BMC Evolutionary Biology[JOURNAL]
Sun
200 papers
Phylogenetic signals in pest abundance and distribution range of spider mites.
Jin PY, Sun JT, Hoffmann A … +5 more , Guo YF, Zhou JC, Zhu YX, Chen L, Hong XY
BMC Evol Biol · 2019 Dec · PMID 31805865 · Full text
BACKGROUND: Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impac...
BACKGROUND: Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide. RESULTS: We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny. CONCLUSIONS: The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable - including the number of known hosts and phylogenetic position of the mites - could therefore be useful in predicting future pest risk of species.
Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica.
Pirie MD, Kandziora M, Nürk NM … +5 more , Le Maitre NC, Mugrabi de Kuppler A, Gehrke B, Oliver EGH, Bellstedt DU
BMC Evol Biol · 2019 Dec · PMID 31805850 · Full text
BACKGROUND: The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here...
BACKGROUND: The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. RESULTS: We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a "stepping stone" between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. CONCLUSIONS: These results highlight the roles of geographical and ecological distance in limiting LDD, but also the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.
Analysis of substitution rates showed that TLR5 is evolving at different rates among mammalian groups.
Pinheiro A, Águeda-Pinto A, Melo-Ferreira J … +3 more , Neves F, Abrantes J, Esteves PJ
BMC Evol Biol · 2019 Dec · PMID 31791244 · Full text
BACKGROUND: Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin,...
BACKGROUND: Toll-like receptors (TLRs) are the most widely studied innate immunity receptors responsible for recognition of invading pathogens. Among the TLR family, TLR5 is the only that senses and recognizes flagellin, the major protein of bacterial flagella. TLR5 has been reported to be under overall purifying selection in mammals, with a small proportion of codons under positive selection. However, the variation of substitution rates among major mammalian groups has been neglected. Here, we studied the evolution of TLR5 in mammals, comparing the substitution rates among groups. RESULTS: In this study we analysed the TLR5 substitution rates in Euungulata, Carnivora, Chiroptera, Primata, Rodentia and Lagomorpha, groups. For that, Tajima's relative rate test, Bayesian inference of evolutionary rates and genetic distances were estimated with CODEML's branch model and RELAX. The combined results showed that in the Lagomorpha, Rodentia, Carnivora and Chiroptera lineages TLR5 is evolving at a higher substitution rate. The RELAX analysis further suggested a significant relaxation of selective pressures for the Lagomorpha (K = 0.22, p < 0.01), Rodentia (K = 0.58, p < 0.01) and Chiroptera (K = 0.65, p < 0.01) lineages and for the Carnivora ancestral branches (K = 0.13, p < 0.01). CONCLUSIONS: Our results show that the TLR5 substitution rate is not uniform among mammals. In fact, among the different mammal groups studied, the Lagomorpha, Rodentia, Carnivora and Chiroptera are evolving faster. This evolutionary pattern could be explained by 1) the acquisition of new functions of TLR5 in the groups with higher substitution rate, i.e. TLR5 neofunctionalization, 2) by the beginning of a TLR5 pseudogenization in these groups due to some redundancy between the TLRs genes, or 3) an arms race between TLR5 and species-specific parasites.
Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6.
Campbell MC, Ashong B, Teng S … +2 more , Harvey J, Cross CN
BMC Evol Biol · 2019 Dec · PMID 31791241 · Full text
BACKGROUND: Lymphotoxin-α (LTα), located in the Major Histocompatibility Complex (MHC) class III region on chromosome 6, encodes a cytotoxic protein that mediates a variety of antiviral responses among other biological f...
