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1.
Proc Biol Sci ; 287(1934): 20200941, 2020 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-32900317

RESUMO

Adaptive radiations (ARs) frequently show remarkable repeatability where single lineages undergo multiple independent episodes of AR in distant places and long-separate time points. Genetic variation generated through hybridization between distantly related lineages can promote AR. This mechanism, however, requires rare coincidence in space and time between a hybridization event and opening of ecological opportunity, because hybridization generates large genetic variation only locally and it will persist only for a short period. Hence, hybridization seems unlikely to explain recurrent AR in the same lineage. Contrary to these expectations, our evolutionary computer simulations demonstrate that admixture variation can geographically spread and persist for long periods if the hybrid population becomes separated into isolated sub-lineages. Subsequent secondary hybridization of some of these can reestablish genetic polymorphisms from the ancestral hybridization in places far from the birthplace of the hybrid clade and long after the ancestral hybridization event. Consequently, simulations revealed conditions where exceptional genetic variation, once generated through a rare hybridization event, can facilitate multiple ARs exploiting ecological opportunities available at distant points in time and space.


Assuntos
Especiação Genética , Hibridização Genética , Animais , Evolução Biológica , Filogenia , Reprodução
2.
Nat Commun ; 11(1): 4763, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32958765

RESUMO

Many animal species remain separate not because their individuals fail to produce viable hybrids but because they "choose" not to mate. However, we still know very little of the genetic mechanisms underlying changes in these mate preference behaviours. Heliconius butterflies display bright warning patterns, which they also use to recognize conspecifics. Here, we couple QTL for divergence in visual preference behaviours with population genomic and gene expression analyses of neural tissue (central brain, optic lobes and ommatidia) across development in two sympatric Heliconius species. Within a region containing 200 genes, we identify five genes that are strongly associated with divergent visual preferences. Three of these have previously been implicated in key components of neural signalling (specifically an ionotropic glutamate receptor and two regucalcins), and overall our candidates suggest shifts in behaviour involve changes in visual integration or processing. This would allow preference evolution without altering perception of the wider environment.


Assuntos
Borboletas/fisiologia , Genes de Insetos , Especiação Genética , Preferência de Acasalamento Animal , Percepção Visual/genética , Animais , Borboletas/genética , Feminino , Regulação da Expressão Gênica , Fluxo Gênico , Genes de Insetos/genética , Genoma de Inseto/genética , Masculino , Mutação , Locos de Características Quantitativas , Especificidade da Espécie , Simpatria , Asas de Animais
3.
Nat Commun ; 11(1): 4048, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873779

RESUMO

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.


Assuntos
Mudança Climática , Especiação Genética , Genoma Mitocondrial , Mastodontes/genética , Animais , DNA Antigo/análise , DNA Antigo/isolamento & purificação , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Feminino , Fósseis , Masculino , Filogeografia
4.
Nat Commun ; 11(1): 4468, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32901021

RESUMO

Speciation constrains the flow of genetic information between populations of sexually reproducing organisms. Gaining control over mechanisms of speciation would enable new strategies to manage wild populations of disease vectors, agricultural pests, and invasive species. Additionally, such control would provide safe biocontainment of transgenes and gene drives. Here, we demonstrate a general approach to create engineered genetic incompatibilities (EGIs) in the model insect Drosophila melanogaster. EGI couples a dominant lethal transgene with a recessive resistance allele. Strains homozygous for both elements are fertile and fecund when they mate with similarly engineered strains, but incompatible with wild-type strains that lack resistant alleles. EGI genotypes can also be tuned to cause hybrid lethality at different developmental life-stages. Further, we demonstrate that multiple orthogonal EGI strains of D. melanogaster can be engineered to be mutually incompatible with wild-type and with each other. EGI is a simple and robust approach in multiple sexually reproducing organisms.


