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1,523 results for “speciation”
The shape of phylogenies under phase-type distributed times to speciation and extinction
<p>Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently, many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous' $\beta$ statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the $\beta$ statistic to sets of trees. This extension produces less biased estimates of $\beta$ compared to using the median $\beta$ values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.</p>
Figure 1 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 1. Distribution of Litoria myola sp. nov. (formerly termed iS) and the northern (N) and southern (S) lineages of Litoria genimaculata in the Wet Tropics, northeast Queensland. CT, Carbine Tableland; BMC, Black Mountain Corridor; LR, Lamb Range; BK, Bellenden Ker Range; AT, Atherton Tableland; MT, Malbon Thompson Range; GR, Graham Range.
Figure 2 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 2. Litoria myola, sp. nov., males (A, a pale individual; B, a heavily marked individual), Kuranda, north-east Queensland.
Figure 3 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 3. Spectrogram of the courtship call of Litoria myola sp. nov. (recorded at an air temperature of 25 °C). The spectrogram displays a single courtship call consisting of six notes ('tocs'). The degree of shading displays call intensity.
Figure 7 in Description, biology and conservation of a new species of Australian tree frog (Amphibia: Anura: Hylidae: Litoria) and an assessment of the remaining populations of Litoria genimaculata Horst, 1883: systematic and conservation implications of an unusual speciation event
Figure 7. Rainforest stream habitat, with rocky (A) and sandy (B) substrate, Kuranda, north-east Queensland. Litoria myola sp. nov. and Litoria genimaculata are present at both sites.
Data from: Extreme elevational migration spurred cryptic speciation in giant hummingbirds
<p>The eco-evolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how 'outlier' species defy constraints. Of the 363 hummingbird species, the giant hummingbird (<em>Patagona gigas</em>) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a three-week, ~4,100 m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a new species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: When the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.</p>
Supplementary Dataset for `Imbalanced speciation pulses sustain the radiation of mammals`
<p>Supplementary Dataset for Quintero, I., Lartillot, N. and Morlon, H. `Imbalanced speciation pulses sustain the radiation of mammals`, Science. This dataset contains all the simulations and the empirical data and results for Mammals using the birth-death diffusion (BDD) diversification models. These dataset were produced with the Tapestree.jl package for the Julia software. Moreover, it contains the fossil data and resulting extinction curves using PyRate as well as other files. Please read the README.md file for detailed description.</p>
Figure 4. A-B in Incipient speciation within the Namalycastis abiuma (Annelida: Nereididae) species group from southern India revealed by combined morphological and molecular data
Figure 4. A-B shows the two equally parsimonious trees recovered from the phylogenetic analysis based on the COI dataset (length: 153, CI: 0.896, RI: 0.935). Specimens pertaining to the N. abiuma species group are indicated in bold font, and morphotype (M1-M6) and haplotype (H1- H4) numbers, as referred to in text, are denoted. Bootstrap support values above 50% are shown at each node. Branch lengths are drawn proportional to change.
Figure 1 in Incipient speciation within the Namalycastis abiuma (Annelida: Nereididae) species group from southern India revealed by combined morphological and molecular data
Figure 1. Map of the collection localities for the specimens of the Namalycastis abiuma species group.
Figure 3 in Incipient speciation within the Namalycastis abiuma (Annelida: Nereididae) species group from southern India revealed by combined morphological and molecular data
Figure 3. Neighbour joining tree derived from the COI dataset. Specimens pertaining to the N. abiuma species group are indicated in bold font, and morphotype (M1-M6) and haplotype (H1-H4) numbers, as referred to in text, are denoted by the brackets
Figure 2 in Incipient speciation within the Namalycastis abiuma (Annelida: Nereididae) species group from southern India revealed by combined morphological and molecular data
Figure 2. Selected morphological characters of the various N. abiuma species group morphotypes (M1-M6). A, M1, jaws with 11 teeth; B, M3, jaws with 10 teeth; C, M2, jaws with 9 teeth; D, M5 and M6 jaws with 8 teeth; E, M5, specimen with eyes absent; F, specimen with merged eyes; G-H, M5, specimens with three eyes; I, M5, specimen with faded eyes; J, M4, specimen with the longer tentacular cirri, indicative of species group 2 (see text); K, M4, specimen with relatively wider parapodium; L-M, M6, specimens showing three acicula; N, multi-incised pygidium.