BACKGROUND: Lymphotoxin-α (LTα), located in the Major Histocompatibility Complex (MHC) class III region on chromosome 6, encodes a cytotoxic protein that mediates a variety of antiviral responses among other biological functions. Furthermore, several genotypes at this gene have been implicated in the onset of a number of complex diseases, including myocardial infarction, autoimmunity, and various types of cancer. However, little is known about levels of nucleotide variation and linkage disequilibrium (LD) in and near LTα, which could also influence phenotypic variance. To address this gap in knowledge, we examined sequence variation across ~ 10 kilobases (kbs), encompassing LTα and the upstream region, in 2039 individuals from the 1000 Genomes Project originating from 21 global populations. RESULTS: Here, we observed striking patterns of diversity, including an excess of intermediate-frequency alleles, the maintenance of multiple common haplotypes and a deep coalescence time for variation (dating > 1.0 million years ago), in global populations. While these results are generally consistent with a model of balancing selection, we also uncovered a signature of positive selection in the form of long-range LD on chromosomes with derived alleles primarily in Eurasian populations. To reconcile these findings, which appear to support different models of selection, we argue that selective sweeps (particularly, soft sweeps) of multiple derived alleles in and/or near LTα occurred in non-Africans after their ancestors left Africa. Furthermore, these targets of selection were predicted to alter transcription factor binding site affinity and protein stability, suggesting they play a role in gene function. Additionally, our data also showed that a subset of these functional adaptive variants are present in archaic hominin genomes. CONCLUSIONS: Overall, this study identified candidate functional alleles in a biologically-relevant genomic region, and offers new insights into the evolutionary origins of these loci in modern human populations.
PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.
Fang Y, Liu C, Lin J … +4 more , Li X, Alavian KN, Yang Y, Niu Y
BMC Evol Biol · 2019 Dec · PMID 31791235 · Full text
BACKGROUND: Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermedia...
BACKGROUND: Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building. RESULTS: Here, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree. CONCLUSIONS: Together with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).
Human-specific mutations in VMAT1 confer functional changes and multi-directional evolution in the regulation of monoamine circuits.
Sato DX, Ishii Y, Nagai T … +2 more , Ohashi K, Kawata M
BMC Evol Biol · 2019 Dec · PMID 31791232 · Full text
BACKGROUND: Neurochemicals like serotonin and dopamine play crucial roles in human cognitive and emotional functions. Vesicular monoamine transporter 1 (VMAT1) transports monoamine neurotransmitters, and its variant (136...
BACKGROUND: Neurochemicals like serotonin and dopamine play crucial roles in human cognitive and emotional functions. Vesicular monoamine transporter 1 (VMAT1) transports monoamine neurotransmitters, and its variant (136Thr) is associated with various psychopathological symptoms and reduced monoamine uptake relative to 136Ile. We previously showed that two human-specific amino acid substitutions (Glu130Gly and Asn136Thr/Ile) of VMAT1 were subject to positive natural selection. However, the potential functional alterations caused by these substitutions (Glu130Gly and Asn136Thr) remain unclear. To assess functional changes in VMAT1 from an evolutionary perspective, we reconstructed ancestral residues and examined the role of these substitutions in monoamine uptake in vitro using fluorescent false neurotransmitters (FFN), which are newly developed substances used to quantitatively assay VMATs. RESULTS: Immunoblotting confirmed that all the transfected YFP-VMAT1 variants are properly expressed in HEK293T cells at comparable levels, and no significant difference was seen in the density and the size of vesicles among them. Our fluorescent assays revealed a significant difference in FFN206 uptake among VMAT1 variants: 130Glu/136Asn, 130Glu/136Thr, and 130Gly/136Ile showed significantly higher levels of FFN206 uptake than 130Gly/136Asn and 130Gly/136Thr, indicating that both 130Glu and 136Ile led to increased neurotransmitter uptake, for which 136Thr and 136Asn were comparable by contrast. CONCLUSIONS: These findings suggest that monoamine uptake by VMAT1 initially declined (from 130Glu/136Asn to 130Gly/136Thr) in human evolution, possibly resulting in higher susceptibility to the external environment of our ancestors.
Local origin or external input: modern horse origin in East Asia.
Ning T, Ling Y, Hu S … +9 more , Ardalan A, Li J, Mitra B, Chaudhuri TK, Guan W, Zhao Q, Ma Y, Savolainen P, Zhang Y
BMC Evol Biol · 2019 Nov · PMID 31775623 · Full text
BACKGROUND: Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. RESULTS: The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial g...
