Molecular Divergence Time Estimates Research Articles

Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes)

The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.

Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes

Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams.

Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life.

Simple SummaryAll life is derived from a single common ancestor, whose descendants coevolved with the planet, shaping the structure of biodiversity and the physical processes that operate on Earth. This complex history cannot be inferred solely by studying the genomes of living organisms, nor through analysis of the fossil remains of their extinct relatives. Only a unified approach integrating living and extinct species and drawing from both genomic and anatomical evidence can achieve this aim. In this review, we highlight recent advances, challenges, and opportunities in this endeavour. These include the development of models for analysis of anatomical data; methods for combined analysis of fossil and living species, as well as anatomical and genomic data; and the combined estimation of evolutionary relationships, geographic range, and evolutionary rates. However, the application of such methods is limited by a shortage of expertise in taxonomy and comparative anatomy, which are skills required for the compilation of anatomical datasets. Whereas there is a common concern for the incompleteness of the fossil record, knowledge with respect to the comparative anatomy of living species is equally incomplete. We anticipate that the increased demand for an integrative phylogenetic approach to reconstruct the tree of life and evolutionary patterns and processes will encourage researchers to overcome these challenges with the aim of elucidating the complexities behind organismal evolution across broad taxonomic and time scales.The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.

Revisiting R.H. Tschudy’s fern-spore spike concept 40 years later: connecting Tschudy’s ‘disaster taxon’ concept with paleopolyploidization in Stenochlaena J. Sm

The Cretaceous/Paleogene (K/Pg) boundary fern-spore spike concept was first introduced by R.H. Tschudy 40 years ago and established the precept that ferns are so-called ‘disaster taxa’ that flourish after natural disasters because of the high colonization potential of their wind-blown spores. Among the least understood topics at the crux of contemporary K/Pg boundary fern-spike studies is whether Stenochlaena-like or other stem blechnaceous ferns were among those that flourished after the K/Pg event, contributing to the Laevigatosporites-dominated phase of the fern-spore spike. For instance, dispersed Stenochlaena-like spores – e.g. Polypodiisporites usmensis (van der Hammen) Khan & Martin – first appear in the upper Eocene stratigraphic record of South America, whereas megafossils of Stenochlaena-like ferns are first known from the upper Paleocene strata of this same region. Beyond this traditional focus on taphonomic and taxonomic uncertainty regarding the identity of dispersed spore producers, however, there is further discordance between contemporary paleobotanical and molecular phylogenetic perspectives on the timing of diversification of stem lineages of blechnaceous ferns in relation to the K/Pg boundary. This investigation reconciles these two perspectives by constraining molecular clock divergence time estimates using contemporary fossil data. If this reconciliation is correct, then paleopolyploidization (whole genome duplication or WGD) associated with the origin of the genus Stenochlaena J. Sm. predated evolution of polocytic stomata, a heavily ornamented exospore, and a hemi-epiphytic to epiphytic habit observed in the crown lineage. Critically, this novel perspective elicits a merger of the K/Pg boundary fern spike and K/Pg boundary-WGD concepts, suggesting a link between polyploidy and the ‘disaster taxon’ concept.

Dense sampling of taxa and characters improves phylogenetic resolution among deltocephaline leafhoppers (Hemiptera: Cicadellidae: Deltocephalinae)

AbstractWe analysed a phylogenomic dataset comprising 730 terminal taxa and >160,000 nucleotide positions obtained using anchored hybrid enrichment of genomic DNA for a sample of deltocephaline leafhoppers and outgroups. Maximum likelihood analyses of concatenated nucleotide and amino acid sequences as well as coalescent gene tree analysis, yielded well‐resolved phylogenetic estimates that were highly congruent with most branches receiving maximum support. Some topological incongruence occurs among the trees resulting from different analyses, mainly distributed among very short branches at intermediate levels in the phylogeny, pertaining to relationships among some tribes and multi‐tribe lineages restricted to particular continents. Coalescent gene tree analysis revealed extensive gene tree conflict at these nodes, suggesting that certain relationships may remain difficult to resolve consistently even with genome‐scale datasets and dense taxon sampling. Ancestral character state reconstruction of feeding preference indicates that grass specialization has been acquired three or fewer times in some highly diverse but relatively derived lineages. Molecular divergence time estimation suggests that the earliest divergences in the subfamily occurred during the Cretaceous but that most modern tribes did not appear until after the Cretaceous–Palaeogene boundary and that grass specialist lineages generally diversified and spread at the same time as grasslands were becoming widespread globally. These analyses also show a high level of global biogeographic structure, with several large lineages of primarily arboreal deltocephalines restricted to particular regions or continents and long‐distance dispersal among continents occurring primarily among grass‐specialist lineages. The results represent a major improvement over previous analyses of this diverse subfamily, which were based on 152 or fewer taxa and data from morphology and partial sequences of two genes.

