Monitoring occurrence,extinction, and colonization probabilities for gibbon populations

All gibbon species (Family: Hylobatidae) are considered threatened with extinction and recognized on the International Union for Conservation of Nature Red List of Threatened Species. Because gibbons are one of the most threatened families of primates, monitoring their status is now critically important. Long-term monitoring programs applying occupancy approaches, in addition to assessing occurrence probability, improves understanding of other population parameters such as site extinction or colonization probabilities, which elucidate temporal and spatial changes and are therefore important for guiding conservation efforts. In this study, we used multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities for northern yellow-cheeked crested gibbon Nomascus annamensis in three adjacent protected areas in the Central Annamites mountain range, Vietnam. We collected data at 30 listening posts in 2012, 2014, and 2016 using the auditory point count method. Occurrence probabilities were highest in 2012 (0.74, confidence interval [CI]: 0.56–0.87) but slightly lower in 2014 (0.66, CI: 0.51–0.79) and 2016 (0.67, CI: 0.49–0.81). Extinction probabilities during the 2012–2014 and 2014–2016 intervals were 0.26 (0.14–0.44) and 0.25 (0.12–0.44), respectively. Colonization probabilities during 2012–2014 were 0.44 (0.19–0.73) and between 2014 and 2016 was 0.51 (0.26–0.75). Although local site extinctions have occurred, high recolonization probability helped to replenish the unoccupied sites and kept the occurrence probability stable. Long-term monitoring programs which use occurrence probability alone might not fully reveal the true dynamics of gibbon populations. We strongly recommend including multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities in long-term gibbon monitoring programs.     

Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach

Gibbons are believed to have diverged from the larger great apes ∼16.8 MYA and today reside in the rainforests of Southeast Asia. Based on their diploid chromosome number, the family Hylobatidae is divided into four genera, Nomascus, Symphalangus, Hoolock, and Hylobates. Genetic studies attempting to elucidate the phylogenetic relationships among gibbons using karyotypes, mitochondrial DNA (mtDNA), the Y chromosome, and short autosomal sequences have been inconclusive . To examine the relationships among gibbon genera in more depth, we performed second-generation whole genome sequencing (WGS) to a mean of ∼15× coverage in two individuals from each genus. We developed a coalescent-based approximate Bayesian computation (ABC) method incorporating a model of sequencing error generated by high coverage exome validation to infer the branching order, divergence times, and effective population sizes of gibbon taxa. Although Hoolock and Symphalangus are likely sister taxa, we could not confidently resolve a single bifurcating tree despite the large amount of data analyzed. Instead, our results support the hypothesis that all four gibbon genera diverged at approximately the same time. Assuming an autosomal mutation rate of 1 × 10⁻⁹/site/year this speciation process occurred ∼5 MYA during a period in the Early Pliocene characterized by climatic shifts and fragmentation of the Sunda shelf forests. Whole genome sequencing of additional individuals will be vital for inferring the extent of gene flow among species after the separation of the gibbon genera.     

Comparison of point transect distance and traditional acoustic point-count sampling of hoolock gibbons in Htamanthi Wildlife Sanctuary,Myanmar

Effective conservation demands more accurate and reliable methods of survey and monitoring of populations. Surveys of gibbon populations have relied mostly on mapping of groups in “listening areas” using acoustical point-count data. Traditional methods of estimating density in have usually used counts of gibbon groups within fixed-radius areas or areas bounded by terrain barriers to sound transmission, and have not accounted for possible decline in detectability with distance. In this study we sampled the eastern hoolock gibbon (Hoolock leucogenys) population in Htamanthi Wildlife Sanctuary (WS), Myanmar, using two methods: the traditional point-count method with fixed-radius listening areas, and a newer method using point-transect Distance analysis from a sample point established in the center of each listening point array. The basic data were obtained by triangulating on singing groups from four LPs for 4 days, in 10 randomly selected sample areas within the sanctuary. The point transect method gave an average density of 3.13 groups km⁻², higher than the estimates of group density within fixed-radius areas without correction for detectability. A new method of analysis of singing probability per day (p[1]) gave an estimate of 0.547. Htamanthi WS is an important conservation area containing an estimated 7000 (95% confidence interval: 5000–10,000) hoolock groups. Surveys at Htamanthi WS and locations in the Hukaung Valley suggest that the extensive evergreen forests in northern Myanmar have the capacity to support 2–4 (average about 3) groups of hoolock gibbons per km², but most forests in its range have yet to be surveyed.     

