Phylogenetic relationships and divergence times of Charadriiformes genera: multigene evidence for the Cretaceous origin of at least 14 clades of shorebirds

Comparative study of character evolution in the shorebirds is presently limited because the phylogenetic placement of some enigmatic genera remains unclear. We therefore used Bayesian methods to obtain a well-supported phylogeny of 90 recognized genera using 5 kb of mitochondrial and nuclear sequences. The tree comprised three major clades: Lari (gulls, auks and allies plus buttonquails) as sister to Scolopaci (sandpipers, jacanas and allies), and in turn sister to Charadrii (plovers, oystercatchers and allies), as in previous molecular studies. Plovers and noddies were not recovered as monophyletic assemblages, and the Egyptian plover Pluvianus is apparently not a plover. Molecular dating using multiple fossil constraints suggests that the three suborders originated in the late Cretaceous between 79 and 102 Mya, and at least 14 lineages of modern shorebirds survived the mass extinction at the K/T boundary. Previous difficulties in determining the phylogenetic relationships of enigmatic taxa reflect the fact that they are well-differentiated relicts of old, genus-poor lineages. We refrain from suggesting systematic revisions for shorebirds at this time because gene trees may fail to recover the species tree when long branches are connected to deep, shorter branches, as is the case for some of the enigmatic taxa.     

RAG-1 sequences resolve phylogenetic relationships within Charadriiform birds

The Charadriiformes is a large and diverse order of shorebirds currently classified into 19 families, including morphologically aberrant forms that are of uncertain phylogenetic placement within non-passerine birds in general. Recent attempts using morphological characters have failed to recover a well-supported phylogeny depicting higher level relationships within Charadriiformes and the limits to the order, primarily because of inconsistency and homoplasy in these data. Moreover, these trees are incongruent with the relationships presented in the DNA hybridization tapestry of, including the location of the root and the branching order of major clades within the shorebirds. To help clarify this systematic confusion we therefore sequenced the large RAG-1 nuclear exon (2850 bp) from 36 species representing 17 families of shorebirds for which DNA was available. Trees built with maximum parsimony, maximum likelihood or Bayesian methods are topologically identical and fully resolved, with high support at basal nodes. This further attests to the phylogenetic utility of the RAG-1 sequences at higher taxonomic levels within birds. The RAG-1 tree is topologically similar to the DNA hybridization tree in depicting three major subordinal clades of shorebirds, the Charadrii (thick-knees, sheathbills, plovers, oystercatchers, and allies), Scolopaci (sandpipers and jacanas) and the Lari (coursers, pratincoles, gulls, terns, skimmers, and skuas). However, the basal split in the RAG-1 tree is between Charadrii and (Scolopaci+Lari), whereas in the DNA hybridization tree Scolopaci is the sister group to the (Charadrii+Lari). Thus in both of these DNA-based trees the Alcidae (auks, murres, and allies) are not basal among shorebirds as hypothesized in morphological trees, but instead are placed as a tip clade within Lari. The enigmatic buttonquails (Turnicidae), variously hypothesized as being allied to either the Galliformes, Gruiformes, or Charadriiformes, are shown to be a basal lineage in the more conventional Lari clade. Divergence times estimated with rate-smoothing methods and minimum time constraints imposed at nodes with key fossils suggest that Charadriiformes originated in Gondwanaland.     

Population identification of western hemisphere shorebirds throughout the annual cycle

Identification of relationships among geographically distinct populations of migratory species can provide an understanding of breeding and natal philopatry, migration pathways, and population mixing during winter. We used random amplified polymorphic DNA (RAPD) analyses to search for markers specific to difficult-to-differentiate shorebird species (e.g. long-billed dowitcher Limnodromus scolopaceus and short-billed dowitcher L. griseus ) as well as geographically distinct breeding populations of Hudsonian godwits Limosa haemastica , red-necked phalaropes Phalaropus lobatus , semipalmated plovers Charadrius semipalmatus , dunlin Calidris alpina , pectoral sandpipers C. melanotos , semipalmated sandpipers C. pusilla and western sandpipers C. mauri . Markers clearly differentiated all shorebird species. Estimates of population differentiation varied greatly among species ( F _ST= 0.095–0.685) and correlated with interspecific variation in philopatry and geographical separation of breeding populations. We assigned individuals to putative breeding locales with greater certainty in well-differentiated species than in poorly differentiated species. Our findings indicate specific phylogeographical structure varies among species, which has strong implications for conservation of habitats within migratory corridors. We suggest that RAPDs are useful in identifying geographical populations of migratory species and that molecular markers should be considered for tracking migratory birds throughout the annual cycle.     

