BMC Evolutionary Biology[JOURNAL]
Sun
200 papers
New haplochromine cichlid from the upper Miocene (9-10 MYA) of Central Kenya.
Altner M, Ruthensteiner B, Reichenbacher B
BMC Evol Biol · 2020 Jun · PMID 32503417 · Full text
BACKGROUND: The diversification process known as the Lake Tanganyika Radiation has given rise to the most speciose clade of African cichlids. Almost all cichlid species found in the lakes Tanganyika, Malawi and Victoria,...
BACKGROUND: The diversification process known as the Lake Tanganyika Radiation has given rise to the most speciose clade of African cichlids. Almost all cichlid species found in the lakes Tanganyika, Malawi and Victoria, comprising a total of 12-16 tribes, belong to this clade. Strikingly, all the species in the latter two lakes are members of the tribe Haplochromini, whose origin remains unclear. The 'out of Tanganyika' hypothesis argues that the Haplochromini emerged simultaneously with other cichlid tribes and lineages in Lake Tanganyika, presumably about 5-6 million years ago (MYA), and that their presence in the lakes Malawi and Victoria and elsewhere in Africa today is due to later migrations. In contrast, the 'melting pot Tanganyika hypothesis' postulates that Haplochromini emerged in Africa prior to the formation of Lake Tanganyika, and that their divergence could have begun about 17 MYA. Haplochromine fossils could potentially resolve this debate, but such fossils are extremely rare. RESULTS: Here we present a new fossil haplochromine from the upper Miocene site Waril (9-10 million years) in Central Kenya. Comparative morphology, supported by Micro-CT imaging, reveals that it bears a unique combination of characters relating to dentition, cranial bones, caudal skeleton and meristic traits. Its most prominent feature is the presence of exclusively unicuspid teeth, with canines in the outer tooth row. †Warilochromis unicuspidatus gen. et sp. nov. shares this combination of characters solely with members of the Haplochromini and its lacrimal morphology indicates a possible relation to the riverine genus Pseudocrenilabrus. Due to its fang-like dentition and non-fusiform body, †W. unicuspidatus gen. et sp. nov. might have employed either a sit-and-pursue or sit-and-wait hunting strategy, which has not been reported for any other fossil haplochromine cichlid. CONCLUSIONS: The age of the fossil (9-10 MYA) is incompatible with the 'out of Tanganyika' hypothesis, which postulates that the divergence of the Haplochromini began only 5-6 MYA. The presence of this fossil in an upper Miocene palaeolake in the Central Kenya Rift, as well as its predatory lifestyle, indicate that Haplochromini were already an important component of freshwater drainages in East Africa at that time.
An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola).
Vasilikopoulos A, Misof B, Meusemann K … +20 more , Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U
BMC Evol Biol · 2020 Jun · PMID 32493355 · Full text
BACKGROUND: The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has b...
BACKGROUND: The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS: Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION: Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
Computed tomography sheds new light on the affinities of the enigmatic euarthropod Jianshania furcatus from the early Cambrian Chengjiang biota.
Liu Y, Ortega-Hernández J, Chen H … +3 more , Mai H, Zhai D, Hou X
BMC Evol Biol · 2020 Jun · PMID 32487135 · Full text
BACKGROUND: The Chengjiang biota is one of the most species-rich Cambrian Konservat-Lagerstätten, and preserves a community dominated by non-biomineralized euarthropods. However, several Chengjiang euarthropods have an u...
BACKGROUND: The Chengjiang biota is one of the most species-rich Cambrian Konservat-Lagerstätten, and preserves a community dominated by non-biomineralized euarthropods. However, several Chengjiang euarthropods have an unfamiliar morphology, are extremely rare, or incompletely preserved. RESULTS: We employed micro-computed tomography to restudy the enigmatic euarthropod Jianshania furcatus. We reveal new morphological details, and demonstrate that the specimens assigned to this species represent two different taxa. The holotype of J. furcatus features a head shield with paired anterolateral notches, stalked lateral eyes, and an articulated tailspine with a bifurcate termination. The other specimen is formally redescribed as Xiaocaris luoi gen. et sp. nov., and is characterized by stalked eyes connected to an anterior sclerite, a subtrapezoidal head shield covering three small segments with reduced tergites, a trunk with 15 overlapping tergites with a well-developed dorsal keel, and paired tail flukes. CONCLUSIONS: The presence of antennae, biramous appendages with endopods composed of 15 articles, and multiple appendage pairs associated with the trunk tergites identify X. luoi nov. as a representative of Fuxianhuiida, an early branching group of stem-group euarthropods endemic to the early Cambrian of Southwest China. X. luoi nov. represents the fifth fuxianhuiid species described from the Chengjiang biota, and its functional morphology illuminates the ecological diversity of this important clade for understanding the early evolutionary history of euarthropods.