Combining species distribution modeling and distance sampling to assess wildlife population size: A case study with the northern yellow-cheeked gibbon (Nomascus annamensis)

Population size and distribution data for wildlife species play an important role in conservation and management, especially for endangered species. However, scientists seriously lack data on the population status of many species. The northern yellow-cheeked gibbon (Nomascus annamensis) is found in southern Lao PDR, central Vietnam, and northeastern Cambodia. The population of the species has significantly declined due to hunting, habitat loss, and the wildlife trade. To examine the population size and distribution of N. annamensis, we conducted a field survey in Song Thanh Nature Reserve, Quang Nam Province, central Vietnam from February to April 2019 using the audio point count method. We combined Distance Sampling and Ecological Niche Modeling to estimate the population of the gibbons. Results showed that the total suitable area for the gibbons was about 302.32 km², with the two most important variables of the habitat model being the distance-to-villages and forest type. We detected 36 gibbon groups through field surveys and estimated 443 (95% CI, 278–707) gibbon groups in Song Thanh Nature Reserve. Our results indicate that the gibbon population in Song Thanh Nature Reserve is the largest known population of N. annamensis in Vietnam. In addition, our study was the first to combine species distribution modeling with distance sampling to estimate gibbon density and population size. This approach might be useful in surveying and monitoring gibbon populations because it takes imperfect detection probability into account in estimating gibbon population density while estimating the area of potential habitat using environmental variables.     

Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South‐West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high‐elevation, semi‐aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each situated on islands on either side of Wallace's Line. One radiation is composed of Philippine species of Platymantis and the other contains all taxa from the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian archipelagos. Several additional genera (Batrachylodes, Discodeles, Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of these Batrachylodes and Discodeles are nonmonophyletic. To address the widespread paraphyly of the genus Platymantis and several additional nomenclatural issues, we undertook a wholesale nomenclatural reorganization of the family. Given our partially unresolved phylogeny, and in order to impart a conservative, stable taxonomy, involving a minimal number of genus‐species couplet changes, we propose a conservative classification representing a few compromises. These changes are designed to preserve maximally the presumed original intent of taxonomy (widely used group names associated with morphological and ecological diversity of particular species or groups of species) while implementing a hierarchical system that is consistent with the estimate of phylogeny based on new molecular data. © 2015 The Linnean Society of London     

Phylogenetic and mixed Yule‐coalescent analyses reveal cryptic lineages within two South American marine snails of the genus Crepipatella (Gastropoda: Calyptraeidae)

The presence of sibling species within the marine gastropod genus Crepipatella has complicated the taxonomy of members of the group. Since the establishment of the genus, 15 species have been described, but recent studies have indicated that there are only five valid species, two of which inhabit the coasts of Chile, namely C. dilatata and C. fecunda. The two species are morphologically indistinguishable as adults, but can be differentiated on the basis of their encapsulated developmental stages. The primary aim of this study was to reconstruct phylogeny within the genus, and to establish species limits of C. dilatata and C. fecunda, using mitochondrial DNA data. To this end, we used maximum parsimony, maximum likelihood, and Bayesian inference to reconstruct phylogenies using 589 bp of the cytochrome oxidase I (COI) gene. The mtDNA phylogenies were then used as input in a general mixed Yule‐coalescent (GMYC) analysis to estimate species boundaries. In addition, quarter likelihood mapping was used to test a posteriori the confidence of inner branch patterns in the phylogenetic tree. Both DNA tree‐based and GMYC methods provide support for five isolated lineages within this species complex. Our data also suggest that Late Pleistocene and Holocene fragmentation and subsequent range expansion events may have shaped contemporary genetic patterns of Crepipatella in South America.     

