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The ornithologist Alfred Russel Wallace and the controversy surrounding the dinosaurian origin of birds

Ibrahim N, Kutschera U

Theory Biosci, 2013 Dec;132(4):267-75.
PMID: 23975643 DOI: 10.1007/s12064-013-0192-5

Over many years of his life, the British naturalist Alfred Russel Wallace (1823-1913) explored the tropical forests of Malaysia, collecting numerous specimens, including hundreds of birds, many of them new to science. Subsequently, Wallace published a series of papers on systematic ornithology, and discovered a new species on top of a volcano on Ternate, where he wrote, in 1858, his famous essay on natural selection. Based on this hands-on experience, and an analysis of an Archaeopteryx fossil, Wallace suggested that birds may have descended from dinosaurian ancestors. Here, we describe the "dinosaur-bird hypothesis" that originated with the work of Thomas H. Huxley (1825-1895). We present the strong evidence linking theropod dinosaurs to birds, and briefly outline the long and ongoing controversy around this concept. Dinosaurs preserving plumage, nesting sites and trace fossils provide overwhelming evidence for the dinosaurian origin of birds. Based on these recent findings of paleontological research, we conclude that extant birds indeed descended, with some modifications, from small, Mesozoic theropod dinosaurs. In the light of Wallace's view of bird origins, we critically evaluate recent opposing views to this idea, including Ernst Mayr's (1904-2005) arguments against the "dinosaur-bird hypothesis", and document that this famous ornithologist was not correct in his assessment of this important aspect of vertebrate evolution.

Matched MeSH terms: Biological Evolution*
The prominent absence of Alfred Russel Wallace at the Darwin anniversaries in Germany in 1909, 1959 and 2009

Hossfeld U, Olsson L

Theory Biosci, 2013 Dec;132(4):251-7.
PMID: 23975642 DOI: 10.1007/s12064-013-0189-0

It is well known that the contribution of Alfred Russell Wallace (1823-1913) to the development of the "Darwinian" principle of natural selection has often been neglected. Here we focus on how the three anniversaries to celebrate the origin of the Darwin-Wallace theory in Germany in 1909, in 1959 in the divided country, as well as in 2009, have represented Charles Robert Darwin's and Alfred Russell Wallace's contributions. We have analyzed books and proceedings volumes related to these anniversaries, and the main result is that Wallace was almost always ignored, or only mentioned in passing. In 1909, Ernst Haeckel gave a talk in Jena, later published under the title The worldview of Darwin and Lamarck (Das Weltbild von Darwin und Lamarck), but not as the Darwin-Wallace concept. Haeckel mentions Wallace only once. In two important proceedings volumes from the 1959 anniversaries, Wallace was ignored. The only fair treatment of Wallace is given in another book, a collection of documents edited by Gerhard Heberer, for which the author selected nine key documents and reprinted excerpts (1959). Three of them were articles by Wallace, including the Sarawak- and Ternate-papers of 1855 and 1858, respectively. An analysis of the dominant themes during the celebrations of 2009 shows that none of the six topics had much to do with Wallace and his work. Thus, the tendency to exclude Alfred Russell Wallace is an international phenomenon, and largely attributable to the "Darwin industry".

Matched MeSH terms: Biological Evolution*
Engaging with Lyell: Alfred Russel Wallace's Sarawak Law and Ternate papers as reactions to Charles Lyell's Principles of Geology

Costa JT

Theory Biosci, 2013 Dec;132(4):225-37.
PMID: 24014172 DOI: 10.1007/s12064-013-0188-1

Alfred Russel Wallace (1823-1913) and Charles Darwin (1809-1882) are honored as the founders of modern evolutionary biology. Accordingly, much attention has focused on their relationship, from their independent development of the principle of natural selection to the receipt by Darwin of Wallace's essay from Ternate in the spring of 1858, and the subsequent reading of the Wallace and Darwin papers at the Linnean Society on 1 July 1858. In the events of 1858 Wallace and Darwin are typically seen as central players, with Darwin's friends Charles Lyell (1797-1875) and Joseph Dalton Hooker (1817-1911) playing supporting roles. This narrative has resulted in an under-appreciation of a more central role for Charles Lyell as both Wallace's inspiration and foil. The extensive anti-transmutation arguments in Lyell's landmark Principles of Geology were taken as the definitive statement on the subject. Wallace, in his quest to solve the mystery of species origins, engaged with Lyell's arguments in his private field notebooks in a way that is concordant with his engagement with Lyell in the 1855 and 1858 papers. I show that Lyell was the object of Wallace's Sarawak Law and Ternate papers through a consideration of the circumstances that led Wallace to send his Ternate paper to Darwin, together with an analysis of the material that Wallace drew upon from the Principles. In this view Darwin was, ironically, intended for a supporting role in mediating Wallace's attempted dialog with Lyell.

