‘Local adaptation fuels cryptic speciation in terrestrial annelids’
Publication date: Available online 17 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Daniel Fernández Marchán, Marta Novo, Nuria Sánchez, Jorge Domínguez, Darío J. Díaz Cosín, Rosa FernándezAbstractUncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as it is the case with integrative taxonomy. The earthwo...
Source: Molecular Phylogenetics and Evolution - February 17, 2020 Category: Molecular Biology Source Type: research

Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study
Publication date: Available online 17 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Justin C. Bagley, Simon Uribe-Convers, Mónica M. Carlsen, Nathan MuchhalaAbstractTargeted sequence capture is a promising approach for large-scale phylogenomics. However, rapid evolutionary radiations pose significant challenges for phylogenetic inference (e.g. incomplete lineages sorting (ILS), phylogenetic noise), and the ability of targeted nuclear loci to resolve species trees despite such issues remains poorly studied. We test the utility of targeted sequence capture for inferring phylogenetic relationship...
Source: Molecular Phylogenetics and Evolution - February 17, 2020 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: March 2020Source: Molecular Phylogenetics and Evolution, Volume 144Author(s): (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - February 7, 2020 Category: Molecular Biology Source Type: research

Phylogenetic relationships of the Chinese torrent frogs (Ranidae: Amolops) revealed by phylogenomic analyses of AFLP-Capture data
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Zhaochi Zeng, Dan Liang, Jiaxuan Li, Zhitong Lyu, Yingyong Wang, Peng ZhangAbstractThe torrent frog genus Amolops contains nearly sixty species distributed in swift mountain streams throughout southeast Asia. The taxonomy of this genus has proven complicated due to unstable morphological diagnostic characters. The relationships of Amolops species and species groups were not readily resolved with a small number of molecular markers. Here, we applied the novel AFLP-Capture approach and acquired two large datasets (242 an...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

A comprehensive phylogeny and taxonomic evaluation of the waxbills (Aves: Estrildidae)
We present a revised taxonomy of Estrildidae based on the first time-calibrated phylogeny of the family Estrildidae estimated from a data set including the majority of the species, and all genera except the monospecific Paludipasser, using two mitochondrial and five nuclear markers. We find that most differences in current taxonomy reflect alternative opinions among authors regarding inclusiveness of genera, which are usually not in conflict with the phylogeny. The most notable exception is the current circumscriptions of the genera Neochmia, Nesocharis and Taeniopygia, which are incompatible with the phylogeny.Estrildidae...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

Freshwater mussels (Bivalvia: Unionidae) from the Rising Sun (Far East Asia): Phylogeny, systematics, and distribution
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Manuel Lopes-Lima, Akimasa Hattori, Takaki Kondo, Jin Hee Lee, Sang Ki Kim, Akihisa Shirai, Hironori Hayashi, Taira Usui, Kanta Sakuma, Taishi Toriya, Youhei Sunamura, Haruki Ishikawa, Naoki Hoshino, Yushi Kusano, Hinata Kumaki, Yuya Utsugi, Shinnosuke Yabe, Yuma Yoshinari, Hazuki Hiruma, Akiko TanakaAbstractFreshwater mussels (Bivalvia: Unionidae) is a diverse family with around 700 species being widespread in the Northern Hemisphere and Africa. These animals fulfill key ecological functions and provide important serv...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): R. Alexander Pyron, Kyle A. O'Connell, Emily Moriarty Lemmon, Alan R. Lemmon, David A. BeamerAbstractGene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, m...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

The evolutionary history of the cellophane bee genus Colletes Latreille (Hymenoptera: Colletidae): molecular phylogeny, biogeography and implications for a global infrageneric classification
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Rafael R. Ferrari, Thomas M. Onuferko, Spencer K. Monckton, Laurence PackerAbstractColletes Latreille (Hymenoptera: Colletidae) is a diverse genus with 518 valid species distributed in all biogeographic realms, except Australasia and Antarctica. Here we provide a comprehensive dated phylogeny for Colletes based on Bayesian analysis of DNA sequence data of six loci: 28S rDNA, cytochrome c oxidase subunit 1, elongation factor-1α copy F2, long-wavelength rhodopsin, RNA polymerase II and wingless. In total, our multi...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

