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Aim Understanding the phylogeography of a species complex can provide important insights into its evolutionary history. However, phylogeographic inference often faces the dilemma of regionally inadequate sampling. Pungitius sticklebacks are a case in point: although the highest species diversity is found in Northeast Asia, their phylogeography in this region is still poorly understood. Location Northeast Asia. Methods With the aid of whole-genome resequencing data, we investigated the phylogeography of Northeast Asian Pungitius sticklebacks, with newly sampled 83 worldwide Pungitius individuals from 11 locations including eight Chinese locations reported to host only P. sinensis. Results We discovered that three of the eight Chinese locations hosted populations of P. kaibarae and P. bussei, species new to the fauna of China. Phylogeographic analyses further clarified the sequence and timing of colonization of Northeast Asia by different Pungitius species, shedding new light on their origins and current distribution ranges. Colonization of inland Northeast Asia by Pungitius sticklebacks occurred in multiple waves, and the widespread P. sinensis expanded its range relatively late in the Pleistocene. Main conclusions This study complements our understanding of the phylogeography of Pungitius sticklebacks by extending sampling to cover an area that comprises nearly half of the known distribution area of this genus in Northeast Asia. The discovery of three Pungitus species from China is of particular interest, as translocations to support locally declining populations have occurred under the assumption that all sticklebacks in China-except the endangered P. stenurus-are P. sinensis, raising conservation concerns associated with unintentional translocations and possible admixture.

Two nature-inspired computing techniques, i.e. the Firefly and the controlled Genetic Algorithm in a restricted divergence environment has been combined to propose an improved Clinical Decision Support System (CDSS) query optimizer. The proposed model is intended to get better query execution plan which will detract the input-output, processing and communication lust for the execution of the CDSS queries. The amalgamated use of the proposed CDSS query optimizer framework will yield substantial variation in two consecutive generations which will efficaciously resolve the slow convergence problem of the controlled Genetic Algorithm. Furthermore, the results of the proposed CDSS query optimizer are tested against the effects of other genetic algorithm based CDSS query optimizers. It is experimentally found that the results produced using RDFG_CDQO are 13%, 10%, 7% and 3.5% better than the outcomes of the other CDSS query optimizers designed using simple, novel, restricted and entropy-based restricted genetic algorithm respectively. To get the best possible solution using RDFG_CDQO, the value of divergence rate should be set up to 50%. Furthermore, to statistically approve the proposed framework, the results obtained using RDFG_CDQO are validated using different measures of regression analysis viz. assumption of linearity, independence, and constant variance.

Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in coloration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common color pattern in African cichlids, vertical bars, and potential interactions between the two color patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both color patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in Ne. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.

A record of 44Ti activity measured in 20 stony meteorites fallen during CE 1766–2001 was compared to six series of 44Ti activity, calculated from the data on modulation parameter Φ based on cosmogenic isotopes 14C and 10Be. It was shown that both experimental and computed records have appreciable divergences. The secular trends of many model curves are flatter than that of the measured record and the difference in amplitude of the century-scale cycle of Gleissberg is highly significant (p

The resolution of cryptic diversity is essential for understanding the evolutionary diversification of lineages and establishing conservation priorities. We examine relationships in Eriogoneae (Polygonaceae), a diverse lineage in western North America. We ask whether Eriogonum umbellatum, a morphologically and ecologically diverse species, is monophyletic and whether its varieties represent evolutionary lineages. We use genotyping-by-sequencing to assemble a SNP dataset for 51 species in the genera Chorizanthe, Eriogonum and Sidotheca. We report a hierarchical phylogenetic analysis using maximum likelihood to estimate the evolutionary history of Eriogoneae. We illustrate admixture components for 21 populations of E. umbellatum, representing four varieties, and test for lineage structure using TreeMix. We identify strongly supported clades within Eriogoneae. Many relationships in the Eucycla + Oregonium and Latifolia clades are supported, while most relationships within the Eriogonum subg. Oligogonum clade and a clade with most Chorizanthe remain unresolved. Eriogonum congdonii resolves within the main E. umbellatum clade, while populations of three varieties of E. umbellatum are closely related to E. ursinum and are associated with serpentine soils. ADmixture and TreeMix analyses suggest E. umbellatum varieties represent evolutionary lineages. These results from SNP data are largely consistent with previous phylogenetic studies of Eriogoneae based on sequence variation. Structure within Oligogonum suggests consistent environmental association and radiation after initial colonization of serpentine. Morphology is unreliable for the infraspecific taxonomy of E. umbellatum. Additional molecular studies are needed to resolve the evolutionary relationships and ecological diversification within this species, in Oligogonum, and in Eriogoneae. We thank SGIker research support services at the University of the Basque Country, Leioa, Spain for DNA extraction and quality control, and acknowledge Centro Nacional de d-Analisi Genomica in Barcelona, Spain for GBS sequencing. We thank J. Andre, N.J. Jensen and J. Steele for contributing samples and D. Marino for collaboration in nucleic acid extractions. We acknowledge the contributions of O. Lao Grueso to the ADmixture and TreeMix analyses. We thank U.S. Forest Service employees D. Austin, J. Fedorchuk, M. Friend, J. Haas, D. Ikeda, L. Janeway, J. Nelson, D. Netz, A. Sanger, and S. Weis among others for facilitating permitting and collecting. This work was supported by funds from the Basque Government in support of the Terrestrial Plant Diversity group of the Department of Plant Biology and Ecology, University of the Basque Country, and an ERC Advanced Grant, FP7-IDEAS-ERC, `ADAPT', project 339941 awarded to T. Brown.

