3,865 results match your criteria BMC Evolutionary Biology [Journal]


Sex ratios and bimaturism differ between temperature-dependent and genetic sex-determination systems in reptiles.

BMC Evol Biol 2019 Feb 18;19(1):57. Epub 2019 Feb 18.

MTA-PE Evolutionary Ecology Research Group, University of Pannonia, Pf. 158, Veszprém, 8201, Hungary.

Background: Sex-determining systems may profoundly influence the ecology, behaviour and demography of animals, yet these relationships are poorly understood. Here we investigate whether species with temperature-dependent (TSD) and genetic sex determination (GSD) differ in key demographic traits, using data from 181 species representing all major phylogenetic lineages of extant reptiles.

Results: We show that species with TSD exhibit significantly higher within-species variance in sex ratios than GSD species in three major life stages: birth or hatching, juvenility and adulthood. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1386-3DOI Listing
February 2019
1 Read

The role of genetic diversity in the evolution and maintenance of environmentally-cued, male alternative reproductive tactics.

BMC Evol Biol 2019 Feb 18;19(1):58. Epub 2019 Feb 18.

Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, The Netherlands.

Background: Alternative reproductive tactics (ARTs) are taxonomically pervasive strategies adopted by individuals to maximize reproductive success within populations. Even for conditionally-dependent traits, consensus postulates most ARTs involve both genetic and environmental interactions (GEIs), but to date, quantifying genetic variation underlying the threshold disposing an individual to switch phenotypes in response to an environmental cue has been a difficult undertaking. Our study aims to investigate the origins and maintenance of ARTs within environmentally disparate populations of the microscopic bulb mite, Rhizoglyphus robini, that express 'fighter' and 'scrambler' male morphs mediated by a complex combination of environmental and genetic factors. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1385-4DOI Listing
February 2019

Identification and co-evolution pattern of stem cell regulator miR394s and their targets among diverse plant species.

BMC Evol Biol 2019 Feb 14;19(1):55. Epub 2019 Feb 14.

National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.

Background: Micro RNAs (miRNAs), a class of small non-coding RNAs, have been implicated in various aspects of plant development. miR394 is required for shoot apical meristem organization, stem cell maintenance and abiotic stress responses in Arabidopsis, where it functions by negatively regulating the transcript level of target LEAF CURLING RESPONSIVENESS (LCR), which is an F-box protein-coding gene. The evolutionary conservation of stem cell regulatory miR394-LCR module among plants remains elusive. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1382-7DOI Listing
February 2019

Correction to: Evolutionary biogeography of the centipede genus Ethmostigmus from Peninsular India: testing an ancient vicariance hypothesis for Old World tropical diversity.

BMC Evol Biol 2019 Feb 14;19(1):56. Epub 2019 Feb 14.

The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.

Following publication of the original article [1], the authors notified us of an error in the Results section of the Abstract. The original article has been corrected. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1383-6DOI Listing
February 2019

Phyloproteomic and functional analyses do not support a split in the genus Borrelia (phylum Spirochaetes).

BMC Evol Biol 2019 Feb 13;19(1):54. Epub 2019 Feb 13.

UMR BIPAR, INRA, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, 94700, Maisons-Alfort, France.

Background: The evolutionary history of a species is frequently derived from molecular sequences, and the resulting phylogenetic trees do not include explicit functional information. Here, we aimed to assess the functional relationships among bacteria in the Spirochaetes phylum, based on the biological processes of 42,489 proteins in reference proteomes of 34 Spirochaetes species. We tested the hypothesis that the species in the genus Borrelia might be sufficiently different to warrant splitting them into two separate genera. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1379-2DOI Listing
February 2019

DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation.

BMC Evol Biol 2019 Feb 11;19(1):52. Epub 2019 Feb 11.

School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.

Background: DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1346-yDOI Listing
February 2019

Contrasting patterns of molecular evolution in metazoan germ line genes.

BMC Evol Biol 2019 Feb 11;19(1):53. Epub 2019 Feb 11.

Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.

Background: Germ lines are the cell lineages that give rise to the sperm and eggs in animals. The germ lines first arise from primordial germ cells (PGCs) during embryogenesis: these form from either a presumed derived mode of preformed germ plasm (inheritance) or from an ancestral mechanism of inductive cell-cell signalling (induction). Numerous genes involved in germ line specification and development have been identified and functionally studied. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1363-xDOI Listing
February 2019
2 Reads

Invasion triple trouble: environmental fluctuations, fluctuation-adapted invaders and fluctuation-mal-adapted communities all govern invasion success.

BMC Evol Biol 2019 Feb 1;19(1):42. Epub 2019 Feb 1.

Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylä, Finland.

Background: It has been suggested that climate change will lead to increased environmental fluctuations, which will undoubtedly have evolutionary consequences for all biota. For instance, fluctuations can directly increase the risk of invasions of alien species into new areas, as these species have repeatedly been proposed to benefit from disturbances. At the same time increased environmental fluctuations may also select for better invaders. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1348-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359858PMC
February 2019

Evolutionary biogeography of the centipede genus Ethmostigmus from Peninsular India: testing an ancient vicariance hypothesis for Old World tropical diversity.

BMC Evol Biol 2019 Feb 1;19(1):41. Epub 2019 Feb 1.

The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.

Background: Understanding the relative influence of vicariance and dispersal in shaping Old World tropical biodiversity remains a challenge. We aimed to infer the roles of these alternative biogeographic processes using a species time-tree for the centipede genus Ethmostigmus from the Old World tropics. Additionally, we explored fine-scale biogeographic patterns for an endemic radiation of Ethmostigmus from the peninsular Indian Plate (PIP), an area with complex geological and climatic history. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1367-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359765PMC
February 2019

Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity.

BMC Evol Biol 2019 Jan 31;19(1):40. Epub 2019 Jan 31.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.

Background: Cilia and flagella are complex cellular structures thought to have first evolved in a last ciliated eukaryotic ancestor due to the conserved 9 + 2 microtubule doublet structure of the axoneme and associated proteins. The Tektin family of coiled-coil domain containing proteins was previously identified in cilia of organisms as diverse as green algae and sea urchin. While studies have shown that some Tektins are necessary for ciliary function, there has been no comprehensive phylogenetic survey of tektin genes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1360-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357514PMC
January 2019

Is there adaptation in the human genome for taste perception and phase I biotransformation?

BMC Evol Biol 2019 Jan 31;19(1):39. Epub 2019 Jan 31.

Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Catalonia, Spain.

Background: During the modern human expansion, new environmental pressures may have driven adaptation, especially in genes related to the perception of ingested substances and their detoxification. Consequently, positive (adaptive) selection may have occurred in genes related to taste, and in those related to the CYP450 system due to its role in biotransformation of potentially toxic compounds. A total of 91 genes (taste receptors and CYP450 superfamily) have been studied using Hierarchical Boosting, a powerful combination of different selection tests, to detect signatures of recent positive selection in three continental human populations: Northern Europeans (CEU), East Asians (CHB) and Africans (YRI). Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1366-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357387PMC
January 2019
3 Reads

Morphological diversification of biomechanical traits: mustelid locomotor specializations and the macroevolution of long bone cross-sectional morphology.

BMC Evol Biol 2019 Jan 30;19(1):37. Epub 2019 Jan 30.

Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK.

Background: Morphological diversity of limb bone lengths, diameters, and proportions in mammals is known to vary strongly with locomotor habit. It remains less well known how different locomotor habits are correlated with cross-sectional traits of the limb skeleton, such as cross-sectional area (CSA), second moments of area (SMA), and section modulus (MOD) and whether these traits have evolved adaptively. CSA and SMA represent the bone's resistance to axial compression and bending, respectively, whereas MOD represents bone structural strength related to shape. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1349-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354431PMC
January 2019

Evolution of vertebrate nicotinic acetylcholine receptors.

BMC Evol Biol 2019 Jan 30;19(1):38. Epub 2019 Jan 30.