形目15种鸟类线粒体ND6基因序列差异及其系统进化关系

采用PCR和质粒克隆测序方法 ,首次获得形目 15种鸟类线粒体基因组的ND6基因全长 5 2 2bp的序列。经对位排列 ,序列间未见有插入和缺失 ,共有 2 16个变异位点 ,种间序列差异为 5 17%～ 19 92 %。以白鹳为外群 ,用NJ法构建 15种鸟类的进化关系树。研究结果表明 :构建的系统树将形目 15种鸟类分为 2个支系。第 1支系包括蒙古沙、环颈、灰斑和反嘴鹬。第 2支系包括红脚鹬、林鹬、青脚鹬、翘嘴鹬、翻石鹬、大滨鹬、尖尾滨鹬、斑尾塍鹬、中杓鹬、大杓鹬和白腰杓鹬 ,其中鹬属的 3个种和杓鹬属的 3个种分别组成一个单系 ;翘嘴鹬和翻石鹬、大滨鹬和尖尾滨鹬分别聚为姊妹群 ,表现出较近的亲缘关系 ;斑尾塍鹬独立分支出来。分子证据提示 :鹬科中的塍鹬属、科中的斑属应提升为亚科分类阶元 ;反嘴鹬与科鸟类亲缘关系较近 ,组成一个单系 ,将其归入科下属的一个类群更为合理 ,与核型研究结果及Sibley新分类体系的观点相一致 [动物学报 49(1) :6 1～ 6 7,2 0 0 3]。     

Foraging behaviour of western sandpipers changes with sediment temperature: implications for their hemispheric distribution

Migratory shorebirds need to replenish their energy reserves by foraging at stop-over sites en route. Adjusting their foraging behaviour to accommodate variation in local prey availability would therefore be advantageous. We test whether western sandpipers (Calidris mauri), a sexually dimorphic shorebird, adjust their foraging behaviour in response to local changes in prey availability, as inferred by changes in diurnal time and sediment temperature. Both males and females showed quantitative changes to foraging mode in relation to each of these variables. Probing, for example, which is used to exploit infaunal prey, was significantly more common at higher temperatures. The results presented here are consistent with the notion that western sandpipers can adjust their foraging behaviour in response to variation in prey availability. Further, we speculate that temperature-induced changes to prey location may contribute to the striking sexual segregation observed for this species during the non-breeding season.     

Niche dynamics of shorebirds in Delaware Bay: Foraging behavior,habitat choice and migration timing

Niche differentiation through resource partitioning is seen as one of the most important mechanisms of diversity maintenance contributing to stable coexistence of different species within communities. In this study, I examined whether four species of migrating shorebirds, dunlins (Calidris alpina), semipalmated sandpipers (Calidris pusilla), least sandpipers (Calidris minutilla) and short-billed dowitchers (Limnodromus griseus), segregate by time of passage, habitat use and foraging behavior at their major stopover in Delaware Bay during spring migration. I tested the prediction that most of the separation between morphologically similar species will be achieved by differential migration timing. Despite the high level of overlap along observed niche dimensions, this study demonstrates a certain level of ecological separation between migrating shorebirds. The results of analyses suggest that differential timing of spring migration might be the most important dimension along which shorebird species segregate while at stopover in Delaware Bay. Besides differences in time of passage, species exhibited differences in habitat use, particularly least sandpipers that foraged in vegetated areas of tidal marshes more frequently than other species, as well as short-billed dowitchers that foraged in deeper water more often than small sandpipers did. Partitioning along foraging techniques was less prominent than segregation along temporal or microhabitat dimensions. Such ranking of niche dimensions emphasizes significance of temporal segregation of migratory species – separation of species by time of passage may reduce the opportunity for interspecific aggressive encounters, which in turn can have positive effects on birds' time and energy budget during stopover period.     

Surface tension prey transport in shorebirds: how widespread is it?