The slow-worm lizards of the genus Anguis show significant morphological, behavioural and ecological uniformity owing to their limbless, elongated bodies and semifossorial lifestyle. This makes the delimitation of species challenging. Five monophyletic, deeply divergent and mostly parapatric mitochondrial lineages are currently recognized, although hybridization occurs along contact zones. In the southern edge of the range of the genus, two endemic Balkan Anguis (Anguis graeca and Anguis cephallonica) share a broad area of co-distribution and intermediate morphological characteristics. Expecting to retrieve hybrids within the overlap in their distributions, we used genome-wide single nucleotide polymorphisms but did not recover any evidence of interspecific gene flow. Within each species, genomic data revealed shallow population structuring influenced by spatial isolation, with the exception of the southernmost population of A. cephallonica from the Mani Peninsula. Species distribution modelling showed a lack of strong niche overlap and specific environmental preferences; both species showed a precipitation dependence, but A. cephallonica was better acclimatized to high temperatures. Finally, geometric morphometrics of the head shape suggested morphological divergence, mostly seen in the elongation of the head of A. cephallonica. All the evidence supports a long and complete reproductive isolation between the two southern slow worms and raises questions about how ecomorphological divergence might have acted to promote their speciation.

By shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage disequilibrium prespeciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and Drosophila persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between D. pseudoobscura and D. persimilis over three distinct timescales: (1) segregation of ancestral polymorphism early in the speciation process, (2) gene flow after the split of D. pseudoobscura and D. persimilis, but prior to the split of D. pseudoobscura subspecies, and (3) recent gene flow between sympatric D. pseudoobscura and D. persimilis, after the split of D. pseudoobscura subspecies. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in other systems.

Given a complex, elliptic coefficient function we investigate for which values of p the corresponding second-order divergence form operator, complemented with Dirichlet, Neumann or mixed boundary conditions, generates a strongly continuous semigroup on $$\mathrm {L}^p(\Omega )$$ . Additional properties like analyticity of the semigroup, $$\mathrm {H}^\infty $$ -calculus and maximal regularity are also discussed. Finally, we prove a perturbation result for real coefficients that gives the whole range of p’s for small imaginary parts of the coefficients. Our results are based on the recent notion of p-ellipticity, reverse Holder inequalities and Gaussian estimates for the real coefficients.

Given n ≥ 2 and $$\alpha > \tfrac{1}{2}$$ , we obtained an improved upbound of Hausdorff’s dimension of the fractional Schrodinger operator; that is, $$\mathop {\sup }\limits_{f \in {H^s}({\mathbb{R}^n})} {\dim _H}\left\{ {x \in {{\mathbb{R}^n}}:\;\mathop {\lim }\limits_{t \to 0} {e^{{\rm{i}}t{{( - \Delta )}^\alpha }}}f(x) \ne f(x)} \right\} \le n + 1 - {{2(n + 1)s} \over n}$$ for $$\tfrac{n}{{2(n + 1)}} < s \le \tfrac{n}{2}$$

The correct choice of parents that will compose optimal segregating populations is the key to success for breeding programs. It was postulated the hypothesis that this choice of these parents could be made based on information of molecular markers analyzed in the context of population structure. Ten parental populations were simulated and 45 hybrid combinations were obtained from the dialel crosses. Each population consisted of 200 individuals with 50 independent loci. The populations were evaluated for the Hardy-Weinberg Equilibrium (HWE), Coefficient of Inbreeding (F), Heterozygosity (H), and the Polymorphic Information Content (PIC). Genetic diversity between pairs of parental populations was evaluated using five dissimilarity measures. Values of Mantel correlation were obtained for the pairs of the dissimilarity matrices, and the PIC, H, and F values ​​were obtained in the hybrid combinations. All parental populations were under HWE, and the combination that emerged from this condition was the hybrid 3x5, with only 26% of the loci manifesting HWE. This same hybrid was among those with lower F estimates and higher values ​​of H, which indicated the existence of greater divergence between their parentals. There was agreement on the indication of the more and less divergent hybrid combinations for the dissimilarity measures. This fact is important because the variability, associated with the good average potential, are important criteria for the formation of an initial population in breeding programs of any kind, involving sexual processes.

A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population-specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naive Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naive Bayes, could be used as the valuable tool for ancestry analysis.

Urbanisation changes the structure of natural habitats and alters trophic interactions, pressuring urban species to adjust and adapt. Unlike behavioural shifts that tend to be more flexible, morphological characteristics in vertebrates are less plastic and changes may come at a greater cost. We explored the hypothesis that morphological characteristics in a tropical agamid lizard Psammophilus dorsalis are not only selected to suit altered habitat conditions in urbanised areas but reflect predation risk in urban habitats. In addition, we explored differences in tail loss in both sexes from urban and rural habitats. First, we find that predation risk did not differ between urban and rural habitats, but differed between sexes. Conspicuous courtship-coloured male lizards were more likely to be attacked compared to cryptically-coloured female lizards. Next, we find that P. dorsalis differed in key morphological characteristics, with greater urban-rural differences in males than females. Urban lizards had shorter proximal limb elements, longer 4th digits and greater body mass than rural lizards; and among males, urban lizards had significantly larger head sizes and longer distal limb elements than rural lizards. Finally, we find that the rates of tail loss differed between habitats and sexes, with urban male lizards having greater rates of tail loss than rural males and all females. Inter-sexual difference in tail loss was consistent with the difference in predation risk between sexes, but tail loss differences between urban and rural habitats could not be explained by predation risk. In sum, we find that adaptations to novel urban environments are not exclusively driven by a single promoter (e.g. predation risk) but are influenced by multiple selection pressures with associated fitness costs, such as tail loss.

Summary ・Phytochromes play a central role in mediating adaptive responses to light and temperature throughout plant life cycles. Despite evidence for adaptive importance of natural variation in phytochromes, little information is known about molecular mechanisms that modulate physiological responses of phytochromes in nature. ・We show evolutionary divergence in physiological responses relevant to thermal stability of a physiologically active form of phytochrome (Pfr) between two sister species of Brassicaceae growing at different latitudes. The higher latitude species (Cardamine bellidifolia; Cb) responded more strongly to light‐limited conditions compared with its lower latitude sister (C. nipponica; Cn). Moreover, CbPHYB conferred stronger responses to both light‐limited and warm conditions in the phyB‐deficient mutant of Arabidopsis thaliana than CnPHYB: that is Pfr CbphyB was more stable in nuclei than CnphyB. ・Our findings suggest that fine tuning Pfr stability is a fundamental mechanism for plants to optimise phytochrome‐related traits in their evolution and adapt to spatially varying environments, and open a new avenue to understand molecular mechanisms that fine tune phytochrome responses in nature.