Department of Neuroscience, Unit of Pharmacology, Science for Life Laboratory, Uppsala University, Box 593, SE-751 24, Uppsala, Sweden.

Background: Many physiological processes are influenced by nicotinic acetylcholine receptors (nAChR), ranging from neuromuscular and parasympathetic signaling to modulation of the reward system and long-term memory. Due to the complexity of the nAChR family and variable evolutionary rates among its members, their evolution in vertebrates has been difficult to resolve. In order to understand how and when the nAChR genes arose, we have used a broad approach of analyses combining sequence-based phylogeny, chromosomal synteny and intron positions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1341-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354393PMC
January 2019

Evolution of salivary glue genes in Drosophila species.

BMC Evol Biol 2019 Jan 29;19(1):36. Epub 2019 Jan 29.

Institut Jacques Monod-CNRS UMR7592-Université Paris Diderot, 15 rue Hélène Brion, 75013, Paris, France.

Background: At the very end of the larval stage Drosophila expectorate a glue secreted by their salivary glands to attach themselves to a substrate while pupariating. The glue is a mixture of apparently unrelated proteins, some of which are highly glycosylated and possess internal repeats. Because species adhere to distinct substrates (i. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1364-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6352337PMC
January 2019
1 Read

Paleozoic diversification of terrestrial chitin-degrading bacterial lineages.

BMC Evol Biol 2019 Jan 28;19(1):34. Epub 2019 Jan 28.

Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

Background: Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1357-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348609PMC
January 2019
2 Reads

Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have.

BMC Evol Biol 2019 Jan 28;19(1):35. Epub 2019 Jan 28.

MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.

Background: Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1365-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350292PMC
January 2019
3.368 Impact Factor

Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane.

BMC Evol Biol 2019 Jan 25;19(1):33. Epub 2019 Jan 25.

Agronomy Department, University of Florida, Gainesville, FL, USA.

Background: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1356-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347779PMC
January 2019

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation.

BMC Evol Biol 2019 Jan 23;19(1):32. Epub 2019 Jan 23.

Zoological Institute and Museum, University of Greifswald, D-17489, Greifswald, Germany.

Background: Phenotypic plasticity is a pervasive property of all organisms and considered to be of key importance for dealing with environmental variation. Plastic responses to temperature, which is one of the most important ecological factors, have received much attention over recent decades. A recurrent pattern of temperature-induced adaptive plasticity includes increased heat tolerance after exposure to warmer temperatures and increased cold tolerance after exposure to cooler temperatures. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1362-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345059PMC
January 2019

Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales.

BMC Evol Biol 2019 Jan 23;19(1):31. Epub 2019 Jan 23.

Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.

Background: The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1359-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343362PMC
January 2019
4 Reads

Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species.

BMC Evol Biol 2019 Jan 22;19(1):29. Epub 2019 Jan 22.

Department of Biology, University of Ottawa, Gendron Hall, Room 160, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada.

Background: Plukenetia is a small pantropical genus of lianas and vines with variably sized edible oil-rich seeds that presents an ideal system to investigate neotropical and pantropical diversification patterns and seed size evolution. We assessed the biogeography and seed evolution of Plukenetia through phylogenetic analyses of a 5069 character molecular dataset comprising five nuclear and two plastid markers for 86 terminals in subtribe Plukenetiinae (representing 20 of ~ 23 Plukenetia species). Two nuclear genes, KEA1 and TEB, were used for phylogenetic reconstruction for the first time. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1308-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341577PMC
January 2019
3 Reads

Morphological evolution and modularity of the caecilian skull.

BMC Evol Biol 2019 Jan 22;19(1):30. Epub 2019 Jan 22.

Department of Life Sciences, Natural History Museum, London, UK.

