Multilocus phylogeny and recent rapid radiation of the viviparous sea snakes (Elapidae: Hydrophiinae)

The viviparous sea snakes (Hydrophiinae: Hydrophiini) comprise a young but morphologically and ecologically diverse clade distributed throughout the Indo-Pacific. Despite presenting a very promising model for marine diversification studies, many relationships among the 62 species and 16 genera in Hydrophiini remain unresolved. Here, we extend previous taxonomic and genomic sampling for Hydrophiini using three mitochondrial fragments and five nuclear loci for multiple individuals of 39 species in 15 genera. Our results highlight many of the impediments to inferring phylogenies in recent rapid radiations, including low variation at all five nuclear markers, and conflicting relationships supported by mitochondrial and nuclear trees. However, concatenated Bayesian and likelihood analyses, and a multilocus coalescent tree, recovered concordant support for primary clades and several previously unresolved inter-specific groupings. The Aipysurus group is monophyletic, with egg-eating specialists forming separate, early-diverging lineages. All three monotypic semi-aquatic genera (Ephalophis, Parahydrophis and Hydrelaps) are robustly placed as early diverging lineages along the branch leading to the Hydrophis group, with Ephalophis recovered as sister to Parahydrophis. The molecular phylogeny implies extensive evolutionary convergence in feeding adaptations within the Hydrophis group, especially the repeated evolution of small-headed (microcephalic) forms. Microcephalophis (Hydrophis) gracilis is robustly recovered as a relatively distant sister lineage to all other sampled Hydrophis group species, here termed the ‘core Hydrophis group’. Within the ‘core Hydrophis group’, Hydrophis is recovered as broadly paraphyletic, with several other genera nested within it (Pelamis, Enhydrina, Astrotia, Thalassophina, Acalyptophis, Kerilia, Lapemis, Disteira). Instead of erecting multiple new genera, we recommend dismantling the latter (mostly monotypic) genera and recognising a single genus, Hydrophis Latreille 1802, for the core Hydrophis group. Estimated divergence times suggest that all Hydrophiini last shared a common ancestor ～6 million years ago, but that the majority of extant lineages diversified over the last ～3.5 million years. The core Hydrophis group is a young and rapidly speciating clade, with 26 sampled species and 9 genera and dated at only ～1.5–3 million years old.     

Molecular phylogeny of elapid snakes and a consideration of their biogeographic history

Evolutionary relationships among the major elapid clades, particularly the taxonomic position of the partially aquatic sea kraits (Latkauda) and the fully aquatic true sea snakes have been the subject of much debate. To discriminate among existing phylogenetic and biogeographic hypotheses, portions of both the 16S rRNA and cytochrome b mitochondrial DNA genes were sequenced from 16 genera and 17 species representing all major elapid snake clades from throughout the world and two non-elapid outgroups. This sequence data yielded 181 informative sites under parsimony. Parsimony analyses of the separate data sets produced trees of broad agreement although less well supported than the single most parsimonious tree resulting from the combined analyses. These results support the following hypotheses: (1) the Afro-Asian cobra radiation forms one or more sister groups to other elapids, (2) American and Asian coral snakes form a clade, corroborating morphological studies, (3) Bungarus forms a sister group to the hydrophiines comprised of Latkauda, terrestrial Australo-Papuan elapids and true sea snakes, (4) Latkauda and true sea snakes do not form a monophyletic group but instead each group shares an independent history with terrestrial Australo-Papuan elapids, corroborating previous studies, (5) a lineage of Melanesian elapids forms the sister group to Latkauda, terrestrial Australian species and true sea snakes. In agreement with previous morphologically based studies, the sequence data suggests that Bungarus and Latkauda represent transitional clades between the elapine 'palatine erectors' and hydrophiine 'palatine draggers'. Both intra and inter-clade genetic distances are considerable, implying that each of the major radiations have had long independent histories. I suggest an African, Asian, or Afro-Asian origin for elapids as a group, with independent Asian origins for American coral snakes and the hydrophiines.     

Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (hydrophiinae): evidence from seven genes for rapid evolutionary radiations

One of the most prolific radiations of venomous snakes, the Australo-Melanesian Hydrophiinae includes approximately 100 species of Australasian terrestrial elapids plus all approximately 60 species of viviparous sea snakes. Here, we estimate hydrophiine relationships based on a large data set comprising 5800 bp drawn from seven genes (mitochondrial: ND4, cytb, 12S, 16S; nuclear: rag1, cmos, myh). These data were analysed using parsimony, likelihood and Bayesian methods to better resolve hydrophiine phylogeny and provide a timescale for the terrestrial and marine radiations. Among oviparous forms, Cacophis, Furina and Demansia are basal to other Australian elapids (core oxyuranines). The Melanesian Toxicocalamus and Aspidomorphus group with Demansia, indicating multiple dispersal events between New Guinea and Australia. Oxyuranus and Pseudonaja form a robust clade. The small burrowing taxa form two separate clades, one consisting of Vermicella and Neelaps calanotus, and the other including Simoselaps, Brachyurophis and Neelaps bimaculatus. The viviparous terrestrial elapids form three separate groups: Acanthophis, the Rhinoplocephalus group and the Notechis-Hemiaspis group. True sea snakes (Hydrophiini) are robustly united with the Notechis-Hemiaspis group. Many of the retrieved groupings are consistent with previous molecular and morphological analyses, but the polyphyly of the viviparous and burrowing groups, and of Neelaps, are novel results. Bayesian relaxed clock analyses indicate very recent divergences: the approximately 160 species of the core Australian radiation (including sea snakes) arose within the last 10 Myr, with most inter-generic splits dating to between 10 and 6 Ma. The Hydrophis sea snake lineage is an exceptionally rapid radiation, with > 40 species evolving within the last 5 Myr.     

Venom glands and some associated muscles in sea snakes

The venom glands and related muscles of sea snakes conform in their general structure to those of the terrestrial elapids. The venom gland, however, is smaller in size and the accessory gland is considerably reduced. A similar pattern is found in the Australian elapid Notechis. The musculus compressor glandulae is well developed in the sea snakes and in some species its posterior-medial portion runs uninterruptedly from the origin to the insertion of the muscle. This might be considered as a primitive condition suggesting an early divergence of the sea snakes from an ancestral elapid stock. Three species of sea snakes, Aipysurus eydouxi, Emydocephalus annulatus, and E. ijimae, feed on fish eggs and have very small, but still functioning, venom glands. The reduced accessory gland of the sea snakes is apparently connected with their aquatic environment, as a similar condition is found also in the elapine Boulengerina annulata which lives in large lakes of Central Africa. The similarity in structure of the venom gland between sea snakes and Notechis scutatus may point to a possible phylogenetic relationship between this group of Australian elapids and hydrophiine snakes.     

A combined morphological and molecular phylogeny of the genus Chironius Fitzinger, 1826 (Serpentes: Colubridae)

Chironius is one of the most speciose genera of the South American colubrid snakes. Although the genus represents a well‐known radiation of diurnal racers, its monophyly, affinities with other Neotropical colubrid genera, and intrageneric relationships are open questions. Here, we present a phylogenetic analysis of Chironius based on a data matrix that combines one nuclear (c‐mos) and two mitochondrial (12S and 16S rRNA) genes with 37 morphological characters derived from scutellation, skull, and hemipenial features. Phylogenetic relationships were inferred using maximum parsimony (MP) and maximum likelihood (ML). Our combined morphological and molecular analyses strongly support the monophyly of the genus Chironius and its sister‐group relationship with a clade formed by the genera Dendrophidion and Drymobius. Phylogenetic relationships within the genus Chironius is still controversial, although five clades are retrieved with medium to strong support. © 2014 The Linnean Society of London     

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1217–1243.     

Inferring Species Trees from Gene Trees: A Phylogenetic Analysis of the Elapidae (Serpentes) Based on the Amino Acid Sequences of Venom Proteins

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A₂and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.     