A global molecular phylogeny of 147 periwinkle species (Gastropoda,Littorininae)

Reid, D. G., Dyal, P. & Williams, S.T. (2012) A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae). —Zoologica Scripta, 41, 125–136. Complete species‐level molecular phylogenies have been published for several genera of Littorinidae (e.g. Echinolittorina, Littoraria). Here we add new sequence data from three genes (28S rRNA, 12S rRNA, cytochrome oxidase c subunit I) for single specimens of an additional 24 species, to make a data set of 147 (97%) of the 152 recognized species of the subfamily Littorininae. This three‐gene data set is analysed to produce a phylogenetic hypothesis for the subfamily, which includes the first complete species‐level phylogeny of the genus Peasiella and the first three‐gene phylogeny of all Littorina species. The non‐planktotrophic species of Littorina have previously been classified together (as subgenus Neritrema), implying a single origin of this developmental mode. Tests of this hypothesis with the new data are inconclusive, and resolution is not improved in a tree constructed from five genes (adding previously published sequences of 16S rRNA and cytochrome b). Using available fossils for calibration we generate a BEAST chronogram, which emphasizes that the radiation of Littorina is more recent than that of other littorinine genera. A database is provided, listing all known species of Littorininae, with their distributions, development, ecology and gene sequences, as a tool for future evolutionary studies of this model group.     

Molecular evolution of IgG subclass among nonhuman primates: implication of differences in antigenic determinants among Apes

The cross-reactivity of five different rabbit polyclonal antibodies to human IgG and IgG subclass (IgG1, IgG2, IgG3, and IgG4) was determined by competitive ELISA with nine nonhuman primate species including five apes, three Old World monkeys, and one New World monkey. As similar to those previously reported, the reactivity of anti-human IgG antibody with plasma from different primate species was closely related with phylogenic distance from human. Every anti-human IgG subclass antibody showed low cross-reactivity with plasma from Old World and New World monkeys. The plasma from all apes except for gibbons (Hylobates spp.) showed 60 to 100% of cross-reactivity with anti-human IgG2 and IgG3 antibodies. On the other hand, chimpanzee (Pan troglodytes andPan paniscus) and orangutan (Pongo pygmaeus) plasma showed 100% cross-reactivity with anti-human IgG1 antibody, but gorilla (Gorilla gorilla) and gibbon plasma showed no cross-reactivity. The chimpanzee and gorilla plasma cross-reacted with anti-human IgG4 antibody at different reactivity, 100% in chimpanzee and 50% in gorilla, but no cross-reactivity was observed in orangutan and gibbon plasma. These results suggest the possibilities that the divergence of “human-type” IgG subclasses might occur at the time of divergence ofHomo sapience fromHylobatidae, and that the molecular evolution of IgG1 as well as IgG4 is different from that of IgG2 and IgG3 in great apes, this is probably caused by different in development of immune function in apes during the course of evolution.     

Phylogeny of Neotropical Monkeys: The Interplay of Morphological, Molecular, and Parasitological Data

Separate independent hypotheses of the phylogenetic relationships among the Platyrrhini monkeys have been produced in a recent past, either based upon morphological or molecular data, but the results are generally conflicting and the phylogeny of the group still is debated. The high host specificity observed among primates and their oxyurid parasites allows to consider the result of a morphologically based cladistic analysis of the pinworms of the Platyrrhini as an estimate of the phylogeny of these monkeys. Using the matrix representation method this “parasite-tree” is combined, using parsimony analysis, with several conflicting molecular or morphological hypothesis of the phylogeny of the host group. The results are discussed with respect to previously published classification, or composite computations of the phylogeny, of the Neotropical monkeys. Comparison of different hypothesis makes apparent several stable groups: (i) the Callithrichidae +Saimiri,(ii) the Atelidae/Alouattidae, (iii) the Pitheciidae, and (iv) the Alouattidae/Atelidae + Pitheciidae. In addition, the parasite and the molecular trees support close relationships betweenCallimicoandCallithrix/Cebuella.The study also makes apparent that the parasite tree generally portrays the results of other studies, both when they are congruous and when they are conflicting. This is interpreted to be additional evidence for close coevolution between the Platyrrhini and their specific pinworms. Because, whatever the combination of data being considered no consensus can be found on the exact position ofAotusandCallicebus,and because it is likely that the earliest radiation of the Platyrrhini could be comparable to an evolutionary burst, which renders identification of homologous characters difficult, it is suggested that, possibly, not enough discriminating tracks of the evolutionary paths have been conserved to allow to resolve this uncertainty in the future.     