Background: Caecilians (Gymnophiona) are the least speciose extant lissamphibian order, yet living forms capture approximately 250 million years of evolution since their earliest divergences. This long history is reflected in the broad range of skull morphologies exhibited by this largely fossorial, but developmentally diverse, clade. However, this diversity of form makes quantification of caecilian cranial morphology challenging, with highly variable presence or absence of many structures. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-018-1342-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343317PMC
January 2019
2 Reads

Defining novel plant polyamine oxidase subfamilies through molecular modeling and sequence analysis.

BMC Evol Biol 2019 Jan 21;19(1):28. Epub 2019 Jan 21.

Laboratorio de Fisiología de Estrés Abiótico en Plantas, Unidad de Biotecnología, INTECH - CONICET - UNSAM, Intendente Marino KM 8.2 - B7130IWA Chascomús, Buenos Aires, Argentina.

Background: The polyamine oxidases (PAOs) catabolize the oxidative deamination of the polyamines (PAs) spermine (Spm) and spermidine (Spd). Most of the phylogenetic studies performed to analyze the plant PAO family took into account only a limited number and/or taxonomic representation of plant PAOs sequences.

Results: Here, we constructed a plant PAO protein sequence database and identified four subfamilies. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1361-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6341606PMC
January 2019
2 Reads

Origin and diversification of the plasminogen activation system among chordates.

BMC Evol Biol 2019 Jan 17;19(1):27. Epub 2019 Jan 17.

Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.

Background: The plasminogen (PLG) activation system is composed by a series of serine proteases, inhibitors and several binding proteins, which together control the temporal and spatial generation of the active serine protease plasmin. As this proteolytic system plays a central role in human physiology and pathophysiology it has been extensively studied in mammals. The serine proteases of this system are believed to originate from an ancestral gene by gene duplications followed by domain gains and deletions. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-019-1353-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337849PMC
January 2019
7 Reads

Nature of selection varies on different domains of IFI16-like PYHIN genes in ruminants.

BMC Evol Biol 2019 Jan 17;19(1):26. Epub 2019 Jan 17.

Animal Genomics Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, 132001, India.

Background: ALRs (AIM2-like Receptors) are germline encoded PRRs that belong to PYHIN gene family of cytokines, which are having signature N-terminal PYD (Pyrin, PAAD or DAPIN) domain and C-terminal HIN-200 (hematopoietic, interferon-inducible nuclear protein with 200 amino acid repeat) domain joined by a linker region. The positively charged HIN-200 domain senses and binds with negatively charged phosphate groups of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) purely through electrostatic attractions. On the other hand, PYD domain interacts homotypically with a PYD domain of other mediators to pass the signals to effector molecules downwards the pathways for inflammatory responses. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1334-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335826PMC
January 2019
2 Reads
3.368 Impact Factor

Measurements of hybrid fertility and a test of mate preference for two house mouse races with massive chromosomal divergence.

BMC Evol Biol 2019 Jan 16;19(1):25. Epub 2019 Jan 16.

Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.

Background: Western house mice Mus musculus domesticus are among the most important mammalian model species for chromosomal speciation. Hybrids between chromosomal races of M. m. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1322-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335807PMC
January 2019
1 Read

Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae).

BMC Evol Biol 2019 Jan 16;19(1):24. Epub 2019 Jan 16.

Department of Biology and Marine Biology, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA.

Background: Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1343-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335727PMC
January 2019
1 Read

Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates.

BMC Evol Biol 2019 Jan 14;19(1):22. Epub 2019 Jan 14.

Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada.

Background: An excess of nonsynonymous substitutions, over neutrality, is considered evidence of positive Darwinian selection. Inference for proteins often relies on estimation of the nonsynonymous to synonymous ratio (ω = d/d) within a codon model. However, to ease computational difficulties, ω is typically estimated assuming an idealized substitution process where (i) all nonsynonymous substitutions have the same rate (regardless of impact on organism fitness) and (ii) instantaneous double and triple (DT) nucleotide mutations have zero probability (despite evidence that they can occur). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1326-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332903PMC
January 2019
2 Reads

Biogeography of Korea's top predator, the yellow-throated Marten: evolutionary history and population dynamics.

BMC Evol Biol 2019 Jan 14;19(1):23. Epub 2019 Jan 14.

