Relaxed Clock Methods Research Articles

Morphological and Molecular Analysis Identified a Subspecies of Crassostrea ariakensis (Fujita, 1913) along the Coast of Asia.

Crassostrea ariakensis (Fujita, 1913) is one of the most important economic and ecological oysters that is naturally distributed along the coast of Asia, separated by the Yangtze River estuary. They are usually compared as different populations, while there is no consensus on whether C. ariakensis in northern and southern areas should be considered as two species or subspecies. Here, we analyzed morphological characteristics, COI, 16s rRNA, mitogenome sequences, and species delimitation analysis (ASAP and PTP) to resolve the intraspecific taxonomic status of the C. ariakensis. Phylogenetic and ASAP analysis highlight that C. ariakensis was divided into N-type and S-type. PTP was unable to differentiate between the two types of C. ariakensis. The divergence time of N-type and S-type C. ariakinsis is estimated to be 1.6 Mya, using the relaxed uncorrelated lognormal clock method. Additionally, significant morphological differences exist between the two groups in terms of the adductor muscle scar color. Despite these differences, the COI (0.6%) and 16S rRNA (0.6%) genetic distance differences between N-type and S-type C. ariakensis has not yet reached the interspecific level. These results suggest that N-type and S-type C. ariakensis should be treated as different subspecies and renamed as C. ariakensis ariakensis subsp. nov and C. ariakensis meridioyangtzensis subsp. nov.

Molecular timetrees using relaxed clocks and uncertain phylogenies.

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.

Timescale lessons of Durinskia baltica (Kryptoperidiniaceae, Dinophyta) from freshwater through a molecular phylogeny

Background: The evolutionary pattern of dinophytes is complex and requires comprehensive taxonomic studies addressing the species' development and morphology, ecology, evolution, and genetics.
 Questions: How recent was the transition of D. baltica from Mexico to freshwater based on a calibrated phylogeny tree of the Kryptoperidiniaceae?
 Studied species and data description: Durinskia baltica, Kryptoperidiniaceae and the known fossil record of dinotoms (endosymbiont diatom-host dinophytes).
 Study sites and dates: Xochimilco, Mexico City. 2010 to 2019.
 Methods: Phylogenies were constructed with Bayesian inferences and host sequences were calibrated with a relaxed clock method.
 Results: We obtained genetic sequences of the 18S rDNA sector in the host and the rbcL sector in the endosymbiont. The Nitzschia-type endosymbiont is genetically distinct from endosymbionts of other dinotomes with the same diatom type. In contrast, considering the known freshwater species of Durinskia, the genetic relationship between hosts is robust and of recent origin. The antiquity of the Mexican sequence coincides with the geological origin of the Xochimilco basin, suggesting particularities in the evolutionary history of dinotomes linked to the geographic regions they inhabit.
 Conclusions: Our evolutionary scenario with a calibrated phylogeny indicates that the transition of Durinskia baltica to freshwater in the Xochimilco basin is geologically contextualized. The historical environmental change of Lake Xochimilco with respect to salinity corresponds with an initial colonization of D. baltica in a brackish environment and its subsequent adaptation to freshwater.

Macro-evolutionary patterns of East Asian opsariichthyin-xenocyprinin-cultrin fishes related to the formation of river and river-lake environments under monsoon climate

Although the East Asian monsoon is believed to be an important driver for the origin and evolution of the biotas in this region, the association has rarely been rigorously tested. Here, using phylogenetic comparative methods and analyses of key innovations of adaptive traits, we investigated evolutionary patterns of the East Asian cyprinid opsariichthyin-xenocyprinin-cultrin clade; the dominant species in lakes and rivers, which are the typical productions of monsoon climate. Our molecular phylogenetic analyses revealed the relationships as (Opsariichthys-tribe + (((Oxygaster-tribe ​+ ​Aphyocypris-tribe) ​+ ​Metzia-tribe) ​+ ​(Paralaubuca-tribe + (Squaliobarbus-tribe + (Hypophthalmichthys-tribe + (xenocyprinins ​+ ​cultrins)))))). Based on Bayesian relaxed-clock methods, we found that origins of the Squaliobarbus- and Hypophthalmichthys-tribes bearing the key adaptation of riverine spawning with drifting eggs occurred 22.5 and 21.1 Mya, respectively. These times are consistent with the Early Miocene origin of major rivers (e.g., Yangtze River) and the appearance of the East Asian monsoon climate. Diversification of the cultrins, characterized by spawning of adhesive eggs as well as swimming and feeding in lentic waters, were estimated to have evolved 16.6 to 0.2 Mya. This period covers three phases of enhancement of the East Asian monsoon from the Middle Miocene to the Pliocene (around 15–13, 10–7, and 3.5 Mya). The habitats of these cultrins and their evolution also suggest the appearance and development of a lake-river environment during those periods. Therefore, our results suggest close relationships between the evolution of these fishes and geological events in East Asia. Further, they provide knowledge that may help facilitate future conservation strategies such as the maintenance of high river flows during dam construction and operation.