Assuntos
Drosophila melanogaster/genética , Engenharia Genética/métodos , Especiação Genética , Animais , Animais Geneticamente Modificados , Cruzamentos Genéticos , Feminino , Genes de Insetos , Genes Letais , Genótipo , Hibridização Genética , Masculino , Modelos Genéticos , Transgenes
5.
PLoS One ; 15(8): e0237744, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32841246

RESUMO

Both the Mediterranean (MED) species of the Bemisia tabaci whitefly complex and the greenhouse whitefly (Trialeurodes vaporariorum, TV) are important agricultural pests. The two species of whiteflies differ in many aspects such as morphology, geographical distribution, host plant range, plant virus transmission, and resistance to insecticides. However, the molecular basis underlying their differences remains largely unknown. In this study, we analyzed the genetic divergences between the transcriptomes of MED and TV. In total, 2,944 pairs of orthologous genes were identified. The average identity of amino acid sequences between the two species is 93.6%. The average nonsynonymous (Ka) and synonymous (Ks) substitution rates and the ratio of Ka/Ks of the orthologous genes are 0.0389, 2.23 and 0.0204, respectively. The low average Ka/Ks ratio indicates that orthologous genes tend to be under strong purified selection. The most divergent gene classes are related to the metabolisms of xenobiotics, cofactors, vitamins and amino acids, and this divergence may underlie the different biological characteristics between the two species of whiteflies. Genes of differential expression between the two species are enriched in carbohydrate metabolism and regulation of autophagy. These findings provide molecular clues to uncover the biological and molecular differences between the two species of whiteflies.


Assuntos
Produção Agrícola , Genes de Insetos/genética , Especiação Genética , Hemípteros/genética , Proteínas de Insetos/genética , Sequência de Aminoácidos/genética , Substituição de Aminoácidos/genética , Aminoácidos/metabolismo , Animais , Hemípteros/metabolismo , Proteínas de Insetos/metabolismo , Resistência a Inseticidas/genética , Inseticidas/farmacologia , Região do Mediterrâneo , Anotação de Sequência Molecular , RNA-Seq , Homologia de Sequência de Aminoácidos , Especificidade da Espécie , Vitaminas/metabolismo , Xenobióticos/metabolismo
6.
Mol Ecol ; 29(16): 2954-2956, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32745299

RESUMO

In this issue of Molecular Ecology, Yamasaki et al. (2020) use genetic data from extensive sampling of Rhinogobius goby fish across the Ryukyu Archipelago in Japan to demonstrate the parallel speciation of a freshwater form from an ancestral amphidromous form. They then show that ecosystem size strongly predicts the probability of speciation between the two forms across islands. In doing so, this study connects population-level processes (microevolution) to broad-scale biodiversity patterns (macroevolution), an important but understudied link in evolutionary biology. Moving forward, we can build on this research to (a) more directly determine how geographic, ecological and historical factors influence the different stages of the speciation process, and (b) understand whether mechanisms inferred from insular radiations extend to those on continents, where both demographic histories and environmental regimes are likely more complex.


Assuntos
Ecossistema , Especiação Genética , Animais , Biodiversidade , Evolução Biológica , Água Doce , Japão , Probabilidade
7.
Proc Biol Sci ; 287(1931): 20201162, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32693723

RESUMO

The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional redundancy. However, current knowledge is based on short timescales and an understanding of how functional diversity responds to long-term biodiversity dynamics has been limited by the availability of deep-time, trait-based data. Here, we compile an exceptional trait dataset of fossil molluscs from a 23-million-year interval in the Caribbean Sea (34 011 records, 4422 species) and develop a novel Bayesian model of multi-trait-dependent diversification to reconstruct mollusc (i) diversity dynamics, (ii) changes in functional diversity, and (iii) extinction selectivity over the last 23 Myr. Our results identify high diversification between 23-5 Mya, leading to increases in both functional richness and redundancy. Conversely, over the last three million years, a period of high extinction rates resulted in the loss of 49% of species but only 3% of functional richness. Extinction rates were significantly higher in small, functionally redundant species suggesting that competition mediated the response of species to environmental change. Taken together, our results identify long-term diversification and selective extinction against redundant species that allowed functional diversity to grow over time, ultimately buffering the ecological functions of biological communities against extinction.