BACKGROUND: Despite decades of research, the horse domestication scenario in East Asia remains poorly understood. RESULTS: The study identified 16 haplogroups with fine-scale phylogenetic resolution using mitochondrial genomes of 317 horse samples. The time to the most recent common ancestor of the 16 haplogroups ranges from [0.8-3.1] thousand years ago (KYA) to [7.9-27.1] KYA. With combined analyses of the mitochondrial control region for 35 extant Przewalski's horses, 3544 modern and 203 ancient horses across the world, researchers provide evidence for that East Asian prevalent haplogroups Q and R were indigenously domesticated or they were involved in numerous distinct genetic components from wild horses in the southern part of East Asia. These events of haplotypes Q and R occurred during 4.7 to 16.3 KYA and 2.1 to 11.5 KYA, respectively. The diffusion of preponderant European haplogroups L from west to East Asia is consistent with the external gene input. Furthermore, genetic differences were detected between northern East Asia and southern East Asia cohorts by Principal Component Analysis, Analysis of Molecular Variance test, the χ test and phylogeographic analyses. CONCLUSIONS: All results suggest a complex picture of horse domestication, as well as geographic pattern in East Asia. Both local origin and external input occurred in East Asia horse populations. And besides, there are at least two different domestication or hybridization centers in East Asia.
The evolution of reproductive isolation in Daphnia.
Chin TA, Cáceres CE, Cristescu ME
BMC Evol Biol · 2019 Nov · PMID 31775606 · Full text
BACKGROUND: The process by which populations evolve to become new species involves the emergence of various reproductive isolating barriers (RIB). Despite major advancements in understanding this complex process, very li...
BACKGROUND: The process by which populations evolve to become new species involves the emergence of various reproductive isolating barriers (RIB). Despite major advancements in understanding this complex process, very little is known about the order in which RIBs evolve or their relative contribution to the total restriction of gene flow during various stages of speciation. This is mainly due to the difficulties of studying reproductive isolation during the early stages of species formation. This study examines ecological and non-ecological RIB within and between Daphnia pulex and Daphnia pulicaria, two recently diverged species that inhabit distinct habitats and exhibit an unusual level of intraspecific genetic subdivision. RESULTS: We find that while ecological prezygotic barriers are close to completion, none of the non-ecological barriers can restrict gene flow between D. pulex and D. pulicaria completely when acting alone. Surprisingly, we also identified high levels of postzygotic reproductive isolation in 'conspecific' interpopulation crosses of D. pulex. CONCLUSIONS: While the ecological prezygotic barriers are prevalent during the mature stages of speciation, non-ecological barriers likely dominated the early stages of speciation. This finding indicates the importance of studying the very early stages of speciation and suggests the contribution of postzygotic isolation in initiating the process of speciation.
Natriuretic peptides appeared after their receptors in vertebrates.
Grandchamp A, Tahir S, Monget P
BMC Evol Biol · 2019 Nov · PMID 31771521 · Full text
BACKGROUND: In mammals, the natriuretic system contains three natriuretic peptides, NPPA, NPPB and NPPC, that bind to three transmembrane receptors, NPR1, NPR2 and NPR3. The natriuretic peptides are known only in vertebr...
BACKGROUND: In mammals, the natriuretic system contains three natriuretic peptides, NPPA, NPPB and NPPC, that bind to three transmembrane receptors, NPR1, NPR2 and NPR3. The natriuretic peptides are known only in vertebrates. In contrast, the receptors have orthologs in all the animal taxa and in plants. However, in non-vertebrates, these receptors do not have natriuretic properties, and most of their ligands are unknown. How was the interaction of the NP receptors and the NP established in vertebrates? Do natriuretic peptides have orthologs in non-vertebrates? If so, what was the function of the interaction? How did that function change? If not, are the NP homologous to ancestral NPR ligands? Or did the receptor's binding pocket completely change during evolution? METHODS: In the present study, we tried to determine if the pairs of natriuretic receptors and their ligands come from an ancestral pair, or if the interaction only appeared in vertebrates. Alignments, modeling, docking, research of positive selection, and motif research were performed in order to answer this question. RESULTS: We discovered that the binding pocket of the natriuretic peptide receptors was completely remodeled in mammals. We found several peptides in non vertebrates that could be related to human natriuretic peptides, but a set of clues, as well as modeling and docking analysis, suggest that the natriuretic peptides undoubtedly appeared later than their receptors during animal evolution. We suggest here that natriuretic peptide receptors in non vertebrates bind to other ligands. CONCLUSIONS: The present study further support that vertebrate natriuretic peptides appeared after their receptors in the tree of life. We suggest the existence of peptides that resemble natriuretic peptides in non-vertebrate species, that might be the result of convergent evolution.