Figure 3 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 3. Bayesian inference (BI) phylogram of Gyrodactylus spp. parasitizing Nearctic Cypriniformes based on sequences of the ITS regions (927 bp). Values above branches indicate posterior probabilities (PP) from BI analyses and bootstrap support (BS) from ML. Values below 0.80 (BI) and 70 (ML) are shown as dashes.
Figure 2 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 2. Photomicrographs (A–C) and line drawings (B–D) of Gyrodactylus mediotorus King, Marcogliese, Forest, McLaughlin and Bentzen, 2013 from the blacktail shiner, Cyprinella venusta (A–B) and from the sand shiner, Notropis cf. stramineus (Guadalupe River) (C–D).
Figure 1 in Intraspecific variation in Gyrodactylus mediotorus and G. crysoleucas (Gyrodactylidae) from Nearctic shiners (Leuciscidae): evidence for ongoing speciation, host-switching, and parasite translocation
Figure 1. Photomicrographs (A) and line drawings (B) of Gyrodactylus crysoleucas from the blacktail shiner, Cyprinella venusta.
Data from: Caught in the act: Incipient speciation at the southern limit of Viburnum in the Central Andes
<p>A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of <em>Viburnum </em>has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa of have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized as <em>V. seemenii </em>f. <em>minor </em>has recently occupied the drier Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in northern Argentina. Plants in these populations form a well-supported clade with a distinctive genetic signature and they have evolved smaller, narrower leaves. We interpret this as the beginning of a within-species divergence process that has elsewhere in the neotropics resulted repeatedly in Viburnum species with a particular set of leaf ecomorphs. Specifically, the southern populations are in the process of evolving the small, glabrous, and entire leaf ecomorph that has evolved in four other montane areas of endemism. As predicted based on our studies of leaf ecomorphs in Chiapas, Mexico, these southern populations experience generally drier conditions, with large diurnal temperature fluctuations. In a central portion of the range of <em>V. seemenii</em>, characterized by wetter climatic conditions, we also document what may be the initial differentiation of the leaf ecomorph with larger, pubescent, and toothy leaves. The emergence of these ecomorphs thus appears to be driven by adaptation to subtly different climatic conditions in separate geographic regions, as opposed to parapatric differentiation along elevational gradients as suggested by Viburnum species distributions in other parts of the neotropics.</p>
Data from: Understanding species boundaries that arise from complex histories: Gene flow across the speciation continuum in the spotted whiptail lizards
<p>Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus <em>Aspidoscelis </em>(<em>A. gularis </em>complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.</p>
Fig. 9 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 9 Macroscopic symptoms of the infection of Juncus oxycarpus (a, healthy plant) roots by Juncorrhiza oxycarpi (b). Scale bars: a approx. 1 cm, b = 1 mm
Fig. 5 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 5 Macroscopic symptoms of the infection of Fuirena ciliaris roots by Entorrhiza fuirenae (arrows). Scale bar = approx. 1 cm
Fig. 7 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 7 Macroscopic symptoms of the infection of Juncus ranarius roots by Juncorrhiza maritima (arrows). Scale bar = 5 mm
Fig. 4 in The origin and diversification of the Entorrhizales: deep evolutionary roots but recent speciation with a phylogenetic and phenotypic split between associates of the Cyperaceae and Juncaceae
Fig. 4 Tanglegram between host plant (left) and fungal (right) phylogenies reconstructed from the ITS + rbcL and ITS + LSU sequences, respectively. Nodal support is given as maximum likelihood bootstrap (≥
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