National Institute of Ecology, 1210, Geumgang-ro, Maseo-myeon, Seocheon-gun, South Chungcheong province, 33657, Republic of Korea.

Background: Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr). Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1347-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6332909PMC
January 2019
1 Read

Decrease of gene expression diversity during domestication of animals and plants.

BMC Evol Biol 2019 Jan 11;19(1):19. Epub 2019 Jan 11.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

Background: The genetic mechanisms underlying the domestication of animals and plants have been of great interest to biologists since Darwin. To date, little is known about the global pattern of gene expression changes during domestication.

Results: We generated and collected transcriptome data for seven pairs of domestic animals and plants including dog, silkworm, chicken, rice, cotton, soybean and maize and their wild progenitors and compared the expression profiles between the domestic and wild species. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-018-1340-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330456PMC
January 2019
12 Reads
3.368 Impact Factor

Contrasting evolutionary origins of two mountain endemics: Saxifraga wahlenbergii (Western Carpathians) and S. styriaca (Eastern Alps).

BMC Evol Biol 2019 Jan 11;19(1):18. Epub 2019 Jan 11.

W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Krakow, Poland.

Background: The Carpathians and the Alps are the largest mountain ranges of the European Alpine System and important centres of endemism. Among the distinctive endemic species of this area is Saxifraga wahlenbergii, a Western Carpathians member of the speciose genus Saxifraga. It was frequently considered a taxonomically isolated Tertiary palaeopolyploid and palaeoendemic, for which the closest relatives could not yet be traced. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1355-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329101PMC
January 2019
2 Reads

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences.

BMC Evol Biol 2019 Jan 11;19(1):21. Epub 2019 Jan 11.

Station d'Ecologie Théorique et Expérimentale de Moulis, CNRS, Moulis, France.

Background: Multiple Sequence Alignments (MSAs) are the starting point of molecular evolutionary analyses. Errors in MSAs generate a non-historical signal that can lead to incorrect inferences. Therefore, numerous efforts have been made to reduce the impact of alignment errors, by improving alignment algorithms and by developing methods to filter out poorly aligned regions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1350-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330419PMC
January 2019
1 Read

Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation.

BMC Evol Biol 2019 Jan 11;19(1):20. Epub 2019 Jan 11.

Department of Biology, Chungnam National University, Daejeon, 34134, South Korea.

Background: The Synurophyceae is one of most important photosynthetic stramenopile algal lineages in freshwater ecosystems. They are characterized by siliceous scales covering the cell or colony surface and possess plastids of red-algal secondary or tertiary endosymbiotic origin. Despite their ecological and evolutionary significance, the relationships amongst extant Synurophyceae are unclear, as is their relationship to most other stramenopiles. Read More

View Article

Download full-text PDF

Source
https://bmcevolbiol.biomedcentral.com/articles/10.1186/s1286
Publisher Site
http://dx.doi.org/10.1186/s12862-018-1316-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330437PMC
January 2019
6 Reads

Pectoral myology of limb-reduced worm lizards (Squamata, Amphisbaenia) suggests decoupling of the musculoskeletal system during the evolution of body elongation.

BMC Evol Biol 2019 Jan 10;19(1):16. Epub 2019 Jan 10.

Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany.

Background: The evolution of elongated body forms in tetrapods has a strong influence on the musculoskeletal system, including the reduction of pelvic and pectoral girdles, as well as the limbs. However, despite extensive research in this area it still remains unknown how muscles within and around bony girdles are affected by these reductions. Here we investigate this issue using fossorial amphisbaenian reptiles, or worm lizards, as a model system, which show substantial variation in the degree of reductions of girdles and limbs. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1303-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329177PMC
January 2019
1 Read

Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare.

BMC Evol Biol 2019 Jan 10;19(1):17. Epub 2019 Jan 10.

Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece.

Background: The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1354-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329171PMC
January 2019
2 Reads

Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries.

BMC Evol Biol 2019 Jan 10;19(1):13. Epub 2019 Jan 10.