Phylogeny and biogeography of the Daniellia clade (Leguminosae: Detarioideae), a tropical tree lineage largely threatened in Africa and Madagascar
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Le Min Choo, Félix Forest, Jan J. Wieringa, Anne Bruneau, Manuel de la EstrellaAbstractThe legume subfamily Detarioideae is exceptionally diverse in tropical Africa and Madagascar, compared to South America or Asia, a trend contrary to that shown by most other pantropical plant groups. We aim to elucidate the process of diversification giving rise to these high diversity levels by focussing our investigations on the Daniellia clade, which is present in both Africa and Madagascar. The Daniellia clade is an early-...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

A taxonomic conundrum: Characterizing a cryptic radiation of Asian gracile skinks (Squamata: Scincidae: Riopa) in Myanmar
Publication date: Available online 3 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Elyse S. Freitas, Aryeh H. Miller, R. Graham Reynolds, Cameron D. SilerAbstractRecognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using multilocus molecular data, phylogenetic analyses, species delimitation analyses, and morphologica...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers
In this study, we used a double digest RADseq protocol to provide a high resolution (∼ 4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results sugge...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

ddRAD analyses reveal a credible phylogenetic relationship of the four main genera of Bambusa-Dendrocalamus-Gigantochloa complex (Poaceae: Bambusoideae)
Publication date: Available online 4 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Jing-Xia Liu, Meng-Yuan Zhou, Guo-Qian Yang, Yu-Xiao Zhang, Peng-Fei Ma, Maria S. Vorontsova, De-Zhu LiAbstractThe Bambusa-Dendrocalamus-Gigantochloa complex (BDG complex) is the most diversified and phylogenetically recalcitrant group of the paleotropical woody bamboos. Species of this complex occur in tropical and subtropical Asia and most of them are of great economic, cultural and ecological value. The lack of resolution achieved through the analyses of previous molecular datasets has long confounded its phylogenet...
Source: Molecular Phylogenetics and Evolution - February 5, 2020 Category: Molecular Biology Source Type: research

Cryptic diversity and non-adaptive radiation of montane New Guinea skinks (Papuascincus; Scincidae)
Publication date: Available online 31 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Alex Slavenko, Karin Tamar, Oliver J.S. Tallowin, Allen Allison, Fred Kraus, Salvador Carranza, Shai MeiriAbstractNew Guinea, the world’s largest and highest tropical island, has a rich but poorly known biota. Papuascincus is a genus of skinks endemic to New Guinea’s mountain regions, comprising two wide-ranging species and two species known only from their type series. The phylogeny of the genus has never been examined and the relationships among its species – as well as between it and closely relate...
Source: Molecular Phylogenetics and Evolution - February 1, 2020 Category: Molecular Biology Source Type: research

Phylogeny and biogeography of Astraea with new insights into the evolutionary history of Crotoneae (Euphorbiaceae)
Publication date: Available online 27 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Otávio Luis Marques da Silva, Ricarda Riina, Inês CordeiroAbstractWe investigated species relationships in Astraea, a primarily Neotropical genus of tribe Crotoneae centered in Brazil, using data from the nuclear ribosomal ITS, and the plastid trnL-trnF and psbA-trnH spacers. With all species of Astraea sampled along with representatives from across Crotoneae, the evolutionary history of Astraea was interpreted in a broader framework, as well as divergence time estimates and reconstructions of ancestral ar...
Source: Molecular Phylogenetics and Evolution - January 29, 2020 Category: Molecular Biology Source Type: research

