Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella

Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantella madagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantella aurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantella crocea + Mantella milotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.

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Individual and Geographic Variation of Skin Alkaloids in Three Swamp-Forest Species of Madagascan Poison Frogs (Mantella)

Journal of Chemical Ecology ◽

10.1007/s10886-015-0616-4 ◽

2015 ◽

Vol 41 (9) ◽

pp. 837-847 ◽

Cited By ~ 7

Author(s):

Nirina R. Andriamaharavo ◽

H. Martin Garraffo ◽

Thomas F. Spande ◽

Lesley-Ann Giddings ◽

David R. Vieites ◽

...

Keyword(s):

Geographic Variation ◽

Forest Species ◽

Swamp Forest ◽

Poison Frogs

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Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa035 ◽

2020 ◽

Vol 194 (1) ◽

pp. 84-99

Author(s):

Inelia Escobar ◽

Eduardo Ruiz-Ponce ◽

Paula J Rudall ◽

Michael F Fay ◽

Oscar Toro-Núñez ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Incomplete Lineage Sorting ◽

Morphological Evolution ◽

Strong Support ◽

Plastid Dna ◽

Lineage Sorting ◽

Generic Level ◽

Molecular Analyses ◽

Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

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A new species of Vespula, and first record of Vespa crabro L. (Hymenoptera: Vespidae) from Guatemala, Central America

Zootaxa ◽

10.11646/zootaxa.2629.1.4 ◽

2010 ◽

Vol 2629 (1) ◽

pp. 61 ◽

Cited By ~ 5

Author(s):

PETER J. LANDOLT ◽

JOSÉ MONZÓN SIERRA ◽

THOMAS R. UNRUH ◽

RICHARD S. ZACK

Keyword(s):

New Species ◽

Central America ◽

Dna Sequences ◽

First Record ◽

Color Pattern ◽

Species Group ◽

Mountain Range ◽

Vespa Crabro ◽

Vespula Vulgaris ◽

A New Species

Vespula akrei Landolt sp. nov. is described from Guatemala. The first record of Vespa crabro L. in Guatemala is given, and Vespula inexspectata Eck from Mexico is re-described. We place Vespula akrei sp. nov. in the Vespula vulgaris (L.) species group (= Paravespula Bluthgen) based on morphology, color pattern, and DNA sequences from two mitochrondrial genes. It is presently known only from the Sierra de las Minas mountain range in southeastern Guatemala.

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Description of a new genus and two new species of killifish (Cyprinodontiformes: Nothobranchiidae) from West Africa, with a discussion of the taxonomic status of Aphyosemion maeseni Poll, 1941

Zootaxa ◽

10.11646/zootaxa.2294.1.1 ◽

2009 ◽

Vol 2294 (1) ◽

pp. 1-22 ◽

Cited By ~ 3

Author(s):

RAINER SONNENBERG ◽

ECKHARD BUSCH

Keyword(s):

New Species ◽

Dna Sequences ◽

New Genus ◽

Nuclear Dna ◽

Taxonomic Status ◽

Morphological Characters ◽

Color Pattern ◽

Monophyletic Group ◽

Morphological Data ◽

Adult Males

The phylogeny of the West African genus Archiaphyosemion was studied with mitochondrial and nuclear DNA sequences. The results of the combined dataset presented here did not support a monophyletic group. After the exclusion of the type species of the genus, A. guineense, the remaining species form a well-supported monophyletic group. Based on these molecular results and supported by morphological data, we suggest a new name for this group, Nimbapanchax, new genus. Additionally, based on a recent collection in Guinea, two new Nimbapanchax species were described. The taxon Nimbapanchax leucopterygius, new species, is described for a nothobranchiid fish formerly misidentified as Archiaphyosemion maeseni (Poll, 1941). Nimbapanchax melanopterygius, new species, is described from the Mount Nimba region in southeastern Guinea. Both new Nimbapanchax species are clearly distinguished from their congeners by the coloration pattern of adult males. The results of the DNA data support the assumption based on color pattern and morphological characters that the new described species are sister taxa. The type of Aphyosemion maeseni Poll, 1941 was reexamined and transferred to the genus Epiplatys, a decision based on diagnostic morphological characters.