Matched MeSH terms: Biological Evolution*
Alfred Russel Wallace (1823-1913): the forgotten co-founder of the Neo-Darwinian theory of biological evolution

Kutschera U, Hossfeld U

Theory Biosci, 2013 Dec;132(4):207-14.
PMID: 23982797 DOI: 10.1007/s12064-013-0187-2

The British naturalist Alfred Russel Wallace (1823-1913), who had to leave school aged 14 and never attended university, did extensive fieldwork, first in the Amazon River basin (1848-1852) and then in Southeast Asia (1854-1862). Based on this experience, and after reading the corresponding scientific literature, Wallace postulated that species were not created, but are modified descendants of pre-existing varieties (Sarawak Law paper, 1855). Evolution is brought about by a struggle for existence via natural selection, which results in the adaptation of those individuals in variable populations who survive and reproduce (Ternate essay, 1858). In his monograph Darwinism (1889), and in subsequent publications, Wallace extended the contents of Darwin's Origin of Species (1859) into the Neo-Darwinian theory of biological evolution, with reference to the work of August Weismann (1834-1914). Wallace also became the (co)-founder of biogeography, biodiversity research, astrobiology and evolutionary anthropology. Moreover, he envisioned what was later called the anthropocene (i.e., the age of human environmental destructiveness). However, since Wallace believed in atheistic spiritualism and mixed up scientific facts and supernatural speculations in some of his writings, he remains a controversial figure in the history of biology.

Matched MeSH terms: Biological Evolution*
Evaluating Frugivore-fruit Interactions Using Avian Eye Modelling

Fadzly N, Burns KC, Zuharah WF

Trop Life Sci Res, 2013 Dec;24(2):31-50.
PMID: 24575247 MyJurnal

Fruit phenotypes are often hypothesised to be affected by selection by frugivores. Here, we tested two hypotheses concerning frugivore-fruit interactions from the perspective of fruit colours. We measured the spectral properties of 26 fruits and the associated leaves of plants from 2 islands in New Zealand. Visual observations were also performed to record the birds that fed on the fruits. First, we tested the fruit-foliage hypothesis, where fruit colours are assumed to be evolutionarily constrained by their own leaf colour to maximise colour contrast and fruit conspicuousness. We ran a null model analysis comparing fruit colour contrast using an avian eye model. Second, we tested the frugivore specificity hypothesis, where specific fruit colours are thought to be connected with a specific bird frugivore. We performed a regression on the number of bird visits against the fruit colour in tetrahedral colour space based on an avian eye calculation using Mantel's test. The results show that fruit colours are not constrained by their own leaf colours. There is also no relationship or pattern suggesting a link between a specific fruit colour and specific bird visitors. We suggest that although fruit colour is one of the most highly discussed components, it is not the most important single deciding factor in frugivore fruit selection.

Matched MeSH terms: Biological Evolution
Fulltext Divergence of iron metabolism in wild Malaysian yeast

Lee HN, Mostovoy Y, Hsu TY, Chang AH, Brem RB

G3 (Bethesda), 2013 Dec 09;3(12):2187-94.
PMID: 24142925 DOI: 10.1534/g3.113.008011

Comparative genomic studies have reported widespread variation in levels of gene expression within and between species. Using these data to infer organism-level trait divergence has proven to be a key challenge in the field. We have used a wild Malaysian population of S. cerevisiae as a test bed in the search to predict and validate trait differences based on observations of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron. Malaysian yeast also showed a hyperactive regulatory response during culture in the presence of excess iron and had a unique growth defect in conditions of high iron. Molecular validation experiments pinpointed the iron metabolism factors AFT1, CCC1, and YAP5 as contributors to these molecular and cellular phenotypes; in genome-scale sequence analyses, a suite of iron toxicity response genes showed evidence for rapid protein evolution in Malaysian yeast. Our findings support a model in which iron metabolism has diverged in Malaysian yeast as a consequence of a change in selective pressure, with Malaysian alleles shifting the dynamic range of iron response to low-iron concentrations and weakening resistance to extreme iron toxicity. By dissecting the iron scarcity specialist behavior of Malaysian yeast, our work highlights the power of expression divergence as a signpost for biologically and evolutionarily relevant variation at the organismal level. Interpreting the phenotypic relevance of gene expression variation is one of the primary challenges of modern genomics.