Zoological Institute, University of Basel, Basel, Switzerland.

Background: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1345-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327445PMC
January 2019
1 Read

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength.

BMC Evol Biol 2019 Jan 10;19(1):15. Epub 2019 Jan 10.

Molecular Genetics Group, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

Background: A central theme in (micro)biology is understanding the molecular basis of fitness i.e. which strategies are successful under which conditions; how do organisms implement such strategies at the molecular level; and which constraints shape the trade-offs between alternative strategies. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1331-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327505PMC
January 2019
1 Read

Reduced bonobo MHC class I diversity predicts a reduced viral peptide binding ability compared to chimpanzees.

BMC Evol Biol 2019 Jan 10;19(1):14. Epub 2019 Jan 10.

Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.

Background: The highly polymorphic genes of the major histocompatibility complex (MHC) class I are involved in defense against viruses and other intracellular pathogens. Although several studies found reduced MHC class I diversity in bonobos in comparison to the closely related chimpanzee, it is unclear if this lower diversity also influences the functional ability of MHC class I molecules in bonobos. Here, we use a bioinformatic approach to analyze the viral peptide binding ability of all published bonobo MHC class I molecules (n = 58) in comparison to all published chimpanzee MHC class I molecules (n = 161) for the class I loci A, B, C and A-like. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1352-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327438PMC
January 2019
1 Read

Live fast, diversify non-adaptively: evolutionary diversification of exceptionally short-lived annual killifishes.

BMC Evol Biol 2019 Jan 9;19(1):10. Epub 2019 Jan 9.

MacroBiodiversity Lab, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.

Background: Adaptive radiations are triggered by ecological opportunity - the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when 'spatial opportunity' (i. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1344-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327596PMC
January 2019
1 Read

Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects.

BMC Evol Biol 2019 Jan 9;19(1):11. Epub 2019 Jan 9.

Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113, Germany.

Background: Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor.

Results: Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1324-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327564PMC
January 2019
1 Read

Duplication and expression of horizontally transferred polygalacturonase genes is associated with host range expansion of mirid bugs.

BMC Evol Biol 2019 Jan 9;19(1):12. Epub 2019 Jan 9.

State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.

Backgroud: Horizontal gene transfer and gene duplication are two major mechanisms contributing to the evolutionary adaptation of organisms. Previously, polygalacturonase genes (PGs) were independently horizontally transferred and underwent multiple duplications in insects (e.g. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-019-1351-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327464PMC
January 2019
1 Read

Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes.

BMC Evol Biol 2019 Jan 8;19(1). Epub 2019 Jan 8.

Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.

Background: Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1323-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325677PMC
January 2019
1 Read

First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species.

BMC Evol Biol 2019 Jan 8;19(1). Epub 2019 Jan 8.

Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, B-3000, Leuven, Belgium.

Background: Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1325-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323704PMC
January 2019
2 Reads

Genetic divergence, population differentiation and phylogeography of the cicada Subpsaltria yangi based on molecular and acoustic data: an example of the early stage of speciation?

BMC Evol Biol 2019 Jan 8;19(1). Epub 2019 Jan 8.

State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: Geographical isolation combined with historical climatic fluctuations have been identified as two major factors that contribute to the formation of new species. On the other hand, biotic factors such as competition and predation are also able to drive the evolution and diversification of organisms. To determine whether geographical barriers contributed to population divergence or speciation in the rare endemic cicada Subpsaltria yangi the population differentiation, genetic structure and phylogeography of the species were investigated in the Loess Plateau and adjacent areas of northwestern China by analysing mitochondrial and nuclear DNA and comparing the calling song structure of 161 male individuals. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1317-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323834PMC
January 2019
1 Read

Changes in ontogenetic patterns facilitate diversification in skull shape of Australian agamid lizards.

BMC Evol Biol 2019 Jan 8;19(1). Epub 2019 Jan 8.

School of Biological Sciences, University of Adelaide, Room 205E, Darling Building North Terrace, Adelaide, SA, 5005, Australia.

