On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

Background  

The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution.     

Phenotypic traits evolution and morphological traits associated with echolocation calls in cryptic horseshoe bats (Rhinolophidae)

Bats provide an excellent casestudy for studying evolution due to their remarkable flight and echolocation capabilities. In this study, we sought to understand the phenotypic evolution of key traits in Rhinolophidae (horseshoe bats) using phylogenetic comparative methods. We aimed to test the phylogenetic signals of traits, and evaluated the best-fit evolutionary models given the data for each trait considering different traits may evolve under different models (i.e., Brownian Motion [BM], Ornstein-Uhlenbeck [OU], and Early Burst [EB]) and reconstruct ancestral character states. We examined how phenotypic characters are associated with echolocation calls and minimum detectable prey size. We measured 34 traits of 10 Asian rhinolophids species (187 individuals). We found that the majority of traits showed a high phylogenetic signal based on Blomberg′s K and Pagel′s λ, but each trait may evolve under different evolutionary models. Sella traits were shown to evolve under stabilizing selection based on OU models, indicating sella traits have the tendency to move forward along the branches toward some medial value in equilibrium. Our findings highlight the importance of sella characters in association with echolocation call emissions in Rhinolophidae, as calls are important for spatial cognition and also influence dietary preferences. Minimum detectable prey size in Rhinolophidae was associated with call frequency, bandwidth, call duration, wingspan, and wing surface area. Ultimately, understanding trait evolution requires sensitivity due to the differential selective pressures which may apply to different characteristics.     

Growth of horseshoe bats (Chiroptera: Rhinolophidae) in temperate continental conditions and the influence of climate

Growth characteristics of three species of horseshoe bats (Rhinolophus ferrumequinum, R. euryale and R. mehelyi) were studied in northern Bulgaria, and measurements of cohorts born there in different years were compared interannually. Bulgarian horseshoe bats are usually born in the first 3 weeks of June and start to leave the roost at an age of about 3 weeks. Young horseshoe bats of all three species had attained more than 95% of the adult dimensions at the time when they started to regularly leave the cave to forage on their own in mid of July. Individually marked juvenile R. ferrumequinum reached adult dimensions in most external wing measurements in the first half of August. Accordingly the pooled measurements of all juveniles did not differ anymore from those of adult bats in the second half of August. The same pattern was found in R. mehelyi and R. euryale.We found a clear relationship between the climatic conditions prevailing in each year and the final size of individuals born respectively in those years. Whereas previous studies have addressed climatic effects only on several bat species along their northern limits of distribution, these data provide the first evidence for an influence of climate on the growth of individuals in the centre of the species’ distributions.     

Molecular evolution of the phytochrome gene family in sorghum: changing rates of synonymous and replacement evolution

The photoreceptor phytochromes, encoded by a small gene family, are responsible for controlling the expression of a number of light-responsive genes and photomorphogenic events, including agronomically important phenotypes such as flowering time and shade-avoidance behavior. The understanding and control of flowering time are particularly important goals in sorghum cultivar development for diverse environments, and naturally occurring variation in the phytochrome genes might prove useful in breeding programs. Also of interest is whether variation observed at the phytochrome loci in domesticated sorghum, or in particular races, is a result of human selection. Population genetic studies can reveal evidence of such selection in patterns of polymorphism and divergence. In this study we report a population genetic analysis of the PHY gene family in Sorghum bicolor (L.) Moench in a diverse panel including both cultivated and wild accessions. We show that the level of nucleotide variation in all gene family members is about half the average for this species, consistent with purifying selection acting on these loci. However, the rate of amino acid substitution is accelerated at PHYC compared to the other two loci. In comparisons to a closely related sorghum species, PHYC shows a pattern of intermediate frequency amino acid changes that differ from the patterns observed in comparisons across longer evolutionary distances. There is also a departure from expected patterns of polymorphism and divergence at synonymous sites in PHYC, although the data do not fit a simple model of directional or diversifying selection. Cultivated sorghum has a level of variation similar to that of wild relatives (ssp. verticilliflorum), but many polymorphisms are subspecies-specific, including several amino acid variants.     

The evolution of echolocation in bats

Recent molecular phylogenies have changed our perspective on the evolution of echolocation in bats. These phylogenies suggest that certain bats with sophisticated echolocation (e.g. horseshoe bats) share a common ancestry with non-echolocating bats (e.g. Old World fruit bats). One interpretation of these trees presumes that laryngeal echolocation (calls produced in the larynx) probably evolved in the ancestor of all extant bats. Echolocation might have subsequently been lost in Old World fruit bats, only to evolve secondarily (by tongue clicking) in this family. Remarkable acoustic features such as Doppler shift compensation, whispering echolocation and nasal emission of sound each show multiple convergent origins in bats. The extensive adaptive radiation in echolocation call design is shaped largely by ecology, showing how perceptual challenges imposed by the environment can often override phylogenetic constraints.     

Flight and echlocation in the ecology and evolution of bats

Flight and echolocation are key characters distinguishing most bats from other mammals.The number of ecolological niches for bats is limited by the concurent constraints of the mammalian physiology and reproductive system and the high cost of flight and echolocation. The recent discovery of a biomechanical coupling between echolocation and flight highlights the need to incorporate both chracters as parts of a single adaptive complex in future research on the ecology and evolution of bats.     

