Chromosomal evolution in Malagasy lemurs. IX. Chromosomal banding studies of Lepilemur mustelinus, L. dorsalis, and L. edwardsi

The karyotypes of three Lepilemuridae species, Lepilemur mustelinus, L. edwardsi, and L. dorsalis, are described and compared to those of three Lepilemur species previously reported. The phylogenetic relationships between the six species and their presumed last common ancestor are given. The results obtained, and the comparison with other groups, strongly suggest a monophyletic origin for all Malagasy lemurs.     

Chromosomal evolution in Malagasy lemurs. VIII. Chromosome banding studies of Lepilemur ruficaudatus, L leucopus, and L septentrionalis

The karyotypes of three Lepilemuridae species, Lepilemur ruficaudatus, L leucopus, and L septentrionalis, are described and compared. An almost complete analogy of chromosome banding is exhibited. Several complex chromosomal rearrangements, especially end-to-end translocations, have occurred in the evolution of these species. The chromosomal data indicate that the species studied are well separated. In addition, their common chromosomal characters show that they constitute a clearly distinct family among the lemurs.     

Taxonomic relationships and sampling effects among Lepilemuridae and Lemuridae using a partial cytochrome b gene

Partial cytochrome b sequences were used to study relationships between three Lepilemuridae species (Lepilemur dorsalis, L. septentrionalis and L. leucopus) and other Lemuridae species. L. dorsalis were subdivided into two sub-groups, according to their capture area (Nosy-Be island and Sahamalaza peninsula). Relationships deduced from phylogenetic trees as well as genetic distances lead to the classification of the Lepilemurs analysed here into separate species. These Lepilemurs form a monophyletic clade which is the sister clade of all other Lemurs used in this study. Reconstructions using randomly chosen sequences and step by step addition of sequences indicate that phylogenetic results for closely related species need to be analysed with caution, if only a small number of sequences are used to obtain them.     

First evidence of prey capture and meat eating by wild Yunnan snub-nosed monkeys Rhinopithecus bieti in Yunnan,China

Most extant nonhuman primates occasionally prey on fast-moving, warm-blooded animals; however, Indriidae, Lepilemuridae, and Colobinae either scavenged for meat or did not eat meat at all. Here we report six cases of animal consumption by the snub-nosed monkey Rhinopithecus bieti in a wild, habituated group between 2004 and 2009 in Yunnun, China. At present,only males in an all-male unit within the study group were involved in active hunting. Such a male-biased activity may be related to the group structure and spatial spread of R. bieti. Two females were observed eating freshly killed birds. The findings confirmed that R. bieti engaged in scavenging and, when hunting, employed a cranio-cervical bite to kill their prey. Meat eating is likely a nutrient maximization feeding strategy in R. bieti, especially in males. A begging behavior occurred after successful prey capture. Although begging was observed, no sharing of the meat was seen. The present findings illuminate the dietary diversity of R. bieti and their ability to expand their dietary spectrum.     

Application of molecular cytogenetics for chromosomal evolution of the Lemuriformes (Prosimians)

R-banding chromosomal studies of 21 species of Lemuriformes allowed us to reconstruct the presumed ancestral karyotype of all the Lemuriformes except for Daubentoniidae and permitted the construction of their phylogenetic tree. Chromosome painting with fluorescently labeled heterologous DNA probes permitted comparative chromosome maps to be established. The Zoo-FISH method was used to reassess the karyotypes of 22 species or subspecies. While our results largely confirm the previous reconstruction of the ancestral karyotype, they resulted in a modification of the previously established phylogenetic tree. The Daubentoniidae emerged first followed by the divergence of the families Cheirogaleidae, Indriidae, Lepilemuridae and Lemuridae. Eight chromosome rearrangements occurred in all Lemuriformes except for Daubentoniidae in the common trunk. The present findings do not allow us to propose the occurrence of any rearrangement common to Daubentoniidae and other Lemuriformes, and probably other Prosimii. Conserved syntenies previously described in various mammalian orders were also conserved, while others were specific to the Lemuriformes.     