Let $$ \{X, X_{n};~n \ge 1 \}$$ be a sequence of independent and identically distributed Banach space valued random variables. This paper is devoted to providing a divergence criterion for a class of random series of the form $$\sum _{n=1}^{\infty } f_{n}\left( \left\| S_{n} \right\| \right) $$ where $$S_{n} = X_{1} + \cdots + X_{n}, ~n \ge 1$$ and $$\left\{ f_{n}(\cdot ); n \ge 1 \right\} $$ is a sequence of nonnegative nondecreasing functions defined on $$[0, \infty )$$ . More specifically, it is shown that (i) the above random series diverges almost surely if $$\sum _{n=1}^{\infty } f_{n} \left( cn^{1/2} \right) = \infty $$ for some $$c > 0$$ and (ii) the above random series converges almost surely if $$\sum _{n=1}^{\infty } f_{n} \left( cn^{1/2} \right) < \infty $$ for some $$c > 0$$ provided additional conditions are imposed involving X, the sequences $$\left\{ S_{n};~n \ge 1 \right\} $$ and $$\left\{ f_{n}(\cdot ); n \ge 1 \right\} $$ , and c. A special case of this criterion is a divergence/convergence criterion for the random series $$\sum _{n=1}^{\infty } a_{n} \left\| S_{n} \right\| ^{q}$$ based on the series $$\sum _{n=1}^{\infty } a_{n} n^{q/2}$$ where $$\left\{ a_{n};~n \ge 1 \right\} $$ is a sequence of nonnegative numbers and $$q > 0$$ .

Morphometric and meristic data were used in this study to establish morphological variations within the largest genetically consistent groups of five wild populations of tilapia from Kyushu and Okinawa ecological regions of Japan. The genetic analysis based on mitochondrial DNA relatedness was used to determine the data range used for the morphological analyses. During the morphological analyses, the morphometric and meristic data were correlated by two multivariate statistical methods, such as PCA and LDA. Both statistical methods observed morphological differences of higher divergence in Okinawa contrary to Kyushu. Additionally, the statistical relationship between the estimated non-parametric test of ANOSIM (R = 0.21; p ˂ 0.05) and PERMANOVA (F = 4.20; p ˂ 0.05) indicated a higher magnitude of morphological separation, especially in Okinawa; nevertheless, water temperature, conductivity, and salinity levels vary widely in Kyushu than in Okinawa. All observed differences could be attributed to either genetic and/or environmental factors, which are major variables in influencing phenotypic variability. However, since tilapia in Japan experienced multiple introductions from different countries and environmental backgrounds, we recommend further studies under a controlled environment to ascertain the environmental responsiveness during morphological differentiation within a genetically consistent group of tilapia.

Describing the rules of community assembly is a central topic of ecology. Studying successional processes through a trait-based null model approach can help to better understand the rules of community assembly. According to theoretical considerations, at the beginning of succession - after getting over the dispersal limitation stage - community composition is primarily shaped by environmental filters (generating functional convergence), while in later stages limiting similarity (generating functional divergence) will be dominant. However, empirical evidence does not clearly support theoretical expectations. Our aim was to detect the presence and changes of trait-based assembly processes during old-field succession based on twelve traits. Changes in vegetation composition were evaluated by a combination of time series and space-for-time substitution: conducting three resurveys of permanent plots on four old-field age-groups. The individual dispersion of traits was transformed into effect size (i.e. departure from null model expectation). The impact of time since abandonment on effect sizes was tested by generalized additive mixed effect models. We detected a non-random pattern for each trait in at least some part of the succession. Departure from randomness did not change significantly over time for six traits: seed mass, lateral spread and pollination type were divergent, while leaf size, generative height and length of flowering were convergent. Six traits had changing patterns along the succession. Four of them showed increasing divergence (e.g. dispersal type, LDMC), which supports our hypothesis. While two (SLA, life form) displayed increasing convergence, contrary to expectations. We confirmed the general hypothesis that convergence is predominant initially and that divergence can be detected later in succession for four traits. However, the large variation found in trait dispersion indicates that complex processes operate during succession.

Many plant families lack substantive fossil records, limiting our understanding of their origin and evolution. The abundance and preservation potential of pollen through geological time have helped to overcome such limitations and have provided reliable fossils for reconstructing biogeographical history and character evolution in many angiosperm families. Here, using scanning electron microscopy, we identified six Ebenaceae-type fossil pollen grains from early Palaeogene sediments of western India. Phenetic and phylogenetic analyses using pollen characters of fossil and extant taxa reavealed affinities of these fossils to three genera of Ebenaceae (Euclea, Royena and Diospyros). Furthermore, our divergence dating analysis using these fossils as priors suggested a Gondwanan origin for the family during the mid-Cretaceous [c. 107 Mya, 95% highest posterior density (HPD): 100–112 Mya] and supports the boreotropical and ‘out of India’ dispersal hypotheses as the most probable explanations for the present global distribution of the family. The study also supports the dispersal of the family into India, from Africa, through the Kohistan–Ladakh Arc during the Palaeocene. Finally, comparative phylogenetic analyses suggest significant synapomorphic and phylogenetic signals for a few selected pollen characters in Ebenaceae. Our findings have important implications for understanding the biogeography and evolution of the highly diverse and ecologically and economically important family Ebenaceae.