Surface tension prey transport is a feeding mechanism employing the surface tension of water surrounding prey to transport prey from bill tip to mouth. Previously, it has been demonstrated only in the Red-necked Phalarope Phalaropus lobatus. On the basis of a model of the bill morphology necessary for this method of prey transport, I suggest that many species of shorebird should be capable of surface tension feeding. Laboratory investigations of the feeding mechanics of Wilson's Phalarope Phalaropus tricolor , Western Sandpiper Calidris mauri and Least Sandpiper Calidris minutilla demonstrated that all three use surface tension transport of prey when feeding in water. I examined interspecific variation in the performance of this feeding mechanism with a high-speed video system and a customized motion analysis system. Exploratory analyses indicated significant interspecific variation in distance the prey is transported per cycle of mandibular spreading, gape increase per unit transport, speed of transport, total number of cycles necessary to complete transport and total time to complete transport. The calidrid sandpipers also occasionally used other feeding mechanisms in conjunction with surface tension transport of prey. The discovery that these sandpipers, which normally obtain prey by probing, are capable of surface tension transport of prey implies that the capacity to employ this feeding mechanism may be widespread in the Scolopacidae and may have been a significant factor in the evolutionary radiation of phalaropes into aquatic environments.     

长江口杭州湾鸻形目鸟类群落季节变化和生境选择

在长江口南岸杭州湾北岸滨海滩涂进行了鸻形目鸟类的资源调查,以及鸟类栖息地选择模式分析,2004年3月至2005年1月共统计到鸟类25种,春季优势种为大缤鹬(Calidris tenuirostris)、尖尾缤鹬(Calidris alpine)和红颈滨鹬(Calidris ruficollis);夏季为环颈(Charadrius alexandrinus)、青脚鹬(Tringa nebularia)和蒙古沙(Charadrius mongolus),秋季为环颈、红颈滨鹬和青脚鹬,冬季为黑腹滨鹬(Calidris alpina)、环颈和泽鹬(Tringa stagnatilis),鸟类总体数量呈春季>秋季>冬季>夏季,海堤外(自然滩涂)和堤内(人工湿地)鸟类种数四季大致相等,但鸟类平均密度季节差异显著。通过对样点内鸟类与环境因子进行多元分析,初步总结出堤外滩宽和光滩宽是影响鸟类栖息的最关键因子,海三棱草(Scirpus× mariquete)覆盖比例和潮上坪宽度的影响程度次之。堤内浅水塘比例和裸地比例是影响形目鸟类分布的关键因子,海三棱草覆盖比例也起正向作用。而人类干扰大、芦苇(Phragmites communis)/互花米草(Spartina alternifloral)密植和高水位的区域不利于鸟类利用。     

Foraging Ecology of Fall-Migrating Shorebirds in the Illinois River Valley

Populations of many shorebird species appear to be declining in North America, and food resources at stopover habitats may limit migratory bird populations. We investigated body condition of, and foraging habitat and diet selection by 4 species of shorebirds in the central Illinois River valley during fall migrations 2007 and 2008 (Killdeer [Charadrius vociferus], Least Sandpiper [Calidris minutilla], Pectoral Sandpiper [Calidris melanotos], and Lesser Yellowlegs [Tringa flavipes]). All species except Killdeer were in good to excellent condition, based on size-corrected body mass and fat scores. Shorebird diets were dominated by invertebrate taxa from Orders Diptera and Coleoptera. Additionally, Isopoda, Hemiptera, Hirudinea, Nematoda, and Cyprinodontiformes contribution to diets varied by shorebird species and year. We evaluated diet and foraging habitat selection by comparing aggregate percent dry mass of food items in shorebird diets and core samples from foraging substrates. Invertebrate abundances at shorebird collection sites and random sites were generally similar, indicating that birds did not select foraging patches within wetlands based on invertebrate abundance. Conversely, we found considerable evidence for selection of some diet items within particular foraging sites, and consistent avoidance of Oligochaeta. We suspect the diet selectivity we observed was a function of overall invertebrate biomass (51.2±4.4 [SE] kg/ha; dry mass) at our study sites, which was greater than estimates reported in most other food selection studies. Diet selectivity in shorebirds may follow tenants of optimal foraging theory; that is, at low food abundances shorebirds forage opportunistically, with the likelihood of selectivity increasing as food availability increases. Nonetheless, relationships between the abundance, availability, and consumption of Oligochaetes for and by waterbirds should be the focus of future research, because estimates of foraging carrying capacity would need to be revised downward if Oligochaetes are truly avoided or unavailable for consumption.     

