The embryonic development of the Egyptian cobra Naja h. haje (Squamata: Serpentes: Elapidae)

The Egyptian cobra, Naja h. haje, is the largest of the African cobras and is a member of a successful and medically important species complex found throughout Africa, north and south of the Sahara, as well as across the Arabian Peninsula to Oman. Although its phylogenetic position and venom characteristics have been well studied, its development has not. Here, we present a normal staging table for N. h. haje, based on external features. Comparison with firstly the Asian monocled cobra, Naja kaouthia, and then with the small number of other oviparous snake species, allowed us to examine whether differences between two species in the same genus were of the same type and magnitude as those between unrelated genera. In fact, at least with respect to external features, we found a similar level of disparity. N. h. haje embryos lagged behind those of N. kaouthia in body and head scale development, size in ovo and hatchling length, despite having a slightly shorter incubation period and a somewhat larger adult size. Some of these differences may have been the result of differing incubation temperatures. Nonetheless, there does appear to be a broadly conserved pattern of in ovo development in at least macrostomatan snakes.     

Monophyly of elapid snakes (Serpentes: Elapidae). An assessment of the evidence

The defining morphological characters of the family Elapidae are analysed in an attempt to evaluate whether the front-fanged, proteroglyphous, snakes constitute a natural (monophyletic) group or whether proteroglyphy is more likely to be a condition achieved independently by a number of higher snake lineages. The evidence relating to presumed elapids whose affinities have been questioned, namely a South African genus Homoroselaps and New World proteroglyphs (Micrurus and Micruroides) , is examined. It concluded that Homoroselaps is a genuinely equivocal case, the evidence for its inclusion in the Elapidae is balanced by features which suggest that it is more closely related to the Aparallactinae. However, Micrurus and Micruroides seem clearly to be more closely related to undisputed elapids than to any other caenophidians. It is suggested that, at least for the present, the family Elapidae be retained in its broad sense to include all proteroglyphous snakes.     

Notes on the Australian sea-snake Ephalophis greyi M. Smith (Serpentes:Elapidae, Hydrophiinae) and the origin and classification of sea-snakes

The type and two other specimens of Ephalophis greyi are described. The venom gland musculature is of the Demansia type, with an isolated muscle running from the quadrate to the rear of the venom gland. The only other hydrophiine with the Demansia pattern of venom gland musculature, Hydrophis mertoni Roux, is referred, for this and other reasons, to the genus Ephalophis as E. mertoni (Roux). Some notes on a skull of E. mertoni are presented, along with a revised diagnosis of Ephalophis. The Demansia pattern of venom gland muscles seen in Ephalophis is primitive for the Hydrophiinae and other members of that subfamily have secondarily taken on a Glyphodon type of musculature of the venom gland by loss of the muscle slip from quadrate to gland. The Demansia group of terrestrial elapids, particularly the genus Drepanodontis Worrell, stand close to the origin of the Hydrophiinae. A classification of the Hydrophiinae into three generic groups is presented, with Ephalophis, Aipysurus , and Emydocephalus referred to an Aipysurus group.     

A multivariate morphometric analysis and systematic review of Pseudonaja (Serpentes,Elapidae, Hydrophiinae)

Pseudonaja is a clade of seven nominal species of elapid snakes distributed throughout Australia and in southern New Guinea. The species‐level systematics of this group is generally considered to be problematic. A recent phylogenetic analysis of mitochondrial DNA sequences for a geographically extensive series of Pseudonaja specimens revealed nine major clades, of which six largely coincide with nominal species (P. affinis, P. guttata, P. inframacula, P. ingrami, P. modesta and P. textilis). The three remaining clades are composed of specimens currently referred to P. nuchalis. This paper presents a multivariate analysis of 30 morphometric variables recorded for 220 specimens, representing the P. affinis, P. inframacula, P. textilis and three P. nuchalis clades (P. guttata, P. ingrami and P. modesta are well‐demarcated species and, accordingly, were not considered). The morphometric data readily separate these putative lineages, affording compelling evidence that they constitute evolutionary species. The names aspidorhyncha and mengdeni are resurrected for two of the three species presently recognized as P. nuchalis. These species, P. affinis, P. inframacula, P. nuchalis and P. textilis are redescribed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 171–197.     