The impact of Miocene orogeny for the diversification of Caucasian Epeorus (Caucasiron) mayflies (Ephemeroptera: Heptageniidae)
This study focuses on mayflies of the subgenus Caucasiron, one of the most diversified stenotopic mayflies inhabiting various types of streams throughout the Caucasus. Using the time-calibrated phylogeny based on two mitochondrial (COI, 16S) and three nuclear (EF-1α, wg, 28S) gene fragments, we tested the role of Caucasian orogeny in biogeography, diversification patterns, and altitudinal diversification of Caucasiron mayflies. We found that orogeny promoted the lineage diversification of Caucasiron in the Miocene. The highest diversification rate corresponding with the uplift of mountains was followed by a significa...
Source: Molecular Phylogenetics and Evolution - January 29, 2020 Category: Molecular Biology Source Type: research

RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae)
Publication date: April 2020Source: Molecular Phylogenetics and Evolution, Volume 145Author(s): Étienne Léveillé-Bourret, Bing-Hua Chen, Marie-Ève Garon-Labrecque, Bruce A. Ford, Julian R. StarrAbstractTrichophoreae is a nearly cosmopolitan Cyperaceae tribe that contains ~17 species displaying striking variation in size, inflorescence complexity, and perianth morphology. Although morphologically distinct, the status of its three genera (Cypringlea, Oreobolopsis and Trichophorum) is controversial because recent phylogenetic studies have suggested they might not be reciprocally monophyletic. Howev...
Source: Molecular Phylogenetics and Evolution - January 29, 2020 Category: Molecular Biology Source Type: research

Phylogeny and highland adaptation of Chinese species in Allium Section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing
Publication date: Available online 23 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Deng-Feng Xie, Yan Yu, Jun Wen, Jiao Huang, Jun-Pei Chen, Juan Li, Song-Dong Zhou, Xing-Jin HeAbstractAllium L. is one of the largest monocotyledonous genera with an extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous s...
Source: Molecular Phylogenetics and Evolution - January 24, 2020 Category: Molecular Biology Source Type: research

Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae)
In this study, we present the first tribal-level phylogeny of Lamiinae, inferred from 130 terminals (representing 46 tribes, prioritizing generic type species of the tribes) and fragments of two mitochondrial and three nuclear markers (cox1, rrnL, Wg, CPS and LSU; 5,024 aligned positions total). Analyses were performed under Maximum Likelihood and Bayesian methods based on two datasets: a dataset including all taxa available for the study, and a reduced dataset with 111 terminals where taxa only contributing with mitochondrial markers were excluded from the matrix. The monophyly of Lamiinae was corroborated in three of the...
Source: Molecular Phylogenetics and Evolution - January 23, 2020 Category: Molecular Biology Source Type: research

Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types
Publication date: Available online 21 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Huihui Chang, Zhongying Qiu, Hao Yuan, Xiaoyang Wang, Xuejuan Li, Huimin Sun, Xiaoqiang Guo, Yingchun Lu, Xiaolei Feng, Muhammad Majid, Yuan HuangAbstractOrthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a dat...
Source: Molecular Phylogenetics and Evolution - January 21, 2020 Category: Molecular Biology Source Type: research

Further discussion with Li et al. (2013, 2019) regarding the “ITS pseudogene hypothesis” for Ophiocordyceps sinensis
Publication date: Available online 2 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Xiu-Zhang Li, Yu-Ling Li, Yi-Sang Yao, Wei-Dong Xie, Jia-Shi Zhu (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - January 17, 2020 Category: Molecular Biology Source Type: research

Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage
Publication date: Available online 11 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Gautério Thaísa Bozzetti, Machado Stela, Loreto Elgion Lucio da Silva, Gottschalk Marco Silva, Robe Lizandra JaquelineAbstractThe Neotropical region harbors an astonishing diversity of species, but still encompasses the least studied biogeographic region of the world. These properties apply for different taxonomic groups, and can be exemplified by drosophilids. In fact, high levels of cryptic diversity have recently been discovered for Neotropical species of the Zygothrica genus group, but relationships a...
Source: Molecular Phylogenetics and Evolution - January 11, 2020 Category: Molecular Biology Source Type: research

