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203 results for “Divergence times”
Data from: A jungle tale: molecular phylogeny and divergence time estimates of the Desmopsis - Stenanona clade (Annonaceae) in Mesoamerica
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels
Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards endemic to the New World. The clade is characterized by several features that would benefit from interpretation in a phylogenetic context, including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma, and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of disputed age; (3) origins of the parthenogenetic species of Lepidophyma; (4) pronounced micro-habitat differences accompanied by distinct morphologies in both Xantusia and Lepidophyma; and (5) placement of Xantusia riversiana, the only vertebrate species endemic to the California Channel Islands, which is highly divergent from its mainland relatives. This study incorporates extensive new character data from multiple gene regions to investigate the phylogeny of Xantusiidae using the most comprehensive taxonomic sampling available to date. Parsimony and partitioned Bayesian analyses of more than 7 kb of mitochondrial and nuclear sequence data from 11 loci all confirm that Xantusiidae is monophyletic, and comprises three well-supported clades: Cricosaura, Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well supported as the sister to all other xantusiids. Estimates of divergence time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia) clade ∼81 million years ago (Ma), a time frame consistent with the separation of the Antilles from North America. Our results also confirm and extend an earlier study suggesting that parthenogenesis has arisen at least twice within Lepidophyma without hybridization, that rock-crevice ecomorphs evolved numerous times (>9) within Xantusia and Lepidophyma, and that the large-bodied Channel Island endemic X. riversiana is a distinct, early lineage that may form the sister group to the small-bodied congeners of the mainland.
Fossilization processes have little impact on tip-calibrated divergence time analyses
<p>The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian Total-Evidence Dating methods which utilise fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non-random distribution of missing data. The impact of non-random missing data on the accuracy and precision of clade age estimation is unknown. In an attempt to constrain the impact of taphonomy on tip-calibrated dating analyses, we compared clade ages estimated from a very complete morphological matrix to ages estimated from the same matrix permuted to simulate the progressive loss of anatomical information resulting from taphonomic processes. We demonstrate that systematically distributed missing data negatively influence clade age estimates, but that successive stages within the taphonomic process introduce greater differences in age estimates, when compared to estimates obtained from untreated data. Despite these effects, the general influence of missing data is weak, presumably due to the compensatory effect of extensive morphological data from extant taxa. We suggest that, in the absence of models that can explicitly account for taphonomic processes, morphological datasets should be constructed to minimise the impact of taphonomy on divergence time estimation.</p>
The implications of lineage-specific rates for divergence time estimation
<p>Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets.</p>
Data from: Maintenance of soil ecotypes of Solidago virgaurea in close parapatry via divergent flowering time and selection against immigrants
1. The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural laboratory to understand how divergent selection drives the process of local adaptation in edaphically endemic plant species. In case where the serpentine ecotype is surrounded by related non-soil specialists, a balance of natural selection and potential gene flow should be a key factor to maintain the different ecotypes over very short distances. We aimed to reveal the mechanisms to enable soil ecotypes of a goldenrod species to occur almost sympatric situations in Japan. 2. We performed field surveys to characterize microenvironments and reproductive timings of each ecotype, common garden and reciprocal transplant experiments, artificial crossing, and population genetic analysis. 3. Growth chamber experiments show that serpentine plants showed higher leaf mass per area and greater resource allocation to their root systems than did their non-serpentine counterparts, a potential adaptation to drier soil condition in serpentine habitats. Reciprocal transplants demonstrated a clear pattern of local adaptation in the plant growth rate. Importantly, serpentine populations completed flowering by mid-summer versus late summer in non-serpentine plants. This pattern is consistent with the hypothesis that early flowering ensures reproductive success, before the microclimatic conditions becomes severest in open habitats. Although prezygotic isolation was a strong barrier to gene flow, genetic differentiation was very low, indicating a recent origin for the serpentine ecotypes and/or gene flow at low frequencies. 4. Synthesis. The findings indicate that the early-flowering times of serpentine ecotypes, which would have been selected for by microclimates in serpentine areas, can play roles in local adaptation, but also population isolation via a by-product of diverged reproductive timings. This study contributes to general understanding of the initial stages of plant ecological speciation under potential gene flow in very small geographic scales.
Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades
Estimating divergence times on phylogenies is critical in paleontological and neontological studies. Chronostratigraphically-constrained fossils are the only direct evidence of absolute timing of species divergence. Strict temporal calibration of fossil-only phylogenies provides minimum divergence estimates, and various methods have been proposed to estimate divergences beyond these minimum values. We explore the utility of simultaneous estimation of tree topology and divergence times using BEAST tip-dating on datasets consisting only of fossils by using relaxed morphological clocks and birth-death tree priors that include serial sampling (BDSS) at a constant rate through time. We compare BEAST results to those from the traditional maximum parsimony (MP) and undated Bayesian inference (BI) methods. Three overlapping datasets were used that span 250 million years of archosauromorph evolution leading to crocodylians. The first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes (101 taxa, 340 chars.). For each dataset three time-calibrated trees (timetrees) were calculated: a minimum-age timetree with node ages based on earliest occurrences in the fossil record; a 'smoothed' timetree using a range of time added to the root that is then averaged over zero-length internodes; and a tip-dated timetree. Comparisons within datasets show that the smoothed and tip-dated timetrees provide similar estimates. Only near the root node do BEAST estimates fall outside the smoothed timetree range. The BEAST model is not able to overcome limited sampling to correctly estimate divergences considerably older than sampled fossil occurrence dates. Conversely, the smoothed timetrees consistently provide node-ages far older than the strict dates or BEAST estimates for morphologically conservative sister-taxa when they sit on long ghost lineages. In this latter case, the relaxed-clock model appears to be correctly moderating the node-age estimate based on the limited morphological divergence. Topologies are generally similar across analyses, but BEAST trees for crocodyliforms differ when clades are deeply nested but contain very old taxa. It appears that the constant-rate sampling assumption of the BDSS tree prior influences topology inference by disfavoring long, unsampled branches.
Data from: Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations.
Reconstructing the chronology of mammalian evolution is a debated issue between molecule- and fossil-based inferences. A methodological limitation of molecules is the evolutionary rate variation among lineages, precluding the application of the global molecular clock. We considered 2422 first and second codon positions of the combined ADRA2B, IRBP, and vWF nuclear genes for a well-documented set of placentals including an extensive sampling of rodents. Using seven independent calibration points and a maximum-likelihood framework, we evaluated whether molecular and paleontological estimates of mammalian divergence dates may be reconciled by the local molecular clocks approach, allowing local constancy of substitution rates with variations at larger phylogenetic scales. To handle the difficulty of choosing among all possible rate assignments for various lineages, local molecular clocks were based on the results of branch-length and two-cluster tests. Extensive lineage-specific variation of evolutionary rates was detected, even among rodents. Cross-calibrations indicated some incompatibilities between divergence dates based on different paleontological references. To decrease the impact of a single calibration point, estimates derived from independent calibrations displaying only slight reciprocal incompatibility were averaged. The divergence dates inferred for the split between mice and rats (approximately 13-19 Myr) was younger than previously published molecular estimates. The most recent common ancestors of rodents, primates and rodents, boreoeutherians, and placentals were estimated to be, respectively, approximately 60, 70, 75, and 78 Myr old. Global clocks, local clocks, and quartet dating analyses suggested a Late Cretaceous origin of the crown placental clades followed by a Tertiary radiation of some placental orders like rodents.
FIGURE 3 in The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)
FIGURE 3. Tip calibrated fundulid phylogeny derived from the BEAST analysis. Numbers above nodes are estimated mean ages subtended by lines indicating 95% confidence intervals. Branches subtending nodes not present in the maximum likelihood analysis are depicted as gray and do not include age estimates. Nodes with asterisks (*) have posterior probabilities of 95% or greater. Nodes with dots () have posterior probabilities of 90%–95%. Subgenera within Fundulus are indicated by shaded bars. The outgroup, Profundulus guatemalensis, is not depicted.
FIGURE 2 in The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)
FIGURE 2. Cyprinodontoid phylogeny derived from the maximum likelihood analysis. Nodes with asterisks (*) were present in 95% or greater of bootstrap replicates. Nodes with dots () were present in 60%–94% of bootstrap replicates. Nodes present in fewer than 60% of bootstrap replicates not indicated with a symbol. Alternating outgroup families or subfamilies are shaded to increase clarity. Subgenera within Fundulus are indicated by shading. Outgroup taxa used to root the phylogeny, Kryptolebias marmoratus and Aplocheilus panchax, are not depicted.
FIGURE 4 in The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)
FIGURE 4. Distribution of the genus Fundulus. Fossil localities are indicated by daggers (†). The distribution of subgenus Fundulus is depicted with gray horizontal hatching. The distribution of subgenus Plancterus is outlined by a dotted line and indicated in yellow. The distribution of subgenus Zygonectes is depicted with solid blue and the distribution of Wileyichthys is indicated with solid red.
