source of food when vegetation was scarce.

Applying the AAPM 293 report to estimate the absorbed dose during head computed tomography: using head circumference for rapid dose estimation.

The American Association of Physicists in Medicine (AAPM) report 293 is more accurate than report 220 in evaluating the absorbed radiation dose during head computed tomography (CT) examination. We aimed to investigate the associations between age, head circumference (HC), the conversion factor (f293), and specific-size dose estimation (SSDE293) during these procedures. The rapid radiation dose was also estimated based on the AAPM report 293. In this retrospective, cross-sectional study, unenhanced CT images of the head were retrospectively collected from 1,222 participants from Union Hospital and Hubei Cancer Hospital between December 2018 and September 2019. Scan parameters, including age, HC, water-equivalent diameter (DW), and volumetric computed tomography dose index (CTDIvol), were generated automatically using indigenously-developed image processing software. The corresponding f293 and SSDE293 were calculated according to the AAPM report 293. The analyses were performed using linear regression. In the younger group, age and HC were significantly negatively correlated with SSDE293 (r=-0.33 and -0.44, respectively; both P values ≤0.001). No significant correlation was reported between age, HC, and SSDE293 in the older group. Moreover, age was significantly negatively associated with f293 in the younger and older groups (r=-0.80 and -0.13, respectively; both P values ≤0.001). A significantly negative association was seen between f293 and increased HC in both age groups (r=-0.92 and -0.82, respectively; both P values ≤0.001). The HC of patients was associated with head conversion. HC is a feasible indicator for rapidly estimating the radiation dose in head CT examinations based on the AAPM report 293.

Diversification and Biogeography of North American Thistles (Cirsium: Carduoideae: Compositae): Drivers of a Rapid Continent-Wide Radiation

Previous articleNext article No AccessDiversification and biogeography of North American thistles (Cirsium: Carduoideae: Compositae): drivers of a rapid continent-wide radiationCarolina M. Siniscalchi, Jennifer Ackerfield, and Ryan A. FolkCarolina M. Siniscalchi Search for more articles by this author , Jennifer Ackerfield Search for more articles by this author , and Ryan A. Folk Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by International Journal of Plant Sciences Just Accepted Article DOIhttps://doi.org/10.1086/724310 Views: 34Total views on this site HistoryAccepted November 28, 2022 © 2023 The University of Chicago. All Rights reserved.PDF download Crossref reports no articles citing this article.

The genome of the pygmy right whale illuminates the evolution of rorquals

BackgroundBaleen whales are a clade of gigantic and highly specialized marine mammals. Their genomes have been used to investigate their complex evolutionary history and to decipher the molecular mechanisms that allowed them to reach these dimensions. However, many unanswered questions remain, especially about the early radiation of rorquals and how cancer resistance interplays with their huge number of cells. The pygmy right whale is the smallest and most elusive among the baleen whales. It reaches only a fraction of the body length compared to its relatives and it is the only living member of an otherwise extinct family. This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. Apart from that, genomic data of this species might help to investigate cancer resistance in large whales, since these mechanisms are not as important for the pygmy right whale as in other giant rorquals and right whales.ResultsHere, we present a first de novo genome of the species and test its potential in phylogenomics and cancer research. To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. Furthermore, a genome-wide comparison of selection rates between large and small-bodied baleen whales revealed a small set of conserved candidate genes with potential connections to cancer resistance.ConclusionsOur results suggest that the evolution of rorquals is best described as a hard polytomy with a rapid radiation and high levels of introgression. The lack of shared positive selected genes between different large-bodied whale species supports a previously proposed convergent evolution of gigantism and hence cancer resistance in baleen whales.

The oldest known bat skeletons and their implications for Eocene chiropteran diversification.

The Fossil Lake deposits of the Green River Formation of Wyoming, a remarkable early Eocene Lagerstätte (51.98 ±0.35 Ma), have produced nearly 30 bat fossils over the last 50 years. However, diversity has thus far been limited to only two bat species. Here, we describe a new species of Icaronycteris based on two articulated skeletons discovered in the American Fossil Quarry northwest of Kemmerer, Wyoming. The relative stratigraphic position of these fossils indicates that they are the oldest bat skeletons recovered to date anywhere in the world. Phylogenetic analysis of Eocene fossil bats and living taxa places the new species within the family Icaronycteridae as sister to Icaronycteris index, and additionally indicates that the two Green River archaic bat families (Icaronycteridae and Onychonycteridae) form a clade distinct from known Old World lineages of archaic bats. Our analyses found no evidence that Icaronycteris? menui (France) nor I. sigei (India) belong to this clade; accordingly, we therefore remove them from Icaronycteridae. Taken in sum, our results indicate that Green River bats represent a separate chiropteran radiation of basal bats, and provide additional support for the hypothesis of a rapid radiation of bats on multiple continents during the early Eocene.

Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia

The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocephalus helioscopus, and their associations with geography and past climate change. We obtained the mtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via the genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21–10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zeravshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.