A supertree approach to shorebird phylogeny

Background

Order Charadriiformes (shorebirds) is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species. Here we use the matrix representation with parsimony method to produce the first fully inclusive supertree of Charadriiformes. We also provide preliminary estimates of ages for all nodes in the tree.

Results

Three main lineages are revealed: i) the plovers and allies; ii) the gulls and allies; and iii) the sandpipers and allies. The relative position of these clades is unresolved in the strict consensus tree but a 50% majority-rule consensus tree indicates that the sandpiper clade is sister group to the gulls and allies whilst the plover group is placed at the base of the tree. The overall topology is highly consistent with recent molecular hypotheses of shorebird phylogeny.

Conclusion

The supertree hypothesis presented herein is (to our knowledge) the only complete phylogenetic hypothesis of all extant shorebirds. Despite concerns over the robustness of supertrees (see Discussion), we believe that it provides a valuable framework for testing numerous evolutionary hypotheses relating to the diversity of behaviour, ecology and life-history of the Charadriiformes.

     

Western sandpipers have altered migration tactics as peregrine falcon populations have recovered

The presence of top predators can affect prey behaviour, morphology and life history, and thereby can produce indirect population consequences greater and further reaching than direct depredation would have alone. Raptor species in the Americas are recovering since restrictions on the use of dichlorodiphenyltrichloroethane (DDT) and the implementation of conservation measures, in effect constituting a hemisphere-wide predator-reintroduction experiment, and profound effects on populations of their prey are to be expected. Here, we document changes in the behaviour of western sandpipers (Calidris mauri) at migratory stopover sites over two decades. Since 1985, migratory body mass and stopover durations of western sandpipers have fallen steadily at some stopovers in the Strait of Georgia, British Columbia. Comparisons between years, sites and seasons strongly implicate increasing danger from the recovery of peregrine falcons (Falco peregrinus) as a causal factor. A decade-long ongoing steep decline in sandpiper numbers censused on our study site is explained entirely by the shortening stopover duration, rather than fewer individuals using the site. Such behavioural changes are probably general among migratory shorebird species, and may be contributing to the widespread census declines reported in North America.     

An Experimental Assessment of Vehicle Disturbance Effects on Migratory Shorebirds

ABSTRACT Off-road vehicle (ORV) traffic is one of several forms of disturbance thought to affect shorebirds at migration stopover sites. Attempts to measure disturbance effects on shorebird habitat use and behavior at stopover sites are difficult because ORV disturbance is frequently confounded with habitat and environmental factors. We used a before-after-control-impact experimental design to isolate effects of vehicle disturbance from shorebird responses to environmental and habitat factors. We manipulated disturbance levels within beach closures along South Core Banks, North Carolina, USA, and measured changes in shorebird abundance and location, as well as the activity of one focal species, the sanderling (Calidris alba), within paired control and impact plots. We applied a discrete treatment level of one flee-response-inducing event every 10 minutes on impact plots. We found that disturbance reduced total shorebird and black-bellied plover (Pluvialis squatarola) abundance and reduced relative use of microhabitat zones above the swash zone (wet sand and dry sand) by sanderlings, black-bellied plovers, willets (Tringa semipalmata), and total shorebirds. Sanderlings and total shorebirds increased use of the swash zone in response to vehicle disturbance. Disturbance reduced use of study plots by sanderlings for resting and increased sanderling activity, but we did not detect an effect of vehicle disturbance on sanderling foraging activity. We provide the first estimates of how a discrete level of disturbance affects shorebird distributions among ocean beach microhabitats. Our findings provide a standard to which managers can compare frequency and intensity of disturbance events at other shorebird stopover and roosting sites and indicate that limiting disturbance will contribute to use of a site by migratory shorebirds.     

The effects of habitat on the vigilance of shorebirds: Is visibility important?

