Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations

AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the hitherto controversial species M. japana (Jacoby, 1885) is confirmed. The pattern of nucleotide and amino acid substitutions is discussed in the light of functional domains of the COI molecule. Although the data are preliminary, the results provide new data on the distribution of the species. Together with the phylogenetic analysis they allow for a discussion of the phylogeography of the genus.

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

Zootaxa ◽

10.11646/zootaxa.4320.3.6 ◽

2017 ◽

Vol 4320 (3) ◽

pp. 505 ◽

Cited By ~ 4

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.

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Comparative morphology of internal reproductive systems in leaf beetles of the Donaciinae and Criocerinae (Coleoptera: Chrysomelidae) and its implication for the phylogeny

Zootaxa ◽

10.11646/zootaxa.1845.1.1 ◽

2008 ◽

Vol 1845 (1) ◽

pp. 1 ◽

Cited By ~ 16

Author(s):

YOKO MATSUMURA ◽

KUNIO SUZUKI

Keyword(s):

Phylogenetic Analysis ◽

Reproductive System ◽

Comparative Morphology ◽

Reproductive Organs ◽

Leaf Beetle ◽

Reproductive Systems ◽

Japanese Species ◽

Morphological Comparison ◽

Leaf Beetles ◽

Phylogenetic Hypotheses

We compared the morphology of the internal and external reproductive organs of both sexes among species of the leaf beetle subfamily Donaciinae and its sister taxon Criocerinae. Using nine characters of the reproductive system, we attempted to reconstruct the phylogenetic tree for the two subfamilies combined. For this study, we used 11 Japanese species (including 2 subspecies) of 2 genera in the Donaciinae and 16 Japanese species of 4 genera in the Criocerinae. Morphological comparison revealed that the internal reproductive system exhibits a large diversity even in each subfamily. In particular, the morphology of the spermathecal organ varies greatly among genera or subgenera. In the subgenus Lema, we found a marked apomorphic state, that is, an extremely extended spermathecal duct in females and a similarly extended filiform structure on the internal sac in males. Phylogenetic analysis yielded two most parsimonious trees, which differ in criocerine relationship. In seven of the nine characters, the evolution of an apomorphic state was consistent with previous phylogenetic hypotheses.

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DNA Barcoding of Penaeidae (Decapoda; Crustacea): Non-Distance-Based Species Delimitation of the Most Economically Important Shrimp Family

Diversity ◽

10.3390/d13100460 ◽

2021 ◽

Vol 13 (10) ◽

pp. 460

Author(s):

Jorge L. Ramirez ◽

Luisa Simbine ◽

Carla G. Marques ◽

Eliana Zelada-Mázmela ◽

Lorenzo E. Reyes-Flores ◽

...

Keyword(s):

Dna Barcoding ◽

Species Delimitation ◽

Mitochondrial Gene ◽

Single Gene ◽

Penaeid Shrimp ◽

Genetic Distances ◽

Structured Populations ◽

Nominal Species ◽

Data Set ◽

Shrimp Fishery

The Penaeidae family includes some of the most economic and ecological important marine shrimp, comprising hundreds of species. Despite this importance and diversity, the taxonomic classification for penaeid shrimp has constantly been revised, and issues related to the species identification are common. In this study, we implemented DNA barcoding analyses in addition to single-gene species delimitation analyses in order to identify molecular operational taxonomy units (MOTUs) and to generate robust molecular information for penaeid shrimp based on the cytochrome oxidase subunit I (COI) mitochondrial gene. Our final data set includes COI sequences from 112 taxa distributed in 23 genera of penaeids. We employed the general mixed Yule coalescent (GMYC) model, the Poisson tree processes (PTP), and the Bayesian PTP model (bPTP) for MOTUs delimitation. Intraspecific and interspecific genetic distances were also calculated. Our findings evidenced a high level of hidden diversity, showing 143 MOTUs, with 27 nominal species not agreeing with the genetic delimitation obtained here. These data represent potential new species or highly structured populations, showing the importance of including a non-distance-based species delimitation approach in biodiversity studies. The results raised by this study shed light on the Penaeidae biodiversity, addressing important issues about taxonomy and mislabeling in databases and contributing to a better comprehension of the group, which can certainly help management policies for shrimp fishery activity in addition to conservation programs.