Unusual interplay of contrasting selective pressures on β-defensin genes implicated in male fertility of the Buffalo (Bubalus bubalis).
Batra V, Maheshwarappa A, Dagar K … +5 more , Kumar S, Soni A, Kumaresan A, Kumar R, Datta TK
BMC Evol Biol · 2019 Nov · PMID 31771505 · Full text
BACKGROUND: The buffalo, despite its superior milk-producing ability, suffers from reproductive limitations that constrain its lifetime productivity. Male sub-fertility, manifested as low conception rates (CRs), is a maj...
BACKGROUND: The buffalo, despite its superior milk-producing ability, suffers from reproductive limitations that constrain its lifetime productivity. Male sub-fertility, manifested as low conception rates (CRs), is a major concern in buffaloes. The epididymal sperm surface-binding proteins which participate in the sperm surface remodelling (SSR) events affect the survival and performance of the spermatozoa in the female reproductive tract (FRT). A mutation in an epididymal secreted protein, beta-defensin 126 (DEFB-126/BD-126), a class-A beta-defensin (CA-BD), resulted in decreased CRs in human cohorts across the globe. To better understand the role of CA-BDs in buffalo reproduction, this study aimed to identify the BD genes for characterization of the selection pressure(s) acting on them, and to identify the most abundant CA-BD transcript in the buffalo male reproductive tract (MRT) for predicting its reproductive functional significance. RESULTS: Despite the low protein sequence homology with their orthologs, the CA-BDs have maintained the molecular framework and the structural core vital to their biological functions. Their coding-sequences in ruminants revealed evidence of pervasive purifying and episodic diversifying selection pressures. The buffalo CA-BD genes were expressed in the major reproductive and non-reproductive tissues exhibiting spatial variations. The Buffalo BD-129 (BuBD-129) was the most abundant and the longest CA-BD in the distal-MRT segments and was predicted to be heavily O-glycosylated. CONCLUSIONS: The maintenance of the structural core, despite the sequence divergence, indicated the conservation of the molecular functions of the CA-BDs. The expression of the buffalo CA-BDs in both the distal-MRT segments and non-reproductive tissues indicate the retention the primordial microbicidal activity, which was also predicted by in silico sequence analyses. However, the observed spatial variations in their expression across the MRT hint at their region-specific roles. Their comparison across mammalian species revealed a pattern in which the various CA-BDs appeared to follow dissimilar evolutionary paths. This pattern appears to maintain only the highly efficacious CA-BD alleles and diversify their functional repertoire in the ruminants. Our preliminary results and analyses indicated that BuBD-129 could be the functional ortholog of the primate DEFB-126. Further studies are warranted to assess its molecular functions to elucidate its role in immunity, reproduction and fertility.
Fossil amber reveals springtails' longstanding dispersal by social insects.
Robin N, D'Haese C, Barden P
BMC Evol Biol · 2019 Nov · PMID 31752661 · Full text
BACKGROUND: Dispersal is essential for terrestrial organisms living in disjunct habitats and constitutes a significant challenge for the evolution of wingless taxa. Springtails (Collembola), the sister-group of all insec...