Ottia meiospora (Ottiaceae,Rhodophyta), a new genus and family endophytic within the thallus of Nothocladus (Batrachospermales,Rhodophyta)

A new genus, Ottia, and family, Ottiaceae, are proposed within the Acrochaetiales to accommodate the uniseriate red algal endophyte of batrachspermalean taxa previously named Balbiania meiospora. Prior to this study, Balbiania investiens was transferred to its own family and order (Balbianiales) based on comparative DNA sequence data and a distinctive reproductive morphology. However, the second species described in this genus, B. meiospora, continued to be treated as a species of Audouinella (A. meiospora) pending further investigation. Phylogenetic analyses of sequence data confirmed only a distant relationship between the two endophytes, and a closer alliance of B. meiospora to Acrochaetiales. The data also showed that Ottia meiospora was the deepest diverging lineage in the Acrochaetiales, sister to all of the currently recognized genera and families. In this study, we review the classification of what we now call O. meiospora – reported from Australia, New Zealand and Brazil – based on sequence and morphological data. Morphological observations provided little clarity around the reproductive morphology or the life cycle of this endophyte of Nothocladus s. lat. found commonly in mainland Australia but, to date, less so in New Zealand.     

Dictyonema Hall and its importance for the evolutionary history of the Graptoloidea

Dictyonema retiforme has been regarded as the benthic ancestor to the planktic Graptoloidea, represented by the earliest planktic Rhabdinopora flabelliformis and its descendants. The revision of the type material of Dictyonema retiforme, the type species of the genus Dictyonema, from the Silurian of New York State shows compound stipes formed by the complexly growing and overlapping tubular thecae of acanthograptid type. The connections between adjacent stipes are formed by thecal tubes or thecal bridges and not by dissepiments. Thus, the species has to be transferred to the Acanthograptidae and cannot be regarded as being related to the early planktic Graptoloidea. The tubarium meshwork of Dictyonema is phylogenetically unrelated to the meshwork of the planktic Rhabdinopora, and represents a case of convergent evolution. The origins of the planktic graptoloids lie among members of middle to upper Cambrian Dendrograpidae, as can be seen from the thecal style and the triad budding patterns with regularly developed bithecae in this group.     

The evolutionary history of the ‘alba’ polymorphism in the butterfly subfamily Coliadinae (Lepidoptera: Pieridae)

Polymorphisms are common in the natural world and have played an important role in our understanding of how selection maintains multiple phenotypes within extant populations. Studying the evolutionary history of polymorphisms has revealed important features of this widespread form of phenotypic diversity, including its role in speciation, niche breadth, and range size. In the present study, we examined the evolutionary history of a ubiquitous colour polymorphism in the sulphur butterflies (subfamily: Coliadinae) termed the ‘alba’ polymorphism. We investigated the origin and stability of the ‘alba’ polymorphism using ancestral state reconstruction analysis. Our results indicate that the ancestor of the Coliadinae was polymorphic and that this polymorphism has undergone repeated transitions to monomorphism. Repeated loss of polymorphism suggests that the ‘alba’ polymorphism may be relatively unstable over evolutionary time. These results provide a framework for future studies on the origin and maintenance of the ‘alba’ polymorphism and guide the direction of future hypotheses. We discuss these results in light of current understandings of how the ‘alba’ polymorphism is maintained in extant populations.     

Adaptive radiations in butterflies: evolutionary history of the genus Erebia (Nymphalidae: Satyrinae)

We studied the speciose butterfly genus Erebia by reconstructing its phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification for its lineages and employed a biogeographical analysis in order to reconstruct its evolutionary history. DNA sequence data from one mitochondrial gene and three nuclear genes were analyzed for a total of 74 species in Erebia. The estimated dates of origin and diversification for clades, in combination with a biogeographical analysis, suggest that the genus originated in Asian Russia and started its diversification process around 23 Myr. An important event was the dispersal of a lineage from Asia to Western Europe between 23 and 17 Myr, which allowed the radiation of most of species in the genus. The diversification pattern is consistent with a model of diversity limited by clade richness, which implies an early rapid diversification followed by deceleration due to a decrease in speciation. We argue that these characteristics of the evolutionary history of Erebia are consistent with a density‐dependent scenario, with species radiation limited by filling of niche space and reduced resources. We found that the Boeberia parmenio appears strongly supported in the genus Erebia and therefore we place Boeberia Prout, 1901 as a junior synonym of Erebia Dalman, 1816 ( syn. nov. ).     

