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.

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.

The distribution, taxonomy, and redescription of the geckos Cnemaspis affinis (Stoliczka 1887) and C. flavolineata (Nicholls 1949) with descriptions of a new montane species and two new lowland, karst- dwelling species from Peninsular Malaysia

Zootaxa ◽  
2008 ◽  
Vol 1931 (1) ◽  
pp. 1-24 ◽  
Author(s):  
L. LEE GRISMER ◽  
JESSE L. GRISMER ◽  
PERRY L. WOOD, JR. ◽  
CHAN KIN ONN
Keyword(s):  
Southeast Asia ◽  
Color Pattern ◽  
Southeast Asian ◽  
Peninsular Malaysia ◽  
Scale Morphology ◽  
Separate Species ◽  
New Name ◽  
Scale Characteristics

We provide data supporting the continued recognition of Cnemaspis affinis (Stoliczka) and Cnemaspis flavolineata (Nicholls) as separate species and restrict their distribution to Pulau Pinang, Penang for the former and the Titi Wangsa Range and Gunung Benom, Peninsular Malaysia for the latter. For the montane population of Cnemaspis from Bukit Larut, Perak, which has been referred to as both C. affinis and C. kendallii, we demonstrate that it is discretely diagnosable from all other Southeast Asian Cnemaspis on the basis of size and numerous color pattern and scale characteristics and for it we provide the new name Cnemaspis mcguirei sp. nov. Two new lowland, karst-dwelling species from isolated locations along the foothills of the Titi Wangsa and Timur ranges in northern Peninsular Malaysia are demonstrably differentiable from all other Southeast Asia Cnemaspis on the basis of color pattern and scale morphology and are described herein as Cnemaspis karsticola sp. nov. from Gunung Reng, Kelantan and Cnemaspis bayuensis sp. nov. from Kampung Bayu, Kelantan.

scholarly journals Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael K. Young ◽  
Rebecca Smith ◽  
Kristine L. Pilgrim ◽  
Michael K. Schwartz
Keyword(s):  
North America ◽  
Species Delimitation ◽  
Evolutionary History ◽  
Conservation Status ◽  
Single Locus ◽  
Total Evidence ◽  
Separate Genus ◽  
Interspecific Differences ◽  
Candidate Species ◽  
Scientific Name

AbstractBeing able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.

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

Minimal clustering and species delimitation based on multi-locus alignments vs SNPs: the case of the Seriphium plumosum L. complex (Gnaphalieae: Asteraceae)

2021 ◽  
Author(s):  
Zaynab Shaik ◽  
Nicola Georgina Bergh ◽  
Bengt Oxelman ◽  
Anthony George Verboom
Keyword(s):  
Species Delimitation ◽  
Bayes Factor ◽  
Cape Floristic Region ◽  
Parametric Models ◽  
Western Cape ◽  
Nucleotide Polymorphisms ◽  
Sequence Alignments ◽  
Separate Species ◽  
Multiple Sequence ◽  
Data Set

We applied species delimitation methods based on the Multi-Species Coalescent (MSC) model to 500+ loci derived from genotyping-by-sequencing on the South African Seriphium plumosum (Asteraceae) species complex. The loci were represented either as multiple sequence alignments or single nucleotide polymorphisms (SNPs), and analysed by the STACEY and Bayes Factor Delimitation (BFD)/SNAPP methods, respectively. Both methods supported species taxonomies where virtually all of the 32 sampled individuals, each representing its own geographical population, were identified as separate species. Computational efforts required to achieve adequate mixing of MCMC chains were considerable, and the species/minimal cluster trees identified similar strongly supported clades in replicate runs. The resolution was, however, higher in the STACEY trees than in the SNAPP trees, which is consistent with the higher information content of full sequences. The computational efficiency, measured as effective sample sizes of likelihood and posterior estimates per time unit, was consistently higher for STACEY. A random subset of 56 alignments had similar resolution to the 524-locus SNP data set. The STRUCTURE-like sparse Non-negative Matrix Factorisation (sNMF) method was applied to six individuals from each of 48 geographical populations and 28023 SNPs. Significantly fewer (13) clusters were identified as optimal by this analysis compared to the MSC methods. The sNMF clusters correspond closely to clades consistently supported by MSC methods, and showed evidence of admixture, especially in the western Cape Floristic Region. We discuss the significance of these findings, and conclude that it is important to a priori consider the kind of species one wants to identify when using genome-scale data, the assumptions behind the parametric models applied, and the potential consequences of model violations may have.