Previous studies of vigilance have concentrated on situations where the prey species has an unimpaired view of its surroundings. Here the effects of reduced visibility caused by objects adjacent to the prey are studied in two species of shorebird. A reduction in visibility causes an increase in the level of vigilance, indicating an increase in vulnerability despite the greater degree of camouflaging. This increase is due to individuals being less able to see both approaching predators and their neighbours. Turnstones, Arenaria interpres, and purple sandpipers, Calidris maritima, show very similar increases in the level of vigilance with decreasing visibility, but achieve these increases by different means: turnstones lengthen the duration of each vigilant scan, while purple sandpipers scan more often. Increasing scanning rate produces a shortened interval between scans, which reduces the risk of being caught unawares by an approaching predator. However, it may also reduce feeding efficiency, and it is suggested that this might be more serious in turnstones due to greater handling times for food items, so causing them to adopt a different strategy to increase vigilance.     

Seasonal change and habitat selection of shorebird community at the South Yangtze River Mouth and North Hangzhou Bay, China

Coastal regions are important habitats for migratory shorebirds. The aim of the study is to understand habitat use by migratory shorebirds and to develop a conservation strategy in the sustainable use of wetlands. From March 2004 to January 2005, we conducted a seasonal shorebirds census in ten coastal habitats along the South Yangtze River mouth and North Hangzhou Bay, simultaneously examining the relative seasonal abundance of shorebirds and their spatial distribution. A total of 25 species were identified, the dominant seasonal species were Great Knot (Calidris tenuirostris), Sharp-tailed Sandpiper (Calidris alpine) and Red-necked Stint (Calidris ruficollis) in spring; Kentish Plover (Charadrius alexandrinus), Common Greenshank(Tringa nebularia) and Lesser Sand Plover (Charadrius mongolus) in summer; Kentish Plover, Red-necked Stint and Common Greenshank in autumn; Dunlin(Calidris alpine), Kentish Plover and Marsh Sandpiper (Tringa stagnatilis) in winter. These species accounted for more than 85% of the total shorebirds. The numbers of shorebirds counted was highest in spring and then in autumn, winter and summer respectively. Among the four seasons, there were few significant differences in the number of bird species between the sites outside the seawall (intertidal mudflat) and the sites inside the seawall (artificial wetland), but the average density of shorebirds was obviously different. The habitat-selection analysis of the environmental factors (outside and inside the seawall) impacting on the shorebird community was made in the 10 study sites with Canonical Correspondence Analysis. The study results indicated that: (1) Outside the seawall, the widths of the total intertidal mudflat and bare mudflat were the key factors affecting the shorebirds; the proportion of bulrush (Scirpusmariquete) covering and supertidal mudflat width had a positive correlation with the abundance of birds, while human disturbance and the proportion of both reed (Phragmites communis) and smooth cord-grass (Spartina alterniflora) covering in total surveyed areas had negative impacts on bird numbers; (2) Inside the seawall, the proportions of areas with shallow water and mudflats occupying the total surveyed area were key factors influencing the number of birds; the size of the bulrush area should have a positive impact on the appearance of shorebirds. Habitats with heavy human disturbance, dense reed and smooth cord-grass or a high water level were not conducive to be inhabited by shorebirds.     

鸟类核型研究Ⅳ.鸻形目(CHARADRIIFORMES,AVES)10种

本文报道了鸻形目鸟类2科10种的核型。并和已报道过的鸻形目6种21种的核型进行了比较研究。我们发现鸻形目鸟类中存在两种截然不同的核型,推断它们可能有不同的进化起源。这与Sibley等人(1987)通过对DNA—DNA杂交数据的分析得出的结果相似。     

True and false gharials: a nuclear gene phylogeny of crocodylia

The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.     

Seasonal change and habitat selection of shorebird community at the South Yangtze River Mouth and North Hangzhou Bay, China