BACKGROUND: Dispersal is essential for terrestrial organisms living in disjunct habitats and constitutes a significant challenge for the evolution of wingless taxa. Springtails (Collembola), the sister-group of all insects (with Diplura), are reported since the Lower Devonian and are thought to have originally been subterranean. The order Symphypleona is reported since the early Cretaceous with genera distributed on every continent. This distribution implies an ability to disperse over oceans, however symphypleonan Collembola have never been reported in marine water contrary to other springtail orders. Despite being highly widespread, modern springtails are rarely reported in any kind of biotic association. Interestingly, the fossil record has provided occasional occurrences of Symphypleona attached by the antennae onto the bodies of larger arthropods. RESULTS: Here, we document the case of a ~ 16 Ma old fossil association: a winged termite and ant displaying not some, but 25 springtails attached or in close proximity to the body. The collembola exhibit rare features for fossils, reflecting their courtship and phoretic behaviours. By observing the modes of attachment of springtails on different arthropods, the sex representation and ratios in springtail antennal anatomies in new and previously reported cases, we infer a likely mechanism for dispersal in Symphypleona. By revealing hidden evidence of modern springtail associations with other invertebrates such as ants and termites, new compelling assemblages of fossil springtails, and the drastic increase of eusocial insects' abundance during the Cenozoic (ants/termites comprising more than a third of insects in Miocene amber), we stress that attachment on winged castes of ants and termites may have been a mechanism for the worldwide dispersal of this significant springtail lineage. Moreover, by comparing the general constraints applying to the other wingless soil-dwelling arthropods known to disperse through phoresy, we suggest biases in the collection and observation of phoretic Symphypleona related to their reflexive detachment and infer that this behaviour continues today. CONCLUSIONS: The specific case of tree resin entrapment represents the (so far) only condition uncovering the phoretic dispersal mechanism of springtails - one of the oldest terrestrial arthropod lineages living today.
Correction to: Genetic diversity of the Thao people of Taiwan using Y-chromosome, mitochondrial DNA and HLA gene systems.
Trejaut JA, Muyard F, Lai YH … +5 more , Chen LR, Chen ZS, Loo JH, Huang JY, Lin M
BMC Evol Biol · 2019 Nov · PMID 31747896 · Full text
Following publication of the original article [1], we have been notified that Additional file 3 was published with track changes.
Following publication of the original article [1], we have been notified that Additional file 3 was published with track changes.
Bolder guppies do not have more mating partners, yet sire more offspring.
Herdegen-Radwan M
BMC Evol Biol · 2019 Nov · PMID 31726971 · Full text
BACKGROUND: Intra-individual stable but inter-individually variable behaviours, i.e. personalities, are commonly reported across diverse animal groups, yet the reasons for their maintenance remain controversial. Therefor...
BACKGROUND: Intra-individual stable but inter-individually variable behaviours, i.e. personalities, are commonly reported across diverse animal groups, yet the reasons for their maintenance remain controversial. Therefore, studying fitness consequences of personality traits is necessary to discriminate between alternative explanations. RESULTS: Here, I measured boldness, a highly repeatable personality trait, and reproductive success in male guppies, Poecilia reticulata. I found that bolder males had higher reproductive success than their shyer conspecifics and they sired offspring with females who had larger clutches. CONCLUSIONS: This result provides direct evidence for fitness consequences of boldness in the guppy. It suggests that the effect may be driven by bolder males mating with more fecund females.
Learning from beautiful monsters: phylogenetic and morphogenetic implications of left-right asymmetry in ammonoid shells.
Jattiot R, Fara E, Brayard A … +2 more , Urdy S, Goudemand N
BMC Evol Biol · 2019 Nov · PMID 31722660 · Full text
BACKGROUND: Many pathologies that modify the shell geometry and ornamentation of ammonoids are known from the fossil record. Since they may reflect the developmental response of the organism to a perturbation (usually a...