The spiral arrangement (phyllotaxis) of leaves is a shared morphology in land plants, and exhibits diversity constrained to the Fibonacci sequence. Phyllotaxis in vascular plants is produced at a multicellular meristem, whereas bryophyte phyllotaxis emerges from a single apical stem cell (AC) that is embedded in a growing tip of the gametophyte. An AC is asymmetrically divided into itself and a single ‘merophyte’, producing a future leaf and a portion of the stem. Although it has been suggested that the arrangement of merophytes is regulated by a rotation of the division plane of an AC, the quantitative description of the merophyte arrangement and its regulatory mechanism remain unclear. To clarify them, we examined three moss species, Tetraphis pellucida, Physcomitrium patens, and Niphotrichum japonicum, which exhibit 1/3, 2/5, and 3/8 spiral phyllotaxis, respectively. We measured the angle between the centroids of adjacent merophytes relative to the AC centroid on cross-transverse sections. At the outer merophytes, this divergence angle converged to nearly 120 $$^\circ$$ in T. pellucida, 136 $$^\circ$$ in N. japonicum, and 141 $$^\circ$$ in P. patens, which was nearly consistent with phyllotaxis, whereas the divergence angle deviated from the converged angle at the inner merophytes near an AC. A mathematical model, which assumes scaling growth of AC and merophytes and a constant angle of division plane rotation, quantitatively reproduced the sequence of the divergence angles. This model showed that successive relocations of the centroid position of an AC upon its division inevitably result in the transient deviation of the divergence angle. As a result, the converged divergence angle was equal to the rotation angle, predicting that the latter is a major regulator of the spiral phyllotaxis diversity in mosses.

The frequency and spatial distributions of precipitation extremes (PEs) and deep convective clouds (DCC) across the Amazon region were assessed using satellite-derived data. For PEs, CHIRPS dataset for the period 1981–2018 were used to calculate a set of absolute, threshold, duration, and percentile-based threshold indices defined by the Expert Team on Climate Change Detection and Indices. DCC occurrence was assessed based on the Advanced Microwave Sounding Unit data for the period 2002–2018. In northern Amazon (north of $$5^\circ \hbox {S}$$ ) PEs and DCC are more frequent ( $$\ge 60\%$$ frequency) during February–June. Averaged trends over these months have shown increase in daily rainfall above 20 mm of near 3 days over the 1981–2018 period, and an increase of 2 consecutive wet days (P $$\ge 1\,\hbox {mm}$$ ) in the same period. South of $$5^\circ \hbox {S}$$ prevalence of PEs and DCC is largely observed during November–March ( $$\ge 60\%$$ frequency), whereas the longest persistence of dry days is observed during June–August. Though all PE trends point to an intensification of rainfall in November–March, only consecutive dry days in winter (JJA) and spring (SON) show significant trends, pointing to an increase of 7 days over the 38-yr winters. Rainfall extremes over the entire Amazon region were found to be moderate to strongly correlated with the mean vertically integrated moisture divergence, and in southern Amazon also to upper level divergence and upward vertical velocity. Increased frequency of DCC were found over the whole basin ( $$\sim 18\% \,\, \hbox {yr}^{-1}$$ ), in contrast to decreased convective overshooting (up to $$\sim 15.4\% \,\, \hbox {yr}^{-1}$$ ).

Cuscuta gronovii Willd. ex Roem. & Schult. is a parasitic plant and widely distributed in Europe and North America. Here, we compared the plastome sequences of a C. gronovii plant collected from China and other 16 Cuscuta plastomes, including one C. gronovii plastome from North America. The plastome was 86,727 bp in size with a pair of inverted repeats (IRs) of 14,354 bp, a large single-copy (LSC) region of 50,956 bp, and a small single-copy (SSC) region of 7,063 bp. We predicted 97 genes in the plastome, including 61 protein-coding genes, eight ribosomal RNA genes, and 28 transfer RNA genes. We detected a total of 21 microsatellite, 16 tandem, and ten interspersed repeats in the genome. Gene contents analysis of 17 Cuscuta plastomes showed the loss of the entire ndh gene family. The phylogenomic analysis using 22 shared protein sequences shows that the two C. gronovii formed a cluster. Thirteen of Cuscuta plastomes showed no rearrangement. The other three showed smaller inversions and smaller numbers of gene deletion. Next, we identified the two INDELs, one SNP site between the two C. gronovii plastomes. And we identified two putative RNA editing sites. Lastly, to distinguish between C. gronovii and two medicinal Cuscuta species, C. chinensis and C. australis, we identified ten molecular markers based on the genome sequences. The overall large-scale gene loss, conserved gene order, low intraspecific divergence are consistent with the adaptation of C. gronovii to a parasitic lifestyle.

Life-history variation plays a central role in evolutionary and ecological processes and might be especially pertinent to divergence in closely related species. We investigated differences in life history in a pair of parapatric species of ambush bugs (Phymata) and a putative hybrid population. Despite the evidence of gene flow among these species, we found clear divergence between these parapatric populations for a suite of juvenile and adult life-history traits, including components of fitness. The higher latitude species was also less active, suggestive of potential divergence in dispersal. Increased melanism was correlated with longevity in one species, although it was unclear whether this relationship was causal. Observed differences in the life history between species were consistent with expectations of high-latitude species putting a premium on early or rapid development and increased reproductive rates. However, these results were not consistent with ‘pace-of-life syndromes’ at the species level. Individuals from the putative hybrid zone exhibited intermediate values for most traits, although they had slower development and reduced mobility, consistent with some previous work suggesting natural selection via hybrid breakdown.

Species of burrowing animals have changed substantially over evolutionary time scales, but, surprisingly, burrows display persisting morphological patterns throughout the Phanerozoic. Deep-sea burrows are geometrically patterned, whereas shallow-marine burrows display simpler morphologies. This divergence between burrow associations is one of the central conundrums of paleontology, but it has never been quantitatively demonstrated, and the organizing principles responsible for this structure remain unknown. We show that the divergence of burrow associations has been shaped by small-world dynamics, which is proposed as a major macroevolutionary force in marine environments. Using network analysis, our study reveals that the association patterns between burrow morphotypes in 45 paleontological sites span ∼500 m.y. Strong statistical support is demonstrated for a surprising association pattern, according to which the data set is optimally partitioned into two subgroups of tightly associated burrow types. These groups correspond to shallow- and deep-marine biomes. Our analysis demonstrates that across the Phanerozoic Eon, burrows did not assemble randomly nor regularly, following instead small-world assembly rules remarkably similar to those that shape human social networks. As such, small-world dynamics deeply influenced gene flow and natural variation in heritable behavior across evolutionary time.