Matched MeSH terms: Biological Evolution
Fulltext Multiple gene analyses of caligid copepods indicate that the reduction of a thoracic appendage in Pseudocaligus represents convergent evolution

Freeman MA, Anshary H, Ogawa K

Parasit Vectors, 2013;6(1):336.
PMID: 24286135 DOI: 10.1186/1756-3305-6-336

The Caligidae is a family of parasitic copepods containing over 30 recognised genera. They are commercially important parasites as they cause disease in numerous finfish aquaculture facilities globally. Morphological features are used to distinguish between the genera and Pseudocaligus has traditionally been differentiated from Caligus solely by the presence of a much reduced form of the fourth thoracic leg. Currently there are numerous DNA sequences available for Caligus spp. but only the type species, Pseudocaligus brevipedis, has molecular data available, so systematic studies using molecular phylogenetic analyses have been limited.

Matched MeSH terms: Biological Evolution*
Fulltext An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters

Abdullah A, Deris S, Anwar S, Arjunan SN

PLoS One, 2013;8(3):e56310.
PMID: 23469172 DOI: 10.1371/journal.pone.0056310

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.

Matched MeSH terms: Biological Evolution*
Fulltext Phylogeographical pattern and evolutionary history of an important Peninsular Malaysian timber species, Neobalanocarpus heimii (Dipterocarpaceae)

Tnah LH, Lee SL, Ng KK, Lee CT, Bhassu S, Othman RY

J Hered, 2013 Jan-Feb;104(1):115-26.
PMID: 23132907 DOI: 10.1093/jhered/ess076

Tectonic movements, climatic oscillations, and marine transgressions during the Cenozoic have had a dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber species, Neobalanocarpus heimii (Dipterocarpaceae). A total of 32 natural populations of N. heimii, with 8 samples from each population were investigated. Fifteen haplotypes were identified from five noncoding chloroplast DNA (cpDNA) regions. Overall, two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to have survived in multiple refugia during climatic oscillations: the northwestern region (R1), the northeastern region (R2), and the southern region (R3). These putative glacial refugia exhibited higher levels of genetic diversity, population differentiation, and the presence of unique haplotypes. Recolonization of refugia R1 and R2 could have first expanded into the northern region and migrated both northeastwards and northwestwards. Meanwhile, recolonization of N. heimii throughout the southern region could have commenced from refugia R3 and migrated toward the northeast and northwest, respectively. The populations of Tersang, Pasir Raja, and Rotan Tunggal exhibited remarkably high haplotype diversity, which could have been the contact zones that have received an admixture of gene pools from the northerly and also southerly regions. As a whole, the populations of N. heimii derived from glacial refugia and contact zones should be considered in the conservation strategies in order to safeguard the long-term survival of the species.

Matched MeSH terms: Biological Evolution*
Hunter-gatherers in southeast Asia: from prehistory to the present

Higham C

Hum Biol, 2013 Feb-Jun;85(1-3):21-43.
PMID: 24297219

Anatomically modern hunter-gatherers expanded from Africa into Southeast Asia at least 50,000 years ago, where they probably encountered and interacted with populations of Homo erectus and Homo floresiensis and the recently discovered Denisovans. Simulation studies suggest that these hunter-gatherers may well have followed a coastal route that ultimately led to the settlement of Sahul, while archaeology confirms that they also crossed significant seas and explored well into the interior. They also adapted to marked environmental changes that alternated between relatively cool and dry conditions and warmer, wetter interludes. During the former, the sea fell by up to 120 m below its present level, which opened up a vast low-lying area known as Sundaland. Three principal alignments can be identified: the first involved the occupation of rock shelters in upland regions, the second has identified settlement on broad riverine floodplains, and the last concentrated on the raised beaches formed from about five millennia ago when the sea level was elevated above its present position. This cultural sequence was dislocated about 4 kya when rice and millet farmers infiltrated the lowlands of Southeast Asia ultimately from the Yangtze River valley. It is suggested that this led to two forms of interaction. In the first, the indigenous hunter-gatherers integrated with intrusive Neolithic communities and, while losing their cultural identity, contributed their genes to the present population of Southeast Asia. In the second, hunter-gatherers withdrew to rainforest refugia and, through selective pressures inherent in such an environment, survived as the small-bodied, dark-skinned humans found to this day in the Philippines, Peninsular Malaysia and Thailand, and the Andaman Islands. Beyond the impact of expansive rice farmers in Melanesia and Australia, hunter-gatherers continued to dominate until they encountered European settlement.