BACKGROUND: Many pathologies that modify the shell geometry and ornamentation of ammonoids are known from the fossil record. Since they may reflect the developmental response of the organism to a perturbation (usually a sublethal injury), their study is essential for exploring the developmental mechanisms of these extinct animals. Ammonoid pathologies are also useful to assess the value of some morphological characters used in taxonomy, as well as to improve phylogenetic reconstructions and evolutionary scenarios. RESULTS: We report on the discovery of an enigmatic pathological middle Toarcian (Lower Jurassic) ammonoid specimen from southern France, characterized by a pronounced left-right asymmetry in both ornamentation and suture lines. For each side independently, the taxonomic interpretations of ornamentation and suture lines are congruent, suggesting a Hildoceras semipolitum species assignment for the left side and a Brodieia primaria species assignment for the right side. The former exhibits a lateral groove whereas the second displays sinuous ribs. This specimen, together with the few analogous cases reported in the literature, lead us to erect a new forma-type pathology herein called "forma janusa" for specimens displaying a left-right asymmetry in the absence of any clear evidence of injury or parasitism, whereby the two sides match with the regular morphology of two distinct, known species. CONCLUSIONS: Since "forma janusa" specimens reflect the underlying developmental plasticity of the ammonoid taxa, we hypothesize that such specimens may also indicate unsuspected phylogenetic closeness between the two displayed taxa and may even reveal a direct ancestor-descendant relationship. This hypothesis is not, as yet, contradicted by the stratigraphical data at hand: in all studied cases the two distinct taxa correspond to contemporaneous or sub-contemporaneous taxa. More generally, the newly described specimen suggests that a hitherto unidentified developmental link may exist between sinuous ribs and lateral grooves. Overall, we recommend an integrative approach for revisiting aberrant individuals that illustrate the intricate links among shell morphogenesis, developmental plasticity and phylogeny.
Gain and loss events in the evolution of the apolipoprotein family in vertebrata.
Liu JQ, Li WX, Zheng JJ … +3 more , Tian QN, Huang JF, Dai SX
BMC Evol Biol · 2019 Nov · PMID 31722659 · Full text
BACKGROUND: Various apolipoproteins widely distributed among vertebrata play key roles in lipid metabolism and have a direct correlation with human diseases as diagnostic markers. However, the evolutionary progress of ap...
BACKGROUND: Various apolipoproteins widely distributed among vertebrata play key roles in lipid metabolism and have a direct correlation with human diseases as diagnostic markers. However, the evolutionary progress of apolipoproteins in species remains unclear. Nine human apolipoproteins and well-annotated genome data of 30 species were used to identify 210 apolipoprotein family members distributed among species from fish to humans. Our study focused on the evolution of nine exchangeable apolipoproteins (ApoA-I/II/IV/V, ApoC-I~IV and ApoE) from Chondrichthyes, Holostei, Teleostei, Amphibia, Sauria (including Aves), Prototheria, Marsupialia and Eutheria. RESULTS: In this study, we reported the overall distribution and the frequent gain and loss evolutionary events of apolipoprotein family members in vertebrata. Phylogenetic trees of orthologous apolipoproteins indicated evident divergence between species evolution and apolipoprotein phylogeny. Successive gain and loss events were found by evaluating the presence and absence of apolipoproteins in the context of species evolution. For example, only ApoA-I and ApoA-IV occurred in cartilaginous fish as ancient apolipoproteins. ApoA-II, ApoE, and ApoC-I/ApoC-II were found in Holostei, Coelacanthiformes, and Teleostei, respectively, but the latter three apolipoproteins were absent from Aves. ApoC-I was also absent from Cetartiodactyla. The apolipoprotein ApoC-III emerged in terrestrial animals, and ApoC-IV first arose in Eutheria. The results indicate that the order of the emergence of apolipoproteins is most likely ApoA-I/ApoA-IV, ApoE, ApoA-II, ApoC-I/ApoC-II, ApoA-V, ApoC-III, and ApoC-IV. CONCLUSIONS: This study reveals not only the phylogeny of apolipoprotein family members in species from Chondrichthyes to Eutheria but also the occurrence and origin of new apolipoproteins. The broad perspective of gain and loss events and the evolutionary scenario of apolipoproteins across vertebrata provide a significant reference for the research of apolipoprotein function and related diseases.
Geographic body size variation of a tropical anuran: effects of water deficit and precipitation seasonality on Asian common toad from southern Asia.
Guo C, Gao S, Krzton A … +1 more , Zhang L
BMC Evol Biol · 2019 Nov · PMID 31706264 · Full text
BACKGROUND: Two previous studies on interspecific body size variation of anurans found that the key drivers of variation are the species' lifestyles and the environments that they live in. To examine whether those findin...