Geographical origin of Leucobryum boninense Sull. & Lesq. (Leucobryaceae,Musci) endemic to the Bonin Islands,Japan

Leucobryum boninense is endemic to the Bonin Islands, Japan, and its related species are widely distributed in Asia and the Pacific. We aimed to clarify the phylogenetic relationships among Leucobryum species and infer the origin of L. boninense. We also describe the utility of the chloroplast trnK intron including matK for resolving the phylogenetic relationships among Leucobryum species, as phylogenetic analyses using trnK intron and/or matK have not been performed well in bryophytes to date. Fifty samples containing 15 species of Leucobryum from Asia and the Pacific were examined for six chloroplast DNA regions including rbcL, rps4, partial 5′ trnK intron, matK, partial 3′ trnK intron, and trnL‐F intergenic spacer plus one nuclear DNA region including ITS. A molecular phylogenetic tree showed that L. boninense made a clade with L. scabrum from Japan, Taiwan and, Hong Kong; L. javense which is widely distributed in East and Southeast Asia, and L. pachyphyllum and L. seemannii restricted to the Hawaii Islands, as well as with L. scaberulum from the Ryukyus, Japan, Taiwan, and southeastern China. Leucobryum boninense from various islands of the Bonin Islands made a monophylic group that was closely related to L. scabrum and L. javense from Japan. Therefore, L. boninense may have evolved from L. scabrum from Japan, Taiwan, or Hong Kong, or L. javense from Japan. We also described the utility of trnK intron including matK. A percentage of the parsimony‐informative characters in trnK intron sequence data (5.8%) was significantly higher than that from other chloroplast regions, rbcL (2.4%) and rps4 (3.2%) sequence data. Nucleotide sequence data of the trnK intron including matK are more informative than other chloroplast DNA regions for identifying the phylogenetic relationships among Leucobryum species.     

Early diversification of sperm size in the evolutionary history of the old world leaf warblers (Phylloscopidae)

Sperm morphological traits are highly variable among species and are commonly thought to evolve by post‐copulatory sexual selection. However, little is known about the evolutionary dynamics of sperm morphology, and whether rates of evolutionary change are variable over time and among taxonomic groups. Here, we examine sperm morphology from 21 species of Old World leaf warblers (Phylloscopidae), a group of generally dull, sexually monochromatic birds, which are known to have high levels of extra‐pair paternity. We found that sperm length differs markedly across species, spanning about 40% of the range observed across a larger selection of passerine birds. Furthermore, we found strong support for an ‘early‐burst’ model of trait evolution, implying that the majority of divergence in sperm length has occurred early in the evolutionary history of this clade with subsequent evolutionary stasis. This large early divergence matches the early divergence reported in ecological traits (i.e. body size and feeding behaviour). Our findings demonstrate that rates of evolution in sperm morphology can change over time in passerine taxa, and that evolutionary stasis in sperm traits can occur even in species exhibiting characteristics consistent with moderate‐to‐high levels of sperm competition. It remains a major challenge to identify the selection mechanisms and possible constraints responsible for these variable rates of sperm evolution.     

Beta‐globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta‐globin haplotypes. Haplotype A is very similar to the goat beta‐globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta‐C globin, which encodes a globin with high oxygen affinity. We surveyed the beta‐globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2–3 million years old. Approximately 40 kb of the sequence flanking the ~37‐kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta‐globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40‐kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40‐kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non‐Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.     

The evolutionary history and taxonomic reevaluation of the Japanese coral snake,Sinomicrurus japonicus (Serpentes,Elapidae), endemic to the Ryukyu Archipelago,Japan, by use of molecular and morphological analyses

Sinomicrurus japonicus has a conspicuous colour pattern of longitudinal black stripes and transverse sets of black and white bands with an orange‐reddish background colour. The pattern varies markedly among island populations, and thus, three subspecies have been recognized. We conducted molecular phylogenetic analyses on the island populations to clarify the evolutionary trajectory of such colour patterns and reevaluate the current classification accordingly. The results indicated relatively deep allopatric divergences within S. j. boettgeri, paraphyly of S. j. boettgeri against other two subspecies, and two independent derivations of S. j. takarai from boettgeri‐like ancestors. Detailed morphological analyses revealed that variations in the boettgeri and takarai forms were more or less continuous and that differences between the two takarai populations were very small. From these results, we propose synonymizing S. j. takarai with S. j. boettgeri. Morphological differences between the genetically most distant populations of S. j. boettgeri were also small, whereas the japonicus form was distinct from the remainder. Considering the possible evolution of S. j. japonicus through peripheral isolation, we propose retention of these two subspecies. This study provides a basis for future work on the adaptive significance of geographic variation in the colour pattern of S. japonicus.     