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Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments

Zoosystematics and Evolution ◽

10.3897/zse.95.31658 ◽

2019 ◽

Vol 95 (1) ◽

pp. 49-64 ◽

Cited By ~ 3

Author(s):

Felipe Polivanov Ottoni ◽

José L. O. Mattos ◽

Axel M. Katz ◽

Pedro H.N. Bragança

Keyword(s):

Phylogenetic Analysis ◽

Species Delimitation ◽

Species Recognition ◽

Mitochondrial Gene ◽

Divergence Time ◽

Morphological Characters ◽

Species Group ◽

Nucleotide Substitutions ◽

Divergence Time Estimates ◽

Late Neogene

Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, and we considered the possibility of two slightly variant scenarios. A time-calibrated phylogenetic analysis is proposed based on the predominant congruence of the results of these three species delimitation methods herein applied. The monophyly of theA.autranispecies group was highly supported with maximum node support value and diagnosed by 11 nucleotide substitutions. The sister clade of theA.autranispecies group is the clade comprisingA.sp. Timbé do Sul andA.minuano. The phylogenetic analysis supports three main clades within theA.autranispecies group, supported by maximum node support value, with the Southern Mata Atlântica clade as the most basal clade. Divergence time estimates indicate that the diversification of theAustraloherosoriginated during the early Neogene, but only in the late Neogene did the processes of diversification in the southeast and north regions occur. Diversification within theAustraloherosautranispecies group occurred synchronically for the three main clades during the beginning of the Quaternary. It is demonstrated that molecular characters are valuable tools for species recognition, particularly in speciose groups with inconspicuous or difficult to record morphological characters. The resulting phylogeny of theAustraloherosautranigroup is highly compatible with the geological and biogeographic scenarios proposed for the Neogene and Quarternary shaping of the extant river basins of eastern Brazil. Despite the origin of theA.autranigroup being dated to the late Miocene, species level diversification occurred in the Pleistocene and was probably driven by headwater capture events and sea-level fluctuations.

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Phylogeography of Simulium Subgenus Wilhelmia (Diptera: Simuliidae)—Insights From Balkan Populations

Journal of Medical Entomology ◽

10.1093/jme/tjz034 ◽

2019 ◽

Vol 56 (4) ◽

pp. 967-978 ◽

Cited By ~ 3

Author(s):

Jelena Đuknić ◽

Vladimir M Jovanović ◽

Nataša Popović ◽

Ivana Živić ◽

Maja Raković ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Dna ◽

Dna Barcoding ◽

Balkan Peninsula ◽

Genetic Distances ◽

Coi Gene ◽

Similar Species ◽

Mtdna Sequences ◽

The Balkans ◽

The Status

Abstract Many morphologically similar species of the simuliid (Diptera: Simuliidae) subgenus Wilhelmia, Enderlein are difficult to distinguish. Thus, the revision of the subgenus using various morphological, cytogenetic, and genetic analyses has been attempted. Neglected until now, the Balkan Peninsula, a crossroad between Europe and Anatolia, provides insight which could resolve problematic interrelationships of the taxa within this subgenus. To uncover the status and relations within the subgenus Wilhelmia, mtDNA was extracted from 47 individuals of six morphospecies: Simulium balcanicum (Enderlein, 1924), Simulium turgaicum Rubtsov, 1940, Simulium lineatum (Meigen, 1804), Simulium pseudequinum Séguy, 1921, Simulium equinum (Linnaeus, 1758), and Simulium paraequinum Puri, 1933 from 21 sites throughout the Balkan Peninsula. Phylogenetic analysis of the Wilhelmia species using mitochondrial DNA barcoding (COI) gene showed two major branches, the lineatum branch, which includes the lineages sergenti, paraequinum, and lineatum, and the equinum branch. In the equinum branch, the mtDNA sequences formed six clades, with high genetic distances, suggesting the existence of different species. Historically, the clades of the equinum branch appeared at numerous islands, perhaps as a result of allopatric speciation. The paraequinum lineage (lineatum branch) is composed of two species. However, six clades of the lineatum lineage overlapped with intra- and interspecific genetic distances. Our results revealed that the species S. balcanicum, S. pseudequinum B, and S. equinum were omnipresent in the Balkans. The results point to not only the fair diversity of Wilhelmia species in the Balkans, but also indicate that most Wilhelmia species live in sympatry.