BACKGROUND: Two previous studies on interspecific body size variation of anurans found that the key drivers of variation are the species' lifestyles and the environments that they live in. To examine whether those findings apply at the intraspecific level, we conducted a study of the Asian common toad (Duttaphrynus melanostictus), a terrestrial anuran distributed in tropical regions. The body size of toads from 15 locations, covering the majority of their geographic range, and local environmental data were summarized from published literature. We used a model selection process based on an information-theoretic approach to examine the relationship between toad body size and those environmental parameters. RESULTS: We found a positive correlation between the body size of the Asian common toad and the water deficit gradient, but no linkage between body size and temperature-related parameters. Furthermore, there was a positive correlation between the seasonality of precipitation and body size of females from different sampled populations. CONCLUSIONS: As a terrestrial anuran, the Asian common toad should experience greater pressure from environmental fluctuations than aquatic species. It is mainly distributed in tropical regions where temperatures are generally warm and stable, but water availability fluctuates. Therefore, while thermal gradients are not strong enough to generate selection pressure on body size, the moisture gradient is strong enough to select for larger size in both males and females in dryer regions. Larger body size supports more efficient water conservation, a pattern in accordance with the prediction that lifestyles of different species and their local habitats determine the relationship between body size and environment. In addition, larger females occur in regions with greater seasonality in precipitation, which may happen because larger females can afford greater reproductive output in a limited reproductive season.
Hooked on you: shape of attachment structures in cymothoid isopods reflects parasitic strategy.
Baillie C, Welicky RL, Hadfield KA … +3 more , Smit NJ, Mariani S, D Beck RM
BMC Evol Biol · 2019 Nov · PMID 31703555 · Full text
BACKGROUND: Parasite attachment structures are critical traits that influence effective host exploitation and survival. Morphology of attachment structures can reinforce host specificity and niche specialisation, or even...
BACKGROUND: Parasite attachment structures are critical traits that influence effective host exploitation and survival. Morphology of attachment structures can reinforce host specificity and niche specialisation, or even enable host switching. Therefore, it is important to understand the determinants of variation in attachment structures. Cymothoid isopods are striking ectoparasites of fishes that include the infamous 'tongue-biters.' They are known to parasitise hosts in one of four qualitatively distinct anatomical regions. Here, we quantify variation in cymothoid attachment structures - hook-like appendages called dactyli - and test whether differences in dactylus shape are correlated with parasite mode (where they attach), allometry, or both, using multivariate ordinary least squares regression. We also assess the influence of shared ancestry on shape using a molecular phylogeny to weight our models using phylogenetic generalised least squares regression. RESULTS: We find clear differences in shape between externally-attaching and internally-attaching cymothoids but also between anterior and posterior dactyli across various species with the same attachment mode. Allometric effects are significant for anterior but not posterior dactyli. Mouth-attaching species show greater shape variability than gill- and mouth-attaching species. We find no evidence that there are clade-specific patterns of association between parasite mode and dactylus shape. CONCLUSIONS: Parasite mode appears to be the main driver of attachment morphology. This likely reflects several components of parasite ecology including feeding and functional demands of attachment in different microhabitats. Geometric morphometric approaches to the quantification of shape variation of simple structures is an effective tool that provides new insights into the evolvability of parasite attachment.
Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex.
Davis JS, Moyle LC
BMC Evol Biol · 2019 Nov · PMID 31694548 · Full text
BACKGROUND: Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies-especially in Drosophila-have documented trait variation along latitudinal or altitudina...
BACKGROUND: Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies-especially in Drosophila-have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation. RESULTS: Using environmental data from collection locations of three North American Drosophila species-D. americana americana, D. americana texana and D. novamexicana-we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits. CONCLUSIONS: Our multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.
The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life.
Du Y, Wu S, Edwards SV … +1 more , Liu L
BMC Evol Biol · 2019 Nov · PMID 31694538 · Full text
BACKGROUND: The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that auto...