Crab in amber reveals an early colonization of nonmarine environments during the Cretaceous.

Amber fossils provide snapshots of the anatomy, biology, and ecology of extinct organisms that are otherwise inaccessible. The best-known fossils in amber are terrestrial arthropods—principally insects—whereas aquatic organisms are rarely represented. Here, we present the first record of true crabs (Brachyura) in amber—from the Cretaceous of Myanmar [~100 to 99 million years (Ma)]. The new fossil preserves large compound eyes, delicate mouthparts, and even gills. This modern-looking crab is nested within crown Eubrachyura, or “higher” true crabs, which includes the majority of brachyuran species living today. The fossil appears to have been trapped in a brackish or freshwater setting near a coastal to fluvio-estuarine environment, bridging the gap between the predicted molecular divergence of nonmarine crabs (~130 Ma) and their younger fossil record (latest Cretaceous and Paleogene, ~75 to 50 Ma) while providing a reliable calibration point for molecular divergence time estimates for higher crown eubrachyurans.

Morphological and molecular phylogenetic analyses ofZepedanulus ishikawai(Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

AbstractHarvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestmanZepedanulus ishikawai(Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based onCO1and16SrRNA sequences of mtDNA, the28SrRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals ofZ. ishikawaiwere monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades ofZ. ishikawai.

Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times.

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.

Phylogeny and temporal diversification of mosquitoes (Diptera: Culicidae) with an emphasis on the Neotropical fauna

AbstractUnderstanding phylogenetic relationships within the family Culicidae informs mosquito evolution and may have public health implications as this family includes numerous species of medical and veterinary importance. We investigated the mitochondrial genomes of 102 mosquitoes, including six newly sequenced species, representing 21 genera with an emphasis on the Neotropical region. We estimated divergence times based on sequence data and three fossil calibration points, using Bayesian relaxed clock methods. Bayesian and maximum‐likelihood phylogenetic analyses based on the DNA sequences of 13 PCGs of the 102 species provided robust support for the monophyly of the subfamily Anophelinae and the tribes Aedini, Culicini, Mansoniini and Sabethini. Despite the current genera of Anophelinae being consistently recovered as monophyletic, relationships among them proved to be quite variable depending on the method used (concatenated or partitioned) and the number of taxa sampled. Molecular divergence time estimates revealed that the two mosquito subfamilies, Anophelinae and Culicinae, diverged in the early Jurassic (approximately 197.5 Mya). However, most major lineages of these groups arose after the Cretaceous, coincident with the emergence of angiosperms and the expansion of mammals and birds. The diversification and worldwide distribution of Culicidae may also be determined in part by geographic isolation as a result of continental drift during the Cretaceous.

Восточно-азиатская – восточно-североамериканская дизъюнкция в видовом комплексе Onoclea sensibilis: викариантность или перипатрия?

Disjunction between East Asian and eastern North American plants has been recognized since the time of Darwin. Although there is considerable evidence for congruent vicariance associated with late Neogene/Quaternary cooling among angiosperms, similar studies among specific fern families (e.g., Osmundaceae Martinov) have appeared incongruous with this pattern. Pteridologists continue to debate whether long-distance dispersal of wind-blown spores could have produced intercontinental disjunctions among ferns. To date, however, state-of-the-art historical biogeographical approaches have not been applied to this problem. In this investigation, multiple chloroplast gene (rbcL, atpA, atpB, and matK) sequences for ferns in the family Onocleaceae Pic. Serm. are drawn from GenBank, including those from the recently sequenced chloroplast genome of the East Asian fern O. sensibilis L. var. interrupta Maxim., and used to create molecular phylogenies using Bayesian (BEAUTi and BEAST) techniques. Using contemporary approaches for relaxed molecular clock divergence time estimation with fossil calibration, divergence time estimates for East Asian and eastern North American populations in the Onoclea sensibilis species complex are consistently reconstructed as the Pliocene (ca. 5 – 3.4 Ma), and the best-fitting historical biogeographic model is a DIVA-like (exclusively vicariant) model using BIOGEOBEARS in RASP4, with a low probability of peripatry. Accordingly, these molecular and fossil data appear congruent with the pattern observed among angiosperms, despite the propensity for long-distance dispersal of wind-blown spores in pteridophytes. The lack of evidence for peripatry in this lineage may be related to the presence of short-lived green spores in onocleoid ferns; however, this hypothesis requires further investigation.

A Narrow Endemic or a Species Showing Disjunct Distribution? Studies on Meehania montis-koyae Ohwi (Lamiaceae).

Meehania montis-koyae Ohwi (Lamiaceae), which has been considered a narrow endemic and endangered species in Japan, was found in eastern China in 2011. China and Japan belong to the same floristic region and share many plant species, but it is very rare that Japanese narrow endemic species are newly found outside of the country. We examined herbarium specimens of both countries, and conducted analyses of molecular phylogenetics, population genetics, and divergence time estimation using two nuclear (ITS and ETS) gene regions and MIG-seq data. Chinese plants tend to become larger than Japanese, and they are different in leaf shape and floral features. Molecular phylogenetic analysis shows Chinese and Japanese M. montis-koyae are the closest relatives to each other. Population genetic analysis indicates no current gene flow between the Chinese and Japanese populations, and divergence time analysis shows they were separated during the late Miocene. We reach the conclusion that Chinese and Japanese M. montis-koyae have already become distinct biological entities, and a new taxon name Meehania zheminensis A. Takano, Pan Li, G.-H.Xia is proposed for the Chinese plants. A key to Asian Meehania species is provided.

Plastome phylogenomics, systematics, and divergence time estimation of the Beilschmiedia group (Lauraceae)

Intergeneric relationships of the Beilschmiedia group (Lauraceae) remain unresolved, hindering our understanding of their classification and evolutionary diversification. To remedy this, we sequenced and assembled complete plastid genomes (plastomes) from 25 species representing five genera spanning most major clades of Beilschmiedia and close relatives. Our inferred phylogeny is robust and includes two major clades. The first includes a monophyletic Endiandra nested within a paraphyletic Australasian Beilschmiedia group. The second includes (i) a subclade of African Beilschmiedia plus Malagasy Potameia, (ii) a subclade of Asian species including Syndiclis and Sinopora, (iii) the lone Neotropical species B. immersinervis, (iv) a subclade of core Asian Beilschmiedia, sister to the Neotropical species B. brenesii, and v) two Asian species including B. turbinata and B. glauca. The rampant non-monophyly of Beilschmiedia we identify necessitates a major taxonomic realignment of the genus, including but not limited to the mergers of Brassiodendron and Sinopora into the genera Endiandra and Syndiclis, respectively. Along these lines, the high degree of continental, clade-wide endemism we identify suggests that geographical distribution may be a good proxy for delineating taxa within this group. Our molecular divergence time estimates indicate that stem Beilschmiedia group members date to the Early Eocene (~50 Ma); their crown age dates to the Eocene–Oligocene boundary (~34 Ma). These findings contradict older estimates of the group and support mounting evidence that the origin and diversification of many pantropical angiosperm clades are not easily attributed to strict western Gondwanan vicariance. Finally, our study highlights the phylogenetic utility of plastomes in Lauraceace, and lays a solid foundation for future phylogenomic and biogeographic investigations within the family.