Gnidia (Thymelaeaceae) is not monophyletic: taxonomic implications for Thymelaeoideae and a partial new generic taxonomy for Gnidia

We address the generic limits of Gnidia (Thymelaeaceae) through a phylogenetic analysis of nuclear ribosomal DNA internal transcribed spacer (ITS) and plastid rbcL, trnL intron and trnL‐F intergenic spacer regions. Maximum parsimony and Bayesian inference were used to produce trees and assess internal support. The most significant conclusion drawn from the molecular analysis is that Gnidia is polyphyletic as currently circumscribed, comprising at least four distinct lineages that are each related to other genera within Thymelaeoideae. Gnidia pinifolia and G. racemosa are members of a clade within which Struthiola is embedded; a second group of species allies with Drapetes as sister to Passerina; and a third lineage corresponds to the previously recognized genus Lasiosiphon. The remaining species of Gnidia included in this study are allied with the Australian genus Pimelea. The taxonomic implications of these findings are discussed in relation to the principle of monophyly. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 402–417.     

Diversification and biogeographical history of Neotropical plethodontid salamanders

The Neotropical bolitoglossine salamanders represent an impressive adaptive radiation, comprising roughly 40% of global salamander species diversity. Despite decades of morphological studies and molecular work, a robust multilocus phylogenetic hypothesis based on DNA sequence data is lacking for the group. We estimated species trees based on multilocus nuclear and mitochondrial data for all major lineages within the bolitoglossines, and used our new phylogenetic hypothesis to test traditional biogeographical scenarios and hypotheses of morphological evolution in the group. In contrast to previous phylogenies, our results place all Central American endemic genera in a single clade and suggest that Central America played a critical role in the early biogeographical history of the group. The large, predominantly Mexican genus Pseudoeurycea is paraphyletic, and analyses of the nuclear data place two lineages of Pseudoeurycea as the sister group of Bolitoglossa. Our phylogeny reveals extensive homoplasy in morphological characters, which may be the result of truncation or alteration of a shared developmental trajectory. We used our phylogenetic results to revise the taxonomy of the genus Pseudoeurycea. © 2015 The Linnean Society of London     

A phylogenetic analysis of the genera of Lejeuneaceae (Hepaticae)

The Lejeuneaceae are the largest family of the liverworts (Hepaticae), with almost a thousand species in 91 currently accepted genera. We analysed phylogenetic relationships of 69 genera, representing all major subfamilies and tribes recognized in the family, by using 49 informative morphological characters (31 gametophytic, 18 sporophytic), one chemical character, and applying equal and successive weighting of characters and parsimony analysis. In all trees recovered, the Lejeuneaceae were monophyletic with Nipponolejeunea (subfam. Nipponolejeuneoideae) forming the basalmost lineage. The remaining genera clustered in two major groups, the monophyletic Lejeuneoideae (52 genera) and the paraphyletic Ptychanthoideae (16 genera). Within each, several multigeneric lineages corresponding in part to previously described taxa were recovered: the Acrolejeuneinae and Ptychanthinae clades in the Ptychanthoideae, and the Brachiolejeuneinae, Lejeuneeae and Tuyamaella–Cololejeunea clades in the Lejeuneoideae. Bryopteris , a genus sometimes treated as a separate family, was nested in the Ptychanthinae clade. The Tuyamaella–Cololejeunea lineage corresponded with three previously recognized subfamilies (Cololejeuneoideae, Myriocoleoideae and Tuyamaelloideae) and contained genera with neotenic features, in two subclades. These features seemed to have originated by multiple heterochronic events: single origins were detected for 'protonemal neoteny' and 'primary neoteny', whereas 'secondary neoteny' probably evolved twice. Relationships within the large Lejeuneeae clade (43 genera) remained largely unresolved, although several putative lineages were detected in majority rule trees. Additional characters such as DNA sequences may provide better phylogenetic resolution in this group.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 391–410.     

