A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (chiroptera)

Bats (Order Chiroptera), the only mammals capable of powered flight and sophisticated laryngeal echolocation, represent one of the most species-rich and ubiquitous orders of mammals. However, phylogenetic relationships within this group are poorly resolved. A robust evolutionary tree of Chiroptera is essential for evaluating the phylogeny of echolocation within Chiroptera, as well as for understanding their biogeographical history. We generated 4 kb of sequence data from portions of four novel nuclear intron markers for multiple representatives of 17 of the 18 recognized extant bat families, as well as the putative bat family Miniopteridae. Three echolocation-call characters were examined by mapping them onto the combined topology: (1) high-duty cycle versus low-duty cycle, (2) high-intensity versus low-intensity call emission, and (3) oral versus nasal emission. Echolocation seems to be highly convergent, and the mapping of echolocation-call design onto our phylogeny does not appear to resolve the question of whether echolocation had a single or two origins. Fossil taxa may also provide insight into the evolution of bats; we therefore evaluate 195 morphological characters in light of our nuclear DNA phylogeny. All but 24 of the morphological characters were found to be homoplasious when mapped onto the supermatrix topology, while the remaining characters provided insufficient information to reconstruct the placement of the fossil bat taxa with respect to extant families. However, a morphological synapomorphy characterizing the Rhinolophoidea was identified and is suggestive of a separate origin of echolocation in this clade. Dispersal-Vicariance analysis together with a relaxed Bayesian clock were used to evaluate possible biogeographic scenarios that could account for the current distribution pattern of extant bat families. Africa was reconstructed as the center of origin of modern-day bat families.     

Australian Oligo-Miocene Mystacinids (Microchiroptera): upper dentition, new taxa and divergence of New Zealand species

The upper dentition of two Australian early Miocene mystacinids, Icaropsparadox and I. aenae, from Riversleigh, Queensland, are described for the first time. Also recognised is a late Oligocene mystacinid from Lake Palankarinna, South Australia. The new fossils help refine understanding about the evolutionary history of mystacinids in Australia, including their temporal and geographical range, possible dietary and roosting habits, and likely separation time of New Zealand mystacinids.     

The origins of graptolites and other pterobranchs: a journey from ‘Polyzoa’

The graptolites, known only from fossils, have been convincingly allied to the pterobranch hemichordates, a group of tiny, mostly colonial marine invertebrates bearing feeding arms. The phylogenetic position of pterobranchs has been subject to debate and revision for over a century. Their colonial lifestyle and feeding arms were originally seen as evidence placing them among the bryozoans, until later and more careful anatomical studies revealed more characters in common with acorn worms. Pterobranchs and acorn worms are now grouped as the phylum Hemichordata. For many decades, it was thought that pterobranchs were closer to the ancestral form of hemichordates, particularly because ‘lophophorate’ invertebrates also possess feeding arms, notably the phoronids and bryozoans, as do crinoid echinoderms. This traditional view has been challenged by recent molecular evidence. First, there is strong molecular evidence to indicate that lophophorates are very distant from hemichordates and echinoderms, in a different major branch of the animal phylogenetic tree. Therefore, similarities between the feeding structures must be due to convergent evolution. Second, there is strong evidence that hemichordates and echinoderms form a clade (Ambulacraria) within the deuterostomes, rather than hemichordates being closer to chordates. Third, there is weaker evidence that pterobranchs may be derived from acorn worms, and hence that the vermiform body plan may be ancestral within hemichordates. This suggestion warrants further testing. Here we review the evidence for these conclusions, highlight strengths and weaknesses in the data and analyses, and consider the implications for the origins of pterobranchs and graptolites.     