Matched MeSH terms: Biological Evolution*
Craniodental affinities of Southeast Asia's "negritos" and the concordance with their genetic affinities

Bulbeck D

Hum Biol, 2013 Feb-Jun;85(1-3):95-133.
PMID: 24297222

Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology have revealed some hints of Southwest Pacific affinities in cranial shape, dental morphology, and dental metrical "shape." On the other hand, the Andamanese have been shown to resemble Africans in their craniometrics and South Asians in their dental morphology, while Philippine negritos resemble Mongoloid Southeast Asians in these respects and also in their dental metrics. This study expands the scope of negrito cranial comparisons by including Melayu Malays and additional coverage of South Asians. It highlights the distinction between the Mongoloid-like Philippine negritos and the Andamanese and Semang (and Senoi of Malaya) with their non-Mongoloid associations. It proposes that the early/mid-Holocene dispersal of the B4a1a mitochondrial DNA clade across Borneo, the Philippines, and Taiwan may be important for understanding the distinction between Philippine and other negritos.

Matched MeSH terms: Biological Evolution*
Why have the peninsular "negritos" remained distinct?

Benjamin G

Hum Biol, 2013 Feb-Jun;85(1-3):445-84.
PMID: 24297237

The primary focus of this article is on the so-called negritos of Peninsular Malaysia and southern Thailand, but attention is also paid to other parts of Southeast Asia. I present a survey of current views on the "negrito" phenotype--is it single or many? If the phenotype is many (as now seems likely), it must have resulted from parallel evolution in the several different regions where it has been claimed to exist. This would suggest (contrary to certain views that have been expressed on the basis of very partial genetic data) that the phenotype originated recently and by biologically well-authenticated processes from within the neighboring populations. Whole-genome and physical-anthropological research currently support this view. Regardless of whether the negrito phenotype is ancient or recent-and to the extent that it retains any valid biological reality (which is worth questioning)-explanations are still needed for its continued distinctiveness. In the Malay Peninsula, a distinctive "Semang" societal pattern followed by most, but not all, so-called negritos may have been responsible for this by shaping familial, breeding, and demographic patterns to suit the two main modes of environmental appropriation that they have followed, probably for some millennia: nomadic foraging in the forest, and facultative dependence on exchange or labor relations with neighboring populations. The known distribution of "negritos" in the Malay Peninsula is limited to areas within relatively easy reach of archaeologically authenticated premodern transpeninsular trading and portage routes, as well as of other non-negrito, Aslian-speaking populations engaged in swidden farming. This suggests that their continued distinctiveness has resulted from a wish to maintain a complementary advantage vis-à-vis other, less specialized populations. Nevertheless, a significant degree of discordance exists between the associated linguistic, societal-tradition, and biological patterns which suggests that other factors have also been at play.

Matched MeSH terms: Biological Evolution
Habitat partitioning and morphological differentiation: the Southeast Asian Draco lizards and Caribbean Anolis lizards compared

Ord TJ, Klomp DA

Oecologia, 2014 Jun;175(2):651-66.
PMID: 24658764

Sympatric species that initially overlap in resource use are expected to partition the environment in ways that will minimize interspecific competition. This shift in resource use can in turn prompt evolutionary changes in morphology. A classic example of habitat partitioning and morphological differentiation are the Caribbean Anolis lizards. Less well studied, but nevertheless striking analogues to the Anolis are the Southeast Asian Draco lizards. Draco and Anolis have evolved independently of each other for at least 80 million years. Their comparison subsequently offers a special opportunity to examine mechanisms of phenotypic differentiation between two ecologically diverse, but phylogenetically distinct groups. We tested whether Draco shared ecological axes of differentiation with Anolis (e.g., habitat use), whether this differentiation reflected interspecific competition, and to what extent adaptive change in morphology has occurred along these ecological axes. Using existing data on Anolis, we compared the habitat use and morphology of Draco in a field study of allopatric and sympatric species on the Malay Peninsula, Borneo and in the Philippines. Sympatric Draco lizards partitioned the environment along common resource axes to the Anolis lizards, especially in perch use. Furthermore, the morphology of Draco was correlated with perch use in the same way as it was in Anolis: species that used wider perches exhibited longer limb lengths. These results provide an important illustration of how interspecific competition can occur along common ecological axes in different animal groups, and how natural selection along these axes can generate the same type of adaptive change in morphology.