We discuss the $0^{+-}$ singlet sector of glueballs in the Klebanov-Strassler theory. We report the results of a numerical study of the linearized equations in the Klebanov-Strasller background and make a comparison with the spectrum of the scalar sector. While for four towers of the total six towers of massive pseudoscalar states our results match the spectrum of the corresponding towers of scalars, the values for the remaining two towers diverge with those of the scalars. We discuss possible interpretations of this divergence., Comment: 7 pages, 2 figures,5 tables -> 7 pages, 2 figures, 5 tables, references added in the second version

The genus Pygopleurus includes some of the most important beetle pollinators of the Eastern Mediterranean islands, showing a particular affinity to red-guild flowers. Focussing on the Aegean Archip...

A tensor v is the sum of at least rank⁡(v) elementary tensors. In addition, a ‘border rank’ is defined: rank_(w)=r holds if r is the minimum integer such that w is a limit of rank-r tensors. Usuall...

Photosynthetic capacity per unit irradiance is greater, and the marginal carbon revenue of water (∂A/∂E) is smaller, in shaded leaves than sunlit leaves, apparently contradicting optimization theory. I tested the hypothesis that these patterns arise from optimal carbon partitioning subject to biophysical constraints on leaf water potential. In a whole plant model with two canopy modules, I adjusted carbon partitioning, nitrogen partitioning and leaf water potential to maximize carbon profit or canopy photosynthesis, and recorded how gas exchange parameters compared between shaded and sunlit modules in the optimum. The model predicted that photosynthetic capacity per unit irradiance should be larger, and ∂A/∂E smaller, in shaded modules compared to sunlit modules. This was attributable partly to radiation-driven differences in evaporative demand, and partly to differences in hydraulic conductance arising from the need to balance marginal returns on stem carbon investment between modules. The model verified, however, that invariance in the marginal carbon revenue of N (∂A/∂N) is in fact optimal. The Cowan-Farquhar optimality solution (invariance of ∂A/∂E) does not apply to spatial variation within a canopy. The resulting variation in carbon-water economy explains differences in capacity per unit irradiance, reconciling optimization theory with observations.

The South American Ctenomys is the most speciose genus among both hystricomorphs and subterranean rodents of the world. Here, we present the most exhaustive phylogenies and timetree of living and e...

Open cloud cells can be described in ideal form as connected clouds that surround spots of isolated clear skies in their centers. This cloud pattern is typically associated with marine stratocumulus (MSc) that form in the oceanic boundary layer. However, it can form in deeper convective clouds as well. Here, we focus on deep-open-cells (with tops reaching up to ~5–7 km) that form in the post-frontal regions of winter Mediterranean cyclones, and examine their properties and evolution. Using a Lagrangian analysis of satellite data, we show that deep-open-cells have a larger equivalent diameter (~58 ± 18 km) and oscillate with a longer periodicity (~3.5 ± 1 h) compared to shallow MSc. A numerical simulation of one Cyprus low event reveals that precipitation-generated convergence and divergence dynamic patterns are the main driver of the open cells’ organization and oscillations. Thus, our findings generalize the mechanism attributed to the behavior of shallow marine cells to deeper convective systems.

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char (Salvelinus sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length‐frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present‐day char populations. Although some lakes exhibit bimodal size distributions, using model‐based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha‐1), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food‐limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation., In this study, we described the morphological and genetic diversity of seven populations of arctic char with varying length‐frequency distributions across two distinct groups of lakes in northern Alaska. Although some lakes exhibit multimodal size distributions, using model‐based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genetic analyses demonstrated differences among lake groups, but within lake groups and within individual lakes, genetic differentiation was not related to total body length.

Buccinum undatum is a subtidal gastropod that exhibits clear spatial variation in several phenotypic shell traits (color, shape, and thickness) across its North Atlantic distribution. Studies of spatial phenotypic variation exist for the species; however, population genetic studies have thus far relied on a limited set of mitochondrial and microsatellite markers. Here, we greatly expand on previous work by characterizing population genetic structure in B. undatum across the North Atlantic from SNP variation obtained by RAD sequencing. There was a high degree of genetic differentiation between Canadian and European populations (Iceland, Faroe Islands, and England) consistent with the divergence of populations in allopatry (FST > 0.57 for all pairwise comparisons). In addition, B. undatum populations within Iceland, the Faroe Islands, and England are typified by weak but significant genetic structuring following an isolation‐by‐distance model. Finally, we established a significant correlation between genetic structuring in Iceland and two phenotypic traits: shell shape and color frequency. The works detailed here enhance our understanding of genetic structuring in B. undatum and establish the species as an intriguing model for future genome‐wide association studies.

By perturbing co-evolved interactions, biological invasions provide an opportunity to study the evolution of interactions between hosts and their parasites on ecological timescales. We studied the interaction between the cane toad (Rhinella marina) and its direct-lifecycle lungworm (Rhabdias pseudosphaerocephala) that was brought from South America to Australia with the toads in 1935. Compared with infective parasite larvae from long-established (range-core) toad populations, parasite larvae from toads near the invasion front were larger, lived longer and were better able to resist exposure to toxin from the parotoid glands of toads. Experimentally, we infected the common-garden-reared progeny of toads from range-core and invasion-front populations within Australia with lungworms from both populations. Infective larvae from invasion-front (vs. range-core) populations of the parasite were more successful at entering toads (by skin penetration) and establishing infections in the lungs. Toads from invasion-front populations were less prone to infection by either type of larvae. Thus, within 84 years, parasites at an invasion front have increased infectivity, whereas hosts have increased resistance to parasite infection compared with range-core populations. Rapid evolution of traits might affect host–parasite interactions during biological invasions, generating unpredictable effects both on the invaders and on native ecosystems.