An extraordinary new genus of spiders from Western Australia with an expanded hypothesis on the phylogeny of Tetragnathidae (Araneae)

We describe Pinkfloydia Hormiga & Dimitrov gen. nov. , a new genus of tetragnathid spiders from Western Australia and study its phylogenetic placement. The taxon sampling from our previous cladistic studies was expanded, with the inclusion of representatives of additional tetragnathid genera and outgroup taxa. Sequences from six genetic markers, 12S, 16S, 18S, 28S, cytochrome c oxidase subunit 1, and histone 3, along with morphological and behavioural data were used to infer tetragnathid relationships. These data were analysed using parsimony (under both static homology and dynamic optimization) and Bayesian methods. Our results indicate that Pinkfloydia belongs to the ‘Nanometa’ clade. We also propose a revised set of synapomorphies to define this lineage. Based on the new evidence presented here we propose a revised hypothesis for the intrafamilial relationships of Tetragnathidae and show that Mimetidae is most likely the sister group of Tetragnathidae. The single species in this genus so far, Pinkfloydia harveii Dimitrov& Hormiga sp. nov. , is described in detail and its web architecture documented and illustrated. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 735–768.     

Leaf epidermal character variation and evolution in Gaultherieae (Ericaceae)

The taxonomic value and evolutionary significance of 30 leaf epidermal characters from 238 samples representing 127 species of all seven genera in the tribe Gaultherieae (Ericaceae) and two outgroup genera were investigated by scanning electron microscopy. The character states were coded and optimized onto a maximum‐likelihood tree based on previous molecular data with Fitch parsimony and hierarchical Bayesian analysis to trace the evolution of character states throughout all internodes in the phylogenetic tree for Gaultherieae. Leaf epidermal characters were found to be largely consistent within species, but highly variable at interspecific and higher taxonomic levels. The most recent common ancestral states of 15 characters diagnosed various lineages recovered from prior studies, some with no prior morphological support. Relatively high frequencies of state change occur in the eastern Asian clade Gaultheria series Gymnobotrys + Diplycosia, the American clade G. subsection Dasyphyta p.p., the core East Asian clade and the Australia/New Zealand clade. The characters with the highest frequencies of state change are the outer stomatal ledge ornamentation type, the stomatal apparatus level, stomatal density and area, and the type of abaxial trichomes. These character state change patterns may provide insight into the ecological adaptions of Gaultherieae during their evolutionary history. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 686–710.     

The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa

The monophyly and phylogeny of the adaptive radiation of Hawaiian finches (Fringillidae: Drepanidini; honeycreepers, auct.) were studied using parsimony analysis of comparative osteology, combined with Templeton (Wilcoxon signed‐ranks) tests of alternative phylogenetic hypotheses. Eighty‐four osteological characters were scored in 59 terminal taxa of drepanidines, including 24 fossil forms, and in 30 outgroup species. The optimal phylogenetic trees show considerable agreement, and some conflict, with independently derived ideas about drepanidine evolution. The monophyly of a large Hawaiian radiation was upheld, although one fossil taxon from Maui fell outside the drepanidine clade. The finch‐billed species were placed as basal drepanidine taxa, and continental cardueline finches (Carduelini) were identified as the radiation's closest outgroups. The study found anatomical as well as phylogenetic evidence that the radiation had a finch‐billed ancestor. The optimal trees identify the red‐and‐black plumage group as a clade, and suggest that the tubular tongue evolved only once in the radiation. Because comparative osteology provides too few characters to strongly support all the nodes of the tree, it was helpful to evaluate statistical support for alternative hypotheses about drepanidine relationships using the Templeton test. Among the alternatives that received significant statistical support are a relationship of the drepanidines with cardueline finches rather than with the Neotropical honeycreepers (Thraupini), classification of the controversial genera Paroreomyza and Melamprosops as drepanidines, and a secondary loss of the tubular tongue in Loxops mana. The hypothesis of monophyly for all the Hawaiian taxa in the study was not rejected statistically. The study provides a framework for incorporating morphological and palaeontological information in evolutionary studies of the Drepanidini. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 141 , 207–255.     

Congruent phylogeographic patterns in a young radiation of live‐bearing marine snakes: Pleistocene vicariance and the conservation implications of cryptic genetic diversity

Aim

To investigate phylogeographic patterns among and within co‐occurring sea snake species from Australia's endemic viviparous Aipysurus lineage, which includes critically endangered species, and evaluate the conservation implications of geographically structured patterns of genetic divergence and diversity.