Glass in the water: Molecular phylogenetics and evolution of Indian glassy perchlets (Teleostei: Ambassidae)

Glassfishes of the family Ambassidae, comprising around 50 species, are distributed in the Indo‐West Pacific where they inhabit marine, estuarine, and freshwater ecosystems. We investigated for the first time the molecular phylogenetic and evolutionary relationships of this group using a combined dataset of mitochondrial and nuclear genes, particularly focusing on the taxa occurring in the Indian subcontinent. Results revealed that marine and freshwater genera of Ambassidae diverged during the Paleocene (~62 mya). The enigmatic monotypic genus Chanda is nested within the larger clade currently recognized as Parambassis, indicating its paraphyly. Based on cleared and stained osteological preparations and phylogenetic placement of Chanda nama, we hypothesize that the elongated and protruding lower jaw is an autapomorphic character that might have evolved for the lepidophagous habit of the species. The southern Indian species of Parambassis, Parambassis dayi, and Parambassis thomassi, which formed a monophyletic group, probably diverged from other species of Parambassis and Chanda nama around the Eocene (~42 mya) and can potentially be recognized as a distinct genus in view of the apomorphic characters such as the presence of serration on the ventral fringe of interopercle, densely serrated palatine and ectopterygoid, and the presence of more than 30 serrations along the lower preopercle and the posterior edge. Our analysis provides new insights into the evolution and phylogenetic relationships of glassy perchlets, including detailed relationships among the Indian species within this family.     

Postovipositional development of the sand snake Psammophis sibilans (Serpentes:Lamprophiidae) in comparison with other snake species

Characterizing and comparing developmental progress across different species helps to interpret how different or similar body forms evolved. We present an embryonic table for the oviparous African Sand Snake Psammophis sibilans from the Lamprophidae family, describing its postovipositional in ovo development. Psammophis is a good model of a genus that is widely distributed in Africa and Asia and includes 22 species. We describe ten embryonic stages based on the development of externally visible morphological characteristics such as; pharyngeal arches, facial processes, eyes, scales, body pigmentation and body colour pattern development. This study discusses the development of this snake and compares it with that of the closely related brown house snake Lamprophis fulliginosus (Lamprophidae) and the medically important venomous cobras Naja haje haje and Naja kaouthia from the sister lineage Elapidae. The distantly related basal snake Python sebae, which displays different morphology and behaviour, was chosen for deeper insight into the evolution of body structures within the snake clade. We found interspecific differences in the relative stage of development of embryonic structures at the time of oviposition and during postovipositional embryonic development. One of the outcomes of this study is that embryonic structures such as the pharyngeal processes, eye pigmentation and scales are interspecifically conservative in regard to timing of morphodifferentiation, while body pigmentation, colour and colour pattern are interspecifically plastic in their temporospatial development.     

A genetic perspective on the taxonomy and evolution of the medically important flea,Dinopsyllus ellobius (Siphonaptera: Dinopsyllinae), and the resurrection of Dinopsyllus abaris

Dinopsyllus ellobius is considered a common and widespread flea in southern Africa and can act as a vector for plague. Due to differences in the interpretation of geographical variation in male sternite VIII, the taxonomy of the species is characterized by uncertainty. In an attempt to provide a better understanding of the systematics of D. ellobius, and also to provide new insights into the mechanisms that play a role in the diversification of the taxon, we sampled 830 small mammals at 31 localities throughout the distribution range of the parasite. Mitochondrial cytochrome c oxidase subunit II (COII) sequence data were generated for 151 D. ellobius specimens from 19 positive localities and this data set was supplemented with partial data derived from an elongation factor 1 alpha (EF1‐α) intron. A parsimony haplotype network of the mtDNA and a Splitstree analyses revealed the existence of two genetic clades that were separated by 5.53% (± 1.78) sequence divergence. Although the nuclear DNA data were unresolved, significant size differences were detected between head, coxa, femur and tibia lengths of male individuals belonging to the two mtDNA lineages. The exact mechanisms that could have caused the diversification among lineages are not clear but the two lineages seem to be geographically separated and may have different ecological requirements. The present study strongly supports the notion that the two lineages are representative of D. ellobius (probably more associated with the host body and better adapted to mesic conditions) and Dinopsyllus abaris (probably more associated with the host nest and diverse climatic conditions) as originally proposed based on the single morphological character confined to male sternite VIII.     