Chromosomal evolution in prosimians

A cytogenetic study of almost all the Malagasy lemurs, of several representative Lorisiforms and one representative each of Tupaiiforms and Tarsiforms is reported. A phylogenic tree was constructed for all species exceptTarsius syrichta, which could not be related to either Prosimians or Simians. Three branches emerge, independentely or after a short common trunk, from the ancestral karyotype of all the Primates. One branch leads to the Lorisiforms, another to the Lemuriforms and the third to the Tupaïa. The chromosomal evolution of the Lorisiforms which gave rise to the Galagidae and the Lorisidae is of a populational mode, while among the Lemuriforms 4 modes of speciation have occurred: populational for the Indriidae, dichotomic for the Lepilemuridae, bushy for the Lemuridae and a catenary one for the Hapelemurs.     

An alu-based phylogeny of lemurs (infraorder: lemuriformes)

LEMURS (INFRAORDER: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ～55-60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera.     

Simulating the evolution of signal transduction pathways

We use a generic model of a network of proteins that can activate or deactivate each other to explore the emergence and evolution of signal transduction networks and to gain a basic understanding of their general properties. Starting with a set of non-interacting proteins, we evolve a signal transduction network by random mutation and selection to fulfill a complex biological task. In order to validate this approach we base selection on a fitness function that captures the essential features of chemotactic behavior as seen in bacteria. We find that a system of as few as three proteins can evolve into a network mediating chemotaxis-like behavior by acting as a "derivative sensor". Furthermore, we find that the dynamics and topology of such networks show many similarities to the natural chemotaxis pathway, that the response magnitude can increase with increasing network size and that network behavior shows robustness towards variations in some of the internal parameters. We conclude that simulating the evolution of signal transduction networks to mediate a certain behavior may be a promising approach for understanding the general properties of the natural pathway for that behavior.     

Modelling autocatalytic networks with artificial microbiology

Cells can usefully be equated to autocatalytic networks that increase in mass and then divide. To begin to model relationships between autocatalytic networks and cell division, we have written a program of artificial chemistry that simulates a cell fed by monomers. These monomers are symbols that can be assembled into linear (non-branched) polymers to give different lengths. A reaction is catalysed by a particular polymer or 'enzyme' that may itself be a reactant of that reaction (autocatalysis). These reactions are only studied within the confines of the 'cell' or 'reaction chamber'. There is a flux of material through the cell and eventually the mass of polymers reaches a threshold at which we analyse the cell. Our results indicate a similarity between the connectivity of the reaction network and that of real metabolic networks. Developing the model will entail attributing increased probabilities of reactions to polymers that are colocalised to evaluate the consequences of the dynamics of large assemblies of diverse molecules (hyperstructures) and of cell division.     

The impairment argument for the immorality of abortion revisited

Eric Vogelstein has defended Don Marquis' ‘future-like-ours' argument for the immorality of abortion against what is known as the Identity Objection, which contends that for a fetus to have a future like ours, it must be numerically identical to an entity like us that possesses valuable experiences some time in the future. On psychological accounts of personal identity, there is no identity relationship between the fetus and the entity with valuable experiences that it will become. Vogelstein maintains that a non-sentient fetus nonetheless has a future like ours because it is numerically identical with a future organism that has a mind that bears valuable experiences. Skott Brill, drawing on Jeff McMahan's embodied mind account, denies that human organisms directly have experiences, claiming that they only have experiences derivatively by virtue of their thinking part, and the loss of a future like ours is not transferred to the organism. I show that on McMahan's account, a strong case can be made for the organism having experiences directly, and the subject having these experiences derivatively. This negates Brill's reasoning, although it does imply that non-sentient fetuses do not have a future like ours in quite the same way as we do. I conclude that this is not problematic for Marquis' argument.     