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Phylogenetic systematics and biogeography of the poison frogs: evidence from mitochondrial DNA sequences

Biological Journal of the Linnean Society ◽

10.1111/j.1095-8312.2000.tb01236.x ◽

2000 ◽

Vol 70 (3) ◽

pp. 515-540 ◽

Cited By ~ 48

Author(s):

MARK CLOUGH ◽

KYLE SUMMERS

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Phylogenetic Systematics ◽

Poison Frogs

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Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys: a mitochondrial selective sweep?

10.1101/2020.08.20.259549 ◽

2020 ◽

Author(s):

Rebecca S. Taylor ◽

Ashley C. Bramwell ◽

Rute Clemente-Carvalho ◽

Nicholas A. Cairns ◽

Frances Bonier ◽

...

Keyword(s):

Mitochondrial Dna ◽

Environmental Changes ◽

Incomplete Lineage Sorting ◽

Mitochondrial Gene ◽

Nuclear Gene ◽

Phylogeographic Structure ◽

Gene Trees ◽

Lineage Sorting ◽

Reciprocal Monophyly ◽

Mitochondrial Introgression

ABSTRACTThe golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results support the true species status of Z. atricapilla and Z. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

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An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

10.1101/709477 ◽

2019 ◽

Cited By ~ 2

Author(s):

Mark S. Springer ◽

John Gatesy

Keyword(s):

Dna Sequences ◽

Incomplete Lineage Sorting ◽

Species Tree ◽

Data Sets ◽

Lineage Sorting ◽

Sequence Alignments ◽

Data Set ◽

Short Branch ◽

Phylogenetic Methods ◽

Branch Lengths

AbstractDNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroposon insertions satisfy the ‘no intralocus recombination’ assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work. Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ2 Quartet-Asymmetry Test to detect hybridization using retroposon data. Both coalescence methods recovered the same topology for each of the three data sets. The ASTRAL species tree for Laurasiatheria has consecutive short branch lengths that are consistent with an anomaly zone situation. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both coalescence methods recovered a topology that supports the paraphyly of Balaenopteridae. Application of the χ2 Quartet-Asymmetry Test to this data set detected 16 different quartets of species for which historical hybridization may be inferred, but significant asymmetry was not detected in the placental root and Laurasiatheria analyses.

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Taxonomic notes on Trigonidium and related groups with one new species from the Philippines (Orthoptera: Trigonidiidae; Trigonidiinae)

Zootaxa ◽

10.11646/zootaxa.4564.2.13 ◽

2019 ◽

Vol 4564 (2) ◽

pp. 573 ◽

Cited By ~ 1

Author(s):

MING KAI TAN ◽

JESSICA B. BAROGA-BARBECHO ◽

SHERYL A. YAP

Keyword(s):

New Species ◽

Dna Sequences ◽

Gene Tree ◽

Molecular Data ◽

The Philippines ◽

Current Data ◽

Considerable Confusion ◽

Future Work ◽

One New Species ◽

A New Species

The taxonomy of Old World Trigonidiinae (sword-tailed crickets) is in need of major revision. This includes its type genus Trigonidium. Various authors have different opinions on what constitutes the subgenera and species of Trigonidium s. l. and this has led to considerable confusion and inconsistencies. Recent use of molecular data has helped make some progress in resolving some of these problems, but there are still limitations. In this paper, we aim to provide a baseline to resolve the confusion in the taxonomy of Trigonidium s. l. Firstly, we provide a literature review of the contentious taxa related to Trigonidium and also provide some recommendations on future work for Trigonidium s. l. Secondly, we reanalysed the gene tree (sensu Lu et al., 2018) using more DNA sequences from GenBank to test whether Trigonidium s. str. and Paratrigonidium should be considered separate genera or subgenera of Trigonidium s. l. However, the gene tree based on current data was not conclusive. Lastly, we describe a new species of Trigonidium s. str. from Siargao Island, Mindanao (Philippines): Trigonidium solis sp. nov.

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