Molecular Clock Dating Research Articles

Molecular Dating of the Teleost Whole Genome Duplication (3R) Is Compatible With the Expectations of Delayed Rediploidization.

Vertebrate evolution has been punctuated by three whole genome duplication events that have been implicated causally in phenotypic evolution, from the origin of phenotypic novelties to explosive diversification. Arguably, the most dramatic of these is the 3R whole genome duplication event associated with the origin of teleost fishes which comprise more than half of all living vertebrate species. However, tests of a causal relationship between whole genome duplication and teleost diversification have proven difficult due to the challenge of establishing the timing of these phenomena. Here we show, based on molecular clock dating of concatenated gene alignments, that the 3R whole genome duplication event occurred in the early-middle Permian (286.18 to 267.20 million years ago; Ma), 52.02 to 12.84 million years (Myr) before the divergence of crown-teleosts in the latest Permian-earliest Late Triassic (254.36 to 234.16 Ma) and long before the major pulses of teleost diversification in Ostariophysi and Percomorpha (56.37 to 100.17 Myr and at least 139.24 to 183.29 Myr later, respectively). The extent of this temporal gap between putative cause and effect precludes 3R as a deterministic driver of teleost diversification. However, these age constraints remain compatible with the expectations of a prolonged rediploidization process following whole genome duplication which, through the effects of chromosome rearrangement and gene loss, remains a viable mechanism to explain the evolution of teleost novelties and diversification.

Vicariance and cryptic diversity revealed by molecular phylogenetic analyses of estuarine Gammarus species (Crustacea: Amphipoda) due to formation of the Labrador Current

The metapopulation of the estuarine species Gammarus tigrinus along the east coast of the United States has been hypothesised to represent two cryptic species divided biogeographically off the coast of North Carolina, USA. This divergence has been attributed to a strong temperature gradient created by the formation of the cold Labrador Current c. 3.0 million years ago. In addition, the northern phylogeographic clade of G. tigrinus has been demonstrated to be invasive in estuarine habitats across a large portion of northern Europe. Recent collections of G. tigrinus from Florida and Maryland, USA, allow for new approaches to test this hypothesis. Using the nuclear 18S and 28S rRNA, and mitochondrial 16S rRNA and cytochrome c oxidase subunit I genes, species delimitation models provide support that the genetic divergence of the northern and southern clades is equivalent to species level. In addition, molecular clock data demonstrate that this phylogeographic divergence coincides with the formation of the Labrador Current. Furthermore, the collections of G. daiberi from Florida, a species with biogeographical and ecological characteristics similar to those of G. tigrinus, provide independent support for the hypothesis. The potential for invasive species to be cryptic highlights the need for accurate identification of taxa to ensure that appropriate biogeographical assessment of potential source populations and mechanisms of dispersal can be made.

Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae.

Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae. Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.

Silica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera

Metazoans use silicon traces but rarely develop extensive silica skeletons, except for the early-diverging lineage of sponges. The mechanisms underlying metazoan silicification remain incompletely understood, despite significant biotechnological and evolutionary implications. Here, the characterization of two proteins identified from hexactinellid sponge silica, hexaxilin and perisilin, supports that the three classes of siliceous sponges (Hexactinellida, Demospongiae, and Homoscleromorpha) use independent protein machineries to build their skeletons, which become non-homologous structures. Hexaxilin forms the axial filament to intracellularly pattern the main symmetry of the skeletal parts, while perisilin appears to operate in their thickening, guiding extracellular deposition of peripheral silica, as does glassin, a previously characterized hexactinellid silicifying protein. Distant hexaxilin homologs occur in some bilaterians with siliceous parts, suggesting putative conserved silicifying activity along metazoan evolution. The findings also support that ancestral Porifera were non-skeletonized, acquiring silica skeletons only after diverging into major classes, what reconciles molecular-clock dating and the fossil record.

Divergence time estimates for the hypoxia-inducible factor-1 alpha (HIF1α) reveal an ancient emergence of animals in low-oxygen environments.