New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates

Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug‐resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum‐like isolates (infecting non‐human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.     

Gerarda prevostiana(Eydoux and Gervais,1837)(Squamata:Serpentes:Homalopsidae),a New Snake for Borneo

A new record of the homalopsid snake, Gerarda prevostiana is presented from a mangrove-dominated patch in the vicinity of Kampung Bako, Sarawak, East Malaysia, and this comprises the first published record from the Sundaic Island of Borneo. A possible second locality for the species is a ca. 6.68 km site to its northeast, Kampung Buntal, based on an unlocated museum specimen. The species is widespread in mainland Southeast Asia, with additional records to the west(the Indian Subcontinent) and east(the Philippines Archipelago), but was previously unrecorded from the islands of the Sundas. The secretive habits of the species, including the occupancy of mud lobster(Thalassinia spp.) mounds in mostly inaccessible, swampy habitats may be a reason for its perceived rarity and few published records.     

Population genetic structure,genetic diversity,and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data

The effect of glaciation on the levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly, complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant communities. We therefore studied the population genetics of three closely related, hybridizing species of Nothofagus (N. obliqua, N. alpina, and N. glauca, all of subgenus Lophozonia; Nothofagaceae) from Chile. To estimate population genetic parameters and infer the influence of the last ice age on the spatial and genetic distribution of these species, we examined and analyzed genetic variability at seven polymorphic microsatellite DNA loci in 640 individuals from 40 populations covering most of the ranges of these species in Chile. Populations showed no significant inbreeding and exhibited relatively high levels of genetic diversity (H_E = 0.502–0.662) and slight, but significant, genetic structure (R_ST = 8.7–16.0%). However, in N. obliqua, the small amount of genetic structure was spatially organized into three well‐defined latitudinal groups. Our data may also suggest some introgression of N. alpina genes into N. obliqua in the northern populations. These results allowed us to reconstruct the influence of the last ice age on the genetic structure of these species, suggesting several centers of genetic diversity for N. obliqua and N. alpina, in agreement with the multiple refugia hypothesis.     

Molecular evolution and diversification of the moss family Daltoniaceae (Hookeriales,Bryophyta) with emphasis on the unravelling of the phylogeny of Distichophyllum and its allies

Phylogenetic relationships in Daltoniaceae (～200 species in 14 genera) are inferred from nucleotide sequences from five genes, representing all genomic compartments, using parsimony, likelihood and Bayesian methods. Alternative classifications for Daltoniaceae have favoured traits from either sporophytes or gametophytes; phylogenetic transitions in gametophytic leaf limbidia and sporophytic exostome ornamentation were evaluated using ancestral state reconstruction to assess the levels of conflict between these generations. Elimbate leaves and the cross‐striate exostome are reconstructed as plesiomorphic states. Limbate leaves and papillose exostomes evolved at least two and six times, respectively, without reversals. The evolution of leaf limbidia is relatively conserved, but exostome ornamentation is highly homoplasious, indicating that superficial similarity in peristomes gives unreliable approximations of phylogenetic relatedness. Our phylogenetic analyses show that Achrophyllum and Calyptrochaeta are reciprocally monophyletic. Within core Daltoniaceae, relationships among taxa with elimbate leaves are generally well understood. However, taxa with limbate leaves form a monophyletic group, but resolved subclades correspond to biogeographical entities, rather than to traditional concepts of genera. Daltonia (～21 species), Distichophyllum (～100 species) and Leskeodon (～20 species) are polyphyletic. Seven nomenclatural changes are proposed here. As the current taxonomy of Daltoniaceae lacks phylogenetic consistency, critical generic revisions are needed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.