Molecular systematics of Thouarella (Octocorallia:Primnoidae) with the description of three new species from the Southern Ocean based on combined molecular and morphological evidence

2021 ◽  
Author(s):  
Mónica Núñez-Flores ◽  
Daniel Gomez-Uchida ◽  
Pablo J. López-González
Keyword(s):  
New Species ◽  
Southern Ocean ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Weddell Sea ◽  
Morphological Evidence ◽  
Three New Species ◽  
Taxonomic Framework ◽  
The Antarctic

Thouarella Gray, 1870, is one of the most speciose genera among gorgonians of the family Primnoidae (Cnidaria:Octocorallia:Anthozoa), being remarkably diverse in the Antarctic and sub-Antarctic seafloor. However, their diversity in the Southern Ocean is likely underestimated. Phylogenetic analyses of mitochondrial and nuclear DNA markers were integrated with species delimitation approaches as well as morphological colonial and polyps features and skeletal SEM examinations to describe and illustrate three new species within Thouarella, from the Weddell Sea, Southern Ocean: T. amundseni sp. nov., T. dolichoespinosa sp. nov. and T. pseudoislai sp. nov. Our species delimitation results suggest, for the first time, the potential presence of Antarctic and sub-Antarctic cryptic species of primnoids, based on the likely presence of sibling species within T. undulata and T. crenelata. With the three new species here described, the global diversity of Thouarella has increased to 41 species, 15 of which are endemic to the Antarctic and sub-Antarctic waters. Consequently, our results provide new steps for uncovering the shelf benthonic macrofauna’s hidden diversity in the Southern Ocean. Finally, we recommend using an integrative taxonomic framework in this group of organisms and species delimitation approaches because the distinctions between some Thouarella species based only on a superficial examination of their macro- and micromorphological features is, in many cases, limited.

Species delimitation of colour polymorphic Cladophorus (Coleoptera: Lycidae) from New Guinea

Zootaxa ◽  
2017 ◽  
Vol 4320 (3) ◽  
pp. 505 ◽  
Author(s):  
ROMANA KALOUSOVA ◽  
LADISLAV BOCAK
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Related Species ◽  
Species Delimitation ◽  
Morphological Differentiation ◽  
Morphological Characters ◽  
Molecular Data ◽  
Closely Related Species ◽  
Dna Fragment ◽  
Colour Patterns

Cladophorus Guérin-Méneville, 1830 are endemic Papuan net-winged beetles which take part in highly diverse Müllerian mimicry rings. Available specimens were sequenced for cox1–tRNA-Leu–cox2 mitochondrial DNA fragment and the species delimitations were based on the genetic distance, phylogenetic analysis, and morphology. Three earlier described species were identified in the recently collected material and further 10 species are described: C. pallescens sp. nov., C. bicolor sp. nov., C. craterensis sp. nov., C. motykai sp. nov., C. mindikensis sp. nov., C. kailakiensis sp. nov., C. manokwarensis sp. nov., C. haiaensis sp. nov., C. humeralis sp. nov., and C. boceki sp. nov. DNA-based identifications provided some ambiguous results and closely related species could not be robustly delimited using solely molecular data. Additionally, the species limits were based on clearly defined morphological characters and the morphological differentiation was found unlinked from the genetic divergence. Colour patterns cannot be used for identification because all species available in more specimens were polymorphic and followed various local co-mimics. The Papuan fauna of Cladophorus is very diverse and the closely related species regularly occur in limited regions. Differentiation within restricted ranges is therefore considered as the main speciation mode. 

scholarly journals The identity of Pseudomystus moeschii (Boulenger, 1890), with the description of two new species of bagrid catfishes from Southeast Asia (Teleostei: Bagridae)

Zootaxa ◽  
2005 ◽  
Vol 851 (1) ◽  
pp. 1 ◽  
Author(s):  
HEOK HEE NG ◽  
KELVIN K.P. LIM
Keyword(s):  
New Species ◽  
Southeast Asia ◽  
Peninsular Malaysia ◽  
The Other ◽  
River Drainage ◽  
Posterior Process ◽  
Two New Species ◽  
The Way

The identity of the poorly known bagrid catfish Pseudomystus moeschii (Boulenger, 1890) is clarified and the species redescribed. Two new species of closely related bagrid catfishes are also described: Pseudomystus carnosus from the Way Seputih River drainage in the province of Lampung in the southern tip of Sumatra, and P. fumosus from the Pahang River drainage in eastern Peninsular Malaysia. Pseudomystus carnosus, P. fumosus and P. moeschii can be distinguished from congeners in having an enlarged posterior process of the post-temporal, presence of long hair-like epithelial projections on the skin and long tubular extensions of the sensory pores. Pseudomystus carnosus differs from the other two species in having a pointed (vs. rounded) tip of the nuchal shield, while P. fumosus differs from the other two species in having very well developed procurrent caudal rays which are sinuously curved along the anterior edges (vs. less developed procurrent caudal rays that slope evenly along the edges). A lectotype is designated for P. moeschii.

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