Background: Morphological diversity among closely related animals can be the result of differing growth patterns. The Australian radiation of agamid lizards (Amphibolurinae) exhibits great ecological and morphological diversity, which they have achieved on a continent-wide scale, in a relatively short period of time (30 million years). Amphibolurines therefore make an ideal study group for examining ontogenetic allometry. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1335-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325775PMC
January 2019
1 Read

A common arthropod from the Late Ordovician Big Hill Lagerstätte (Michigan) reveals an unexpected ecological diversity within Chasmataspidida.

BMC Evol Biol 2019 Jan 8;19(1). Epub 2019 Jan 8.

, Louiseville, USA.

Background: Chasmataspidids are a rare group of chelicerate arthropods known from 12 species assigned to ten genera, with a geologic range extending from the Ordovician to the Devonian. The Late Ordovician (Richmondian) fauna of the Big Hill Lagerstätte includes a new species of chasmataspidid represented by 55 specimens. This taxon is only the second chasmataspidid described from the Ordovician and preserves morphological details unknown from any of the previously described species. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1329-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325806PMC
January 2019
1 Read

Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs.

BMC Evol Biol 2019 Jan 7;19(1). Epub 2019 Jan 7.

Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, USA.

Background: Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1297-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323724PMC
January 2019
1 Read

Allelic diversity and selection at the MHC class I and class II in a bottlenecked bird of prey, the White-tailed Eagle.

BMC Evol Biol 2019 Jan 5;19(1). Epub 2019 Jan 5.

Eagle Conservation Committee, Niepodległości 53/55, 10-044, Olsztyn, Poland.

Background: Genes of the Major Histocompatibility Complex (MHC) are essential for adaptive immune response in vertebrates, as they encode receptors that recognize peptides derived from the processing of intracellular (MHC class I) and extracellular (MHC class II) pathogens. High MHC diversity in natural populations is primarily generated and maintained by pathogen-mediated diversifying and balancing selection. It is, however, debated whether selection at the MHC can counterbalance the effects of drift in bottlenecked populations. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1338-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321662PMC
January 2019
1 Read

A new zygodactylid species indicates the persistence of stem passerines into the early Oligocene in North America.

BMC Evol Biol 2019 Jan 5;19(1). Epub 2019 Jan 5.

University of Texas at Austin, Jackson School of Geosciences, Austin, TX, USA.

Background: The lake deposits of the informal Ruby Paper Shale unit, part of the Renova Formation of Montana, have yielded abundant plant fossils that document Late Eocene - Early Oligocene global cooling in western North America. A nearly complete small bird with feather impressions was recovered from this unit in in 1959, but has only been informally mentioned.

Results: Here we describe this fossil and identify it as a new species of Zygodactylus, a stem lineage passerine with a zygodactyl foot. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1319-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6321701PMC
January 2019
1 Read

Long-term sky islands generate highly divergent lineages of a narrowly distributed stream salamander (Pachyhynobius shangchengensis) in mid-latitude mountains of East Asia.

BMC Evol Biol 2019 Jan 3;19(1). Epub 2019 Jan 3.

Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China.

Background: Climate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands.

Results: The Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1333-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318985PMC
January 2019
2 Reads

The pay-off of hypsodonty - timing and dynamics of crown growth and wear in molars of Soay sheep.

BMC Evol Biol 2018 12 29;18(1):207. Epub 2018 Dec 29.

Department of Biology, University of Hildesheim, Universitätsplatz 1, 31141, Hildesheim, Germany.

Background: Several lineages of herbivorous mammals have evolved hypsodont cheek teeth to increase the functional lifespan of their dentition. While the selective drivers of this trend and the developmental processes involved have been studied in greater detail, thus far no quantitative information is available on the relationship between additional investment into tooth growth and the resulting extension of the functional period of these teeth. To achieve this, we performed a detailed analysis of molar crown growth in known-age Soay sheep repeatedly injected with different fluorochromes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-018-1332-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310973PMC
December 2018
3 Reads