New morphological evidence supports congruent phylogenies and Gondwana vicariance for palaeognathous birds

There has been little agreement on the phylogeny of palaeognathous birds, with major differences amongst and between results from morphological and molecular data. Two recently published phylogenies using nuclear and mitochondrial DNA have substantial agreement in overall topology, with the ostrich as sister group of all other extant palaeognaths and a kiwi‐emu‐cassowary clade. Here I report a morphological phylogeny based mainly on new characters from the tongue apparatus and cranial osteology, with a theoretical ancestor as outgroup. A new interpretation of the evolution of the avian palate is included. This phylogeny is very similar to these recent molecular results; this is the first report of such congruence, and offers a credible basis for understanding the evolution of this clade. This phylogeny is fully consistent with a Gondwana vicariance model of evolution. Dates attributed from known geological events place the first extant radiation (ostrich) in the mid‐Cretaceous, and offer a means of calibration of future molecular clock investigations. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 959–983.     

New insights into tateid gastropods and their radiation on Fiji based on anatomical and molecular methods (Caenogastropoda: Truncatelloidea)

The South Pacific archipelago of Fiji is characterized by a predominantly Indo‐Malesian flora and fauna. We provide a first systematic study on Fiji's tateid gastropods – previously classified as Hydrobiidae – describing 18 new species, combining morphological, anatomical, and molecular data. The molecular phylogeny of tateid gastropods based on 16S rRNA and cytochrome c oxidase subunit I (COI) showed that the species from Fiji were closer related to New Zealand than to Australian or New Caledonian taxa, which is rather exceptional. Performing an ancestral range reconstruction we inferred the colonization history across the two main islands. The radiation had its origin in southern Viti Levu, with a subsequent dispersal over the western and central parts of the island. The chronology of the radiation over eastern Viti Levu and Vanua Levu remained unresolved because of incomplete lineage sorting, a phenomenon typical for young radiations. © 2014 The Linnean Society of London     

Relic of ancient recombinations in gibbon ABO blood group genes deciphered through phylogenetic network analysis

The primate ABO blood group gene encodes a glycosyl transferase (either A or B type), and is known to have large coalescence times among the allelic lineages in human. We determined nucleotide sequences of ca. 2.2 kb of this gene for 23 individuals of three gibbon species (agile gibbon, white-handed gibbon, and siamang), and observed a total of 24 haplotypes. We found relics of five ancient intragenic recombinations, occurred during ca. 2–7 million years ago, through a phylogenetic network analysis. The coalescence time between A and B alleles estimate precede the divergence (ca. 8 MYA) of siamang and common gibbon lineages. This establishes the coexistence of divergent allelic lineages of the ABO blood group gene for a long period in the ancestral gibbon species, and strengthens the non-neutral evolution for this gene.     

Diversification rates in the Australasian endemic grass <Emphasis Type="Italic">Austrostipa</Emphasis>: 15 million years of constant evolution

Patterns seen in other Australian flora have led to hypotheses that early Miocene shifts in climate drove rapid radiation of major taxonomic groups such as Eucalyptus. Little is known about absolute dates and rates for Australian monocots, particularly grasses. I tested this early Miocene radiation hypothesis for Australian grasses using a calibrated phylogeny of the endemic stipoid genus Austrostipa and an analysis of diversification rates. The phylogeny was developed from a Bayesian likelihood analysis of the nuclear internal transcribed spacers region, and three calibration points were set based on fossil evidence. The results indicate that the genus arose in the early Miocene and underwent a species radiation, but the rate of diversification was not rapid compared to the current rate or to those of other taxa. Following an 8 million year period of fast molecular evolution but no taxonomic radiation, diversification rates have been constant for the past 15 million years. Comparable measures such as the gamma statistic can be used across taxa to make general conclusions about evolutionary rate constancy.     