The green-brown polymorphism of the club-legged grasshopper Gomphocerus sibiricus is heritable and appears genetically simple.
Schielzeth H, Dieker P
BMC Evol Biol · 2020 Jun · PMID 32487064 · Full text
BACKGROUND: Local coexistence of distinct, genetically determined color morphs can be unstable and transitional. Stable, long-term coexistence requires some form of balancing selection to protect morphs from getting lost...
BACKGROUND: Local coexistence of distinct, genetically determined color morphs can be unstable and transitional. Stable, long-term coexistence requires some form of balancing selection to protect morphs from getting lost by directional selection or genetic drift. However, not all phenotypic polymorphism need to have a genetic basis. We here report on the genetic basis of two color polymorphisms in the club-legged grasshopper Gomphocerus sibiricus: a green-brown polymorphism that is phylogenetically and geographically widespread among orthopteran insects and a pied-brown pattern polymorphism that is shared among many gomphocerine grasshoppers. RESULTS: We found a remarkably clear outcome of matings within and between morph that suggest not only that the green-brown polymorphism is heritable in this species, but that results can be most parsimoniously explained by a single autosomal locus with two alleles in which the green allele is dominant over the brown allele. A few individuals did not match this pattern and suggest the existence of genetic modifiers and/or developmental phenocopies. We also show that the pied-brown polymorphism is highly heritable, although the evidence for the involvement of one or more loci is less clear-cut. CONCLUSIONS: Overall, our data demonstrate that the two polymorphisms are heritable in the club-legged grasshopper and appear genetically simple, at least with respect to green morphs. The results are consistent with the idea that the synthesis or transport of a pigment involved in the production of green coloration (likely biliverdin) is lost by homozygosity for loss-of-function alleles in brown individuals. The apparently simple genetic architecture of the green-brown polymorphism offer potential for studying balancing selection in the field and for genetic mapping in this species.
Hybridization and introgression between Helicoverpa armigera and H. zea: an adaptational bridge.
Cordeiro EMG, Pantoja-Gomez LM, de Paiva JB … +4 more , Nascimento ARB, Omoto C, Michel AP, Correa AS
BMC Evol Biol · 2020 May · PMID 32450817 · Full text
BACKGROUND: Invasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native...
BACKGROUND: Invasion of organisms into new ecosystems is increasingly common, due to the global trade in commodities. One of the most complex post-invasion scenarios occurs when an invasive species is related to a native pest, and even more so when they can hybridize and produce fertile progeny. The global pest Helicoverpa armigera was first detected in Brazil in 2013 and generated a wave of speculations about the possibility of hybridization with the native sister taxon Helicoverpa zea. In the present study, we used genome-wide single nucleotide polymorphisms from field-collected individuals to estimate hybridization between H. armigera and H. zea in different Brazilian agricultural landscapes. RESULTS: The frequency of hybridization varied from 15 to 30% depending on the statistical analyses. These methods showed more congruence in estimating that hybrids contained approximately 10% mixed ancestry (i.e. introgression) from either species. Hybridization also varied considerably depending on the geographic locations where the sample was collected, forming a 'mosaic' hybrid zone where introgression may be facilitated by environmental and landscape variables. Both landscape composition and bioclimatic variables indicated that maize and soybean cropland are the main factors responsible for high levels of introgression in agricultural landscapes. The impact of multiple H. armigera incursions is reflected in the structured and inbred pattern of genetic diversity. CONCLUSIONS: Our data showed that the landscape composition and bioclimatic variables influence the introgression rate between H. armigera and H. zea in agricultural areas. Continuous monitoring of the hybridization process in the field is necessary, since agricultural expansion, climatic fluctuations, changing composition of crop species and varieties, and dynamic planting seasons are some factors in South America that could cause a sudden alteration in the introgression rate between Helicoverpa species. Introgression between invasive and native pests can dramatically impact the evolution of host ranges and resistance management.