Plastid phylogenomic data yield new and robust insights into the phylogeny of Cleisostoma–Gastrochilus clades (Orchidaceae, Aeridinae)
We present large-scale phylogenomic data sets, incorporating complete chloroplast genome sequences from 53 species (including 41 species sequenced in this study), to compare plastome structure and to resolve the phylogenetic relationships of these clades. The plastomes of Cleisostoma–Gastrochilus clades possessed the quadripartite structure and plastome genes of typical angiosperms with sizes ranging from 142 to 149 kb and encoding a set of 118–120 genes. Unusual structural features were detected in the plastome of Uncifera acuminata, including the presence of a large 17-kb inversion (19 genes) in the Large Sin...
Source: Molecular Phylogenetics and Evolution - January 9, 2020 Category: Molecular Biology Source Type: research

Further discussion with Li et al.(2013, 2019) regarding the “ITS pseudogene hypothesis” for Ophiocordyceps sinensis
Publication date: Available online 2 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Xue-Zhang Li, Yu-Ling Li, Yi-Sang Yao, Wei-Dong Xie, Jia-Shi Zhu (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - January 3, 2020 Category: Molecular Biology Source Type: research

Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from Republic of Madagascar (Africa) with microbiome analysis
Publication date: Available online 3 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Łukasz Kaczmarek, Milena Roszkowska, Izabela Poprawa, Kamil Janelt, Hanna Kmita, Magdalena Gawlak, Edyta Fiałkowska, Monika MioduchowskaAbstractIn a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of the eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and...
Source: Molecular Phylogenetics and Evolution - January 3, 2020 Category: Molecular Biology Source Type: research

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements
Publication date: Available online 3 January 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Perry L. Wood, Xianguang Guo, Scott L. Travers, Yong-Chao Su, Karen V. Olson, Aaron M. Bauer, L. Lee Grismer, Cameron D. Siler, Robert G. Moyle, Michael J. Andersen, Rafe M. BrownAbstractRecent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in Aus...
Source: Molecular Phylogenetics and Evolution - January 3, 2020 Category: Molecular Biology Source Type: research

RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a rapid recent radiation (Cyperaceae)
Publication date: Available online 30 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Étienne Léveillé-Bourret, Bing-Hua Chen, Marie-Ève Garon-Labrecque, Bruce A. Ford, Julian R. StarrAbstractTrichophoreae is a nearly cosmopolitan Cyperaceae tribe that contains ∼17 species displaying striking variation in size, inflorescence complexity, and perianth morphology. Although morphologically distinct, the status of its three genera (Cypringlea, Oreobolopsis and Trichophorum) are controversial because recent phylogenetic studies have suggested they might not be reciprocally mon...
Source: Molecular Phylogenetics and Evolution - January 1, 2020 Category: Molecular Biology Source Type: research

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex
Publication date: Available online 28 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Adam Bessa-Silva, Marcelo Vallinoto, Iracilda Sampaio, Oscar A. Flores-Villela, Eric N. Smith, Fernando SequeiraAbstractThe high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites and...
Source: Molecular Phylogenetics and Evolution - December 29, 2019 Category: Molecular Biology Source Type: research

Phylogenomics, co-evolution of ecological niche and morphology, and historical biogeography of buckeyes, horsechestnuts, and their relatives (Hippocastaneae, Sapindaceae) and the value of RAD-Seq for deep evolutionary inferences back to the Late Cretaceous
In this study, we used RAD-seq data to resolve the phylogeny of the tribe Hippocastaneae and conducted comparative analyses to gain insights into the evolution and biogeography of the group that had fossils dating back to the late Cretaceous. Hippocastaneae, including the horsechestnuts and buckeyes, is a well-supported clade in Sapindaceae that comprises 12–14 species in Aesculus, two in Billia, and one in Handeliodendron. Most species in the tribe are distributed in Eurasia and North America and exhibit a classic pattern of intercontinental disjunction in the northern hemisphere, while Billia occurs from southern M...
Source: Molecular Phylogenetics and Evolution - December 29, 2019 Category: Molecular Biology Source Type: research