Habitats can select for specialized phenotypic characteristics in animals. However, the consistency of evolutionary responses to particular environmental conditions remains difficult to predict. One trait of great ecological importance is brain form, which is expected to vary between habitats that differ in their cognitive requirements. Here, we compared divergence in brain form and oral jaw size across a common littoral-pelagic ecological axis in two sunfishes at both the intraspecific and interspecific levels. Brain form differed between habitats at every level of comparison; however, divergence was inconsistent, despite consistent differences in oral jaw size. Pumpkinseed and bluegill species differed in cerebellum, optic tectum and olfactory bulb size. These differences are consistent with a historical ecological divergence because they did not manifest between littoral and pelagic ecotypes within either species, suggesting constraints on changes to these regions over short evolutionary time scales. There were also differences in brain form between conspecific ecotypes, but they were inconsistent between species. Littoral pumpkinseed had larger brains than their pelagic counterpart, and littoral bluegill had smaller telencephalons than their pelagic counterpart. Inconsistent brain form divergence between conspecific ecotypes of pumpkinseed and bluegill sharing a common littoral-pelagic habitat axis suggests that contemporary ecological conditions and historic evolutionary context interact to influence evolutionary changes in brain form in fishes.

In East Asia, genetic divergence is usually considered to be correlated to different floristic regions, however, subtropical-tropical divergence is largely ignored, compared to widely explored temperate-subtropical divergence. Lindera aggregata (Lauraceae), a dominant species in South-East China was selected to address this issue. Fifteen low-copy nuclear genes (LCGs) and four chloroplast DNA (cpDNA) fragments were used to detect its evolutionary history. In LCGs, STRUCTURE and dated Bayesian phylogeny analyses detect distinct subtropical-tropical divergence since late Pleistocene. Approximate Bayesian calculation (ABC) further supports the distinct subtropical-tropical divergence, and close related Taiwan and South China populations are diverged at the last interglacial. Isolation by distance, isolation by environment and isolation by resistance analyses suggest the current climatic difference rather than geographical distance contributes to the genetic differentiation. Principle component analysis shows populations of tropical cluster occur in warmer area with higher precipitation. Ancestral area reconstruction based on Bayesian phylogeny indicates that ancestral L. aggregata populations are distributed in tropical region. In cpDNA, although unique haplotypes are found in tropical region, distinct subtropical-tropical divergence is absent. In conclusion, distinct late Pleistocene subtropical-tropical divergence of L. aggregata is triggered by climate. It is likely that L. aggregata is originated in Southwest-South China and experienced hierarchical dispersal from south to north. The South China Sea land bridge has dual role in connecting or isolating Taiwan and mainland populations since the last glaciation.

Dobinea is a dioecious genus endemic to East Asia that consists of two extant species: Dobinea delavayi and Dobinea vulgaris. Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between Dobinea and related taxa by sequencing the whole plastome DNA sequences for both extant species of Dobinea and comparing them to published plastomes within Sapindales. The complete plastomes of D. vulgaris and D. delavayi were 160,683 and 160, 154 base pairs (bp) in length, including a pair of inverted repeat regions (IRs, 26,889 and 26,759 bp) divided by the large single-copy region (LSC, 87,962 and 87,555 bp) and small single-copy region (SSC, 18,943 and 19,081 bp), and identically encoded 113 unique genes (79 protein-coding genes, 30 tRNAs, and 4 rRNA genes). Plastid phylogenomic analyses showed that Dobinea was a well-supported monophyletic unit and sister to the clade including tribes Anacardieae and Rhoideae, which suggests that Dobinea is a member of Anacardiaceae. In addition, molecular dating inferred D. delavayi and D. vulgaris diverged approximately 10.76 Ma, suggesting the divergence between these two species may have been driven by the intensification of the Asian summer monsoon and the establishment of distinct monsoon regimes in East Asia.

Adaptive diversification is a product of both phylogenetic constraint and ecological opportunity. The species-rich parrotfish genera Scarus and Chlorurus display considerable variation in trophic cranial morphology, but these parrotfishes are often described as generalist herbivores. Recent work has suggested that parrotfish partition trophic resources at very fine spatial scales, raising the question of whether interspecific differences in cranial morphology reflect trophic partitioning. We tested this hypothesis by comparing targeted feeding substrata with a previously published dataset of nine cranial morphological traits. We sampled feeding substrata of 15 parrotfish species at Lizard Island, Great Barrier Reef, Australia, by following individuals until focused biting was observed, then extracting a bite core 22 mm in diameter. Three indices were parameterized for each bite core: substratum taphonomy, maximum turf height and cover of crustose coralline algae. Parrotfish species were spread along a single axis of variation in feeding substrata: successional status of the substratum taphonomy and epilithic and endolithic biota. This axis of trophic variation was significantly correlated with cranial morphology, indicating that morphological disparity within this clade is associated with interspecific partitioning of feeding substrata. Phylogenetic signal and phylomorphospace analyses revealed that the evolution of this clade involved a hitherto-unrecognized level of trophic diversification.

The biodiversity of the tropical Americas is a consequence of the interplay between geological and climatic events, with the Andean uplift being a major driver of speciation. Multiple studies have shown that species diversification promoted by the Andes can occur in the presence or absence of gene flow. However, to date, the majority of research addressing this aspect has been conducted in vertebrates, whereas other highly diverse tropical organisms such as arthropods remain uninvestigated. We used a combination of phylogenetics, population genetic analyses and species distribution models to explore whether the northern Andes played a role in the diversification of Ancylometes bogotensis. We detected two major lineages that are separated by the Eastern Cordillera of the Colombian Andes, and they share the same climatic niche. These groups diverged at ~3.85 Mya and exhibit no signatures of gene flow, which can be a consequence of the Andean highlands being poorly suited habitats for this species, thus preventing their genetic connectivity. Our study reveals that the genetic structure of an arachnid species that has limited dispersal capacity and is highly dependent on water bodies is shaped by the Andean orogeny. The generality of this observation remains to be assessed in other invertebrates.