The puzzling mitochondrial phylogeography of the black soldier fly (Hermetia illucens), the commercially most important insect protein species.
Ståhls G, Meier R, Sandrock C … +14 more , Hauser M, Šašić Zorić L, Laiho E, Aracil A, Doderović J, Badenhorst R, Unadirekkul P, Mohd Adom NAB, Wein L, Richards C, Tomberlin JK, Rojo S, Veselić S, Parviainen T
BMC Evol Biol · 2020 May · PMID 32448128 · Full text
BACKGROUND: The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying e...
BACKGROUND: The black soldier fly (Diptera: Stratiomyidae, Hermetia illucens) is renowned for its bioconversion ability of organic matter, and is the worldwide most widely used source of insect protein. Despite varying extensively in morphology, it is widely assumed that all black soldier flies belong to the same species, Hermetia illucens. We here screened about 600 field-collected and cultured flies from 39 countries and six biogeographic regions to test this assumption based on data for three genes (mitochondrial COI, nuclear ITS2 & 28S rDNA) and in order to gain insights into the phylogeography of the species. RESULTS: Our study reveals a surprisingly high level of intraspecific genetic diversity for the mitochondrial barcoding gene COI (divergences up to 4.9%). This level of variability is often associated with the presence of multiple species, but tested nuclear markers (ITS2 and 28S rDNA) were invariant and fly strain hybridization experiments under laboratory conditions revealed reproductive compatibility. COI haplotype diversity is not only very high in all biogeographic regions (56 distinct haplotypes in total), but also in breeding facilities and research centers from six continents (10 haplotypes: divergences up to 4.3%). The high genetic diversity in fly-breeding facilities is mostly likely due to many independent acquisitions of cultures via sharing and/or establishing new colonies from field-collected flies. However, explaining some of the observed diversity in several biogeographic regions is difficult given that the origin of the species is considered to be New World (32 distinct haplotypes) and one would expect severely reduced genetic diversity in the putatively non-native populations in the remaining biogeographic regions. However, distinct, private haplotypes are known from the Australasian (N = 1), Oriental (N = 4), and the Eastern Palearctic (N = 4) populations. We reviewed museum specimen records and conclude that the evidence for introductions is strong for the Western Palearctic and Afrotropical regions which lack distinct, private haplotypes. CONCLUSIONS: Based on the results of this paper, we urge the black soldier fly community to apply molecular characterization (genotyping) of the fly strains used in artificial fly-breeding and share these data in research publications as well as when sharing cultures. In addition, fast-evolving nuclear markers should be used to reconstruct the recent invasion history of the species.
Aligning functional network constraint to evolutionary outcomes.
Wollenberg Valero KC
BMC Evol Biol · 2020 May · PMID 32448114 · Full text
BACKGROUND: Functional constraint through genomic architecture is suggested to be an important dimension of genome evolution, but quantitative evidence for this idea is rare. In this contribution, existing evidence and d...
BACKGROUND: Functional constraint through genomic architecture is suggested to be an important dimension of genome evolution, but quantitative evidence for this idea is rare. In this contribution, existing evidence and discussions on genomic architecture as constraint for convergent evolution, rapid adaptation, and genic adaptation are summarized into alternative, testable hypotheses. Network architecture statistics from protein-protein interaction networks are then used to calculate differences in evolutionary outcomes on the example of genomic evolution in yeast, and the results are used to evaluate statistical support for these longstanding hypotheses. RESULTS: A discriminant function analysis lent statistical support to classifying the yeast interactome into hub, intermediate and peripheral nodes based on network neighborhood connectivity, betweenness centrality, and average shortest path length. Quantitative support for the existence of genomic architecture as a mechanistic basis for evolutionary constraint is then revealed through utilizing these statistical parameters of the protein-protein interaction network in combination with estimators of protein evolution. CONCLUSIONS: As functional genetic networks are becoming increasingly available, it will now be possible to evaluate functional genetic network constraint against variables describing complex phenotypes and environments, for better understanding of commonly observed deterministic patterns of evolution in non-model organisms. The hypothesis framework and methodological approach outlined herein may help to quantify the extrinsic versus intrinsic dimensions of evolutionary constraint, and result in a better understanding of how fast, effectively, or deterministically organisms adapt.