Unveiling the tempo and mode of animal evolution is necessary to understand the links between environmental changes and biological innovation. Although the earliest unambiguous metazoan fossils date to the late Ediacaran period, molecular clock estimates agree that the last common ancestor (LCA) of all extant animals emerged ~850 Ma, in the Tonian period, before the oldest evidence for widespread ocean oxygenation at ~635-560 Ma in the Ediacaran period. Metazoans are aerobic organisms, that is, they are dependent on oxygen to survive. In low-oxygen conditions, most animals have an evolutionarily conserved pathway for maintaining oxygen homeostasis that triggers physiological changes in gene expression via the hypoxia-inducible factor (HIFa). However, here we confirm the absence of the characteristic HIFa protein domain responsible for the oxygen sensing of HIFa in sponges and ctenophores, indicating the LCA of metazoans lacked the functional protein domain as well, and so could have maintained their transcription levels unaltered under the very low-oxygen concentrations of their environments. Using Bayesian relaxed molecular clock dating, we inferred that the ancestral gene lineage responsible for HIFa arose in the Mesoproterozoic Era, ~1273 Ma (Credibility Interval 957-1621 Ma), consistent with the idea that important genetic machinery associated with animals evolved much earlier than the LCA of animals. Our data suggest at least two duplication events in the evolutionary history of HIFa, which generated three vertebrate paralogs, products of the two successive whole-genome duplications that occurred in the vertebrate LCA. Overall, our results support the hypothesis of a pre-Tonian emergence of metazoans under low-oxygen conditions, and an increase in oxygen response elements during animal evolution.

Tonian Low‐Latitude Marine Ecosystems Were Cold Before Snowball Earth

AbstractPrecambrian marine carbonate strata are commonly assumed to have formed in warm‐water carbonate factories due to the temperature dependence of non‐skeletal carbonate precipitation rates. However, some climate models and geological observations suggest that global climate was cool for tens of millions of years prior to the onset of Snowball Earth glaciation at ∼717 Ma, in conflict with common interpretations of pre‐glacial carbonates as warm‐water carbonate factories. We report the occurrence of guttulatic microfabric—a petrographic fingerprint of ikaite, a carbonate mineral that only forms in cold sedimentary environments—in the Beck Spring Dolomite, a carbonate succession deposited in a low‐latitude shallow marine environment between ∼780 and 730 Ma. This interpretation of pre‐glacial carbonate factories aligns cold conditions with vase‐shaped microfossils, possible algal fossils, and molecular clock dates for crown‐group metazoans. Our observations indicate that these marine ecosystems were able to thrive in cold low‐latitude environments millions of years before the Snowball glaciations.

Phylogeography and karyotypic evolution of some Deuterodon species from southeastern Brazil (Characiformes, Characidae, Stethaprioninae).

Deuterodon is a genus of the subfamily Stethaprioninae, a group of Neotropical fish known as tetras. Deuterodon hastatus represents a species complex, which is supported by cytogenetic and molecular data. In this study, we show the results of comparative evolutionary analyses of the ATP synthase subunit 6 gene in four Deuterodon species, in addition to ribosomal markers (18S rDNA and 5S rDNA), of a new population of the D. hastatus species complex from the Angra dos Reis/RJ region. The study population comprised a new cytotype, which we refer to as cytotype D, in D. hastatus, with 2n = 50 = 6M+8SM+8ST+28A. We obtained three different clades of D. hastatus in our phylogeny, one of them composed only by specimens of cytotype D. By using molecular clock dating, we observed that the radiation of Deuterodon from southeastern Brazil seemed to be associated with neotectonic events that occurred during the Miocene-Pliocene and Pliocene-Pleistocene transitions, marked by the capture of headwater streams and marine transgressions. The results obtained reinforce the idea that D. hastatus is a species complex, and at least three evolutionary significant units were identified in this group.

A Timeframe for SARS-CoV-2 Genomes: A Proof of Concept for Postmortem Interval Estimations.

Establishing the timeframe when a particular virus was circulating in a population could be useful in several areas of biomedical research, including microbiology and legal medicine. Using simulations, we demonstrate that the circulation timeframe of an unknown SARS-CoV-2 genome in a population (hereafter, estimated time of a queried genome [QG]; tE-QG) can be easily predicted using a phylogenetic model based on a robust reference genome database of the virus, and information on their sampling dates. We evaluate several phylogeny-based approaches, including modeling evolutionary (substitution) rates of the SARS-CoV-2 genome (~10-3 substitutions/nucleotide/year) and the mutational (substitutions) differences separating the QGs from the reference genomes (RGs) in the database. Owing to the mutational characteristics of the virus, the present Viral Molecular Clock Dating (VMCD) method covers timeframes going backwards from about a month in the past. The method has very low errors associated to the tE-QG estimates and narrow intervals of tE-QG, both ranging from a few days to a few weeks regardless of the mathematical model used. The SARS-CoV-2 model represents a proof of concept that can be extrapolated to any other microorganism, provided that a robust genome sequence database is available. Besides obvious applications in epidemiology and microbiology investigations, there are several contexts in forensic casework where estimating tE-QG could be useful, including estimation of the postmortem intervals (PMI) and the dating of samples stored in hospital settings.