Planetary boundary layer parametrization (PBL) is a key factor influencing weather forecast skills. This article provides a quantitative illustration of the segregation of forecast errors and their growth arising from different PBLs of the Weather Research and Forecasting (WRF) model. The systematic (root mean square) components of forecast errors arising from four different PBLs of the WRF over the state of Odisha (India) and its surrounding regions are elucidated. Error characterizations are carried out for the forecast lead time up to 96 h (day-4) for two contrasting monsoon seasons, i.e., 2013 (normal) and 2014 (deficit). A total of 1112 simulations are carried out for each initial condition, i.e., May 15 to September 29 for both monsoon seasons using four PBL schemes, i.e., Yonsei University (YSU), Mellor–Yamada–Nakanishi-Niino (MYNN), Asymmetric Convective Model version 2 (ACM2), and medium-range forecast (MRF). The overall results suggest the errors in thermodynamical variables (i.e., temperature and relative humidity) are large compared to the dynamical variable (i.e., wind). For the normal monsoon year (i.e., 2013), the MRF and MYNN exhibit the lowest root mean square error (RMSE) of temperature compared to ACM2 and YSU, whereas MRF (MYNN) shows the lowest (highest) error growth at 24–48 h (72–96 h). The deficit year (2014) has a higher temperature error compared to that of the normal monsoon year (2013), which might be due to frequent monsoon break periods. The spatial distribution of wind exhibits the lowest systematic error for MRF with lead time up to 48 h. The subsequent decrease (increase) of convergence (divergence) of error flux over northern Odisha and increase (decrease) of the same over southern Odisha suggests that the error propagation occurs from north to south. In general, both the convergence and divergence of error energy are found to be weak in MRF and MYNN, attributable to the lower error growth rate and hence the smaller systematic errors compared to ACM2 and YSU for both these monsoon seasons. It is also found that the systematic component of the linear (nonlinear) error growth rate is contributed by the physics (dynamics) components of the model. These findings will provide guidance for the model community and operational agencies to make an optimal choice of PBL parameterizations, particularly for the monsoon forecast.

Because sister species share a phenotypic axis, they hold morphological and ecological traits in common and, when sympatric, are ideal subjects for examining the extent of morphological divergence associated with the non-shared ecological parameters of the niche. Trematomus lepidorhinus and T. loennbergii have overlapping depth ranges of > 1000 m and occupy the deep shelf-upper slope niche in the waters of East Antarctica, an area where glacial troughs and their 1000-1500 m-deep landward basins (innershelf depressions) encompass 40% of the sea floor. The sense organ and brain divergence between the two species at the gross anatomical and histological levels involves differences in: number of olfactory lamellae, composition of the photoreceptor array and the number of retinal cells, size of the cephalic lateral line pores, and overall size of the brain and degree of development of different brain regions. Size and shape of the sagittal otoliths also differ. The morphology is unequivocally differentiating for habitat depths and conclusively documents a shift toward reliance on non-visual senses in T. loennbergii, consistent with collection data indicating this species lives at greater depths than T. lepidorhinus. Depths of peak abundances--200-500 m for T. lepidorhinus and 600-800 m for T. loennbergii--are the major differentiating parameter, with the ?300 m differential between the peaks providing considerable, although not absolute, habitat separation. This is also reflected in the greater absolute abundances of the shallower-living T. lepidorhinus in trawl catches. Only T. loennbergii is found near the floors of 1000-1500 m-deep innershelf depressions, a distinctive microhabitat on the high latitude shelf.

Walker circulations near East Africa are identified and their influence on the interannual variability of East African rainfall is explored in multiple reanalyses and observational precipitation datasets. The robustness of methodology for identifying 2-dimensional overturning circulations in a three-dimensional flow is investigated. Three Walker circulations with potential relevance to East African rainfall are identified, namely, the East African, the Congo Basin, and the Indian Ocean Walker circulations. Consistent anti-correlations across the reanalyses exist for the upward and downward branches of the Indian Ocean Walker Circulation during September–March, with strongest connections during October–December; they do not emerge for the other two Walker circulations. Less (more) precipitation occurs over East Africa in the short-rains season when the Indian Ocean Walker Circulation is anomalously strong (weak). These rainfall variations are associated with anomalous mid-level moisture divergence that primarily results from variations in wind divergence rather than atmospheric moisture. The anomalous horizontal advection of moist static energy can be important in modulating convection, but this argument is not conclusive considering the unclosed budget and the variations within the composites. The associations above do not indicate causality. Caution is advisable when using the concept of Walker circulations because a two-dimensional stream function can over-simplify the complexity of the three-dimensional circulation.

Differences in reproductive allocation of male and female fishes could lead to sexual divergence in nutritional requirements, trophic ecologies, and metabolisms that may be reflected in isotopic compositions. We compared muscle C:N ratio, δ13C, and δ15N between mature females and males for eight fish species from 21 North American populations. We also compared isotopic compositions between muscle and ova in a subset of females to determine if observed sex differences may be associated with fractionation during oogenesis. Muscle δ13C and δ15N did not vary greatly between males and females for most species but significant differences were observed in walleye (Sander vitreus) and burbot (Lota lota). Among-individual variation in isotopic composition, estimated as dispersion in δ13C–δ15N space, did not differ significantly between the sexes. Ova had significantly higher C:N ratio and lower δ13C than female muscle in all species with the greatest contrast between tissues seen in burbot. Ova had significantly higher δ15N than female muscle in most species with the greatest contrast between tissues in walleye. Sex-based divergence in isotopic composition of northern fishes is most evident in lean-fleshed piscivores, and may be related to selective mobilization of nutrients from soma to ovaries.

The paper gives the results of the first studies on the molecular divergence between native and non-native populations of Speonomus normandi hydrophilus (Jeannel, 1907). This species is endemic to Massif Arize in the Central Pyrenees (France), and represents highly specialised organisms that live underground. In 1982, one hundred specimens of S. normandi hydrophilus had been experimentally introduced into the Dzwonnica Cave (Poland). Since then, a numerous population has developed in the Towarna-Dzwonnica cave system, and the neighbouring Cabanowa Cave. After almost 40 years of isolation between native and non-native populations, the genetic variations were examined using the COI and 28S rDNA genes. Analyses of the haplotypes of 28S showed one common haplogroup, which confirms the origin of the Polish group. The differentiation of haplotypes for the COI marker was high for both the French and Polish populations. Altogether 18 haplotypes of this marker have been detected, 12 in the French population and 9 in the Polish. However, only a portion of the haplotypes is shared between the native and introduced population.