Assuntos
Biodiversidade , Extinção Biológica , Animais , Teorema de Bayes , Região do Caribe , Fósseis , Especiação Genética , Moluscos
8.
Nat Commun ; 11(1): 3333, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620894

RESUMO

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.


Assuntos
Biodiversidade , Especiação Genética , Variação Genética , Rosales/crescimento & desenvolvimento , Temperatura , Algoritmos , Evolução Biológica , Conservação dos Recursos Naturais/métodos , Geografia , Filogenia , Rosales/classificação , Rosales/genética , Especificidade da Espécie , Clima Tropical
9.
Nat Commun ; 11(1): 3375, 2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32632155

RESUMO

Hybridization can drive speciation. We examine the hypothesis that Castanea henryi var. omeiensis is an evolutionary lineage that originated from hybridization between two near-sympatric diploid taxa, C. henryi var. henryi and C. mollissima. We produce a high-quality genome assembly for mollissima and characterize evolutionary relationships among related chestnut taxa. Our results show that C. henryi var. omeiensis has a mosaic genome but has accumulated divergence in all 12 chromosomes. We observe positive correlation between admixture proportions and recombination rates across the genome. Candidate barrier genomic regions, which isolate var. henryi and mollissima, are re-assorted in the hybrid lineage. We further find that the putative barrier segments concentrate in genomic regions with less recombination, suggesting that interaction between natural selection and recombination shapes the evolution of hybrid genomes during hybrid speciation. This study highlights that reassortment of parental barriers is an important mechanism in generating biodiversity.


Assuntos
Diploide , Fagaceae/genética , Genoma de Planta/genética , Hibridização Genética , Mosaicismo , Ploidias , Algoritmos , Evolução Molecular , Fagaceae/classificação , Especiação Genética , Modelos Genéticos , Recombinação Genética , Seleção Genética , Especificidade da Espécie , Sequenciamento Completo do Genoma/métodos
10.
Proc Natl Acad Sci U S A ; 117(28): 16438-16447, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32601213

RESUMO

Chemosensory communication is essential to insect biology, playing indispensable roles during mate-finding, foraging, and oviposition behaviors. These traits are particularly important during speciation, where chemical perception may serve to establish species barriers. However, identifying genes associated with such complex behavioral traits remains a significant challenge. Through a combination of transcriptomic and genomic approaches, we characterize the genetic architecture of chemoperception and the role of chemosensing during speciation for a young species pair of Heliconius butterflies, Heliconius melpomene and Heliconius cydno We provide a detailed description of chemosensory gene-expression profiles as they relate to sensory tissue (antennae, legs, and mouthparts), sex (male and female), and life stage (unmated and mated female butterflies). Our results untangle the potential role of chemical communication in establishing barriers during speciation and identify strong candidate genes for mate and host plant choice behaviors. Of the 252 chemosensory genes, HmOBP20 (involved in volatile detection) and HmGr56 (a putative synephrine-related receptor) emerge as strong candidates for divergence in pheromone detection and host plant discrimination, respectively. These two genes are not physically linked to wing-color pattern loci or other genomic regions associated with visual mate preference. Altogether, our results provide evidence for chemosensory divergence between H. melpomene and H. cydno, two rarely hybridizing butterflies with distinct mate and host plant preferences, a finding that supports a polygenic architecture of species boundaries.


Assuntos
Borboletas/genética , Evolução Molecular , Especiação Genética , Proteínas de Insetos/genética , Animais , Borboletas/classificação , Borboletas/fisiologia , Quimiotaxia , Feminino , Proteínas de Insetos/metabolismo , Masculino , Fenótipo , Sensação
11.
PLoS One ; 15(6): e0234385, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603327

RESUMO

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.