The enigmatic Leiosaurae clade: Phylogeography, species delimitation, phylogeny and historical biogeography of its southernmost species
Publication date: Available online 26 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Martin M. Femenias, Luciano J. Avila, Jack W. Sites, Mariana MorandoAbstractThe clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and understanding of their evolutionary histories. Here, we use data collected over 9 years to study the phylogenetic history, genetic diversity, and biogeographic history of almost all the southernmost specie...
Source: Molecular Phylogenetics and Evolution - December 27, 2019 Category: Molecular Biology Source Type: research

Editorial Board
Publication date: February 2020Source: Molecular Phylogenetics and Evolution, Volume 143Author(s): (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - December 27, 2019 Category: Molecular Biology Source Type: research

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)
Publication date: Available online 24 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Jin-Min Chen, Elizabeth Prendini, Yun-He Wu, Bao-Lin Zhang, Chatmongkon Suwannapoom, Hong-Man Chen, Jie-Qiong Jin, Emily Moriarty Lemmon, Alan R. Lemmon, Bryan L. Stuart, Christopher J. Raxworthy, Robert W. Murphy, Zhi-Yong Yuan, Jing CheAbstractRhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst...
Source: Molecular Phylogenetics and Evolution - December 26, 2019 Category: Molecular Biology Source Type: research

Genetic variation and admixture of red-eared sliders (Trachemys scripta elegans) in the USA
Publication date: Available online 23 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): James F. Parham, Theodore J. Papenfuss, Anna B. Sellas, Bryan L. Stuart, W. Brian SimisonAbstractThe most ubiquitous, abundant, and invasive turtle on Earth, Trachemys scripta elegans (TSE, “red-eared slider”), is one of four taxa in a clade that is native to the USA and adjacent Mexico (three subspecies of Trachemys scripta plus Trachemys gaigeae). The present range-wide study of this clade is based on 173 known-locality mtDNA sequences combined with ddRAD libraries for 43 samples emphasizing the western ...
Source: Molecular Phylogenetics and Evolution - December 24, 2019 Category: Molecular Biology Source Type: research

Plastome evolution and phylogeny of subtribe Aeridinae (Vandeae, Orchidaceae)
Publication date: Available online 21 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Young-Kee Kim, Sangjin Jo, Se-Hwan Cheon, Myounghai Kwak, Young-Dong Kim, Ki-Joong KimAbstractSubtribe Aeridinae (Vandeae, Epidendroideae, Orchidaceae) consists of 83 genera and 2,345 species. The present study completely decoded the plastomes and nuclear ribosomal (nr) RNA gene clusters of seven species of Aeridinae belonging to Gastrochilus, Neofinetia, Pelatantheria, and Thrixspermum and compared them with existing data to investigate their genome evolution and phylogeny. Although no large structural variations wer...
Source: Molecular Phylogenetics and Evolution - December 21, 2019 Category: Molecular Biology Source Type: research

Conservation and innovation: plastome evolution during rapid radiation of Rhodiola on the Qinghai-Tibetan Plateau
Publication date: Available online 18 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Dan-Ni Zhao, Yi Ren, Jian-Qiang ZhangAbstractThe amount of plastome sequence data available has soared in the last decade, but the nature of plastome evolution during rapid radiations is largely unknown. Moreover, although there is increasing evidence showing that plastomes may have undergone adaptive evolution in order to allow adaptation to various environments, few studies have systematically investigated the role of the plastome in alpine adaptation. To address these questions, we sequenced and analyzed 12 represe...
Source: Molecular Phylogenetics and Evolution - December 19, 2019 Category: Molecular Biology Source Type: research