The features of polyglutamine regions depend on their evolutionary stability.
Mier P, Andrade-Navarro MA
BMC Evol Biol · 2020 May · PMID 32448113 · Full text
BACKGROUND: Polyglutamine regions (polyQ) are one of the most studied and prevalent homorepeats in eukaryotes. They have a particular length-dependent codon usage, which relates to a characteristic CAG-slippage mechanism...
BACKGROUND: Polyglutamine regions (polyQ) are one of the most studied and prevalent homorepeats in eukaryotes. They have a particular length-dependent codon usage, which relates to a characteristic CAG-slippage mechanism. Pathologically expanded tracts of polyQ are known to form aggregates and are involved in the development of several human neurodegenerative diseases. The non-pathogenic function of polyQ is to mediate protein-protein interactions via a coiled-coil pairing with an interactor. They are usually located in a helical context. RESULTS: Here we study the stability of polyQ regions in evolution, using a set of 60 proteomes from four distinct taxonomic groups (Insecta, Teleostei, Sauria and Mammalia). The polyQ regions can be distinctly grouped in three categories based on their evolutionary stability: stable, unstable by length variation (inserted), and unstable by mutations (mutated). PolyQ regions in these categories can be significantly distinguished by their glutamine codon usage, and we show that the CAG-slippage mechanism is predominant in inserted polyQ of Sauria and Mammalia. The polyQ amino acid context is also influenced by the polyQ stability, with a higher proportion of proline residues around inserted polyQ. By studying the secondary structure of the sequences surrounding polyQ regions, we found that regarding the structural conformation around a polyQ, its stability category is more relevant than its taxonomic information. The protein-protein interaction capacity of a polyQ is also affected by its stability, as stable polyQ have more interactors than unstable polyQ. CONCLUSIONS: Our results show that apart from the sequence of a polyQ, information about its orthologous sequences is needed to assess its function. Codon usage, amino acid context, structural conformation and the protein-protein interaction capacity of polyQ from all studied taxa critically depend on the region stability. There are however some taxa-specific polyQ features that override this importance. We conclude that a taxa-driven evolutionary analysis is of the highest importance for the comprehensive study of any feature of polyglutamine regions.
MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects.
Chang H, Nie Y, Zhang N … +5 more , Zhang X, Sun H, Mao Y, Qiu Z, Huang Y
BMC Evol Biol · 2020 May · PMID 32429841 · Full text
BACKGROUND: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial...
BACKGROUND: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthoptera-specific mitochondrial amino acid empirical model. RESULTS: We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data. CONCLUSIONS: The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.
The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene.
Linnenbrink M, Ullrich KK, McConnell E … +1 more , Tautz D
BMC Evol Biol · 2020 May · PMID 32414322 · Full text
BACKGROUND: Amylase gene clusters have been implicated in adaptive copy number changes in response to the amount of starch in the diet of humans and mammals. However, this interpretation has been questioned for humans an...
BACKGROUND: Amylase gene clusters have been implicated in adaptive copy number changes in response to the amount of starch in the diet of humans and mammals. However, this interpretation has been questioned for humans and for mammals there is a paucity of information from natural populations. RESULTS: Using optical mapping and genome read information, we show here that the amylase cluster in natural house mouse populations is indeed copy-number variable for Amy2b paralogous gene copies (called Amy2a1 - Amy2a5), but a direct connection to starch diet is not evident. However, we find that the amylase cluster was subject to introgression of haplotypes between Mus musculus sub-species. A very recent introgression can be traced in the Western European populations and this leads also to the rescue of an Amy2b pseudogene. Some populations and inbred lines derived from the Western house mouse (Mus musculus domesticus) harbor a copy of the pancreatic amylase (Amy2b) with a stop codon in the first exon, making it non-functional. But populations in France harbor a haplotype introgressed from the Eastern house mouse (M. m. musculus) with an intact reading frame. Detailed analysis of phylogenetic patterns along the amylase cluster suggest an additional history of previous introgressions. CONCLUSIONS: Our results show that the amylase gene cluster is a hotspot of introgression in the mouse genome, making it an evolutionary active region beyond the previously observed copy number changes.