Phylogeny and classification of the leafhopper subfamily Eurymelinae (Hemiptera: Cicadellidae) inferred from molecules and morphology

AbstractPhylogenetic analysis of the globally distributed arboreal leafhopper subfamily Eurymelinae was conducted based on DNA sequence data from three nuclear and two mitochondrial genes in addition to 86 discrete morphological characters. The analysis included 89 species representing 61 genera from all major biogeographic regions including six species from outgroups, Megophthalminae and Ulopinae. Trees resulting from partitioned Bayesian and maximum likelihood analyses of the combined data were well resolved and largely congruent, differing mainly in the relationships among the earliest diverging lineages. The results are consistent with an expanded concept of Eurymelinae, including tribes Austroagalloidini and Macropsini. Six monophyletic groups are recognized as new tribes, Balocerini, Chiasmodolini, Chileanoscopini, Idioceroidini, Kopamerrini and Nesocerini, tribe n., and the previously recognized tribes Eurymelini, Idiocerini and Megipocerini are redefined. A new synonym, Busonini Zhang & Li, 2015 syn.n. is proposed here for Megipocerini Isaev, 1988. Molecular divergence time estimates were calibrated using two fossil taxa and suggested that the earliest divergences occurred in the Lower Cretaceous and that most major lineages of this group arose during the Cretaceous. Reconstruction of ancestral areas revealed considerable continental‐scale biogeographical structure. The place of origin of Eurymelinae is equivocal but major lineages arose in the Neotropical, Australian and Afrotropical regions. A key to tribes and a checklist of genera showing current tribal placements are provided.

Forest giants on different evolutionary branches: Ecomorphological convergence in helicopter damselflies.

The convergent evolution of analogous features is an evolutionary process occurring independently across the tree of life. From the evolution of echolocation, prehensile tail, viviparity, or winged flight, environmental factors often drive this astonishing phenomenon. However, convergent evolution is not always conspicuous or easily identified. Giant damselflies count among the largest flying insects on Earth, and have astonishing ecologies including orb-web spider plucking and oviposition in phytotelmata. One species occurs in the Afrotropics and 18 species are found in the Neotropics. Convergent evolution was historically hypothesized based on the ecological and morphological affinities of these two geographically distant lineages but was not supported by earlier phylogenetic inferences supporting their monophyly. Using a molecular supermatrix approach and a large selection of outgroups, we revisit and reject the monophyly of Afrotropical and Neotropical giant damselflies that is otherwise supported by a morphological phylogeny. Molecular divergence time estimation suggests an origin of Afrotropical giant damselflies in the late Paleogene, and of Neotropical ones at the Cretaceous/Paleogene boundary, thereby rejecting a long-standing West Gondwana vicariance hypothesis. The strong ecological and morphological resemblances between these two independent lineages represents an astonishing case of Amphi-Atlantic tropical convergent evolution.

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia.

Twenty-five years ago, it was suggested that current-day New Zealand, part of the largely sunken continent of Zealandia, could have been completely inundated during the Oligocene marine transgression (OMT) some 25-23 million years ago. Such an event would, of necessity, imply that all terrestrial, freshwater, and maybe coastal marine species must have dispersed there since. This idea has generated heated debate, on which geological, palaeontological and molecular data are being brought to bear. Here, we review the phylogeographic literature in the form of molecular estimates of divergence times between New Zealand lineages and their closest overseas sister groups. Using an event-based approach, we show that these divergence times follow approximately a smooth exponential over the last 50Ma or more. Approximately 74 of these 248 lineages appear to have survived the OMT in situ; some of these major lineages comprise multiple additional lineages as a result of autochthonous speciation prior to the OMT. Non-volant terrestrial animals, freshwater animals and trees are particularly well represented in surviving lineages, whereas marine animals, herbs and shrubs tend to show more recent arrival times. There is no evidence for a deficit of pre-Oligocene lineages, nor an excess of ones arriving just afterwards. The pattern is one of geometric increase in new lineages with more recent time, reflecting a balance between immigration and extinction. Consequently, this large body of molecular data provides no evidence for complete inundation of New Zealand during the Oligocene. In conjunction with new geological and palaeontological findings, these data suggest that it is time to put the idea to rest.

Molecular survey of basidiomycetes and divergence time estimation: An Indian perspective.