A bat (Chiroptera) survey of Mora rainforest in Trinidad's Victoria-Mayaro Forest Reserve

The bat fauna of the Mora excelsa-dominated rainforest in the Victoria-Mayaro Forest Reserve (VMFR) in south-east Trinidad was assessed over a six-week period. Trapping effort totaled 271 mist net hours and caught 143 bats of 22 species at a rate of one bat every two net-hours. Simpsons diversity index (1/D) was 1.28 for primary Mora forest and extrapolation using Chaos' estimator, a non-parametric method, estimated the total number of species as 39. Phyllostomid bats of the subfamilies Phyllostominae and Stenodermatinae were well represented, and frugivores predominated in number, accounting for 77% of all captures in primary forest. The most abundant bat, the ground-storey frugivore, Carollia perspicillata, accounted for 43% of all captures in primary forest and, in contrast to most bats, was also abundant on man-made paths through the forest. Four species not previously recorded from the reserve, Tonatia bidens, Trachops cirrhosus, a Myotis sp., and the rare Phylloderma stenops, were captured, bringing the total number of bats species known from the reserve to 35. Thus, over half (52%) of Trinidad's 67 bat species occur in this one forest reserve, making it a high priority area for effective protection and management.     

Distribution of cave-dwelling bats and conservation status of underground habitats in the Istanbul area

Populations of cave-dwelling bat species were investigated in the transitory region between the Eastern Thrace and the Western Pontus. Data were collected during 30 surveys in 13 underground sites, 10 of which had not been surveyed previously by bat researchers, between March 1999 and March 2000. Approximately 20 000 bats representing eight species were recorded. Grouping the sites according to their ecological resemblance, by means of cluster and correspondence analyses, yielded different results for the summer and winter data. In summer, there was a partial separation of the sites by their location in biogeographic regions. In winter, no regional grouping was observed. It was concluded that in the transitory region, species distribution does not differ considerably between the Eastern Thracian and Western Pontic ecosystems. In addition, a conservation scoring system is proposed for those sites investigated, their status is evaluated, and the most important local roosts are identified.     

漆树科植物漆酚的多样性及演化关系研究

漆酚是漆树科植物独有的化学成分,具有良好的抗氧化、抗肿瘤、抗病毒等生物活性,极具药物和工业生产开发价值。该研究通过对国内外有关漆树科各类群有关漆酚数据的搜集和整理,开展漆树科漆酚的多样性与分布情况的综合统计;同时在利用核基因ETS和叶绿体基因rps16和trnL-F重建漆树科系统发育树的基础上,探讨漆酚在漆树科及各属间的起源和演化关系。结果表明:(1)漆树科漆酚具有较高的多样性,在其苯环和-R链上都有很大的变异。(2)发现漆酚仅存在于Anacardioideae亚科中,是该亚科的一个重要界定特征。(3)基于漆酚苯环结构和-R链特征的祖先性状重建分析表明,漆树科的漆酚是由邻苯二酚向间苯二酚演化,而漆酚-R链的十五烃(烯)基则是向十七烃(烯)基平行演化。     

PARSIMONY,MOLECULAR EVOLUTION,AND BIOGEOGRAPHY: THE CASE OF THE NORTH AMERICAN GIANT SALAMANDER

To draw biogeographic conclusions about the Central Highlands region of the United States, we reconstructed the phylogeny of hellbender (Cryptobranchus alleganiensis) populations from restriction-site variation in mtDNA. We were unable to root the phylogeny using an outgroup and therefore could not weight restriction-site gains more heavily than site losses. As a result, maximum parsimony results in low phylogenetic resolution because of high levels of homoplasy in the data set. Use of a recently published algorithm based on an explicit model of molecular evolution yielded much greater resolution of the mtDNA relationships. This phylogeny indicates the two subspecies of hellbenders are paraphyletic with respect to one another. Hellbenders found in the southern Ozarks (C. a. bishopi) are either most closely related to populations of C. a. alleganiensis inhabiting the Tennessee River drainage or are so divergent that phylogenetic affinities are undetectable. Extremely low levels of divergence among mtDNA haplotypes found in populations from Pennsylvania, Indiana, Illinois, and the northern Missouri Ozarks suggest a recent, probably post-Pleistocene, invasion of this region from a refugium in one of these areas. Biogeographic hypotheses of the causes and timing of hellbender distributions differ significantly from those postulated from analyses of fish species relationships. Possible reasons for the discrepancy are discussed.     