Improving the performance of Bayesian phylogenetic inference under relaxed clock models.
Zhang R, Drummond A
BMC Evol Biol · 2020 May · PMID 32410614 · Full text
BACKGROUND: Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phyl...
BACKGROUND: Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. RESULTS: This paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software. CONCLUSIONS: The results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude.
The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans.
da Cruz I, Brochier-Armanet C, Benavente R
BMC Evol Biol · 2020 May · PMID 32408858 · Full text
BACKGROUND: Meiosis is essential for sexual reproduction and generates genetically diverse haploid gametes from a diploid germ cell. Reduction of ploidy depends on active chromosome movements during early meiotic prophas...
BACKGROUND: Meiosis is essential for sexual reproduction and generates genetically diverse haploid gametes from a diploid germ cell. Reduction of ploidy depends on active chromosome movements during early meiotic prophase I. Chromosome movements require telomere attachment to the nuclear envelope. This attachment is mediated by telomere adaptor proteins. Telomere adaptor proteins have to date been identified in fission yeast and mice. In the mouse, they form a complex composed of the meiotic proteins TERB1, TERB2, and MAJIN. No sequence similarity was observed between these three mouse proteins and the adaptor proteins of fission yeast, raising the question of the evolutionary history and significance of this specific protein complex. RESULT: Here, we show the TERB1, TERB2, and MAJIN proteins are found throughout the Metazoa and even in early-branching non-bilateral phyla such as Cnidaria, Placozoa and Porifera. Metazoan TERB1, TERB2, and MAJIN showed comparable domain architecture across all clades. Furthermore, the protein domains involved in the formation of the complex as well as those involved for the interaction with the telomere shelterin protein and the LINC complexes revealed high sequence similarity. Finally, gene expression in the cnidarian Hydra vulgaris provided evidence that the TERB1-TERB2-MAJIN complex is selectively expressed in the germ line. CONCLUSION: Our results indicate that the TERB1-TERB2-MAJIN complex has an ancient origin in metazoans, suggesting conservation of meiotic functions.
A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination.
Pang TY
BMC Evol Biol · 2020 May · PMID 32381044 · Full text
BACKGROUND: A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position...
BACKGROUND: A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer the genome tree, and require that a substantial portion of each genome has not been affected by recombination, a sometimes unrealistic assumption. METHODS: Here, we propose a Coarse-Graining approach for Phylogenetic reconstruction (CGP), which is recombination-aware but forgoes ARG reconstruction. It accounts for the tendency of a higher effective recombination rate between genomes with a lower phylogenetic distance. It is applicable even if all genomic regions have experienced substantial amounts of recombination, and can be used on both nucleotide and amino acid sequences. CGP considers the local density of substitutions along pairwise genome alignments, fitting a model to the empirical distribution of substitution density to infer the pairwise coalescent time. Given all pairwise coalescent times, CGP reconstructs an ultrametric tree representing vertical inheritance. RESULTS: Based on simulations, we show that the proposed approach can reconstruct ultrametric trees with accurate topology, branch lengths, and root positioning. Applied to a set of E. coli strains, the reconstructed trees are most consistent with gene distributions when inferred from amino acid sequences, a data type that cannot be utilized by many alternative approaches. CONCLUSIONS: The CGP algorithm is more accurate than alternative recombination-aware methods for ultrametric phylogenetic reconstructions.
A life-history perspective on sexual selection in a polygamous species.
Gao K, van Wijk M, Clement Z … +2 more , Egas M, Groot AT
BMC Evol Biol · 2020 May · PMID 32380947 · Full text
BACKGROUND: Ever since Darwin, evolutionary biologists have studied sexual selection driving differences in appearance and behaviour between males and females. An unchallenged paradigm in such studies is that one sex (us...