Coastal regions are important habitats for migratory shorebirds. The aim of the study is to understand habitat use by migratory shorebirds and to develop a conservation strategy in the sustainable use of wetlands. From March 2004 to January 2005, we conducted a seasonal shorebirds census in ten coastal habitats along the South Yangtze River mouth and North Hangzhou Bay, simultaneously examining the relative seasonal abundance of shorebirds and their spatial distribution. A total of 25 species were identified, the dominant seasonal species were Great Knot (Calidris tenuirostris), Sharp-tailed Sandpiper (Calidris alpine) and Red-necked Stint (Calidris ruficollis) in spring; Kentish Plover (Charadrius alexandrinus), Common Greenshank(Tringa nebularia) and Lesser Sand Plover (Charadrius mongolus) in summer; Kentish Plover, Red-necked Stint and Common Greenshank in autumn; Dunlin(Calidris alpine), Kentish Plover and Marsh Sandpiper (Tringa stagnatilis) in winter. These species accounted for more than 85% of the total shorebirds. The numbers of shorebirds counted was highest in spring and then in autumn, winter and summer respectively. Among the four seasons, there were few significant differences in the number of bird species between the sites outside the seawall (intertidal mudflat) and the sites inside the seawall (artificial wetland), but the average density of shorebirds was obviously different. The habitat-selection analysis of the environmental factors (outside and inside the seawall) impacting on the shorebird community was made in the 10 study sites with Canonical Correspondence Analysis. The study results indicated that: (1) Outside the seawall, the widths of the total intertidal mudflat and bare mudflat were the key factors affecting the shorebirds; the proportion of bulrush (Scirpus×mariquete) covering and supertidal mudflat width had a positive correlation with the abundance of birds, while human disturbance and the proportion of both reed (Phragmites communis) and smooth cord-grass (Spartina alterniflora) covering in total surveyed areas had negative impacts on bird numbers; (2) Inside the seawall, the proportions of areas with shallow water and mudflats occupying the total surveyed area were key factors influencing the number of birds; the size of the bulrush area should have a positive impact on the appearance of shorebirds. Habitats with heavy human disturbance, dense reed and smooth cord-grass or a high water level were not conducive to be inhabited by shorebirds.     

A multigenic perspective on phylogenetic relationships in the largest family of salamanders, the Plethodontidae

Despite several recent studies, the phylogeny of plethodontid salamanders is not yet fully resolved and the phylogenetic positions of several key genera, especially Aneides, Hemidactylium, Hydromantes and Karsenia, are contentious. Here we present a combined dataset of complete mitochondrial genomes and three nuclear loci for 20 species (16 genera) of plethodontids, representing all major clades in the family. The combined dataset without mitochondrial third codon positions provides a fully resolved, statistically well-supported tree. In this topology two major clades are recovered. A northern clade includes Aneides, Desmognathus, Ensatina, Hydromantes, Karsenia, Phaeognathus and Plethodon, with Plethodon being the sister taxon to the rest of the clade. Hydromantes and Karsenia are sister taxa, and Aneides is recovered as the sister taxon to Ensatina. Desmognathus+Phaeognathus form the sister taxon to Aneides+Ensatina. An eastern/southern clade comprises two subclades. One subclade, the spelerpines (Eurycea, Gyrinophilus, Pseudotriton, Stereochilus, Urspelerpes) is the sister taxon to a subclade comprising Hemidactylium, Batrachoseps and the tropical plethodontids (represented by Bolitoglossa, Nototriton and Thorius). In this topology Hemidactylium is well-supported as the sister taxon to Batrachoseps. Only when mitochondrial third codon positions are included using maximum likelihood analysis is Hemidactylium recovered as the sister taxon to Batrachoseps+tropical genera. Hypothesis testing of alternative topologies supports these conclusions. On the basis of these results we propose a conservative taxonomy for Plethodontidae.     

Molecular phylogeny of Malagasy reed frogs, Heterixalus, and the relative performance of bioacoustics and color-patterns for resolving their systematics

The members of the genus Heterixalus constitute one of the endemic frog radiations in Madagascar. Here we present a complete species-level phylogeny based on DNA sequences (4876 base pairs) of three nuclear and four mitochondrial markers to clarify the phylogenetic relationships among and within all known species of this genus, as well as the phylogenetic position of the monospecific Seychellean Tachycnemis seychellensis. Although the performance to resolve supported clades of Heterixalus species differed among the investigated gene fragments when analyzed separately, we could identify five well-supported species groups within Heterixalus in the combined analysis of all gene fragments. Our data strongly support a Heterixalus-Tachycnemis clade, and indicate the probable monophyly of Heterixalus placed sister to Tachycnemis. However, the diversification of these lineages may have happened in a short interval of time, leading to an unstable placement of Tachycnemis in the single-gene fragment phylogenies. Referring to the hitherto existing classification of Heterixalus, which is predominantly based on chromatic and bioacoustic characters, we examined the relative performance of these data sets relative to our molecular phylogeny. A Bayesian tree reconstructed with a bioacoustic data set yielded a higher resemblance to the molecular phylogeny than a tree constructed using a chromatic data set, which supports the importance of bioacoustic characters for systematic analyses of these anurans.     

Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family

Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.