Assuntos
Genoma Mitocondrial , Viverridae/genética , Animais , Ásia Sudeste , DNA Mitocondrial/genética , DNA Mitocondrial/história , Bases de Dados de Ácidos Nucleicos , Evolução Molecular , Extinção Biológica , Fósseis/história , Especiação Genética , História Antiga , Filogenia , Filogeografia , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da Espécie , Viverridae/classificação
12.
PLoS One ; 15(6): e0234437, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32511281

RESUMO

Gene flow and genetic variation were examined within and among populations of five of the most common spider species in shrublands of the mountainous Golden Gate Highlands National Park (GGHNP), South Africa. These species included three active hunters, Dendryphantes purcelli Peckham & Peckham, 1903 (Salticidae), Pherecydes tuberculatus O.P.-Cambridge, 1883 (Thomisidae) and Philodromus browningi Lawrence, 1952 (Philodromidae), and two web-builders, Neoscona subfusca (C.L. Koch, 1837) (Araneidae) and a Theridion Walckenaer, 1802 species (Theridiidae). A total of 249 spiders (57 D. purcelli, 69 N. subfusca, 34 P. browningi, 56 P. tuberculatus and 33 Theridion sp.) were collected and analysed from six shrubland localities in the park. Analyses of sequence variation of the mitochondrial cytochrome oxidase c subunit I (COI) gene for each species revealed relatively low nucleotide diversity (π < 0.0420) but high genetic diversity (Hd > 0.6500) within populations for all species, except P. tuberculatus. Genetic differentiation was also noted to differ between species, with only P. tuberculatus indicating very large divergence (Fst > 0.2500). These results were reflected by gene flow, with D. purcelli, N. subfusca and the Theridion sp. estimated as experiencing more than one disperser per generation. Overall, highest gene flow was found in the two web-building species, indicating possible high dispersal ability of these spiders in the GGHNP. Additionally, constructed phylogenies indicated possible cryptic speciation occurring in the majority of the investigated species. Our current results indicate that the five investigated spider species were able to maintain gene flow between shrubland populations within the GGHNP to some degree, despite the mountainous landscape. However, further analyses incorporating additional molecular markers are needed to properly determine the extent of genetic diversity and gene flow of these species within the GGHNP.


Assuntos
Genes de Insetos/genética , Especiação Genética , Variação Genética , Aranhas/genética , Animais , DNA Mitocondrial/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Comportamento Alimentar , Fluxo Gênico , Pradaria , Proteínas de Insetos/genética , Filogenia , África do Sul
13.
Gene ; 756: 144915, 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-32580009

RESUMO

Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) are key enzymes in the process of phosphatidylinositol signaling pathway and have essential functions in growth, development, and biotic and abiotic stresses responses in plants. However, the evolutionary history and patterns of PIP5K genes in plants have not been examined systematically. Here, we use whole-genome sequences from eight plant species of land plants and algae to define the evolutionary relationships between these proteins in plants. 85 PIP5K genes were identified and divided into two subfamilies based on phylogenetic analyses. PIP5K members in subfamily II underwent several duplication events in land plants, resulting in multiple gene copies in angiosperms, while PIP5K members in subfamily I displayed low-copy numbers and lost in eudicots. Furthermore, PIP5K genes within the same subfamily had similar motifs and intron/exon features. Nine duplicated soybean gene pairs, four duplicated Arabidopsis gene pairs and two rice duplicated gene pairs were identified and many of them localized in synteny genomic regions. These duplicate events were formed by Whole-genome duplication (WGD)/segmental duplications. In addition, the ratios of non-synonymous to synonymous substitutions (Ka/Ks) showed that the PIP5K family had undergone purifying selection in higher plants. Expression analysis showed that PIP5K genes had complex and variable expression patterns in different developmental stages. The specificity of these genes is utilized to provide evidence for selective expression in the evolutionary process.


Assuntos
Fosfotransferases (Aceptor do Grupo Álcool)/genética , Plantas/enzimologia , Cromossomos de Plantas , Evolução Molecular , Duplicação Gênica , Especiação Genética , Genoma de Planta , Filogenia , Plantas/classificação , Plantas/genética
14.
Mol Ecol ; 29(12): 2129-2132, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32392379