BACKGROUND: Ever since Darwin, evolutionary biologists have studied sexual selection driving differences in appearance and behaviour between males and females. An unchallenged paradigm in such studies is that one sex (usually the male) signals its quality as a mate to the other sex (usually the female), who is choosy in accepting a partner. Here, we hypothesize that in polygamous species these roles change dynamically with the mating status of males and females, depending on direct reproductive costs and benefits of multiple matings, and on sperm competition. We test this hypothesis by assessing fitness costs and benefits of multiple matings in both males and females in a polygamous moth species, as in moths not males but females are the signalers and males are the responders. RESULTS: We found that multiple matings confer fitness costs and benefits for both sexes. Specifically, the number of matings did not affect the longevity of males or females, but only 67% of the males and 14% of the females mated successfully in all five nights. In addition, the female's reproductive output increased with multiple matings, although when paired with a new virgin male every night, more than 3 matings decreased her reproductive output, so that the Bateman gradient for females fit a quadratic model better than a linear model. The male's reproductive success was positively affected by the number of matings and a linear regression line best fit the data. Simulations of the effect of sperm competition showed that increasing last-male paternity increases the steepness of the male Bateman gradient and thus the male's relative fitness gain from additional mating. Irrespective of last-male paternity value, the female Bateman gradient is steeper than the male one for up to three matings. CONCLUSION: Our results suggest that choosiness in moths may well change throughout the mating season, with males being more choosy early in the season and females being more choosy after having mated at least three times. This life-history perspective on the costs and benefits of multiple matings for both sexes sheds new light on sexual selection forces acting on sexual signals and responses.
Chloroplast (Cp) Transcriptome of P. davidiana Dode×P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny.
Zhang X, Gu C, Zhang T … +4 more , Tong B, Zhang H, Wu Y, Yang C
BMC Evol Biol · 2020 May · PMID 32375634 · Full text
BACKGROUND: Raw second-generation (2G) lignocellulosic biomass materials have the potential for development into a sustainable and renewable source of energy. Poplar is regarded as a promising 2G material (P. davidiana D...
BACKGROUND: Raw second-generation (2G) lignocellulosic biomass materials have the potential for development into a sustainable and renewable source of energy. Poplar is regarded as a promising 2G material (P. davidiana Dode×P. bolleana Lauch, P. bolleana, P. davidiana, P. euphratica, et al). However, their large-scale commercialization still faces many obstacles. For example, drought prevents sufficient irrigation or rainfall, which can reduce soil moisture and eventually destroy the chloroplast, the plant photosynthetic organelle. Heterosis is widely used in the production of drought-tolerant materials, such as the superior clone "Shanxinyang" selected from the offspring of Populus davidiana Dode×Populus bolleana Lauch. Because it produces good wood and is easily genetically transformed, "Shanxinyang" has become a promising material for use in tree genetics. It is also one of the most abundant biofuel plants in northern China. Understanding the genetic features of chloroplasts, the cp transcriptome and physiology is crucial to elucidating the chloroplast drought-response model. RESULTS: In this study, the whole genome of "Shanxinyang" was sequenced. The chloroplast genome was assembled, and chloroplast structure was analysed and compared with that of other popular plants. Chloroplast transcriptome analysis was performed under drought conditions. The total length of the "Shanxinyang" chloroplast genome was 156,190 bp, the GC content was 36.75%, and the genome was composed of four typical areas (LSC, IRa, IRb, and SSC). A total of 114 simple repeats were detected in the chloroplast genome of "Shanxinyang". In cp transcriptome analysis, we found 161 up-regulated and 157 down-regulated genes under drought, and 9 cpDEGs was randomly selected to conduct reverse transcription (RT)-qPCR., in which the Log2 (fold change) was significantly consistent with the qPCR results. The analysis of chloroplast transcription under drought provided clues for understanding chloroplast function under drought. The phylogenetic position of "Shanxinyang" within Populus was analysed by using the chloroplast genome sequences of 23 Populus plants, showing that "Shanxinyang" belongs to Sect. Populus and is sister to Populus davidiana. Further, mVISTA analysis showed that the variation in non-coding (regulatory) regions was greater than that in coding regions, which suggests that further attention should be paid to the chloroplast in order to obtain new evolutionary or functional insights related to aspects of plant biology. CONCLUSIONS: Our findings indicate that complex prokaryotic genome regulation occurs when processing transcripts under drought stress. The results not only offer clues for understanding the chloroplast genome and transcription features in woody plants but also serve as a basis for future molecular studies on poplar species.
Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves.
Li J, Lemer S, Kirkendale L … +3 more , Bieler R, Cavanaugh C, Giribet G
BMC Evol Biol · 2020 May · PMID 32357841 · Full text
BACKGROUND: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive e...
BACKGROUND: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS: In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS: The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.