Protein–protein interactions of the cytochrome c oxidase DNA barcoding region

Enzymatic amplification of homologous regions of DNA using ‘universal’ polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly called the barcoding region. COI is one of three mitochondrial‐encoded subunits of complex IV (Cox) of the electron transport chain. In addition to the mitochondrial subunits there are nine nuclear‐encoded subunits of the complex in Drosophila. Whereas a number of phylogenetic biases associated with this region have been examined and the quaternary structure of Cox has been modelled, the influence of protein–protein interactions on the observed patterns of evolution in this barcoding region of insects has never been examined critically. Using a well‐resolved independently derived phylogeny of 38 Diptera species, we examined the homogeneity of the substitution processes within the barcoding region. We show that, within Diptera, amino acid residues interacting with nuclear‐encoded subunits of Cox are evolving at elevated rates across the phylogeny. Furthermore, we show that codon position two is biased by protein–protein interactions. In contrast, third codon positions provide a less biased estimate of genetic variation in the region. This study highlights the need to examine the potential for systematic bias in DNA barcoding regions as part of the critical assessment of evidence in systematics and in biodiversity assessments.     

A MOLECULAR PHYLOGENY OF THE DROSOPHILA WILLISTONI GROUP: CONFLICTS BETWEEN SPECIES CONCEPTS?

The six sibling species of the Neotropical Drosophila willistoni group have a long history in studies of evolutionary biology, yet to date only one molecular study, which used allozymes, has been published on the phylogeny of the group. Here we present a phylogeny of the siblings based on the sequences of two nuclear genes, period (per) and Alcohol dehydrogenase (Adh), as well as the mitochondrial gene Cytochrome oxidase I (COI). Taken individually, only per has a strong phylogenetic signal supporting a well-resolved phylogeny of the group, and this phylogeny is different from that obtained using allozymes. The COI dataset by itself produces trees that disagree with per, and neither that data nor the Adh data have a strong phylogenetic signal, as indicated by low bootstrap values for all analyses. Combining the Adh and COI datasets results in the same tree as per alone. Combining all three genes results in the same topology, which is strongly supported. Two problematic taxa, D. pavlovskiana and a “Carmody strain,” which were identified as potentially separate species based on reproductive isolation, clearly cluster in the phylogenetic analyses within D. paulistorum and D. equinoxialis, respectively. Thus, there appears to be a conflict between the biological species concept and the phylogenetic species concept.     

PHYLOGENY OF THE TRIBE CERATAPHIDINI (HOMOPTERA) AND THE EVOLUTION OF THE HORNED SOLDIER APHIDS

The horned soldier aphids of the Cerataphidini, unlike most social insects that reside in nests, live on the open surface of plants. The lack of a nest and other obvious ecological correlates makes it unclear why secondary-host soldiers might have evolved. Here I present a molecular phylogenetic analysis of 32 species of the Cerataphidini, including 10 species from the genera Ceratovacuna and Pseudoregma that produce horned soldiers. The phylogeny suggests that horned soldiers evolved once and were lost once or twice. Most horned soldiers are a morphologically specialized caste and two species that have unspecialized soldiers are independently derived from species with specialized castes. The genus Ceratovacuna appears to have undergone a relatively rapid radiation. Mapping secondary-host plants and geographic ranges onto the phylogeny suggests that bamboos were the ancestral secondary-host plants and that the Asian tropics and subtropics were the ancestral geographic regions for the genera Astegopteryx, Ceratoglyphina, Ceratovacuna Chaitoregma, and Pseudoregma and possibly for the entire tribe. There is evidence for vicariant events that separate the tropical and subtropical lineages in all of the major lineages of the tribe and for dispersal of some lineages. Based on these results, I present hypotheses for the causes and consequences of horned-soldier evolution.     