Parallel Evolution of Ameloblastic scpp Genes in Bony and Cartilaginous Vertebrates.

In bony vertebrates, skeletal mineralization relies on the secretory calcium-binding phosphoproteins (Scpp) family whose members are acidic extracellular proteins posttranslationally regulated by the Fam20°C kinase. As scpp genes are absent from the elephant shark genome, they are currently thought to be specific to bony fishes (osteichthyans). Here, we report a scpp gene present in elasmobranchs (sharks and rays) that evolved from local tandem duplication of sparc-L 5′ exons and show that both genes experienced recent gene conversion in sharks. The elasmobranch scpp is remarkably similar to the osteichthyan scpp members as they share syntenic and gene structure features, code for a conserved signal peptide, tyrosine-rich and aspartate/glutamate-rich regions, and harbor putative Fam20°C phosphorylation sites. In addition, the catshark scpp is coexpressed with sparc-L and fam20°C in tooth and scale ameloblasts, similarly to some osteichthyan scpp genes. Despite these strong similarities, molecular clock and phylogenetic data demonstrate that the elasmobranch scpp gene originated independently from the osteichthyan scpp gene family. Our study reveals convergent events at the sparc-L locus in the two sister clades of jawed vertebrates, leading to parallel diversification of the skeletal biomineralization toolkit. The molecular evolution of sparc-L and its coexpression with fam20°C in catshark ameloblasts provides a unifying genetic basis that suggests that all convergent scpp duplicates inherited similar features from their sparc-L precursor. This conclusion supports a single origin for the hypermineralized outer odontode layer as produced by an ancestral developmental process performed by Sparc-L, implying the homology of the enamel and enameloid tissues in all vertebrates.

Plant migration under long-lasting hyperaridity - phylogenomics unravels recent biogeographic history in one of the oldest deserts on Earth.

The post-Miocene climatic histories of arid environments have been identified as key drivers of dispersal and diversification. Here, we investigate how climatic history correlates with the historical biogeography of the Atacama Desert genus Cristaria (Malvaceae). We analyze phylogenetic relationships and historical biogeography by using next-generation sequencing (NGS), molecular clock dating, Dispersal Extinction Cladogenesis and Bayesian sampling approaches. We employ a novel way to identify biogeographically meaningful regions as well as a rarely utilized program permitting the use of dozens of ancestral areas. Partial incongruence between the established taxonomy and our phylogenetic data argue for a complex historical biogeography with repeated introgression and incomplete lineage sorting. Cristaria originated in the central southern part of the Atacama Desert, from there the genus colonized other areas from the late Miocene onwards. The more recently diverged lineages appear to have colonized different habitats in the Atacama Desert during pluvial phases of the Pliocene and early Pleistocene. We show that NGS combined with near-comprehensive sampling can provide an unprecedented degree of phylogenetic resolution and help to correlate the historical biogeography of plant communities with cycles of arid and pluvial phases.

Phylogenetic reconstruction of the initial stages of the spread of the SARS-CoV-2 virus in the Eurasian and American continents by analyzing genomic data

Samples from complete genomes of SARS-CoV-2 isolated during the first wave (December 2019–July 2020) of the global COVID-19 pandemic from 21 countries (Asia, Europe, Middle East and America) around the world, were analyzed using the phylogenetic method with molecular clock dating. Results showed that the first cases of COVID-19 in the human population appeared in the period between July and November 2019 in China. The spread of the virus into other countries of the world began in the autumn of 2019. In mid-February 2020, the virus appeared in all the countries we analyzed. During this time, the global population of SARS-CoV-2 was characterized by low levels of the genetic polymorphism, making it difficult to accurately assess the pathways of infection. The rate of evolution of the coding region of the SARS-CoV-2 genome equal to 7.3 × 10−4 (5.95 × 10−4–8.68 × 10−4) nucleotide substitutions per site per year is comparable to those of other human RNA viruses (Measles morbillivirus, Rubella virus, Enterovirus C). SARS-CoV-2 was separated from its known close relative, the bat coronavirus RaTG13 of the genus Betacoronavirus, approximately 15–43 years ago (the end of the 20th century).

Chromosome-level genome assembly of Welwitschia mirabilis, a unique Namib Desert species.