Determination of network of residues that regulate allostery in protein families using sequence analysis

Allosteric interactions between residues that are spatially apart and well separated in sequence are important in the function of multimeric proteins as well as single-domain proteins. This observation suggests that, among the residues that are involved in long-range communications, mutation at one site should affect interactions at a distant site. By adopting a sequence-based approach, we present an automated approach that uses a generalization of the familiar sequence entropy in conjunction with a coupled two-way clustering algorithm, to predict the network of interactions that trigger allosteric interactions in proteins. We use the method to identify the subset of dynamically important residues in three families, namely, the small PDZ family, G protein-coupled receptors (GPCR), and the Lectins, which are cell-adhesion receptors that mediate the tethering and rolling of leukocytes on inflamed endothelium. For the PDZ and GPCR families, our procedure predicts, in agreement with previous studies, a network containing a small number of residues that are involved in their function. Application to the Lectin family reveals a network of residues interspersed throughout the C-terminal end of the structure that are responsible for binding to ligands. Based on our results and previous studies, we propose that functional robustness requires that only a small subset of distantly connected residues be involved in transmitting allosteric signals in proteins.     

A role for haemoglobin in all plant roots?

Abstract. We have found haemoglobin in plant roots whereas previously it has been recorded only in nitrogen fixing nodules of plants. Haemoglobin occurs not only in the roots of those plants that are capable of nodulation but also in the roots of species that are not known to nodulate. We suggest that a haemoglobin gene may be a component of the genome of all plants. The gene structure and sequence in two unrelated families of plants suggests that the plant haemoglobins have had a single origin and that this origin relates to the haemoglobin gene of the animal kingdom. At present we cannot completely rule out the possibility of a horizontal transfer of the gene from the animal kingdom to a progenitor of the dicotyledonous angiosperms but we favour a single origin of the gene from a progenitor organism to both the plant and animal kingdoms. We speculate about the possible functions of haemoglobin in plant roots and put the case that it is unlikely to have a function in facilitating oxygen diffusion. We suggest that haemoglobin may act as a signal molecule indicating oxygen deficit and the consequent need to shift plant metabolism from an oxidative to a fermentative pathway of energy generation.     

The Impact of Message Mutation on the Fitness of a Genetic Code

The Standard Genetic Code is organized such that similar codons encode similar amino acids. One explanation suggested that the Standard Code is the result of natural selection to reduce the fitness ``load' that derives from the mutation and mistranslation of protein-coding genes. We review the arguments against the mutational load-minimizing hypothesis and argue that they need to be reassessed. We review recent analyses of the organization of the Standard Code and conclude that under cautious interpretation they support the mutational load-minimizing hypothesis. We then present a deterministic asexual model with which we study the mode of selection for load minimization. In this model, individual fitness is determined by a protein phenotype resulting from the translation of a mutable set of protein-coding genes. We show that an equilibrium fitness may be associated with a population with the same genetic code and that genetic codes that assign similar codons to similar amino acids have a higher fitness. We also show that the number of mutant codons in each individual at equilibrium, which determines the strength of selection for load minimization, reflects a long-term evolutionary balance between mutations in messages and selection on proteins, rather than the number of mutations that occur in a single generation, as has been assumed by previous authors. We thereby establish that selection for mutational load minimization acts at the level of an individual in a single generation. We conclude with comments on the shortcomings and advantages of load minimization over other hypotheses for the origin of the Standard Code. Received: 4 April 2001 / Accepted: 22 October 2001     

Dogs choose a human informant: Metacognition in canines

The presence of metacognition in animals has been suggested by the observation that non-human primates will seek out information about the location of a hidden reward before responding. In experiment 1, dogs failed to make an information-seeking response that involved re-positioning themselves in space so that they could view a cue that indicated the location of food. In experiments 2 and 3, dogs were allowed to choose between two people, an informant that pointed to the location of food and a non-informant that provided no information. Dogs showed a clear preference for the informant, even when choice of the informant led to no greater chance of reward than choice of the non-informant. In a procedure that involves human communication, dogs show information-seeking behavior.     