Characteristics of unit responses of the cochlear nuclei of bats (Rhinolophidae) to single and paired ultrasonic stimuli

Characteristics of single unit responses of the cochlear nuclei of greater horseshoe bats to ultrasonic stimuli with a filling frequency within the echolocation range were investigated. In most neurons three unconnected regions of responses were found, with characteristic frequencies equal to 1/2 and 1/3 of the basic frequency, within the range 80–90 kHz. The response regions had inhibitory zones, one of which was higher than the basic characteristic frequency whereas the other two were overlapped by the complementary response regions. Selectivity of the neurons to the frequency of stimulation increased with a change in the characteristic frequency from 90 to 80 kHz; it was maximal in the band 80–80.5 kHz.     

Structure, sequence, chromosomal location, and evolution of the human ferredoxin gene family

Ferredoxin is an iron-sulfur protein that serves as an electron transport intermediate for mitochondrial cytochromes P450 involved in steroid, vitamin D, and bile acid metabolism. We cloned and characterized the human ferredoxin gene family, which includes two expressed genes and two pseudogenes. Sequence analysis of this gene family revealed that it encodes only one protein product. The expressed genes were assigned to chromosome 11 and pseudogenes to chromosomes 20 and 21 by identifying single-copy probes from each gene segment and hybridizing them to DNA from rodent-human hybrid cells. The pseudogenes lacked introns and contained numerous mutations, including insertion, deletion, and substitution which rendered them inactive. They were 96% and 85% homologous to the expressed gene, yet they were only 78% homologous with each other. The intronless nature, higher diversity among themselves, and distinct chromosomal location of the pseudogenes suggests that they arose by independent, retroposon-mediated events.     

Roosting ecology and the evolution of pelage markings in bats

Multiple lineages of bats have evolved striking facial and body pelage makings, including spots, stripes and countershading. Although researchers have hypothesized that these markings mainly evolved for crypsis, this idea has never been tested in a quantitative and comparative context. We present the first comparative study integrating data on roosting ecology (roost type and colony size) and pelage coloration patterns across bats, and explore the hypothesis that the evolution of bat pelage markings is associated with roosting ecologies that benefit from crypsis. We find that lineages that roost in the vegetation have evolved pelage markings, especially stripes and neck collars, which may function in crypsis through disruptive coloration and a type of countershading that might be unique to bats. We also demonstrate that lineages that live in larger colonies and are larger in size tend not to have pelage markings, possibly because of reduced predation pressures due to the predator dilution effect and a lower number of potential predators. Although social functions for pelage color patterns are also possible, our work provides strong support for the idea that roosting ecology has driven the evolution of pelage markings in bats.     

Adaptive evolution of Leptin in heterothermic bats

Heterothermy (hibernation and daily torpor) is a key strategy that animals use to survive in harsh conditions and is widely employed by bats, which are found in diverse habitats and climates. Bats comprise more than 20% of all mammals and although heterothermy occurs in divergent lineages of bats, suggesting it might be an ancestral condition, its evolutionary history is complicated by complex phylogeographic patterns. Here, we use Leptin, which regulates lipid metabolism and is crucial for thermogenesis of hibernators, as molecular marker and combine physiological, molecular and biochemical analyses to explore the possible evolutionary history of heterothermy in bat. The two tropical fruit bats examined here were homeothermic; in contrast, the two tropical insectivorous bats were clearly heterothermic. Molecular evolutionary analyses of the Leptin gene revealed positive selection in the ancestors of all bats, which was maintained or further enhanced the lineages comprising mostly heterothermic species. In contrast, we found evidence of relaxed selection in homeothermic species. Biochemical assays of bat Leptin on the activity on adipocyte degradation revealed that Leptin in heterothermic bats was more lipolytic than in homeothermic bats. This shows that evolutionary sequence changes in this protein are indeed functional and support the interpretation of our physiological results and the molecular evolutionary analyses. Our combined data strongly support the hypothesis that heterothermy is the ancestral state of bats and that this involved adaptive changes in Leptin. Subsequent loss of heterothermy in some tropical lineages of bats likely was associated with range and dietary shifts.     

Rearrangements and chromosomal evolution

Comparisons of the genome sequences of related species suggests varying patterns of chromosomal rearrangements in different evolutionary lineages. In this review, I focus on the quantitative characterization of rearrangement processes and discuss specific inventories that have been compiled to date. Of particular interest are the statistical distribution of the lengths of inverted or locally transposed chromosome fragments (notably very short ones), inhomogeneities in susceptibility to evolutionary breakpoints in chromosomal regions, the relative importance of genome doubling in the history of multicellular eukaryotes, and of lateral transfer versus gene gain and loss in prokaryotes. These developments provide challenges to computational biologists to refine, revise and scale up mathematical models and algorithms for analyzing genome rearrangements.     

Diet and the evolution of digestion and renal function in phyllostomid bats

Bat species in the monophyletic family Phyllostomidae feed on blood, insects, small vertebrates, nectar, fruit and complex omnivorous mixtures. We used nitrogen stable isotope ratios to characterize bat diets and adopted a phylogenetically informed approach to investigate the physiological changes that accompany evolutionary diet changes in phyllostomids. We found that nitrogen stable isotopes separated plant-eating from animal-eating species. The blood of the latter was enriched in (15)N. A recent phylogenetic hypothesis suggests that with the possible exception of carnivory, which may have evolved twice, all diets evolved only once from insectivory. The shift from insectivory to nectarivory and frugivory was accompanied by increased intestinal sucrase and maltase activity, decreased trehalase activity, and reduced relative medullary thickness of kidneys. The shift from insectivory to sanguinivory and carnivory resulted in reduced trehalase activity. Vampire bats are the only known vertebrates that do not exhibit intestinal maltase activity. We argue that these physiological changes are adaptive responses to evolutionary diet shifts.