Welwitschia mirabilis, which is endemic to the Namib Desert, is the only living species within the family Welwitschiaceae. This species has an extremely long lifespan of up to 2,000years and bears a single pair of opposite leaves that persist whilst alive. However, the underlying genetic mechanisms and evolution of the species remain poorly elucidated. Here, we report on a chromosome-level genome assembly for W.mirabilis, with a 6.30-Gb genome sequence and contig N50 of 27.50Mb. In total, 39,019 protein-coding genes were predicted from the genome. Two brassinosteroid-related genes (BRI1 and CYCD3), key regulators of cell division and elongation, were strongly selected in W.mirabilis and may contribute to their long ever-growing leaves. Furthermore, 29gene families in the mitogen-activated protein kinase signalling pathway showed significant expansion, which may contribute to the desert adaptations of the plant. Three positively selected genes (EHMT1, EIF4E, SOD2) may be involved in the mechanisms leading to long lifespan. Based on molecular clock dating and fossil calibrations, the divergence time of W.mirabilis and Gnetum montanum was estimated at ~123.5million years ago. Reconstruction of population dynamics from genome data coincided well with the aridification of the Namib Desert. The genome sequence detailed in the current study provides insight into the evolution of W.mirabilis and should be an important resource for further study on gnetophyte and gymnosperm evolution.

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication.

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.

A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria)

Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments, displaying an excellent fossil record extremely valuable for paleo-environmental reconstruction studies, from where most of their extant diversity and ecology have been inferred. This study represents a comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high classification ranks. Such reconsideration allows gathering different morphologies with concentric structure and spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Our calibrated molecular clock dates the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), among the first radiolarian representatives in the fossil record. This study allows a direct connection between living specimens and extinct morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction analysis.

Developmental capacity and the early evolution of animals

Disentangling the factors underlying the appearance of macroscopic, often skeletonized, bilaterians during the Ediacaran–Cambrian diversification of animals requires carefully parsing the contributions of ecological opportunity, environmental potential and developmental capacity. The early evolution of animals involved the introduction of genomic, developmental, morphologic and behavioural novelties, identified as the individuation of new characters, which led to the construction of new ecological networks (innovation). Here I employ a recently introduced conceptual framework for novelty and individuation that distinguishes between potentiation, novelty, innovation and adaptive adjustments to the Ediacaran–Cambrian Radiation, and focus on the roles of potentiation and novelty in the expansion of developmental capacity. Comparative developmental studies combined with molecular clock estimates and data from the fossil record suggest that developmental capacity, the potential to generate a range of morphologies, may expand rapidly through developmental novelties without leading directly to morphological novelties, or to innovation. The expected patterns from this framework are markedly different from those in adaptive radiation scenarios. Thematic collection: This article is part of the Advances in the Cambrian Explosion collection available at: https://www.lyellcollection.org/cc/advances-cambrian-explosion

Evolutionary ecology of Agave: distribution patterns, phylogeny, and coevolution (an homage to Howard S. Gentry).

With more than 200 species, the genus Agave is one of the most interesting and complex groups of plants in the world, considering for instance its great diversity and adaptations. The adaptations include the production of a single, massive inflorescence (the largest among plants) where after growing for many years, sometimes more than 30, the rosette dies shortly afterward, and the remarkable coevolution with their main pollinators, nectarivorous bats, in particular of the genus Leptonycteris. The physiological adaptations of Agave species include a photosynthetic metabolism that allows efficient use of water and a large degree of succulence, helping to store water and resources for their massive flowering event. Ecologically, the agaves are keystone species on which numerous animal species depend for their subsistence due to the large amounts of pollen and nectar they produce, that support many pollinators, including bats, perching birds, hummingbirds, moths, and bees. Moreover, in many regions of Mexico and in the southwestern United States, agaves are dominant species. We describe the contributions of H. S. Gentry to the understanding of agaves and review recent advances on the study of the ecology and evolution of the genus. We analyze the present and inferred past distribution patterns of different species in the genus, describing differences in their climatic niche and adaptations to dry conditions. We interpret these patterns using molecular clock data and phylogenetic analyses and information of their coevolving pollinators and from phylogeographic, morphological, and ecological studies and discuss the prospects for their future conservation and management.