Location

Australia's tropical shallow water marine environments spanning four regions: Great Barrier Reef (GBR), Gulf of Carpentaria (GoC), Timor Sea (TS) and coastal WA (WAC).

Methods

Samples from >550 snakes representing all nine nominal Aipysurus group species were obtained from throughout their known Australian ranges. Coalescent phylogenetic analyses and Bayesian molecular dating of mitochondrial DNA, combined with Bayesian and traditional population genetic analyses of 11 microsatellite loci, were used to evaluate genetic divergence and diversity.

Results

Mitochondrial DNA revealed highly congruent phylogeographic breaks among co‐occurring species, largely supported by nuclear microsatellites. For each species, each region was characterized by a unique suite of haplotypes (phylogroups). Divergences between the TS, GoC and/or GBR were invariably shallow and dated as occurring 50,000–130,000 years ago, coinciding with the cyclic Pleistocene emergence of the Torres Strait land bridge. By contrast, sea snakes from coastal WA were consistently highly divergent from other regions and dated as diverging 178,000–526,000 years ago, which was not associated with any known vicariant events.

Main Conclusions

Previously unappreciated highly divergent sea snake lineages in coastal WA potentially represent cryptic species, highlighting this region as a high‐priority area for conservation. The cyclic emergence of the Torres Strait land bridge is consisted with observed divergences between the TS, GoC and/or GBR; however, processes involved in the earlier divergences involving the WAC remain to be determined. The observed strong population genetic structures (as surrogates for dispersal) indicate that sea snakes have limited potential to reverse population declines via replenishment from other sources over time frames relevant to conservation.

     

Morphology agrees with molecular data: phylogenetic affinities of Euptychiina butterflies (Nymphalidae: Satyrinae)

Euptychiina is the most species‐rich subtribe of Neotropical Satyrinae, with over 450 known species in 47 genera (14 monotypic). Here, we use morphological characters to examine the phylogenetic relationships within Euptychiina. Taxonomic sampling included 105 species representing the majority of the genera, as well as five outgroups. A total of 103 characters were obtained: 45 from wing pattern, 48 from genitalia and 10 from wing venation. The data matrix was analysed using maximum parsimony under both equal and extended implied weights. Euptychiina was recovered as monophyletic with ten monophyletic genera, contrasting previous DNA sequence‐based phylogenies that did not recover the monophyly of the group. In agreement with sequence‐based hypotheses, however, three main clades were recognized: the ‘Megisto clade’ with six monophyletic and three polyphyletic genera, the ‘Taygetis clade’ with nine genera of which three were monophyletic, and the ‘Pareuptyhia clade’ with four monophyletic and two polyphyletic genera. This is the first morphology‐based phylogenetic hypothesis for Euptychiina and the results will be used to complement molecular data in a combined analysis and to provide critical synapomorphies for clades and genera in this taxonomically confused group.     

Phylogenetic relationships in the genus Agathemera (Insecta: Phasmatodea) inferred from the genes 16S,COI and H3

We present a phylogenetic analysis that includes all known species of Agathemera, using as outgroup four species of the genera Heteronemia, Spinonemia, Monticomorpha, and Anisomorpha. Phylogenetic inference was based on three genes, 16S, COI (mitochondrial markers) and H3 (nuclear marker), based on the maximum‐parsimony, maximum‐likelihood and Bayesian inference methods. Our results show that the genus Agathemera is monophyletic; six of its eight species showed phylogenetic support, while the group A. claraziana + A. millepunctata was not resolved. The resulting topology shows two major clades, the first with A. maculafulgens, A. luteola, A. crassa, A. millepunctata, and A. claraziana, and the second including A. grylloidea, A. mesoauriculae, and A. elegans. Species of the first clade have large mesonotal processes and are found mainly east of the Andes, except for A. crassa. Members of the second clade have small or absent mesonotal processes and are distributed mainly to the west of the Andes. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 63–72.