This study outlines the biodiversity of mushrooms of India. It reveals the molecular biodiversity and divergence time estimation of basidiomycetes from Gujarat, India. A total of 267 mushrooms were collected from 10 locations across the state. 225 ITS sequences were generated belonging to 105 species, 59 genera and 29 families. Phylogenetic analysis of Agaricaceae reveals monophyletic clade of Podaxis differentiating it from Coprinus. Further, the ancient nature of Podaxis supports the hypothesis that gasteroid forms evolved from secotioid forms. Members of Polyporaceae appeared polyphyletic. Further, our results of a close phylogenetic relationship between Trametes and Lenziteslead us to propose that the genera Trametes may by enlarged to include Lenzites. The tricholomatoid clade shows a clear demarcation for Entolomataceae. However, Lyophyllaceae and Tricholomataceae could not be distinguished clearly. Distribution studies of the mushrooms showed omnipresence of Ganoderma and Schizophyllum. Further, divergence time estimation shows that Dacrymycetes evolved in the Neoproterozoic Era and Hymenochaetales diverged from Agaricomycetes during the Silurian period.

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus.

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

A new Annonaceae genus, Wuodendron, provides support for a post–boreotropical origin of the Asian–Neotropical disjunction in the tribe Miliuseae

AbstractRecent molecular and morphological studies have clarified generic circumscriptions in Annonaceae tribe Miliuseae and resulted in the segregation of disparate elements from the previously highly polyphyletic genus Polyalthia s.l. Several names in Polyalthia nevertheless remain unresolved, awaiting assignment to specific genera, including Polyalthia litseifolia. Phylogenetic analyses of seven chloroplast regions (atpB–rbcL, matK, ndhF, psbA–trnH, rbcL, trnL–F, ycf1; ca. 8.3 kb, 116 accessions, including representatives of all currently accepted genera in subfamily Malmeoideae) unambiguously placed Polyalthia litseifolia in a clade with three accessions from Thailand, which have previously been shown to represent an undescribed genus sister to the Neotropical clade (Desmopsis, Sapranthus, Stenanona, Tridimeris) in the predominantly Asian tribe Miliuseae. The collective clade is sister to Meiogyne. Polyalthia litseifolia shares several diagnostic characters with most species in the Neotropical genera and Meiogyne, including: petals that are similar in shape and size in both whorls; multiple ovules per ovary in one or two rows; and lamelliform endosperm ruminations. It is distinct in being deciduous, bearing subpetiolar buds and having inflorescences growing from the leaf scar of the dropped leaves. Morphological comparisons and phylogenetic analyses corroborate its recognition as a new genus, which is formally described and illustrated here as Wuodendron. Polyalthia litseifolia is furthermore found to be conspecific with Desmos praecox, and the latter name is used as the basis for the name of the type. Molecular divergence time estimates under an uncorrelated lognormal relaxed clock place the Wuodendron–Neotropical clade split within the Miocene (ca. 14–12 Ma), highlighting the importance of post–boreotropical dispersal and vicariance in shaping intercontinental tropical disjunctions in Annonaceae.

Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

The timing of the diversification of placental mammals relative to the Cretaceous-Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs (Dermoptera) and pangolins (Pholidota). Depending on the gene partitioning scheme, molecular clock model, and genic deviation from molecular clock assumptions, extensive sensitivity analyses recovered widely varying diversification scenarios for placental mammals from a given gene set, ranging from a deep Cretaceous origin and diversification to a scenario spanning the KPg boundary, suggesting that the use of suboptimal molecular clock markers and methodologies is a major cause of controversies regarding placental diversification timing. We demonstrate that reconciliation between molecular and paleontological estimates of placental divergence times can be achieved using the appropriate clock model and gene partitioning scheme while accounting for the degree to which individual genes violate molecular clock assumptions. A birth-death-shift analysis suggests that placental mammals underwent a continuous radiation across the KPg boundary without apparent interruption by the mass extinction, paralleling a genus-level radiation of multituberculates and ecomorphological diversification of both multituberculates and therians. These findings suggest that the KPg catastrophe evidently played a limited role in placental diversification, which, instead, was likely a delayed response to the slightly earlier radiation of angiosperms.