Assessing Rapid Relaxed-Clock Methods for Phylogenomic Dating.

Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus, the power and pitfalls of selecting among these approaches remain unclear. We compared the accuracy, bias, and coverage probabilities of RelTime, treePL, and least-squares dating time estimates by applying them to analyze computer-simulated data sets in which evolutionary rates varied extensively among branches in the phylogeny. RelTime estimates were consistently more accurate than the other two, particularly when evolutionary rates were autocorrelated or shifted convergently among lineages. The 95% confidence intervals (CIs) around RelTime dates showed appropriate coverage probabilities (95% on average), but other methods produced rather low coverage probabilities because of overly narrow CIs of time estimates. Overall, RelTime appears to be a more efficient method for estimating divergence times for large phylogenies.

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.

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches.

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer-simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.

Flatfish monophyly refereed by the relationship of Psettodes in Carangimorphariae

BackgroundThe monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained.ResultsThe mitogenomes of five flatfishes were determined. Select mitogenomes of representative carangimorph species were further employed for phylogenetic and molecular clock analyses. Our phylogenetic results do not fully support Psettodes as a sister group to pleuronectoids or other carangimorphs. And results also supported the evidence of long-branch attraction between Psettodes and the adjacent clades. Two chronograms, derived from Bayesian relaxed-clock methods, suggest that over a short period in the early Paleocene, a series of important evolutionary events occurred in carangimorphs.ConclusionBased on insights provided by the molecular clock, we propose the following evolutionary explanation for the difficulty in determining the phylogenetic position of Psettodes: The initial diversification of Psettodes was very close in time to the initial diversification of carangimorphs, and the primary diversification time of pleuronectoids, the other suborder of flatfishes, occurred later than that of some percomorph taxa. Additionally, the clade of Psettodes is long and naked branch, which supports the uncertainty of its phylogenetic placement. Finally, we confirmed the monophyly of flatfishes, which was accepted by most ichthyologists.

Phylogeography of the Central American lancehead Bothrops asper (SERPENTES: VIPERIDAE).

The uplift and final connection of the Central American land bridge is considered the major event that allowed biotic exchange between vertebrate lineages of northern and southern origin in the New World. However, given the complex tectonics that shaped Middle America, there is still substantial controversy over details of this geographical reconnection, and its role in determining biogeographic patterns in the region. Here, we examine the phylogeography of Bothrops asper, a widely distributed pitviper in Middle America and northwestern South America, in an attempt to evaluate how the final Isthmian uplift and other biogeographical boundaries in the region influenced genealogical lineage divergence in this species. We examined sequence data from two mitochondrial genes (MT-CYB and MT-ND4) from 111 specimens of B. asper, representing 70 localities throughout the species’ distribution. We reconstructed phylogeographic patterns using maximum likelihood and Bayesian methods and estimated divergence time using the Bayesian relaxed clock method. Within the nominal species, an early split led to two divergent lineages of B. asper: one includes five phylogroups distributed in Caribbean Middle America and southwestern Ecuador, and the other comprises five other groups scattered in the Pacific slope of Isthmian Central America and northwestern South America. Our results provide evidence of a complex transition that involves at least two dispersal events into Middle America during the final closure of the Isthmus.

Dating early animal evolution using phylogenomic data

Information about the geological timeframe during which animals radiated into their major subclades is crucial to understanding early animal ecology and evolution. Unfortunately, the pre-Cambrian fossil record is sparse and its interpretation controversial. Relaxed molecular-clock methods provide an alternative means of estimating the timing of cladogenesis deep in the metazoan tree of life. So far, thorough molecular clock studies focusing specifically on Metazoa as a whole have been based on relatively small datasets or incomplete representation of the main non-bilaterian lineages (such as sponges and ctenophores), which are fundamental for understanding early metazoan evolution. Here, we use a previously published phylogenomic dataset that includes a fair sampling of all relevant groups to estimate the timing of early animal evolution with Bayesian relaxed-clock methods. According to our results, all non-bilaterian phyla, as well as total-group Bilateria, evolved in an ancient radiation during a geologically relatively short time span, before the onset of long-term global glaciations (“Snowball Earth”; ~720–635 Ma). Importantly, this result appears robust to alterations of a number of important analytical variables, such as models of among-lineage rate variation and sets of fossil calibrations used.

Into Africa: Molecular phylogenetics and historical biogeography of sub-Saharan African woodferns (Dryopteris).

Our goal was to infer the phylogenetic relationships and historical biogeography of the genus Dryopteris with a focus on taxa in sub-Saharan Africa and neighboring islands. In general, little is known about the relationships between African fern species and their congeners in other geographic regions, and our aim was to determine whether the sub-Saharan African species of Dryopteris are monophyletic and evolved within Africa or arrived there via repeated dispersals into Africa from other regions. We obtained sequence data for five chloroplast markers from 214 species of Dryopteris and 18 outgroups. We performed phylogenetic and molecular dating analyses using a Bayesian relaxed clock method in BEAST with fossil and secondary calibration points and estimated ancestral ranges for the genus globally by comparing multiple models in BioGeoBEARS. We found that 22 of 27 accessions of sub-Saharan African Dryopteris belong to a large clade of 31 accessions that also includes taxa from Indian and Atlantic Ocean islands. Additional accessions of taxa from our regions of interest have Asian, Hawaiian, European, or North American species as their closest relatives. The majority of sub-Saharan African Dryopteris species are descended from a shared common ancestor that dispersed to Africa from Asia approximately 10 Ma. There have been subsequent dispersal events from the African mainland to islands in the Atlantic and Indian Oceans, including Madagascar. Several additional species are estimated to have descended from ancestors that reached Africa via separate events over the last roughly 20 million years.

Out of Africa: Biogeography and diversification of the pantropical pond skater genus Limnogonus Stål, 1868 (Hemiptera: Gerridae).

Gondwanan vicariance, long‐distance dispersal (LDD), and boreotropical migration have been proposed as alternative hypotheses explaining the pantropical distribution pattern of organisms. In this study, the historical biogeography of the pond skater genus Limnogonus was reconstructed to evaluate the impact of biogeographical scenarios in shaping their modern transoceanic disjunction. We sampled almost 65% of recognized Limnogonus species. Four DNA fragments including 69 sequences were used to reconstruct a phylogram. Divergence time was estimated using a Bayesian relaxed clock method and three fossil calibrations. Diversification dynamics and ancestral area reconstruction were investigated by using maximum likelihood and Bayesian approaches. Our results showed the crown group of Limnogonus originated and diversified in Africa in the early Eocene (49 Ma, HPD: 38–60 Ma), subsequently expanding into other regions via dispersal. The colonization of the New World originated from the Oriental Region probably via the Bering Land Bridge in the late Eocene. Two split events between the Old World and New World were identified: one between Neotropics and Oriental region around the middle Oligocene (30 Ma, HPD: 22–38 Ma), and the other between Neotropics and Africa during the middle Miocene (14 Ma, HPD: 8–21 Ma). The evolutionary history of Limnogonus involved two biogeographical processes. Gondwanan vicariance was not supported in our analyses. The diversification of Limnogonus among Africa, Oriental, and Neotropical regions corresponded with the age of land bridge connection and dispersed as a member associated with the broad boreotropical belt before local cooling (34 Ma). The current transoceanic disjunctions in Limnogonus could be better explained by the disruption of “mixed‐mesophytic” forest belt; however, the direct transoceanic LDD between the Neotropics and Africa could not be ruled out. In addition, the “LDD” model coupled with island hopping could be a reasonable explanation for the diversification of the Oriental and Australian regions during the Oligocene.

Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts.

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL‐F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum‐likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9–93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2–52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio‐Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long‐distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large‐scale distribution of humid tropical angiosperm forests in the Eocene.

Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera, Nymphalidae) in the evolving Andes

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.

Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes.

This project examines the relationships within the genus Zea using complete plastid genomes (plastomes). While Zea mays has been well studied, congeneric species have yet to be as thoroughly examined. For this study four complete plastomes and a fifth nearly complete plastome were sequenced in the five species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis) by Sanger or next-generation methods. An analysis of the microstructural changes, such as inversions, insertion or deletion mutations (indels) and determination of their frequencies were performed for the complete plastomes. It was determined that 193 indels and 15 inversions occurred across the examined plastomes of Zea. Tandem repeat indels were the most common type of microstructural change observed. Divergence times were estimated using a noncorrelated relaxed clock method. Divergence dates for specific nodes relative to Zea were calculated to fall between 38,000years before present (YBP) for the subspecies included in this study and 23,000 YBP for section Luxuriantes included in this study. The stem lineage of all Zea species was calculated to have diverged at 176,000 YBP. The calculated mutation rates for the genus fell within the range of 1.7E-8 to 3.5E-8 microstructural changes per site per year. These rates of change are not uniform, despite the close relationships of taxa in this study. Phylogenomic analyses using full plastome alignments were also conducted to compare tree topologies from different types of mutations. In most cases, the previous work examining Zea mitochondrial and nuclear data was confirmed.

Multiple transoceanic dispersals and geographical structure in the pantropical leafy liverwort Ceratolejeunea (Lejeuneaceae, Porellales)

AbstractAimHow disjunct distributions arise and why organisms differ in diversification patterns remain some of the most compelling fundamental questions in biogeography. We carry out phylogeographical analyses of the pantropical liverwort genus Ceratolejeunea to identify its geographical origin and the dispersal routes by which it gained its Neotropical‐African disjunction. Furthermore, we investigate whether there is geographical structure in Ceratolejeunea on islands and whether island diversity is a result of radiations or recurrent migration.LocationAmerica, Africa and Australasia.MethodsSequences of two chloroplast regions (trnL–F, rbcL) and the nuclear ribosomal ITS region were obtained for 55 accessions of 20 species to explore the phylogeny, divergence times and ancestral areas of Ceratolejeunea. The phylogeny was reconstructed using maximum likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method and fossil and secondary calibrations. Ancestral areas were estimated using BioGeoBEARS.ResultsCeratolejeunea likely originated in the Neotropics during the Palaeogene (42.2 Ma, 95% HPD: 22.2–64.8) and the initial diversification of its crown group took place between the Eocene and Miocene (25.5 Ma, 95% HPD: 16.6–35.8). Although boreotropical migration and subsequent extinction in northern regions cannot be rejected, the observed disjunctions are best explained by four transoceanic dispersal events from the Neotropics to Africa during the late Oligocene to Pleistocene. Geographical structure is prevalent on islands, particularly in the C. cornuta complex. Three species and the subgenus Ceratolejeunea are recovered as paraphyletic.Main conclusionsWidespread paraphyly and sister group relationships between disjunct taxa indicate an important role of cryptic speciation and transoceanic dispersal with subsequent genetic differentiation in the evolution of Ceratolejeunea. On islands, recurrent migration, rather than radiation, has shaped bryophyte diversity.

Phylogeny and historical biogeography of leafhopper subfamily Iassinae (Hemiptera: Cicadellidae) with a revised tribal classification based on morphological and molecular data

AbstractPhylogenetic relationships among major lineages of the leafhopper subfamily Iassinae were explored by analysing a dataset of 91 discrete morphological characters and DNA sequence data from nuclear 28S rDNA and histone H3 genes and mitochondrial 12S rDNA. Bayesian, maximum‐likelihood and maximum parsimony analyses yielded similar tree topologies that were well resolved with strong branch support except at the base of the tree, resulting in equivocal support for inclusion of Bythoniini as a tribe of Iassinae but strong support for the monophyly of Iassinae (excluding Bythoniini) and most previously recognized iassine tribes. Divergence times for recovered nodes were estimated using a Bayesian relaxed clock method with two fossil calibration points. The results suggest that the deepest divergences coincided with Gondwanan vicariant events but that more recent divergences resulted from long‐range dispersal and colonization. Biogeographical analyses suggest that the group most likely has a Neotropical origin. The following changes to the taxonomic classification are proposed: establishment of three new tribes, Batracomorphini trib.n. (based on type genus Batracomorphus Lewis), Hoplojassini trib.n. (based on type genus Hoplojassus Dietrich and including one other South American genus), Lipokrisnini trib.n. (based on type genus Lipokrisna Freytag and including two other endemic Caribbean genera); Krisnini is redefined to include only the Old World genera Krisna and Gessius; Iassini is redefined to include only the type genus and four endemic Afrotropical genera; Bascarrhinus Fowler and Platyhynna Berg, recently treated as genera incertae sedis, are placed in Hyalojassini; Thalattoscopus Kirkaldy is added to the previously monobasic tribe Trocnadini. Iassinae now includes 12 tribes, all of which appear to be monophyletic. Revised morphological diagnoses of the subfamily and each of the included tribes are provided and a key to tribes is also given.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:41295B68‐2DAB‐4C4F‐B260‐F7C054922173.

Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans.

Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.

The role of wet‐zone fragmentation in shaping biodiversity patterns in peninsular India: insights from the caecilian amphibian Gegeneophis

AbstractAimIndian biodiversity is concentrated in the wet zone, which is disjunctly distributed in the north‐east and in the peninsular Western and Eastern Ghats. The Eastern Ghats region is smaller and less well explored biologically and the affinities and origins of its biota poorly understood. Our aim was to assess whether divergence between east and west lineages might have been caused by fragmentation of the wet zone during Pleistocene climatic fluctuations, by Late Miocene wet‐zone contraction or by more ancient events. We present the first dated phylogenetic test of these alternatives by inferring relationships and dating divergences within a wet‐zone‐restricted lineage endemic to the Eastern and Western Ghats.LocationThe Eastern and Western Ghats regions of peninsular India.MethodsMolecular genetic data (one nuclear and four mitochondrial genes) were newly generated for the only known Eastern Ghats teresomatan caecilian amphibian (Gegeneophis orientalis) and the only Western Ghats congener (G. pareshi) for which molecular data were not previously available. Phylogenetic relationships were inferred for Indian indotyphlids using maximum likelihood and Bayesian inference methods. Divergence times within the inferred phylogeny were estimated using a Bayesian relaxed clock method, with the Seychelles versus Indian indotyphlid divergence calibrated based on the geological separation of their respective continental land masses.ResultsThe single Eastern Ghats species of Gegeneophis is sister to all other (Western Ghats) Gegeneophis. The basalmost (and east–west) split within Gegeneophis likely occurred > 35 Ma.Main conclusionsDivergence between Eastern and Western Ghats Gegeneophis is too ancient to have been caused by wet‐zone contraction in the Miocene or by Pleistocene climatic fluctuations. Our results are consistent with a relatively ancient origin of wet‐zone lineages in the Eastern Ghats and a lack of gene flow between Eastern and Western Ghats Gegeneophis for tens of millions of years.

The Gondwana Breakup and the History of the Atlantic and Indian Oceans Unveils Two New Clades for Early Neobatrachian Diversification.

The largest anuran diversity belongs to the Neobatrachia, which harbor more than five thousand extant species. Here, we propose a new hypothesis for the historical aspects of the neobatrachian evolution with a formal biogeographical analysis. We selected 12 genes for 144 neobatrachian genera and four archaeobatrachian outgroups and performed a phylogenetic analysis using a maximum likelihood algorithm with the rapid bootstrap test. We also estimated divergence times for major lineages using a relaxed uncorrelated clock method. According to our time scale, the diversification of crown Neobatrachia began around the end of the Early Cretaceous. Our phylogenetic tree suggests that the first split of Neobatrachia is related to the geological events in the Atlantic and Indian Oceans. Hence, we propose names for these clades that indicate this connection, i.e., Atlanticanura and Indianura. The Atlanticanura is composed of three major neobatrachian lineages: Heleophrynidae, Australobatrachia and Nobleobatrachia. On the other hand, the Indianura consists of two major lineages: Sooglossoidea and Ranoides. The biogeographical analysis indicates that many neobatrachian splits occurred as a result of geological events such as the separation between South America and Africa, between India and the Seychelles, and between Australia and South America.