No file available
To read the file of this research,
you can request a copy directly from the authors.
Molecular phylogenetics of the superfamily Stromboidea (Caenogastropoda): new insights from increased taxon sampling
Abstract
The superfamily Stromboidea is a clade of morphologically distinctive gastropods which include the iconic Strombidae, or ‘true conchs’. In this study, we present the most taxonomically extensive phylogeny of the superfamily to date, using fossil calibrations to produce a chronogram and extant geographical distributions to reconstruct ancestral ranges. From these results, we confirm the monophyly of all stromboidean families; however, six genera are not monophyletic using current generic assignments (Strombidae: Lentigo, Canarium , Dolomena , Doxander ; Xenophoridae: Onustus, Xenophora ). Within Strombidae, analyses resolve an Indo-West Pacific (IWP) clade sister to an East Pacific/Atlantic clade, together sister to a second, larger IWP clade. Our results also indicate two pulses of strombid diversification within the Miocene, and a Tethyan/IWP origin for Strombidae – both supported by the fossil record. However, conflicts between divergence time estimates and the fossil record warrant further exploration. Species delimitation analyses using the COI barcoding gene support several taxonomic changes. We synonymise Euprotomus aurora with Euprotomus bulla , Strombus alatus with Strombus pugilis , Dolomena abbotti with Dolomena labiosa , and Dolomena operosa with Dolomena vittata . We identified cryptic species complexes within Terebellum terebellum , Lambis lambis , “Canarium” wilsonorum, Dolomena turturella and Maculastrombus mutabilis . We reinstate Rimellopsis laurenti as a species (previously synonymised with R. laurenti ) and recognise Harpago chiragra rugosus and Lambis truncata sowerbyi valid at the rank of species. Finally, we establish several new combinations, rendering Lentigo , Dolomena , and Canarium monophyletic: Lentigo thersites , Dolomena robusta , Dolomena epidromis , Dolomena turturella , Dolomena taeniata, Dolomena vanikorensis , D. vittata , “Canarium” wilsonorum , Hawaiistrombus scalariformis , Maculastrombus mutabilis , Maculastrombus microurceus .
ResearchGate has not been able to resolve any citations for this publication.
Eyes within the marine gastropod superfamily Stromboidea range widely in size, from 0.2 to 2.3 mm, the latter being the largest known eyes of any gastropod. However, the evolutionary pressures underlying this variation remain unknown. Here, we use the wealth of material available in museum collections to explore the impact of ecological factors that affect light availability (ocean depth, turbidity and diel activity) on the evolution of eye size and structure within Stromboidea. We construct the most taxonomically extensive phylogeny of Stromboidea to date as a framework to investigate these relationships. Our results suggest that depth is a key light-limiting factor in stromboid eye evolution; here, increasing water depth is correlated with increasing aperture width relative to lens diameter (p = 0.043), and therefore an increasing investment in sensitivity in dim light environments. In the clade containing all large-eyed families (Strombidae, Rostellariidae and Seraphsidae), cathemeral species had wider eye apertures relative to lens sizes than diurnal species (p = 0.002), thereby prioritising sensitivity over resolution. These cathemeral species also had smaller body sizes than diurnal species (p = 0.002); this may suggest that animals with smaller shells are more vulnerable to shell-crushing predators, and therefore avoid the higher predation pressure experienced by animals active during the day. Within the large-eyed stromboid clade, ancestral state reconstruction estimates that absolute eye size increased above 1 mm twice independently. Due to the high energetic investment associated with large eye sizes, this repeated increase in eye size suggests that higher performance vision is important in behavioural tasks within these families. In addition, we note that species with more robust escape responses tend to have larger eyes than those that do not: for example, strombids have 1.79 times the eye size that would be expected from their body size (based on Stromboidea as a whole) and are known to display either a rapid escape response from an approaching predator or withdrawal into the shell. By contrast, the small-eyed xenophorids have 0.59 times the expected eye size, and are only known to withdraw when threatened.
The Pacificellinae are a group of small, high-spired land snails distributed on islands across the Pacific. Some species are endemic to particular island groups, but others have wide geographic distributions, several of which have been attributed to anthropogenic transport between islands before western contact. We used DNA sequence data (COI, 16S, ITS2, 28S) from recently collected and historical specimens to estimate a phylogeny of the Pacificellinae, with a focus on Hawaiian species. Phylogenetic analyses support recognizing Lamellidea and Pacificella as distinct genera and indicate that the genus group Tornatellinops should be regarded as a synonym of Lamellidea. The number of taxa defined by species delimitation analyses (ASAP, bPTP, mPTP) varies widely, with between 6 and 42 species estimated in the Hawaiian Islands. These candidate species hypotheses were evaluated in an integrative framework, including shell morphology, geography, and a multilocus phylogeny, to revise the taxonomy of Hawaiian pacificellines. Four Lamellidea species and two Pacificella species are recognized from the Hawaiian Islands, including two widespread species introduced to Hawaiʻi from the South Pacific. Lamellidea peponum in Hawaiʻi shows little genetic divergence from Polynesian specimens previously referred to L. oblonga, and the name L. oblonga is now regarded as a junior synonym. Lamellidea polygnampta is recognized here from across the Hawaiian Islands, L. cylindrica from the island of O‘ahu, and the lowland species, L. extincta, from the main Hawaiian Islands and the Northwestern Islands. The only Pacificella specimens found in Hawai‘i in modern surveys are more closely related to specimens of P. variabilis from Polynesia than to historical specimens of P. baldwini, indicating that the only Pacificella species now found in the main Hawaiian Islands appears to be introduced. Pacificellines have declined in abundance in Hawai‘i over the last century and the two species L. extincta and P. baldwini, formerly present across the Hawaiian Islands, are now either critically endangered or extinct.
The marine gastropod Strombidae is widely distributed in tropical and subtropical regions all over the world and possesses high morphological diversity. In order to better understand how morphological characteristics evolved within Strombidae, a robust phylogenetic framework is needed. In the present study, the complete mitochondrial genomes of Lentigo lentiginosus, Euprotomus aratrum, and Canarium labiatum were sequenced. The three newly sequenced mt genomes contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and several non-coding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with those of other strombids reported before. Two different datasets derived from mitochondrial genes were constructed to resolve the internal phylogenetic relationships of Stromboidea and Strombidae. Within Stromboidea, the sister group formed by Clade I [Rostellariidae + (Seraphsidae + Strombidae)] and Clade II [Xenophoridae + (Struthiolariidae + Aporrhaidae)] were fully recovered and supported by morphological synapomorphies as previously suggested. The phylogenetic positions of L. lentiginosus, E. aratrum, and C. labiatum were confirmed within Strombidae, and several morphological similarities were observed corresponding to the present phylogeny. A correlation between strombids speciation events and paleoclimate change was presumed. Our results indicate that complete mt genomes would be a promising tool to reconstruct a robust phylogeny of Strombidae with an increased taxon sampling in the future.
This iconography explores the variability and ranges of members of the Ministrombus and introduces three new species bringing the total to six in the genus. Two of these species are alluded to in previous works but were never described. M. athenius is recircumscribed and the type locality is shifted to reflect this change in taxonomic position. This paper examined 430 specimens, and used morphology and distribution patterns to delineate species. There is considerable variability in the form of each species; however, within each species complex, there are distinctive characteristics that enable taxonomic resolution. This paper adds to the growing understanding of diversity within Neostromboidae, and highlights the revisions of what are currently considered stable taxa increasing our understanding of global biodiversity.
Aim
The aim was to investigate the evolutionary origins of the striking biodiversity contrast between high‐ and low‐latitude regions in the present day. Is this a relatively recent phenomenon, causally linked in some way to the greenhouse–icehouse transition and onset of global cooling c. 34 Myr ago, or does it have deeper temporal roots and thus other potential causes?
Location
Early Cenozoic fossil assemblages from two tropical and one polar region, and modern counterparts from various tropical localities and Antarctica.
Time period
The Cretaceous–Palaeogene (K/Pg) mass extinction event, Early Cenozoic (Palaeocene–Eocene) and the present day.
Major taxa studied
Shelf‐depth marine Mollusca; the four richest modern benthic clades: Imparidentia, Pteriomorphia, Neogastropoda and Littorinimorpha.
Methods
The K/Pg mass extinction and subsequent recovery was compared between two tropical and one polar region at four distinct stratigraphic intervals. Taxa were identified to species level and assigned to principal families within the four largest benthic molluscan clades. Taxon counts were compared between the three regions at each level and also compared with standardized tropical and polar modern faunas.
Results
The mass extinction was followed by a distinct 25 Myr phase of evolutionary radiation, during which the tropical–polar contrast in the taxonomic composition of all four clades was strongly enhanced; as the global molluscan fauna expanded, it differentiated into distinct low‐ and high‐latitude components.
Main conclusions
A marked differentiation of tropical and polar molluscan faunas occurred in the immediate aftermath of the K/Pg mass extinction; it is likely that, at least for the two bivalve clades investigated, this differentiation was initiated well within the Mesozoic era. The greater antiquity of the tropical–polar split suggests that it was not the product of any single controlling factor during the Cenozoic.
The propensity for hybridisation is well established in Strombidae. I propose that there are three forms of hybridisation: first the true hybrids; second reticulatory hybrids; and third diversificatory hybrids. The illustrated putative true hybrid between Conomurex decorus and Conomurex luhuanus is known from a single example from central Indonesia and represents the first example of intrageneric hybridization for Conomurex. Furthermore, this paper introduces and illustrates the novel concept of diktyzonos for regions of morphological reticulation within and between taxa, and how hybrids can be classified after assessing this dikyzonotic region.
This part of the Canarium (Canarium) urceus (Linné, 1758) revision after Abbott (1960) revision examines the northwest Pacific specimens, which are currently synonymised under Canarium (Canarium) urceus (Linné, 1758). Canarium (Canarium) nipponium n. sp. is known from the Ryukyuan Subprovince, Mariana Islands and Palau. The new species differs from others in lacking the fine sculpture on the early whorls and triangulate from. Given the propensity for species of Strombidae to disperse widely, to show a high degree of variability across their ranges, and to hybridise, it is expected that traits of this new species will be present in populations of neighbouring species, particularly within the Canarium (Canarium) complex.
Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.
The present study aims to apply a DNA barcoding tool through amplifying two mitochondrial candidate genes i.e., COI and 16S rRNA for accurate identification of fish, aquatic molluscs and crustaceans of Sundarbans mangrove wetland, to build a reference library of fish and shellfishes of this unique ecosystems. A total of 185 mitochondrial COI barcode sequences and 59 partial sequences of the 16S rRNA gene were obtained from 120 genera, 65 families and 21 orders of fish, crustaceans and molluscs. The collected samples were first identified by examining morphometric characteristics and then assessed by DNA barcoding. The COI and 16S rRNA sequences of fishes and crustaceans were clearly discriminated among genera in their phylogenies. The average Kimura two-parameter (K2P) distances of COI barcode sequences within species, genera, and families of fishes are 1.57±0.06%, 15.16±0.23%, and 17.79±0.02%, respectively, and for 16S rRNA sequences, these values are 1.74±.8%, 0.97±.8%, and 4.29±1.3%, respectively. The minimum and maximum K2P distance based divergences in COI sequences of fishes are 0.19% and 36.27%, respectively. In crustaceans, the K2P distances within genera, families, and orders are 1.4±0.03%, 17.73±0.15%, and 22.81±0.02%, respectively and the minimum and maximum divergences are 0.2% and 33.93%, respectively. Additionally, the present study resolves the misidentification of the mud crab species of the Sundarbans as Scylla olivacea which was previously stated as Scylla serrata. In case of molluscs, values of interspecific divergence ranges from 17.43% to 66.3% in the barcoded species. The present study describes the development of a molecular and morphometric cross-referenced inventory of fish and shellfish of the Sundarbans. This inventory will be useful in future biodiversity studies and in forming future conservation plan.
Abstract.—The gastropod family Strombidae has sparked the recent interest of taxonomists as early revisions of the family are re-examined, with a plethora of new species and genera being described. This has brought a greater understanding of the level of diversity within the family, which has assisted in conceptualizing its evolutionary intergeneric relationships. However, gaps in the revisions remain. This paper examines the extant members of the genus Gibberulus after half a century of neglect. After examination of type material and original descriptions, the species are recircumscribed, and a new species, G. dekkersi, new species, is presented, bringing the total number of species in the genus to four. In addition, information of the geographic range of each species is provided. We suggest that, as further revisions of the Strombidae are conducted, particularly of those species with large fragmented distributions, a greater diversity of species will be found and described.
Aliger gigas is an economically important and vulnerable marine species. We present a new mitogenome of A. gigas from the Mexican Caribbean and use the eight publicly available Strombidae mitogenomes to analyze intra- and interspecific variation. We present the most complete phylogenomic understanding of Hypsogastropoda to date (17 superfamilies, 39 families, 85 genera, 109 species) to revisit the phylogenetic position of the Stromboidea and evaluate divergence times throughout the phylogeny. The A. gigas mitogenome comprises 15,460 bp including 13 PCGs, 22 tRNAs, and two rRNAs. Nucleotide diversity suggested divergence between the Mexican and Colombian lineages of A. gigas . Interspecific divergence showed high differentiation among Strombidae species and demonstrated a close relationship between A. gigas and Strombus pugilis , between Lambis lambis and Harpago chiragra , and among Tridentarius dentatus / Laevistrombus canarium / Ministrombus variabilis . At the intraspecific level, the gene showing the highest differentiation is ATP8 and the lowest is NAD4L, whereas at the interspecific level the NAD genes show the highest variation and the COX genes the lowest. Phylogenomic analyses confirm that Stromboidea belongs in the non-Latrogastropoda clade and includes Xenophoridea. The phylogenomic position of other superfamilies, including those of previously uncertain affiliation, is also discussed. Finally, our data indicated that Stromboidea diverged into two principal clades in the early Cretaceous while Strombidae diversified in the Paleocene, and lineage diversification within A. gigas took place in the Pleistocene.
This revision of the genus Canarium Schumacher, 1817 after Abbott (1960) advances
our understanding of the phylogeny of Strombidae. Morphological characters were used to generate a phylogeny using maximum likelihood and including all of the recognised species. This resulted in the recognition of one tree, and within that tree the existing genera Canarium Schumacher, 1817 Tridentarius Kronenberg & Vermeij, 2002 and Terestrombus Kronenberg & Vermeij, 2002, and two more Maculastrombus n. gen. and Neostrombus n. gen. were recognisable clades. Furthermore, within the genus Canarium, four subgenera, Canarium (Canarium), Canarium (Conundrum), Canarium (Elegantum), and Canarium (Stereostrombus), were identified and described. We describe and define taxa that are compatible with the requirements of the International Code of Phylogenetic Nomenclature (PhyloCode 2020), and also conform to the requirements of the International Code of Zoological Nomenclature (ICZN 1999). This revision assists in generating a system of nomenclature that reflects the hypothetical relationships, and is at the same time practical in its application. We designate type localities and types for included species that were not yet addressed up until now
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10⁴ sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand‐alone program that can be used either through a graphical web‐interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte‐Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.
In this study, we present the first complete mitochondrial genome sequence of the giant clam Lambis chiragra. The total length of the mitogenome is 16,404 bp. It contains the typical mitochondrial genomic structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region (D-loop). Mitogenome base composition is biased toward A + T content, at 66.4%. A phylogenetic tree based on complete mitogenome sequences revealed that, L.chiragra is the closest extant relative of Conomurex luhuanus.
Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics¹. However, there has been considerable debate surrounding the reliability of these inferences2–5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.
This paper presents an examination of the relationships between Dolomena, Doxander, Mirabilistrombus, Neodilatilabrum and Labiostrombus using character state analysis and maximum parsimony. Hypothesized relationships are presented through the introduction of definitions that bridge the understanding of the evolutionary relationships with the applied nomenclature. Dolomenini is introduced to incorporate two new subtribes: Dolomenina which combines parts of Dolomena ex Abbott (1960) and Labiostrombus; and Doxanderina, which encloses Doxander and Neodilatilabrum. Based on the generated phylogeny, Amabiliplicatus, Pacificus and Dominus are introduced, while Ministrombus is validated as monophyletic. The clustering of Neodilatilabrum and Doxander within Doxanderina, and the nesting of Labiostrombus within the Dolomenini are major revisions to Stromboid systematics.
The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS version of the MEGA software. This new version eliminates the need for virtualization and emulation programs previously required to use MEGA on Apple computers. MEGA for macOS utilizes memory and computing resources efficiently for conducting evolutionary analyses on Apple computers. It has a native Cocoa graphical user interface that is programmed to provide a consistent user experience across macOS, Windows, and Linux. MEGA for macOS is available from www.megasoftware.net free of charge.
Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes (“biocodes”), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore’s first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to “Biodiversity of Singapore” (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.
The complete mitochondrial genomes of Harpago chiragra and Lambis lambis (Strombidae) were determined with the size of 15,460 bp and 15,481 bp, respectively, and both sequences contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. H. chiragra and L. lambis have similar mitochondrial features, corresponding to typical gastropod mitochondrial genomes, such as the conserved gene order, a high A + T content (66.22% for H. chiragra and 66.10% for L. lambis), and preference for A + T-rich codons. The start or termination codon of same protein-coding gene in H. chiragra was consistent with that in L. lambis, except for the termination codon of cox1 gene (TAG for H. chiragra and TAA for L. lambis) and the start codon of nad4 (GTG for H. chiragra and ATG for L. lambis). Pairwise sequence alignments detected different degrees of variations in H. chiragra and L. lambis mitochondrial genomes; and the two species had lower levels of genetic distance (0.202 for nucleotide sequence) and closest relationships as compared to Strombus gigas and Oncomelania hupensis. The 13 partitioned nucleotide sequences of protein coding genes of H. chiragra and L. lambis were aligned with representatives of the main lineages of gastropods and their phylogenetic relationships were inferred. H. chiragra and L. lambis share the same gene order as Littorinimorpha species, except Vermetoidea, which demonstrate a gene rearrangement in species. The reconstructed phylogeny supports three major clades within Littorinimorpha: 1) Stromboidea, Tonnoidea, Littorinoidea, and Naticoidea, 2) Rissooidea and Truncatelloidea, and 3) Vermetoidea. In addition, a relaxed molecular clock calibrated with fossils dated the diversification of Strombidae near 112 (44–206) Mya and a possible radiation is detected to occur between 45–75 Mya, providing implications to understand the Cenozoic replacement event (65–135 Mya) of Aporrhaidae by Strombidae.
ModelTest-NG is a re-implementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate, and introduces several new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions. ModelTest-NG is available under a GNU GPL3 license at https://github.com/ddarriba/modeltest.
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.
Complete mitochondrial genome of Onustus exutus has been sequenced and phylogenetic relationships were evaluated. The circular mitochondrial genome is 16,043 bp in length consisting of 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. The nucleotide composition of the complete mitochondrial genome of O. exutus is 30.46% A, 14.32% C, 15.83% G, and 39.38% T. With the exception of eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Thirteen protein-coding genes start with ATG. For the stop codon, CYTB, ND6, ND4L, and ND4 end with TAG, other 9 genes end with TAA. Phylogenetic tree was constructed based on 13 protein-coding gene sequences of 11 species using the neighbor-joining method, and the result showed that O. exutus is most closely related to Conomurex luhuanus. This is the first record of complete mitochondrial genome from the genus in the Onustus. The present study provides additional data for Mesogastropoda phylogeny.
There has been confusion on the status of Terebellum delicatum Kuroda & Kawamoto in Kawamoto & Tanabe 1956, which has often erroneously been referred to as a colour form of Terebellum terebellum Linné 1758. The taxon T. delicatum is revised, giving precision regarding authorship, and a translation of the original Japanese description with a further refinement of the described features that assist in species recognition. Notes on the designation of a lectotype are presented.
A fourth hybrid specimen between the supposed involved parent species Euprotomus bulla (Röding, 1798) and E. vomer (Röding, 1798), is reported here based on morphological characteristics. The set of shell characteristics of this hybrid is slightly different compared to the earlier reported hybrid specimens. The hybrid specimen originates :from New Caledonia
This paper highlights a putative inter-generic Conomurex x Gibberulus hybrid from the Sodwana Bay area, North Natal, Republic of South Africa. Putative hybridisation in the Strombidae is becoming ever more recognised at the intra-generic level. Much rarer are the inter-generic hybrids. The new putative hybrid indicates that inter-generic hybridisation may well be an evolutionary force in the radiation of Strombidae, facilitating both rapid reticulation and speciation.
The radicine pond snails represent a species-rich and widely distributed group, many species
of which are key vectors of human and animal trematodoses. Here we clarify the taxonomy,
distribution and evolutionary biogeography of the radicine lymnaeids in the Old World based on the
most comprehensive multi-locus molecular dataset sampled to date. We show that the subfamily
Amphipepleinae is monophyletic and contains at least ten genus-level clades: Radix Montfort, 1810,
Ampullaceana Servain, 1881, Peregriana Servain, 1881, Tibetoradix Bolotov, Vinarski & Aksenova gen.
nov., Kamtschaticana Kruglov & Starobogatov, 1984, Orientogalba Kruglov & Starobogatov, 1985,
Cerasina Kobelt, 1881, Myxas G. B. Sowerby I, 1822, Bullastra Bergh, 1901, and Austropeplea Cotton,
1942. With respect to our phylogeny, species-delimitation model and morphological data, the Old World
fauna includes 35 biological species of radicines. Tibet and Eastern Europe harbor the richest faunas,
while East Asia and Africa appear to be the most species-poor areas. The radicine clade could have
originated near the Cretaceous – Paleocene boundary. The Miocene great lakes in Eurasia seems to be
the most important evolutionary hotspots shaping spatial patterns of recent species richness. Finally,
we present the first DNA barcode reference library for the reliable molecular identification of species
within this group
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
The Tethys Ocean existed between the continents of Gondwana and Laurasia from the Triassic to the Pliocene. Analyses of multiple biogeographic and phylogenetic histories reveal that the subsequent breakup of the Tethys greatly influenced the distributions of many species. The ancestral Tethyan realm broke into five biogeographic provinces, including the present-day East Pacific, West Atlantic, East Atlantic, Mediterranean Sea, and Indo-West Pacific. Palaeogeographic maps illustrate the Mesozoic Atlantic opening, the Cenozoic closure of the Tethys, the Messinian Salinity Crisis, the mid-Miocene closure of the Central American Seaway, and Quaternary geological changes. Further, we consider Cenozoic sea-level changes and the formation of freshwater habitats. These reconstructions allow assessment of patterns of aquatic diversification for marine and freshwater animals, and comparison of vicariance and dispersal processes. Estimated divergence times indicate that fragmentation of the Tethys was responsible for the vicariant speciation of aquatic animals because these dates are consistent with associated tectonic events. The opening of the Atlantic Ocean during the Cretaceous is responsible for the earliest isolation between the West and East Atlantic. The mid-Miocene closure of the Tethys, which blocked global equatorial currents, appears to have isolated the Atlantic/Mediterranean Sea and Indo-West Pacific. Finally, formation of the Isthmus of Panama isolated East Pacific and West Atlantic marine organisms. Dispersals related to the Messinian Salinity Crisis and Quaternary sea-level changes influenced population structuring. Tethyan changes affected marine habitats, created new freshwater habitats, inland caves and ancient lakes along the Alps and Himalayas, and influenced anchialine caves at the edge of the ancient sea. The extensive new habitats provided opportunities for colonisation and rapid diversification. Future work should focus on testing the biological impact of the series of Tethyan changes.
Divergence time estimation—the calibration of a phylogeny to geological time—is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. These results demonstrate the impact of (potentially common) model violations. Here, we suggest another potential challenge: that the configuration of the statistical inference problem (i.e., the parameters, their relationships, and associated priors) alone may preclude the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the calibration densities specified for fossil-calibrated nodes) that with no data present at all, that an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions when employing routine lognormal fossil calibration priors. These results indicate that there is inadequate information in the data to overrule the joint prior. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they act to anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared to determine whether signal is coming from the data or prior belief, especially for parameters of direct interest. This recommendation is not novel. However, given how rarely such checks are carried out in evolutionary biology, it bears repeating. Our results demonstrate the fundamental importance of prior/posterior comparisons in any Bayesian analysis, and we hope that they further encourage both researchers and journals to consistently adopt this crucial step as standard practice. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently. [marginal priors; information content; diptych; divergence time estimation; fossil record; BEAST; angiosperms.]
Motivation:
In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences.
Results:
We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size.
Availability and implementation:
mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org .
Contact:
: paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org.
Supplementary information:
Supplementary data are available at Bioinformatics online.
The Cretaceous breakup of Gondwana strongly modified the global distribution of shallow tropical seas reshaping the geographic configuration of marine basins. However, the links between tropical reef availability, plate tectonic processes and marine biodiversity distribution patterns are still unknown. Here, we show that a spatial diversification model constrained by absolute plate motions for the past 140 million years predicts the emergence and movement of diversity hotspots on tropical reefs. The spatial dynamics of tropical reefs explains marine fauna diversification in the Tethyan Ocean during the Cretaceous and early Cenozoic, and identifies an eastward movement of ancestral marine lineages towards the Indo-Australian Archipelago in the Miocene. A mechanistic model based only on habitat-driven diversification and dispersal yields realistic predictions of current biodiversity patterns for both corals and fishes. As in terrestrial systems, we demonstrate that plate tectonics played a major role in driving tropical marine shallow reef biodiversity dynamics.
A species, according to the biological concept, is a natural group of potentially interbreeding individuals isolated by diverse mechanisms. Hybridization is considered the production of offspring resulting from the interbreeding of two genetically distinct taxa. It has been documented in over 10% of wild animals, and at least in 34 cases for Artic marine mammals. In Otariids, intergeneric hybridization has been reported though neither confirming it through genetic analyses nor presenting evidence of fertile offspring. In this study, we report the finding of a hybrid adult female between a South American fur seal (Arctocephalus australis) and a South American sea lion (Otaria byronia), and its offspring, a male pup, in Uruguay. Further based on morphological constraints and breeding seasons, sex-biased hybridization between the two species is hypothesized. Morphological and genetic (nuclear and mitochondrial) results confirm de hybrid nature of the female-pup pair. Here we discuss a genetic dilution effect, considering other hybridization events must be occurring, and how isolation mechanisms could be circumvented. Moreover, the results obtained from stable isotope analysis suggest feeding habits may be a trait transmitted maternally, leading to consider broader issues regarding hybridization as an evolutionary innovation phenomenon.
Stromboid gastropods (Superfamily Stromboidea) are one of
the most diverse groups of gastropods present in the Neogene
marine successions of western India. In the present endeavor, we
report eight stromboid species, of which four are described as new,
from the early-middle Miocene marine successions of the Dwarka
Basin, western India. The species are Conomurex indica n. sp.,
Persististrombus deperditus, Persististrombus sp., Dilatilabrum
mahalonobisi n. sp., Tibia indica, Terebellum obtusum,
Hemithersitea kanerus n. sp. and Hemithersitea nadharus n. sp.
Paleobiogeographic distribution of most of the stromboid genera
reported here reveals a unidirectional migration from the Tethys
Region towards the Indo-Pacific Region during the Paleogene and
Neogene. Conomurex originated in the western India and further
radiated to the eastern Indian-Western Pacific localities with the
onset of the Neogene. Persististrombus and Tibia show widespread
distribution in the Mediterranean and gradually radiated towards
the eastern Africa-western India localities during the Paleogene.
However, from the middle Miocene onwards, these two genera
further migrated towards the eastern Indian-Western Pacific
localities and became more diverse. The remaining two genera,
i.e., Dilatilabrum and Hemithersitea originated in the
Mediterranean and later migrated to take refuge in western India
during the late Paleogene, and ultimately succumbed to extinction
during the middle Miocene.
The spider-like strombid Lambis lambis is widely distributed in the Indo-Pacific region and possesses morphological diversity. In the present study, the complete mitochondrial genomes of two morphologically different specimens of L. lambis that were collected in Sanya (SY) and Zhaoshu (ZS) islands of the South China Sea (namely L. lambis-SY and L. lambis-ZS) were sequenced. They were also compared with that of L. lambis previously published and sampled from coastal waters of Quanfu (QF) Island of the South China Sea (namely L. lambis-QF). The newly sequenced mitochondrial genomes L. lambis-SY and L. lambis-ZS contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with that of L. lambis-QF. Although L. lambis-SY and L. lambis-ZS differed in shell morphology, the genetic distance between them was small. On the other hand, considerable genetic distance values were detected between L. lambis-QF and L. lambis-SY/L. lambis-ZS, suggesting that the former might be a possible cryptic species within L. lambis. The divergence of the cryptic lineage L. lambis-QF was dated to 4.6 Mya, falling in the lower Pliocene that corresponded to a paleoclimatic transition from cool to warm conditions. This study, therefore, suggests a correlation between paleoclimate change and speciation event.
Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in tropical and subtropical waters. Although a few strombid mitochondrial genomes have been sequenced, data for the other four Recent families in Stromboidea are lacking. In this study we report seven new stromboid mitogenomes obtained from transcriptomic and genomic data, with taxonomic representation from each Recent stromboid family, including the first mitogenomes for Aporrhaidae, Rostellariidae, Seraphsidae and Struthiolariidae. We also report a new mitogenome for the family Xenophoridae. We use these data, along with published sequences, to investigate the relationships among these and other caenogastropod groups. All analyses undertaken in this study support monophyly of Stromboidea as redefined here to include Xenophoridae, a finding consistent with morphological and behavioural data. Consistent with previous morphological and molecular analyses, including those based on mitogenomes, monophyly of Hypsogastropoda is confirmed but monophyly of Littorinimorpha is again rejected.
Morphological identification of gastropods can be difficult considering the larva of species and high similarity among the same genera. DNA barcoding has been widely used in species identification and biodiversity research. The purpose of this study was to explore the feasibility of using the cytochrome c oxidase subunit I (COI) gene for the identification of gastropod species and to construct a reliable DNA barcoding reference database of gastropods in Hainan island, China. A total of 306 mitochondrial COI barcode sequences were obtained from 120 species, 35 families and 7 orders of gastropods. The average length of the sequence was 640 base pairs. The average genetic distances based on Kimura two parameter (K2P) within species, genera, families, orders and classes were 0.9 %, 14.7 %, 18.9 %, 24.5 % and 28.6 %, respectively. Most of the gastropod species could be identified using COI sequences. Our results confirmed that the identification method combining morphology and DNA barcode greatly improved the efficiency of species identification. In this study, we found three new record species in China, namely Semiricinula tissoti (Petit de la Saussaye, 1852), Engina alveolata (Kiener, 1836) and Wallaconchis ater (Lesson, 1831). Overall, this study revealed that the identification of gastropods by DNA barcoding is efficient, and COI sequencing technology can be used for the identification of gastropod species and thereby can be used to manage fisheries and assess biodiversity.
Marginelliform gastropods are a heterogeneous and diverse group of molluscs encompassing over 1,600 living species, among which are the smallest known neogastropods. The relationships of marginelliform gastropods within the order Neogastropoda are controversial, and the monophyly of the two marginelliform families the Marginellidae J. Fleming, 1828 and the Cystiscidae Stimpson, 1865, remains unconfirmed. DNA sequence data have never been used to assess the relationships of the marginelliform gastropods, making this group the only major branch missing in our current understanding of the neogastropod tree of life. Here we report results of the first multilocus phylogenetic analysis of marginelliform gastropods, which is based on a dataset comprising 63 species (20 genera) of Marginellidae and Cystiscidae, and a wide range of
neogastropod lineages. The Marginellidae and Cystiscidae form a moderately supported clade that is sister to the family Volutidae. Marginellona gigas appears to be sister to all other marginelliforms. The subfamily Marginellinae was recovered as a well-supported clade, and good resolution of this part of the tree makes it possible to propose amendments to the family-level classification of the group. The relationship between Granulina and other marginelliforms could not be resolved and requires further study. Due to poor resolution
of basal relationships within the Marginellidae–Cystiscidae clade, the monophyly of the Cystiscidae was neither confirmed nor convincingly rejected. The shell morphology of most marginellid and cystiscid genera is taxonomically not very informative but, nevertheless, of the traditionally recognized genera only Gibberula and Dentimargo were shown to be polyphyletic. Although a comprehensive systematic revision of the group requires more extensive taxonomic sampling (e.g. with better representation of the type species of nominal
genus-group names), our results support the superfamily Volutoidea, comprising four families (Volutidae, Cystiscidae, Marginellidae and Marginellonidae), with the placement of the Granulinidae uncertain for the time being.