Matched MeSH terms: Biological Evolution
Comparative morphology of spermatozoa and reproductive systems of zorapteran species from different world regions (Insecta, Zoraptera)

Dallai R, Gottardo M, Mercati D, Machida R, Mashimo Y, Matsumura Y, et al.

Arthropod Struct Dev, 2014 Jul;43(4):371-83.
PMID: 24657729 DOI: 10.1016/j.asd.2014.03.001

The male and female reproductive apparatus of Zorotypus magnicaudelli (Malaysia), Zorotypus huxleyi (Ecuador) and Zorotypus weidneri (Brazil) were examined and documented in detail. The genital apparatus and sperm of the three species show only minor differences. The testes are larger in Z. magnicaudelli. Z. huxleyi lacks the helical appendage in the accessory glands. A long cuticular flagellum is present in Z. magnicaudelli and in the previously studied Zorotypus caudelli like in several other species, whereas it is absent in Z. weidneri, Z. huxleyi, Zorotypus hubbardi, Zorotypus impolitus and Zorotypus guineensis. Characteristic features of the very similar sperm are the presence of: a) two dense arches above the axoneme; b) a 9 + 9+2 axoneme with detached subtubules A and B of doublets 1 and 6; c) the axonemal end degenerating with enlarging accessory tubules; d) accessory tubules with 17 protofilaments; e) three accessory bodies beneath the axoneme; and f) two mitochondrial derivatives of equal shape. The first characteristic (a) is unknown outside of Zoraptera and possibly autapomorphic. The sperm structure differs distinctly in Z. impolitus and Z. hubbardi, which produce giant sperm and possess a huge spermatheca. The presence of the same sperm type in species either provided with a sclerotized coiled flagellum in males or lacking this structure indicates that a different organization of the genital apparatus does not necessarily affect the sperm structure. The flagellum and its pouch has probably evolved within Zoraptera, but it cannot be excluded that it is a groundplan feature and was reduced several times. The fossil evidence and our findings suggest that distinct modifications in the genital apparatus occurred before the fragmentation of the Gondwanan landmass in the middle Cretaceous.

Matched MeSH terms: Biological Evolution*
Fulltext Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences

Jelen MM, Chen Z, Kocjan BJ, Burt FJ, Chan PK, Chouhy D, et al.

J Virol, 2014 Jul;88(13):7307-16.
PMID: 24741079 DOI: 10.1128/JVI.00621-14

Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution.
IMPORTANCE: This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.

Matched MeSH terms: Biological Evolution
The genus Hormiops Fage, 1933 (Hormuridae, Scorpiones), a palaeoendemic of the South China Sea: systematics and biogeography

Monod L

C. R. Biol., 2014 Oct;337(10):596-608.
PMID: 25282174 DOI: 10.1016/j.crvi.2014.07.009

The monotypic genus Hormiops Fage, 1933 is so far only known from two groups of granitic islands off the coasts of Peninsular Malaysia and Vietnam. Examination of newly collected material from both archipelagos and of the type series of Hormiops davidovi Fage, 1933 reveals previously disregarded morphological differences sufficient to assign the Malaysian specimens to a distinct species, described here as Hormiops infulcra sp. nov. An updated diagnosis of the genus, as well as a dichotomic key enabling the determination of Hormiops from its close relatives, Hormurus Thorell, 1876 and Liocheles Sundevall, 1833 are also provided. The phylogenetic position, distribution pattern, and ecology of these insular scorpions suggest that they are palaeoendemics, remnants of a previously more widely distributed lineage. A biogeographical model is proposed for the genus based on these observations and on a synthesis of palaeogeographical and palaeoenvironmental data currently available for Sundaland.