The genetic basis of hybrid male sterility in sympatric Primulina species.
Feng C, Yi H, Yang L … +1 more , Kang M
BMC Evol Biol · 2020 Apr · PMID 32349663 · Full text
BACKGROUND: Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct popu...
BACKGROUND: Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility. RESULTS: We mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F population. A Bateson-Dobzhansky-Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits. CONCLUSIONS: Hybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.
Pattern and timing of diversification in the African freshwater fish genus Distichodus (Characiformes: Distichodontidae).
Arroyave J, Denton JSS, Stiassny MLJ
BMC Evol Biol · 2020 Apr · PMID 32336263 · Full text
BACKGROUND: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phyl...
BACKGROUND: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. RESULTS: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. CONCLUSIONS: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa's continental ichthyofaunal communities.
Maladaptive plasticity facilitates evolution of thermal tolerance during an experimental range shift.
Leonard AM, Lancaster LT
BMC Evol Biol · 2020 Apr · PMID 32326878 · Full text
BACKGROUND: Many organisms are responding to climate change with dramatic range shifts, involving plastic and genetic changes to cope with novel climate regimes found at higher latitudes. Using experimental lineages of t...
BACKGROUND: Many organisms are responding to climate change with dramatic range shifts, involving plastic and genetic changes to cope with novel climate regimes found at higher latitudes. Using experimental lineages of the seed beetle Callosobruchus maculatus, we simulated the initial phase of colonisation to progressively cooler and/or more variable conditions, to investigate how adaptation and phenotypic plasticity contribute to shifts in thermal tolerance during colonisation of novel climates. RESULTS: We show that heat and cold tolerance rapidly evolve during the initial stages of adaptation to progressively cooler and more variable climates. The evolved shift in cold tolerance is, however, associated with maladaptive plasticity under the novel conditions, resulting in a pattern of countergradient variation between the ancestral and novel, fluctuating thermal environment. In contrast, lineages exposed to progressively cooler, but constant, temperatures over several generations expressed only beneficial plasticity in cold tolerances and no evolved response. CONCLUSIONS: We propose that thermal adaptation during a range expansion to novel, more variable climates found at high latitudes and elevations may typically involve genetic compensation arising from maladaptive plasticity in the initial stages of adaptation, and that this form of (countergradient) thermal adaptation may represent an opportunity for more rapid and labile evolutionary change in thermal tolerances than via classic genetic assimilation models for thermal tolerance evolution (i.e., selection on existing reaction norms). Moreover, countergradient variation in thermal tolerances may typically mask cryptic genetic variability for these traits, resulting in apparent evolutionary stasis in thermal traits.
Ultramicrostructural reductions in teeth: implications for dietary transition from non-avian dinosaurs to birds.
Li Z, Wang CC, Wang M … +6 more , Chiang CC, Wang Y, Zheng X, Huang EW, Hsiao K, Zhou Z
BMC Evol Biol · 2020 Apr · PMID 32316913 · Full text
BACKGROUND: Tooth morphology within theropod dinosaurs has been extensively investigated and shows high disparity throughout the Cretaceous. Changes or diversification in feeding ecology, i.e., adoption of an herbivorous...
BACKGROUND: Tooth morphology within theropod dinosaurs has been extensively investigated and shows high disparity throughout the Cretaceous. Changes or diversification in feeding ecology, i.e., adoption of an herbivorous diet (e.g., granivorous), is proposed as a major driver of tooth evolution in Paraves (e.g., Microraptor, troodontids and avialans). Here, we studied the microscopic features of paravian non-avian theropod and avialan teeth using high-spatial-resolution synchrotron transmission X-ray microscopy and scanning electron microscopy. RESULTS: We show that avialan teeth are characterized by the presence of simple enamel structures and a lack of porous mantle dentin between the enamel and orthodentin. Reduced internal structures of teeth took place independently in Early Cretaceous birds and a Microraptor specimen, implying that shifts in diet in avialans from that of closely related dinosaurs may correlate with a shift in feeding ecology during the transition from non-avian dinosaurs to birds. CONCLUSION: Different lines of evidence all suggest a large reduction in biting force affecting the evolution of teeth in the dinosaur-bird transition. Changes in teeth microstructure and associated dietary shift may have contributed to the early evolutionary success of stemward birds in the shadow of other non-avian theropods.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe