scholarly journals DNA-based species delimitation reveals cryptic and incipient species in synchronous flashing fireflies (Coleoptera: Lampyridae) of Southeast Asia

2020 ◽  
Vol 130 (3) ◽  
pp. 520-532
Author(s):  
Wan F A Jusoh ◽  
Lesley Ballantyne ◽  
Kin Onn Chan
Keyword(s):  
Southeast Asia ◽  
Species Delimitation ◽  
East Coast ◽  
Morphological Differentiation ◽  
Population Level ◽  
Distinct Species ◽  
Peninsular Malaysia ◽  
Species Boundaries ◽  
Incipient Species ◽  
Genetic Sampling

Abstract Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet fundamental knowledge about their biodiversity is lacking. Recent studies have revealed notable population-level phylogeographical structure within the Pteroptyx tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, morphological and genetic similarities between P. balingiana and P. malaccae have raised questions about the former’s validity as a distinct species. We collected samples from previously unsampled populations and assembled the most comprehensive genetic dataset for Pteroptyx to date, to characterize species boundaries within the P. tener, P. bearni and P. malaccae groups. Using a suite of species delimitation analyses, we show that P. tener along the west coast of Peninsular Malaysia (PM) is distinct from populations from the east coast and Borneo despite the absence of morphological differentiation. However, analyses could not conclusively differentiate P. bearni from Borneo and eastern PM, nor identify P. balingiana and P. malaccae as distinct species, indicating that these populations may be conspecific or represent incipient species. This study underlines the need to increase geographical, taxonomic and genetic sampling of Southeast Asian fireflies to provide a better understanding of their biodiversity.

scholarly journals Phylogeography and Molecular Species Delimitation Reveal Cryptic and Incipient Speciation in Synchronous Flashing Fireflies (Coleoptera: Lampyridae) of Southeast Asia

2019 ◽  
Author(s):  
Wan F. A. Jusoh ◽  
Lesley Ballantyne ◽  
Chan Kin Onn
Keyword(s):  
Southeast Asia ◽  
Species Delimitation ◽  
Evolutionary History ◽  
Nuclear Dna ◽  
Morphological Differentiation ◽  
Population Level ◽  
Peninsular Malaysia ◽  
Total Evidence ◽  
Phylogeographic Structure ◽  
Separate Species

ABSTRACTSynchronous flashing fireflies of the genusPteroptyxare ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within theP. tenerandP. bearnigroups in Malaysia, suggesting that cryptic species may exist. Additionally, the close morphological and genetic affinity of the recently described speciesP. balingianatoP. malaccaehas raised questions about its validity. In this study, we assembled the most densely sampled genetic dataset onPteroptyxto-date to estimate a comprehensive phylogeny using mitochondrial and nuclear DNA and subsequently implemented a suite of distance-, phylogeny-, and coalescent-based species delimitation methods to characterize species boundaries within theP. tener,P. bearni, andP. balingiana/P. malaccaegroups. Using a total evidence approach from multiple lines of evidence, we showed that populations ofP. teneralong the west coast of Peninsular Malaysia are sufficiently divergent from populations from the east coast and Borneo to warrant specific recognition, despite the absence of morphological differentiation. Conversely, divergence ofP. bearnifrom Borneo and eastern Peninsular Malaysia, as well asP. balingianafromP. malaccaewere modest and their distinction as separate species were ambiguous; consistent with incipient species in the gray zone of speciation. Overall, this study contributes to the limited but growing body of genetic work on Southeast Asian fireflies and underscores the urgent need to increase the breadth and depth of geographic, taxonomic, and genetic sampling to provide a deeper understanding of their biodiversity and evolutionary history.

Phylogeny and molecular species delimitation of long-nosed armadillos (Dasypus: Cingulata) supports morphology-based taxonomy

2019 ◽  
Vol 186 (3) ◽  
pp. 813-825 ◽  
Author(s):  
Anderson Feijó ◽  
Júlio F Vilela ◽  
Jilong Cheng ◽  
Marco Antônio A Schetino ◽  
Raphael T F Coimbra ◽  
...  
Keyword(s):  
Molecular Species ◽  
Species Delimitation ◽  
Distinct Species ◽  
Molecular Data ◽  
Species Boundaries ◽  
Morphological Evidence ◽  
Guiana Shield ◽  
Taxonomic History ◽  
Molecular Dataset ◽  
Phylogenetic Hypotheses

AbstractThe armadillo genus Dasypus is the most species-rich and widely distributed genus of the order Cingulata and it has a dynamic taxonomic history. Recent morphology-based studies have proposed new taxonomic arrangements, but these were not yet assessed with molecular data. The two comprehensive phylogenetic hypotheses available for the genus are conflicting and were each based on a subset of taxa, hampering a proper evaluation of species boundaries. Using a multilocus molecular dataset, based on the broadest geographic sampling of Dasypus to date, we inferred the phylogenetic relationships of all species of the genus, including the recently reinstated D. beniensis and D. pastasae. We tested recent taxonomic hypotheses using several species-delimitation approaches. Our phylogeny recovered three main lineages of long-nosed armadillos that we treat as subgenera (Hyperoambon, Muletia and Dasypus) and identified the majority of its diversification as having occurred during the Pliocene. Molecular species delimitation supported morphological evidence in assigning D. hybridus as a subspecies of D. septemcinctus and confirming the split of the D. kappleri complex into three species. Our results strongly support the recognition of Guiana Shield populations formerly assigned to D. novemcinctus as a distinct species. The phylogenetic positions of D. mazzai and D. sabanicola remain uncertain. Further investigation using faster-evolving genes and additional samples may help to clarify the relationships of these young species.

scholarly journals When morphometry meets taxonomy: morphological variation and species boundaries in Proboscoida (Cnidaria: Hydrozoa)

2020 ◽  
Vol 190 (2) ◽  
pp. 417-447
Author(s):  
Amanda F Cunha ◽  
Allen G Collins ◽  
Antonio C Marques
Keyword(s):  
Intraspecific Variation ◽  
Morphological Variation ◽  
Species Delimitation ◽  
Species Boundaries ◽  
Nominal Species ◽  
Genetic Sampling ◽  
Taxonomic Implications ◽  
Obelia Geniculata

Abstract Species delimitation in marine taxa is often problematic given large intraspecific variation. Based on extensive, recently published genetic sampling from specimens of the hydrozoan families Campanulariidae, Clytiidae and Obeliidae, we evaluate morphological variation in this group, correlating morphometric and phylogenetic patterns for species delimitation. Several species of Campanulariidae are confidently delimited based on differences in size (e.g. Bonneviella species, Tulpa tulipifera and Rhizocaulus verticillatus), while others are re-identified and corroborated based on differences in perisarc thickness (e.g. Silicularia rosea, Orthopyxis and Campanularia species). In Clytiidae, the length and diameter of hydrothecae, height of hydrothecal cusps and perisarc thickness delimit the species Clytia linearis, C. elsaeoswaldae and C. noliformis from others. However, few characters reliably differentiate the clades associated with the nominal species C. gracilis and C. hemisphaerica. In Obeliidae, Obelia geniculata is distinctive in its higher perisarc thickness, and corroborated as a widely distributed species. Obelia longissima and clades refered to O. dichotoma are subtly distinguished, showing a few differences in size and branching of colonies. The taxonomic implications of these results are discussed. With a few exceptions, species can be delimited based on morphometric patterns, once morphological variation is compared.

scholarly journals Incorporating the speciation process into species delimitation

2021 ◽  
Vol 17 (5) ◽  
pp. e1008924
Author(s):  
Jeet Sukumaran ◽  
Mark T. Holder ◽  
L. Lacey Knowles
Keyword(s):  
Gene Flow ◽  
Species Delimitation ◽  
Subsequent Development ◽  
Genetic Data ◽  
Distinct Species ◽  
Species Boundaries ◽  
Multispecies Coalescent ◽  
Speciation Process ◽  
Other Information ◽  
Species Population

The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.

scholarly journals Multispecies coalescent delimits structure, not species

2017 ◽  
Vol 114 (7) ◽  
pp. 1607-1612 ◽  
Author(s):  
Jeet Sukumaran ◽  
L. Lacey Knowles
Keyword(s):  
Genetic Structure ◽  
Species Delimitation ◽  
Population Level ◽  
Species Boundaries ◽  
Data Types ◽  
Population Isolation ◽  
Species Discovery ◽  
Multispecies Coalescent ◽  
Units Of Analysis ◽  
Multiple Data

The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent. We show that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries. Because of the misidentification of population structure as putative species, our work raises questions about the practice of genome-based species discovery, with cascading consequences in other fields. Specifically, all fields that rely on species as units of analysis, from conservation biology to studies of macroevolutionary dynamics, will be impacted by inflated estimates of the number of species, especially as genomic resources provide unprecedented power for detecting increasingly finer-scaled genetic structure under the multispecies coalescent. As such, our work also represents a general call for systematic study to reconsider a reliance on genomic data alone. Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.

The Evolutionary Biology of Species

2019 ◽  
Author(s):  
Timothy G. Barraclough
Keyword(s):  
Evolutionary Biology ◽  
Biological Diversity ◽  
Distinct Species ◽  
Species Boundaries ◽  
Central Thesis ◽  
Species Accumulation ◽  
Multicellular Organisms ◽  
Broad Approach ◽  
Over Time

‘Species’ are central to understanding the origin and dynamics of biological diversity; explaining why lineages split into multiple distinct species is one of the main goals of evolutionary biology. However, the existence of species is often taken for granted, and precisely what is meant by species and whether they really exist as a pattern of nature has rarely been modelled or critically tested. This novel book presents a synthetic overview of the evolutionary biology of species, describing what species are, how they form, the consequences of species boundaries and diversity for evolution, and patterns of species accumulation over time. The central thesis is that species represent more than just a unit of taxonomy; they are a model of how diversity is structured as well as how groups of related organisms evolve. The author adopts an intentionally broad approach to consider what species constitute, both theoretically and empirically, and how we detect them, drawing on a wealth of examples from microbes to multicellular organisms.

scholarly journals Antimicrobial susceptibility, serotype distribution, virulence profile and molecular typing of piliated clinical isolates of pneumococci from east coast, Peninsular Malaysia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nurul Diana Dzaraly ◽  
Mohd Nasir Mohd Desa ◽  
AbdulRahman Muthanna ◽  
Siti Norbaya Masri ◽  
Niazlin Mohd Taib ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Antimicrobial Susceptibility ◽  
East Coast ◽  
Tertiary Hospital ◽  
Multidrug Resistant ◽  
Peninsular Malaysia ◽  
Clinical Isolates ◽  
Serotype Distribution ◽  
Antimicrobial Susceptibility Test ◽  
Conjugate Vaccines

AbstractPilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the piliated isolates, in relation to antimicrobial susceptibility, serotypes, and genotypes at a major tertiary hospital on the east coast of Peninsular Malaysia. A total of 100 clinical isolates collected between September 2017 and December 2019 were subjected to serotyping, antimicrobial susceptibility test, and detection of pneumococcal virulence and pilus genes. Multilocus sequence typing (MLST) and phylogenetic analysis were performed only for piliated strains. The most frequent serotypes were 14 (17%), 6A/B (16%), 23F (12%), 19A (11%), and 19F (11%). The majority of isolates were resistant to erythromycin (42%), tetracycline (37%), and trimethoprim-sulfamethoxazole (24%). Piliated isolates occurred in a proportion of 19%; 47.3% of them were multidrug-resistant (MDR) and a majority had serotype 19F. This study showed ST236 was the most predominant sequence type (ST) among piliated isolates, which was related to PMEN clone Taiwan19F-14 (CC271). In the phylogenetic analysis, the piliated isolates were grouped into three major clades supported with 100% bootstrap values. Most piliated isolates belonged to internationally disseminated clones of S. pneumoniae, but pneumococcal conjugate vaccines (PCVs) have the potential to control them.

HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 194 Southeast Asia Chinese from Peninsular Malaysia

2019 ◽  
Vol 80 (11) ◽  
pp. 906-907
Author(s):  
Chun-Lai Too ◽  
Lay-Kim Tan ◽  
Hussein Heselynn ◽  
Shahril Nor-Shuhaila ◽  
Mageswaran Eashwary ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Peninsular Malaysia
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