Phylogenetic relationships of Cornaceae and close relatives inferred from matK and rbcL sequences

Phylogenetic relationships were inferred using nucleotide sequences of the chloroplast gene matK for members of Cornales, a well-supported monophyletic group comprising Cornaceae and close relatives. The shortest trees resulting from this analysis were highly concordant with those based on previous phylogenetic analysis of rbcL sequences. Analysis of a combined matK and rbcL sequence data set (a total of 2652 bp [base pairs]) provided greater resolution of relationships and higher internal support for clades compared to the individual data sets. Four major clades (most inclusive monophyletic groups) of Cornales are indicated by both sets of genes: (1) Cornus-Alangium, (2) nyssoids (Nyssa-Davidia-Camptotheca)- mastixioids (Mastixia, Diplopanax), (3) Curtisia, and (4) Hydrangeaceae-Loasaceae. The combined evidence indicates that clades 2 and 3 are sisters, with clade 4 sister to the remainder of Cornales. These relationships are also supported by other lines of evidence, including synapomorphies in fruit and pollen morphology and gynoecial vasculature. Comparisons of matK and rbcL sequences based on one of the most parsimonious rbcL-matK trees indicate that matK has a much higher A-T content (66.9% in matK vs. 55.8% in rbcL) and a lower transition:transversion ratio (1.23 in matK vs. 2.21 in rbcL). The total number of nucleotide substitutions per site for matK is 2.1 times that of rbcL in Cornales. These findings are similar to recent comparisons of matK and rbcL in other dicots. Variable sites of matK are almost evenly distributed among the three codon positions (1.0:1.0:1.3), whereas variable sites of rbcL are mostly at the third position (1.8:1.0 :7.5). Among- lineages rates of nucleotide substitutions in rbcL are basically homogeneous throughout Cornales, but are more heterogeneous in matK.     

The influence of phylogenetic uncertainty on the detection of positive Darwinian selection

The power of maximum likelihood tests of positive selection on protein-coding genes depends heavily on detecting and accounting for potential biases in the studied data set. Although the influence of transition:transversion and codon biases have been investigated in detail, little is known about how inaccuracy in the phylogeny used during the calculations affects the performance of these tests. In this study, 3 empirical data sets are analyzed using sets of simulated topologies corresponding to low, intermediate, and high levels of phylogenetic uncertainty. The detection of positive selection was largely unaffected by errors in the underlying phylogeny. However, the number of sites identified as being under positive selection tended to be overestimated.     

Naturalists, Molecular Biologists, and the Challenges of Molecular Evolution

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era. This revised version was published online in July 2006 with corrections to the Cover Date.     

Birth and death of orphan genes in Rickettsia

The origin and evolution of the thousands of species-specific genes with unknown functions, the so-called orphan genes, has been a mystery. Here, we have studied the rates and patterns of orphan sequence evolution, using the Rickettsia as our reference system. Of the Rickettsia conorii orphans examined in this study, 80% were found to be short gene fragments or fusions of short segments from neighboring genes. We reconstructed the putative sequences of the full-length genes from which the short orphan fragments are thought to have originated. One of the genes thus reconstructed displays weak similarity to the ankyrin-repeat protein family, an identification that is strongly supported by comparative molecular modeling. Studies of the patterns of gene fragmentation underscore the importance of short repeated sequences as targets for recombination events that result in sequence loss and the formation of short, transient open reading frames. Our analysis demonstrates that gene sequences present in the common ancestor can be inferred even in cases when no full-length open reading frame is present in any of the contemporary species. Such reconstructions support the identification of lost protein functions and hint at important lifestyle changes.