Splice variants of the dual specificity tyrosine phosphorylation-regulated kinase 4 (DYRK4) differ in their subcellular localization and catalytic activity

Dual specificity tyrosine phosphorylation-regulated kinases, DYRKs, are a family of conserved protein kinases that play key roles in the regulation of cell differentiation, proliferation, and survival. Of the five mammalian DYRKs, DYRK4 is the least studied family member. Here, we show that several splice variants of DYRK4 are expressed in tissue-specific patterns and that these variants have distinct functional capacities. One of these variants contains a nuclear localization signal in its extended N terminus that mediates its interaction with importin α3 and α5 and that is capable of targeting a heterologous protein to the nucleus. Consequently, the nucleocytoplasmic mobility of this variant differs from that of a shorter isoform in live cell imaging experiments. Other splicing events affect the catalytic domain, including a three-amino acid deletion within subdomain XI that markedly reduces the enzymatic activity of DYRK4. We also show that autophosphorylation of a tyrosine residue within the activation loop is necessary for full DYRK4 kinase activity, a defining feature of the DYRK family. Finally, by comparing the phosphorylation of an array of 720 peptides, we show that DYRK1A, DYRK2, and DYRK4 differ in their target recognition sequence and that preference for an arginine residue at position P -3 is a feature of DYRK1A but not of DYRK2 and DYRK4. Therefore, we highlight the use of subcellular localization as an important regulatory mechanism for DYRK proteins, and we propose that substrate specificity could be a source of functional diversity among DYRKs.     

On the evolutionary origin of aging

It is generally believed that the first organisms did not age, and that aging thus evolved at some point in the history of life. When and why this transition occurred is a fundamental question in evolutionary biology. Recent reports of aging in bacteria suggest that aging predates the emergence of eukaryotes and originated in simple unicellular organisms. Here we use simple models to study why such organisms would evolve aging. These models show that the differentiation between an aging parent and a rejuvenated offspring readily evolves as a strategy to cope with damage that accumulates due to vital activities. We use measurements of the age-specific performance of individual bacteria to test the assumptions of the model, and find evidence that they are fulfilled. The mechanism that leads to aging is expected to operate in a wide range of organisms, suggesting that aging evolved early and repeatedly in the history of life. Aging might thus be a more fundamental aspect of cellular organisms than assumed so far.     

The recent spread of a vertically transmitted virus through populations of Drosophila melanogaster

The sigma virus is a vertically transmitted pathogen that commonly infects natural populations of Drosophila melanogaster. This virus is the only known host-specific pathogen of D. melanogaster, and so offers a unique opportunity to study the genetics of Drosophila-viral interactions in a natural system. To elucidate the population genetic processes that operate in sigma virus populations, we collected D. melanogaster from 10 populations across three continents. We found that the sigma virus had a prevalence of 0-15% in these populations. Compared to other RNA viruses, we found that levels of viral genetic diversity are very low across Europe and North America. Based on laboratory measurements of the viral substitution rate, we estimate that most European and North American viral isolates shared a common ancestor approximately 200 years ago. We suggest two explanations for this: the first is that D. melanogaster has recently acquired the sigma virus; the second is that a single viral type has recently swept through D. melanogaster populations. Furthermore, in contrast to Drosophila populations, we find that the sigma viral populations are highly structured. This is surprising for a vertically transmitted pathogen that has a similar migration rate to its host. We suggest that the low structure in the viral populations can be explained by the smaller effective population size of the virus.     

Do environmental violations affect corporate loan financing? Evidence from China

This article reports an empirical study suggesting that environmental violations generally have a negative influence on the level of loans that the violating firms hold in China and that after a violation announcement involving waste water discharge, firms are forced to take secured loans. These effects are found to be mitigated for state-owned firms and the media coverage of a certain violation event has a negative effect on the level of loans that firms obtain. Our work presents the evidence of a penalty mechanism in the credit market that fines firms for their environmental violations in a transition economy, and has some implications for business management and governmental policy.