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Restoring the species status of Catharus maculatus (Aves: Turdidae), a secretive Andean thrush, with a critique of the yardstick approach to species delimitation

Zootaxa ◽

10.11646/zootaxa.4276.3.4 ◽

2017 ◽

Vol 4276 (3) ◽

pp. 387 ◽

Cited By ~ 4

Author(s):

MATTHEW R. HALLEY ◽

JOHN C. KLICKA ◽

PAUL R. SESINK CLEE ◽

JASON D. WECKSTEIN

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequences ◽

Species Delimitation ◽

Ecological Niches ◽

Plumage Color ◽

Species Status ◽

The Common ◽

Components Analysis ◽

Independent Species ◽

Lines Of Evidence

In the 1850s, two species of "Spotted" Nightingale-Thrush (Aves: Catharus) were independently described from montane rainforests of Guatemala, C. dryas (Gould, 1855) and Ecuador, C. maculatus (Sclater, 1858). However, due to similarities in plumage color, C. maculatus was reclassified as a subspecies of C. dryas in 1878, a decision that has been upheld for 137 years. We collected multiple lines of evidence including phylogenetic analysis of mitochondrial DNA sequences (ND2), discriminant and principal components analysis of morphometric and vocal data, and statistical modeling of ecological niches, that collectively indicate that C. d. dryas and C. d. maculatus are independent species. We recommend restoring species status to C. maculatus of South America and applying the common name Sclater’s Nightingale-Thrush to this species.

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Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Diversity ◽

10.3390/d12110428 ◽

2020 ◽

Vol 12 (11) ◽

pp. 428

Author(s):

Martin Stervander ◽

Bengt Hansson ◽

Urban Olsson ◽

Mark F. Hulme ◽

Ulf Ottosson ◽

...

Keyword(s):

Mitochondrial Dna ◽

Molecular Species ◽

Species Delimitation ◽

Integrative Taxonomy ◽

West African ◽

Northwest Africa ◽

Sub Saharan ◽

Plateau State ◽

Avian Family ◽

Relic Population

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

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Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines

Genetics ◽

10.1093/genetics/150.4.1605 ◽

1998 ◽

Vol 150 (4) ◽

pp. 1605-1614

Author(s):

Junyuan Wu ◽

Konstantin V Krutovskii ◽

Steven H Strauss

Keyword(s):

Mitochondrial Dna ◽

Population Differentiation ◽

Mitochondrial Gene ◽

Dna Polymorphisms ◽

Neighbor Joining ◽

Closely Related Species ◽

Breeding Programs ◽

Length Polymorphisms ◽

Polymerase Chain ◽

Mitochondrial Genome Diversity

Abstract We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

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Reduced Variation in Drosophila simulans Mitochondrial DNA

Genetics ◽

10.1093/genetics/144.4.1519 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1519-1528

Author(s):

J William O Ballad ◽

Joy Hatzidakis ◽

Timothy L Karr ◽

Martin Kreitman

Keyword(s):

Mitochondrial Dna ◽

Mitochondrial Genome ◽

Evolutionary Dynamics ◽

Selective Sweep ◽

Mitochondrial Gene ◽

Drosophila Simulans ◽

Dramatic Reduction ◽

Nucleotide Variability ◽

Pooled Samples ◽

Mitochondrial Gene Mutation

We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.

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Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.8.2207-2210.2000 ◽

2000 ◽

Vol 44 (8) ◽

pp. 2207-2210 ◽

Cited By ~ 26

Author(s):

Nadia Maggi Solcà ◽

Marco Valerio Bernasconi ◽

Jean-Claude Piffaretti

Keyword(s):

Phylogenetic Analysis ◽

Helicobacter Pylori ◽

Amino Acid ◽

Resistant Strain ◽

Point Mutations ◽

Housekeeping Genes ◽

Amino Acid Substitutions ◽

Metronidazole Resistance ◽

Nucleotide Mutation ◽

Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

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