BACKGROUND: The flood of genomic data to help build and date the tree of life requires automation at several critical junctures, most importantly during sequence assembly and alignment. It is widely appreciated that automated alignment protocols can yield inaccuracies, but the relative impact of various sources error on phylogenomic analysis is not yet known. This study employs an updated mammal data set of 5162 coding loci sampled from 90 species to evaluate the effects of alignment uncertainty, substitution models, and fossil priors on gene tree, species tree, and divergence time estimation. Additionally, a novel coalescent likelihood ratio test is introduced for comparing competing species trees against a given set of gene trees. RESULTS: The aligned DNA sequences of 5162 loci from 90 species were trimmed and filtered using trimAL and two filtering protocols. The final dataset contains 4 sets of alignments - before trimming, after trimming, filtered by a recently proposed pipeline, and further filtered by comparing ML gene trees for each locus with the concatenation tree. Our analyses suggest that the average discordance among the coalescent trees is significantly smaller than that among the concatenation trees estimated from the 4 sets of alignments or with different substitution models. There is no significant difference among the divergence times estimated with different substitution models. However, the divergence dates estimated from the alignments after trimming are more recent than those estimated from the alignments before trimming. CONCLUSIONS: Our results highlight that alignment uncertainty of the updated mammal data set and the choice of substitution models have little impact on tree topologies yielded by coalescent methods for species tree estimation, whereas they are more influential on the trees made by concatenation. Given the choice of calibration scheme and clock models, divergence time estimates are robust to the choice of substitution models, but removing alignments deemed problematic by trimming algorithms can lead to more recent dates. Although the fossil prior is important in divergence time estimation, Bayesian estimates of divergence times in this data set are driven primarily by the sequence data.
Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes.
Bogan SN, Place SP
BMC Evol Biol · 2019 Nov · PMID 31694524 · Full text
BACKGROUND: Antarctic fishes of the Notothenioidei suborder constitutively upregulate multiple inducible chaperones, a highly derived adaptation that preserves proteostasis in extreme cold, and represent a system for stu...
BACKGROUND: Antarctic fishes of the Notothenioidei suborder constitutively upregulate multiple inducible chaperones, a highly derived adaptation that preserves proteostasis in extreme cold, and represent a system for studying the evolution of gene frontloading. We screened for Hsf1-binding sites, as Hsf1 is a master transcription factor of the heat shock response, and highly-conserved non-coding elements within proximal promoters of chaperone genes across 10 Antarctic notothens, 2 subpolar notothens, and 17 perciform fishes. We employed phylogenetic models of molecular evolution to determine whether (i) changes in motifs associated with Hsf1-binding and/or (ii) relaxed purifying selection or exaptation at ancestral cis-regulatory elements coincided with the evolution of chaperone frontloading in Antarctic notothens. RESULTS: Antarctic notothens exhibited significantly fewer Hsf1-binding sites per bp at chaperone promoters than subpolar notothens and Serranoidei, the most closely-related suborder to Notothenioidei included in this study. 90% of chaperone promoters exhibited accelerated substitution rates among Antarctic notothens relative to other perciformes. The proportion of bases undergoing accelerated evolution (i) was significantly greater in Antarctic notothens than in subpolar notothens and Perciformes in 70% of chaperone genes and (ii) increased among bases that were more conserved among perciformes. Lastly, we detected evidence of relaxed purifying selection and exaptation acting on ancestrally conserved cis-regulatory elements in the Antarctic notothen lineage and its major branches. CONCLUSION: A large degree of turnover has occurred in Notothenioidei at chaperone promoter regions that are conserved among perciform fishes following adaptation to the cooling of the Southern Ocean. Additionally, derived reductions in Hsf1-binding site frequency suggest cis-regulatory modifications to the classical heat shock response. Of note, turnover events within chaperone promoters were less frequent in the ancestral node of Antarctic notothens relative to younger Antarctic lineages. This suggests that cis-regulatory divergence at chaperone promoters may be greater between Antarctic notothen lineages than between subpolar and Antarctic clades. These findings demonstrate that strong selective forces have acted upon cis-regulatory elements of chaperone genes among Antarctic notothens.
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