Matched MeSH terms: Biological Evolution
Bacterial microbiome of Coptotermes curvignathus (Isoptera: Rhinotermitidae) reflects the coevolution of species and dietary pattern

King JH, Mahadi NM, Bong CF, Ong KH, Hassan O

Insect Sci, 2014 Oct;21(5):584-96.
PMID: 24123989 DOI: 10.1111/1744-7917.12061

Coptotermes curvignathus Holmgren is capable of feeding on living trees. This ability is attributed to their effective digestive system that is furnished by the termite's own cellulolytic enzymes and cooperative enzymes produced by their gut microbes. In this study, the identity of an array of diverse microbes residing in the gut of C. curvignathus was revealed by sequencing the near-full-length 16S rRNA genes. A total of 154 bacterial phylotypes were found. The Bacteroidetes was the most abundant phylum and accounted for about 65% of the gut microbial profile. This is followed by Firmicutes, Actinobacteria, Spirochetes, Proteobacteria, TM7, Deferribacteres, Planctomycetes, Verrucomicrobia, and Termite Group 1. Based on the phylogenetic study, this symbiosis can be a result of long coevolution of gut enterotypes with the phylogenic distribution, strong selection pressure in the gut, and other speculative pressures that determine bacterial biome to follow. The phylogenetic distribution of cloned rRNA genes in the bacterial domain that was considerably different from other termite reflects the strong selection pressures in the gut where a proportional composition of gut microbiome of C. curvignathus has established. The selection pressures could be linked to the unique diet preference of C. curvignathus that profoundly feeds on living trees. The delicate gut microbiome composition may provide available nutrients to the host as well as potential protection against opportunistic pathogen.

Matched MeSH terms: Biological Evolution*
Fulltext Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora

Chung KF, Leong WC, Rubite RR, Repin R, Kiew R, Liu Y, et al.

Bot Stud, 2014 Dec;55(1):1.
PMID: 28510906 DOI: 10.1186/1999-3110-55-1

BACKGROUND: The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species.
RESULTS: Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area.
CONCLUSIONS: Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

Matched MeSH terms: Biological Evolution
Fulltext Anti-inflammatory and antiplatelet activities of plasma are conserved across twelve mammalian species

Ahmed S, Gul S, Idris F, Hussain A, Zia-Ul-Haq M, Jaafar HZ, et al.

Molecules, 2014;19(8):11385-94.
PMID: 25090125 DOI: 10.3390/molecules190811385

Human plasma inhibits arachidonic acid metabolism and platelet aggregation. This helps human form a haemostatic control system that prevents the progress of certain aggregatory or inflammatory reactions. Whether this property of plasma is unique to human or extends to other species is not well known. It is speculated that this protective ability of plasma remains evolutionarily conserved in different mammals. In order to confirm this, the effect of plasma from 12 different mammalian species was investigated for its inhibitory potential against arachidonic acid metabolism and platelet aggregation. Metabolism of arachidonic acid by cyclooxygenase and lipoxygenase pathways was studies using radio-immuno assay and thin layer chromatography while platelet aggregation in the plasma of various mammals was monitored following turbedmetric method in a dual channel aggregometer. Results indicate that inhibition of AA metabolism and platelet aggregation is a common feature of plasma obtained from different mammalian species, although there exists large interspecies variation. This shows that besides human, other mammals also possess general protective mechanisms against various aggregatory and inflammatory conditions and this anti-inflammatory property of the plasma is evolutionarily conserved in mammalian species. The most likely candidates responsible for these properties of plasma include haptoglobin, albumin and lipoproteins.

Matched MeSH terms: Biological Evolution
Fulltext Genomic reconnaissance of clinical isolates of emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential

Choo SW, Wee WY, Ngeow YF, Mitchell W, Tan JL, Wong GJ, et al.

Sci Rep, 2014;4:4061.
PMID: 24515248 DOI: 10.1038/srep04061

Mycobacterium abscessus (Ma) is an emerging human pathogen that causes both soft tissue infections and systemic disease. We present the first comparative whole-genome study of Ma strains isolated from patients of wide geographical origin. We found a high proportion of accessory strain-specific genes indicating an open, non-conservative pan-genome structure, and clear evidence of rapid phage-mediated evolution. Although we found fewer virulence factors in Ma compared to M. tuberculosis, our data indicated that Ma evolves rapidly and therefore should be monitored closely for the acquisition of more pathogenic traits. This comparative study provides a better understanding of Ma and forms the basis for future functional work on this important pathogen.

Matched MeSH terms: Biological Evolution*

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