Phylogeny of Ips DeGeer Species (Coleoptera: Scolytidae) Inferred from Mitochondrial Cytochrome Oxidase I DNA Sequence

We used 766 bp of DNA sequence data from the mitochondrial cytochrome oxidase I gene to reconstruct a phylogeny for 39 of 43 Ips species, many of which are economically important bark beetles. The phylogeny was reconstructed using equally weighted and weighted parsimony. In both analyses, peripheral clades were well supported while internal clades were poorly supported. Phylogenetic analysis of translated amino acids produced a poorly resolved tree that was discordant with trees reconstructed with nucleotide sequence data. Two main conclusions are drawn about the monophyly of Ips and traditional systematic groups within Ips. First, Ips is monophyletic only when I. mannsfeldi, I. nobilis, and the concinnus and latidens species groups are excluded. The latidens group, I. mannsfeldi, and I. nobilis form a monophyletic group with 3 Orthotomicus species, while the concinnus group has a more basal position. Second, the majority of the species groups in the current classification for Ips are not monophyletic. European Ips species do not form a monophyletic group, contrary to common usage, and are dispersed on the phylogenetic tree among North American species. These results indicate that a formal systematic revision of Ips is needed.     

Patterns of genetic variation within and between Gibbon species

Gibbons are small, arboreal, highly endangered apes that are understudied compared with other hominoids. At present, there are four recognized genera and approximately 17 species, all likely to have diverged from each other within the last 5-6 My. Although the gibbon phylogeny has been investigated using various approaches (i.e., vocalization, morphology, mitochondrial DNA, karyotype, etc.), the precise taxonomic relationships are still highly debated. Here, we present the first survey of nuclear sequence variation within and between gibbon species with the goal of estimating basic population genetic parameters. We gathered ~60 kb of sequence data from a panel of 19 gibbons representing nine species and all four genera. We observe high levels of nucleotide diversity within species, indicative of large historical population sizes. In addition, we find low levels of genetic differentiation between species within a genus comparable to what has been estimated for human populations. This is likely due to ongoing or episodic gene flow between species, and we estimate a migration rate between Nomascus leucogenys and N. gabriellae of roughly one migrant every two generations. Together, our findings suggest that gibbons have had a complex demographic history involving hybridization or mixing between diverged populations.     

Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation

Evolutionary relationships within and between the marine hydrophiine sea snake groups have been inferred primarily using morphological characters, and two major groups traditionally are recognized. The Aipysurus group comprises nine species in two genera, and the taxonomically chaotic Hydrophis group comprises as many as 40 species, of which 27 are generally allocated to the genus Hydrophis and 13 to ten additional genera. In addition to these two major groups are three putatively ‘primitive’ monotypic genera, Hydrelaps darwiniensis, Ephalophis greyi and Parahydrophis mertoni. The present study investigated the evolutionary relationships of 23 representative species of marine hydrophiines, comprising 15 species from the Hydrophis group, six species from the Aipysurus group, and H. darwiniensis and P. mertoni, to address two broad aims. First, the aim was to provide a robust phylogeny for sea snakes to test previous phylogenetic hypotheses based on morphology, and thus provide some taxonomic stability to the group. Second, there was interest in evaluating the hypothesis that the Hydrophis group might represent a rapidly diverged adaptive radiation. A large mitochondrial DNA data set based on the cytochrome b gene (1080 bp, 401 parsimony informative) and the 16S rRNA gene (510 bp, 57 parsimony informative) was assembled and these data were analysed using parsimony, maximum‐likelihood and Bayesian approaches. All analyses yielded virtually the same optimal tree, confirming that hydrophiine sea snakes comprise at least three lineages. The Aipysurus group formed a strongly supported and well‐resolved monophyletic clade. The Hydrophis group also formed a strongly supported clade; however, resolution among the genera and species was very poor. Hydrelaps darwiniensis and P. mertoni formed a sister clade to the Hydrophis lineage. Our phylogeny was used to test the validity of previous taxonomic and phylogenetic hypotheses, and to demonstrate that the genus Hydrophis is not monophyletic. Genetic diversity relative to phenotypic diversity is four to seven times greater in the Hydrophis lineage compared with the Aipysurus lineage. The topology of our phylogenetic hypothesis, combined with the levels of genetic divergence relative to morphological diversity, demonstrate that the Hydrophis lineage represents a rapidly diverged adaptive radiation. The data are consistent with the hypothesis that this adaptive radiation may be due to historical sea level fluctuations that have isolated populations and promoted speciation. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 89 , 523–539.