Ice-sheet mass-balance estimates derived from repeat satellite-altimetry observations require accurate calculation of spatiotemporal variability in firn-air content (FAC). However, firn-compaction models remain a large source of uncertainty within mass-balance estimates. In this study, we investigate one process that is neglected in FAC estimates derived from firn-compaction models: enhanced layer thinning due to horizontal divergence. We incorporate a layer-thinning scheme into the Community Firn Model. At every time step, firn layers first densify according to a firn-compaction model and then thin further due to an imposed horizontal divergence rate without additional density changes. We find that horizontal divergence on Thwaites (THW) and Pine Island Glaciers can reduce local FAC by up to 41% and 18%, respectively. We also assess the impact of temporal variability of horizontal divergence on FAC. We find a 15% decrease in FAC between 2007 and 2016 due to horizontal divergence at a location that is characteristic of lower THW. This decrease accounts for 16% of the observed surface lowering, whereas climate variability alone causes negligible changes in FAC at this location. Omitting transient horizontal divergence in estimates of FAC leads to an overestimation of ice loss via satellite-altimetry methods in regions of dynamic ice flow.

The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of

Pennatulaceans are an important component of benthic marine communities usually related to soft bottoms. Despite their important ecological role, as yet little is known about their origin and divergence time. The first attempts to establish phylogenetic relationships among genera date from the early 20th century, when only morphological characters were available. In the last decade, phylogenetic analyses based on mitochondrial DNA sequences from a selected number of species have proposed a different hypothetical ancestor for this group, but their intergeneric relationships remain obscure. The present study is based on a combination of mitochondrial and nuclear markers (mtMutS, Cox1 and 28S rDNA), adding new molecular information about the phylogenetic relationships among the pennatulacean genera, including 38 new sequences belonging to 13 different species. Some of the phylogenetic relationships inferred in the present study question the current classification of sea pens based on morphology (at different taxonomic levels), clearly indicating that the two main groups Sessiliflorae and Subselliflorae, some of their main families (e.g. Pennatulidae, Umbellulidae, Virgulariidae) and some genera (e.g. Umbellula, Veretillum) are non-monophyletic. In addition, the veretillids, traditionally considered the most primitive pennatulaceans, are not shown as the earliest-diverging taxon. Moreover, an analysis of divergence time performed here suggested that the origin of the pennatulaceans dates from the Lower Cretaceous (Berriasian, ~144 Ma), in agreement with their sparsely known fossil record, while the initial divergence of most extant genera occurred in the Oligocene and Miocene times. Los pennatuláceos son un componente importante de las comunidades bentónicas marinas generalmente relacio- nados con fondos blandos. A pesar de su importante papel ecológico, la información sobre su origen y tiempo de divergencia es aún escasa. Los primeros intentos de establecer relaciones filogenéticas entre géneros datan de principios del siglo XX, cuando sólo estaban disponibles caracteres morfológicos. En la última década, los análisis filogenéticos basados en secuen- cias de ADN mitocondrial procedentes de un limitado número de especies han propuesto un ancestro hipotético diferente para este grupo, pero sus relaciones intergenéricas permanecen oscuras. La presente investigación está basada en una combinación de marcadores mitocondriales y nuclear (mtMutS, Cox1 y ADNr 28S), aportando nueva información molecular sobre las relaciones filogenéticas entre los géneros de pennatuláceos, incluyendo 38 nuevas secuencias pertenecientes a 13 especies. Algunas de las relaciones filogenéticas inferidas en el presente estudio cuestionan la actual clasificación de las plumas de mar basada en la morfología (a diferentes niveles taxonómicos), indicando claramente que los dos grupos principales Sessiliflorae y Subselliflorae, algunas de sus principales familias (por ejemplo Pennatulidae, Umbellulidae, Virgulariidae) y algunos gé- neros (por ejemplo Umbellula, Veretillum) son no-monofiléticos. Asimismo, los veretílidos, tradicionalmente considerados los pennatuláceos más primitivos, no se muestran como el taxón divergente más antiguo. Además, un análisis del tiempo de divergencia realizado en este trabajo sugirió que el origen de los pennatuláceos data del Cretácico Inferior (Berriasiano, ~ 144 Ma), de acuerdo con su escasamente conocido registro fósil, mientras que la divergencia inicial de la mayoría de los géneros existentes ocurrió en tiempos del Oligoceno y Mioceno. LAMPOS, ANT XIX/5-REN2001-4929-E/ANT CLIMANT, ANT XXIII/8-POL2006-06399/CGL INDEMARES Cap de Creus, INDEMARES Alborán e INDEMARES Chica-LIFE07/NAT/E/000732 LIFE+ INDEMARES Comisión Nacional de Investigación Científica y Tecnológica de Chile. (CONICYT)-PCHA/Doctorado Nacional/2017–21170438 Ministerio de Economia, Industria y Competitividad de España. (MINECO)- CTM2017-83920-P (DIVERSICORAL)

BackgroundThe vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored.ResultsHere, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group.ConclusionsWe provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

Objectives Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. Materials and methods Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. Results C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. Discussion We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.

The mechanisms underlying the evolutionary adaptation of animals that transcend the ecological barrier separating the intertidal and supratidal zones of rocky shores are poorly understood. Different wetting frequencies in these zones in tropical regions (daily vs. seasonally, respectively) impose different physical stressors, which should drive phenotypic variation and ultimately speciation in the animals that inhabit them. We studied morphological, physiological and genetic variation in a tropical high-shore gastropod that transcends these zones [Echinolittorina malaccana (Philippi, 1847)]. Variation in melanization, shell features and evaporative water loss was linked to regular seawater wetting, frequent activity and feeding, and solar exposure in intertidal snails, and to inactivity and prolonged aestivation in the shade during continuous air exposure in supratidal snails. Despite selective pressure for phenotypic divergence, and reproductive isolation of the populations in either zone, their mitochondrial COI gene sequences confirmed that they represent a single species. Speciation in our study case is probably constrained by the limitation on activity, mating and reproduction of supratidal snails, such that their populations can only be sustained through intertidal pelagic larval recruitment. Comparisons with other studies suggest that supratidal speciation and specialization for life in this zone probably require moderation of the abiotic (desiccative) conditions, to facilitate greater activity and interaction of animals during air exposure.