Air Breathing in an Exceptionally Preserved 340-Million-Year-Old Sea Scorpion

Arachnids are the second most successful terrestrial animal group after insects [1] and were one of the first arthropod clades to successfully invade land [2]. Fossil evidence for this transition is limited, with the majority of arachnid clades first appearing in the terrestrial fossil record. Furthermore, molecular clock dating has suggested a Cambrian-Ordovician terrestrialization event for arachnids [3], some 60 Ma before their first fossils in the Silurian, although these estimates assume that arachnids evolved from a fully aquatic ancestor. Eurypterids, the sister clade to terrestrial arachnids [4-6], are known to have undergone major macroecological shifts in transitioning from marine to freshwater environments during the Devonian [7, 8]. Discoveries of apparently subaerial eurypterid trackways [9, 10] have led to the suggestion that eurypterids were even able to venture on land and possibly breathe air [11]. However, modern horseshoe crabs undertake amphibious excursions onto land to reproduce [12], rendering trace fossil evidence alone inconclusive. Here, we present details of the respiratory organs of Adelophthalmus pyrrhae sp. nov. from the Carboniferous of Montagne Noire, France [13], revealed through micro computed tomography (μ-CT) imaging. Pillar-like trabeculae on the dorsal surface of each gill lamella indicate eurypterids were capable of subaerial breathing, suggesting that book gills are the direct precursors to book lungs while vascular ancillary respiratory structures known as Kiemenplatten represent novel air-breathing structures. The discovery of air-breathing structures in eurypterids indicates that characters permitting terrestrialization accrued in the arachnid stem lineage and suggests the Cambrian-Ordovician ancestor of arachnids would also have been semi-terrestrial.

A one-billion-year-old multicellular chlorophyte.

Chlorophytes (which represent a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans, and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution, and ecological expansion in the late Neoproterozoic and Paleozoic. This model, however, has not been rigorously tested with paleontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimeter-sized, multicellular, and morphologically differentiated macrofossils from ~1,000 Ma rocks. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity, and cellular differentiation nearly a billion years ago, much earlier than previously thought.

Time of re-emergence of Christmas Island and its biogeographical significance

Christmas Island in the eastern Indian Ocean forms the pinnacle of a once-drowned, coral atoll. Exactly when the seamount re-emerged above the seas is, unfortunately, imprecisely understood. One of the consequences of this uncertainty is that it can hamper studies dealing with its land-locked faunal assemblage. We attempt to address this issue using geological and geophysical information. A first constraint is provided by sub-aerially erupted volcanic rocks that accumulated on a karstified land-surface. Radiometric ages for five associated basalt samples yield a mean of 4.39 ± 0.08 Ma (2σ). These data, together with the geological observations, indicate that the island existed in the mid-Early Pliocene. A second constraint is provided by the seamount's postulated uplift path as it ascended the outer-trench high on its journey towards the subduction zone south of Java. Here, the edifice is estimated to have become sub-aerial between 5.66 and 4.49 Ma (5.03 + 0.63/−0.54 Ma). In terms of biogeography, landmass emergence in the latest Miocene-Early Pliocene is largely concordant with the island's native land-locked reptile and mammal species (eight of the nine extant and recently extirpated forms are endemic) as most show only small to negligible levels of genetic differentiation with respect to their nearest off-island relatives. Significantly, though, molecular-clock data for at least two, possibly three, of the lizard species indicate that they split from their nearest living congeners (incidentally, all from lands to the east of the Wallace Line >1100 km away) prior to Christmas Island's emergence, that is in the Late Miocene or earlier (specifically at c. 7 Ma, c. 13 Ma and c. 26 Ma). Assuming the ages are reliable, these dichotomies could be explained if there are/were intermediate relatives that exist elsewhere/are now-extinct as this would facilitate the ancestors of the Christmas Island species colonizing the landmass sometime in the last five million years or so.

Cenozoic formation and colonisation history of the New Zealand vascular flora based on molecular clock dating of the plastid rbcL gene

ABSTRACTA colonisation history for 411 extant genera and 477 lineages of the vascular flora of New Zealand was constructed using the plastid rbcL gene. Molecular clock crown ages suggest that the Eocene-Oligocene transition extinction at 33.9 Ma was critical to the development of the extant flora as few lineages, mostly ferns and conifers, predate this event. Based on crown dates, almost all extant angiosperm lineages have established after the Eocene-Oligocene transition extinction. The Oligocene marine transgression had little discernible impact on the formation of the extant flora, as at the culmination of the inundation (22.0–25.0 Ma) fifty extant lineages of vascular plant were present and another eight lineages originated during this time. The majority of extant species (89%) originated after the end of the Miocene Thermal Optimum at about 15.0 Ma. Nearly 50% of the extant species have evolved during mountain uplift and glaciation of the late Pliocene-Pleistocene (0–4.99 Ma). Therefore, despite a residual contribution from the Eocene, Oligocene and early to mid Miocene periods, the New Zealand vascular flora essentially originated in the late Miocene and after.