We present the first systematic description of a Tortonian (late Miocene) gastropod assemblage from the Ambug Hill section in the Tutong District in Brunei Darussalam. The low-diversity assemblage comprises 62 species of which 37 are unknown from other
Neogene faunas of the Indo-West Pacific Region (IWP), 23 species are formally described as new. Carnivorous, scavenging and detritus feeding species predominate and the ecological requirements of extant relatives suggest a mud-bottom environment of the inner shelf in several tens of meters water depth with reduced vegetation. The small size of most specimens, the frequent occurrence of subadult shells and small size of several species relative to congeneric species might point to suboptimal environmental conditions during the deposition of this part of the Seria Formation. The very low relations with Neogene gastropod faunas from Indonesia at species level might be explained by the biogeographic isolation between the faunas of the Java and Celebes seas and that from the South China Sea. A severe undersampling and rather spotty taxonomic descriptions of Neogene IWP-faunas and a lack of assemblages from identical depositional environments from Indonesia may also contribute to the seemingly endemic character of the Ambug Hill fauna.
Rhinoclavis pulcherrima n. sp., Rissoina tutongensis n. sp., Ficus parvissima n. sp., Dolomena bruneiensis n. sp., Scalptia verheckeni n. sp., Phos bruneiensis n. sp., Nassarius pseudoovum n. sp., Indomitrella acuticonica n. sp., Hemifusus charlieleei n. sp., Prunum seriaense n. sp., Cymbiola ambugensis n. sp., Ziba waltercernohorskyi n. sp., Amalda bruneiana n. sp., Tomopleura furcata n. sp., Unedogemmula nuttallin. sp., Gemmula sculpturata n. sp., Crassispira strangulata n. sp., Paradrillia pachyspira n. sp., Conasprella paupera n. sp., Conasprella trianginodus n. sp., Triplostephanus wilfordi n. sp., Duplicaria aequalis n. sp. and Architectonica beetsi n. sp. are established as new
species.
The TethysOcean existed between the continents of Gondwana and Laurasia from the Triassic to the Pliocene. Analyses
of multiple biogeographic and phylogenetic histories reveal that the subsequent breakup of the Tethys greatly influenced
the distributions of many species. The ancestral Tethyan realm broke into five biogeographic provinces, including the
present-day East Pacific, West Atlantic, East Atlantic, Mediterranean Sea, and Indo-West Pacific. Palaeogeographic
maps illustrate the Mesozoic Atlantic opening, the Cenozoic closure of the Tethys, the Messinian Salinity Crisis, the
mid-Miocene closure of the Central American Seaway, and Quaternary geological changes. Further, we consider
Cenozoic sea-level changes and the formation of freshwater habitats. These reconstructions allow assessment of patterns
of aquatic diversification for marine and freshwater animals, and comparison of vicariance and dispersal processes.
Estimated divergence times indicate that fragmentation of the Tethys was responsible for the vicariant speciation of
aquatic animals because these dates are consistent with associated tectonic events. The opening of the Atlantic Ocean
during the Cretaceous is responsible for the earliest isolation between the West and East Atlantic. The mid-Miocene
closure of the Tethys, which blocked global equatorial currents, appears to have isolated the Atlantic/Mediterranean
Sea and Indo-West Pacific. Finally, formation of the Isthmus of Panama isolated East Pacific and West Atlantic marine
organisms. Dispersals related to the Messinian Salinity Crisis and Quaternary sea-level changes influenced population
structuring. Tethyan changes affected marine habitats, created new freshwater habitats, inland caves and ancient lakes
along the Alps and Himalayas, and influenced anchialine caves at the edge of the ancient sea. The extensive new
habitats provided opportunities for colonisation and rapid diversification. Future work should focus on testing the
biological impact of the series of Tethyan changes.
Phylogenies that are reconstructed without fossil material often contain approximate dates for lineage splitting. For example, particular nodes on molecular phylogenies may be dated by known geographic events that caused lineages to split, thereby calibrating a molecular clock that is used to date other nodes. On the one hand, such phylogenies contain no information about lineages that have become extinct. On the other hand, they do provide a potentially useful testing ground for ideas about evolutionary processes. Here we first ask what such reconstructed phylogenies should be expected to look like under a birth-death process in which the birth and death parameters of lineages remain constant through time. We show that it is possible to estimate both the birth and death rates of lineages from the reconstructed phylogenies, even though they contain no explicit information about extinct lineages. We also show how such phylogenies can reveal mass extinctions and how their characteristic footprint can be distinguished from similar ones produced by density-dependent cladogenesis.
In this study, we first determined the complete mitochondrial genome of the endangered marine strombid gastropod Strombus luhuanus, an important shellfish traditionally distributed around Hainan island of China and parts of Papua New Guinea. The complete mitogenome sequence was 15,799 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one non-coding control region (D-loop). We further compared the mtDNA sequences of S. luhuanus and S. gigas, and calculated the moderate sequence variations in their protein coding regions, which would further provide valuable genome variation information for conservative studies of S. luhuanus.