RESUMO

One of the main goals of evolutionary biology is to understand the processes behind current patterns of biodiversity. Shared geographic distributions among unrelated species may result from a common history, providing a unique opportunity to assess the evolution of the landscape and the origins of biodiversity. Until recently, vicariance prevailed as the main evolutionary model to be tested, and the riverine barrier hypothesis the null model for taxa with river-bounded distributions. In recent years, however, multispecies comparative approaches have unveiled idiosyncratic scenarios among codistributed species, suggesting that rivers may or may not play a role in the speciation process. In a From the Cover article in this issue of Molecular Ecology, Kopuchian et al. (2020) explore predictions of the riverine barrier hypothesis in a major subtropical river system, evaluating the degree of mitochondrial and nuclear genomic differentiation in seven bird species with allegedly morphological differentiation across the Paraná-Paraguay river system. The authors show that in only one case, the genetic differentiation was concordant with the river. Interestingly, pairs presented disparate divergence times and/or distinct demographic histories. In most cases, putative contact zones broadly coincided with the transition of different ecoregions, such as the Espinal/Chaco ecological ecotone. These findings argue against the role of the Paraná-Paraguay river system as a major biogeographic barrier and highlight the need to explore the role of ecology in species diversification. Here, we feature different perspectives for studying the processes governing species divergence and suggest a basic protocol to advance the study of riverine barriers.


Assuntos
Especiação Genética , Rios , Animais , Biodiversidade , Aves , Filogenia
15.
PLoS One ; 15(5): e0233597, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32453786

RESUMO

While biodiversity hotspots are typically identified on the basis of species number per unit area, their exceptional richness is often attributed, either implicitly or explicitly, to high diversification rates. High species concentrations, however, need not reflect rapid diversification, with the diversity of some hotspots accumulating at modest rates over long timespans. Here we explore the relationship between diversification in time vs. diversification in space and develop the concept of diversification density to describe the spatial scale of species accumulation in a clade. We investigate how plant height is associated with both aspects of diversification in Alooideae, a large plant subfamily with its center of diversity in the Greater Cape Floristic Region. We first reconstruct a time-calibrated phylogeny for Alooideae and demonstrate an evolutionary tendency towards reduced plant height. While plant height does not correlate with diversification rate across Alooideae it does so with diversification per unit space: clades of small plants tend to have the highest diversification densities. Furthermore, we find that diversification in time vs. space are uncorrelated. Our results show that diversification rate and density can be decoupled, and suggest that while some biodiversity hotspots might have been generated by high diversification rates, others are the product of high diversification density.


Assuntos
Biodiversidade , Evolução Biológica , Plantas/genética , Traqueófitas/genética , Especiação Genética , Filogenia , Plantas/classificação , Traqueófitas/classificação
16.
PLoS Genet ; 16(5): e1008769, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32392206

RESUMO

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.


Assuntos
Anuros/classificação , Anuros/genética , Poliploidia , Sequenciamento Completo do Exoma/métodos , Animais , Austrália , Ecossistema , Evolução Molecular , Fluxo Gênico , Especiação Genética , Filogenia , Simpatria
17.
PLoS One ; 15(5): e0232029, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32374732

RESUMO

BACKGROUND: Translationally controlled tumor protein (TCTP) is a conserved, multifunctional protein involved in numerous cellular processes in eukaryotes. Although the functions of TCTP have been investigated sporadically in animals, invertebrates, and plants, few lineage-specific activities of this molecule, have been reported. An exception is in Arabidopsis thaliana, in which TCTP (AtTCTP1) functions in stomatal closuer by regulating microtubule stability. Further, although the development of next-generation sequencing technologies has facilitated the analysis of many eukaryotic genomes in public databases, inter-kingdom comparative analyses using available genome information are comparatively scarce. METHODOLOGY: To carry out inter-kingdom comparative analysis of TCTP, TCTP genes were identified from 377 species. Then phylogenetic analysis, prediction of protein structure, molecular docking simulation and molecular dynamics analysis were performed to investigate the evolution of TCTP genes and their binding proteins. RESULTS: A total of 533 TCTP genes were identified from 377 eukaryotic species, including protozoa, fungi, invertebrates, vertebrates, and plants. Phylogenetic and secondary structure analyses reveal lineage-specific evolution of TCTP, and inter-kingdom comparisons highlight the lineage-specific emergence of, or changes in, secondary structure elements in TCTP proteins from different kingdoms. Furthermore, secondary structure comparisons between TCTP proteins within each kingdom, combined with measurements of the degree of sequence conservation, suggest that TCTP genes have evolved to conserve protein secondary structures in a lineage-specific manner. Additional tertiary structure analysis of TCTP-binding proteins and their interacting partners and docking simulations between these proteins further imply that TCTP gene variation may influence the tertiary structures of TCTP-binding proteins in a lineage-specific manner. CONCLUSIONS: Our analysis suggests that TCTP has undergone lineage-specific evolution and that structural changes in TCTP proteins may correlate with the tertiary structure of TCTP-binding proteins and their binding partners in a lineage-specific manner.