FIGURE 1 in The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)
FIGURE 1. (A) †Fundulus lariversi, Tonopah, NV, Seibert Tuff, Miocene, 17.8–16.2 million years ago (mya), CIMNH 6-75-1, Specimen 2 (paratype specimen). (B) †Fundulus nevadensis, near Hazen, Middle Member of Truckee Formation, NV, Miocene, 10.8–9.8 mya, CIMNH uncataloged. (C) †Fundulus detillae, Logan County, KS, Ogallala Formation, Middle Pliocene, 5–3 mya; KUVP 865. D) †Fundulus nevadensis, near Hazen, Middle Member of Truckee Formation, NV, Miocene, 10.8–9.8 mya, LACM 17320. Scale bars equal 1 mm. Angled lines indicate the angle of the posterior coracoid.
FIGURE 1 in Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)
FIGURE 1. ML phylogeny for penaeidae family, reconstructed using 16S, COI and concatenated sequences. For 16S and COI phylogenies only ML bootstrap values are shown. For the concatenated sequence tree bootstrap support values for ML, BI, and NJ are shown near interior branches. Bootstrap values lower than 50 are not shown. Species with circles, triangles and squares belong respectively to Penaeini, Trachypenaeini, and Parapenaeini clades, following Burkenroad's (1953) traditional classification. The Penaeini clade (bold branches) was used in divergence times estimates. Letters A, B and C are references for the nodes where time constrains were set.
Dataset from: Parapatric and sympatric adaptation of Setaria viridis populations in Japan to heterogeneous coastal habitats via trait divergence of plant form, salt spray tolerance and flowering time
<p>This study aimed to determine how coastal variants of<em> </em>plants arise from local populations under natural selection by studying variations in phenotypic variations and survival of <em>Setaria viridis</em> populations inhabiting mosaic environments of two seashores in Japan. <em>S.viridis</em> populations comprised five coastal variants showing significantly higher salt spray tolerance than the inland variant: ST, short and tolerant (common variant); TM, tall and mid-tolerant (Inland Sea); TT, tall and tolerant; PT, prostrate and tolerant; L, extremely late flowering; I, inland and susceptible variants. These variations imply that maritime plants first acquired salt spray tolerance for survival, after which compact plants evolved in habitats where strong winds caused damage from salt spray. Results indicate that diverse intensities of salt spray and winds as well as summer drought generated various coastal variations in parapatry and sympatry.</p>
Figure 1 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 1. Geographical regions of cypriniform fish distribution at the continental scale. The seven region scheme presented here [Africa (Af), South Asia (Sa), East Asia (Ea), Europe (Eu), Siberia (Sb), and western and eastern North America (Wn & En)] is a modification of the conventional Wallace's six region system (Berra, 2001). East Asia, Europe, and Siberia are subdivisions of the Palaearctic region, overlapping with each other. Western and eastern North America are subdivisions of the Nearctic region.
Figure 5. A in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 5. A reconciled dispersal-vicariance analysis (DIVA; upper) and a simple parsimonious reconstruction (lower) inference of past ranges at the subfamilial level superimposed over divergence time estimates. Open rectangular bars stand for 95% confidence ranges of the divergence time estimates. The scale bar at the bottom represents the geological time scale according to Gradstein, Ogg & Smith (2004). Maps drawn from Smith, Smith & Funnel (1994) indicate onset (220 Mya) and completion (160 Mya) of the Pangaean breakup, and separation of the Indian land mass from Africa (130 Mya), which allowed marine permeation. Arrowheads indicate rifting margins; hatched pattern indicates area of black shale deposits (Olsen, 1997).
Figure 2. The maximum likelihood tree inferred from 14 594 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 2. The maximum likelihood tree inferred from 14 594 nucleotide sites of 60 Cypriniformes and six outgroups (lnL = -203 966.535). Numbers at each branch indicate the resampling the estimated log likelihood (RELL) local bootstrap probabilities. Asterisks indicate 100% local bootstrap support. Two major clades of Cyprinidae (A and B) correspond with those presented in Cavender & Coburn (1992).
Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification
Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. Results: We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of pines is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. Conclusions: Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods.
FIGURE 2 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)
FIGURE 2. Phylogenetic trees of the genus Chelonoidis, including the C. chilensis complex, obtained by three different criteria. A: Maximum Parsimony, B: Maximum Likelihood, C: Bayesian Inference. The numbers above the nodes indicate bootstrap support scores (A and B) and posterior probability scores (C). Clade colors refer to the corresponding eco–regions (see Fig. 1).
FIGURE 1 in Phylogenetic and divergence time analysis of the Chelonoidis chilensis complex (Testudines: Testudinidae)
FIGURE 1. Map of Argentina showing the localities from which the tissue samples were taken. Different colors indicate different eco–regions. Legends near sample localities are in accordance with the haplotypes shown in the phylogenetic trees (Fig. 2).
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