Assuntos
Biomarcadores Tumorais/genética , Biomarcadores Tumorais/fisiologia , Evolução Molecular , Especiação Genética , Sequência de Aminoácidos , Animais , Biomarcadores Tumorais/química , Sequência Conservada , Células Eucarióticas/classificação , Células Eucarióticas/metabolismo , Fungos/classificação , Fungos/genética , Humanos , Invertebrados/classificação , Invertebrados/genética , Mamíferos/classificação , Mamíferos/genética , Simulação de Acoplamento Molecular , Filogenia , Células Vegetais/classificação , Células Vegetais/metabolismo , Células Procarióticas/classificação , Células Procarióticas/metabolismo , Ligação Proteica , Estrutura Secundária de Proteína , Especificidade da Espécie
18.
Nat Commun ; 11(1): 2669, 2020 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-32472063

RESUMO

Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish diversification is strongly associated with species' trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent diversification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish diversification.


Assuntos
Biodiversidade , Evolução Biológica , Peixes/classificação , Especiação Genética , Animais , Coevolução Biológica , Tamanho Corporal , Recifes de Corais , Peixes/genética , Geografia , Herbivoria , Filogenia
19.
Am Nat ; 195(5): 899-917, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32364786

RESUMO

Is speciation generally a "special time" in morphological evolution, or are lineage-splitting events just "more of the same" where the end product happens to be two separate lineages? Data on evolutionary dynamics during anagenetic and cladogenetic events among closely related lineages within a clade are rare, but the fossil record of the bryozoan genus Metrarabdotos is considered a textbook example of a clade where speciation causes rapid evolutionary change against a backdrop of morphological stasis within lineages. Here, we point to some methodological and measurement theoretical issues in the original work on Metrarabdotos. We then reanalyze a subset of the original data that can be meaningfully investigated using quantitative statistical approaches similar to those used in the original studies. We consistently fail to find variation in the evolutionary process during within-lineage evolution compared with cladogenetic events: the rates of evolution, the strength of selection, and the directions traveled in multivariate morphospace are not different when comparing evolution within lineages and at speciation events in Metrarabdotos, and genetic drift cannot be excluded as a sufficient explanation for the morphological differentiation within lineages and during speciation. Although widely considered the best example of a punctuated mode of evolution, morphological divergence and speciation are not linked in Metrarabdotos.


Assuntos
Evolução Biológica , Briozoários/anatomia & histologia , Animais , Fósseis/anatomia & histologia , Especiação Genética , Seleção Genética
20.
Trends Ecol Evol ; 35(6): 512-522, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32396818

RESUMO

Recent biological analyses suggest that reductions in dispersal ability have been key drivers of diversification across numerous lineages. We synthesise emerging data to highlight similarities regarding the causes and consequences of dispersal reduction across taxa and ecosystems, as well as the diverse genomic mechanisms underpinning these shifts. Natural selection has acted on standing genetic variation within taxa to drive often rapid - and in some cases parallel - losses of dispersal, and ultimately speciation. Such shifts can thus represent an important nexus between adaptive and neutral diversification processes, with substantial evolutionary consequences. Recognition of the links between these concepts that are emerging from different fields, taxa and ecosystems is transforming our understanding of the fascinating role of dispersal reduction in the formation of biodiversity.


Assuntos
Evolução Biológica , Ecossistema , Biodiversidade , Especiação Genética , Genômica , Filogenia
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