Phylogeographic evidence that the distribution of cryptic euryhaline species in the Gambusia punctata species group in Cuba was shaped by the archipelago geological history
In this study, we analyzed the cryptic diversification of G. punctata species group in Cuba, based on a comprehensive sampling of its distribution and including habitats with different salinity levels. We evaluated the patterns of molecular divergence of the samples by sequencing a set of mitochondrial DNA (mtDNA) regions and genotyping nine nuclear microsatellite loci. We also used cytochrome b gene (cytb) partial sequences and these microsatellite loci to analyze population structure inside putative species. Five mtDNA well-differentiated haplogroups were found, four of them also identified by the analysis of the microsa...
Source: Molecular Phylogenetics and Evolution - December 18, 2019 Category: Molecular Biology Source Type: research

Phylogeny and biogeography of the Cavernicola (Platyhelminthes: Tricladida): Relicts of an epigean group sheltering in caves?
Publication date: Available online 17 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Lisandra Benítez-Alvarez, Ana Maria Leal-Zanchet, Alejandro Oceguera-Figueroa, Rodrigo Lopes Ferreira, Diego de Medeiros Bento, João Braccini, Ronald Sluys, Marta RiutortAbstractThe planarian suborder Cavernicola Sluys, 1990 was originally created to house five species of triclad flatworms with special morphological features and a surprisingly discontinuous and broad geographic distribution. These five species could not be accommodated with any degree of certainty in any of the three taxonomic groups exi...
Source: Molecular Phylogenetics and Evolution - December 18, 2019 Category: Molecular Biology Source Type: research

Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus
We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥ 2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, ...
Source: Molecular Phylogenetics and Evolution - December 17, 2019 Category: Molecular Biology Source Type: research

Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods
Publication date: Available online 15 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Elena V. Romanova, Yurij S. Bukin, Kirill V. Mikhailov, Maria D. Logacheva, Vladimir V. Aleoshin, Dmitry Yu. SherbakovAbstractThe evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amp...
Source: Molecular Phylogenetics and Evolution - December 15, 2019 Category: Molecular Biology Source Type: research

Phylogeny, biogeography and systematics of the hyper-diverse blister beetle genus Hycleus (Coleoptera: Meloidae)
In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species...
Source: Molecular Phylogenetics and Evolution - December 11, 2019 Category: Molecular Biology Source Type: research

Multigene Phylogeny Uncovers Oviposition-related Evolutionary History of Cerambycinae (Coleoptera: Cerambycidae)
In this study, we reconstructed a first multi-locus phylogeny of Cerambycinae representing a wide range of oviposition strategies, host plants, and ovipositor lengths. Ancestral state reconstruction analyses showed that the shortened ovipositor in Cerambycinae evolved at least four times independently and that the use of host plant has evolved from stressed hosts to dead or living hosts and from broad-leaved trees to conifers. The correlated evolution test revealed the correlation between ovipositor length and oviposition strategy. Our study elucidates for the first time the complex evolutionary history of the ovipositor, ...
Source: Molecular Phylogenetics and Evolution - December 11, 2019 Category: Molecular Biology Source Type: research

Out of Africa: the origins of the protozoan blood parasites of the Trypanosoma cruzi clade found in bats from Africa
We present here results based on the molecular characterization of trypanosome isolates obtained from 1,493 bats representing 74 species and sampled over 16 countries across four continents.After estimating the appropriate number of hypothetical species in our data set using GMYC models in combination with Poisson Tree Processes (mPTP) and ABGD, the 18S rRNA and gGAPDH genes were used for phylogenetic analyses to infer the major evolutionary relationships in the T. cruzi clade. Then, biogeographical processes influencing the distribution of this cosmopolitan group of parasites was inferred using BioGeoBEARS. Results reveal...
Source: Molecular Phylogenetics and Evolution - December 10, 2019 Category: Molecular Biology Source Type: research

Spatio-temporal formation of the genetic diversity in the Mediterranean dwelling lichen during the Neogene and Quaternary epochs
This study presents the first comprehensive lichen phylogeography from the Mediterranean region and simultaneously reports for the first time the glacial survival of a warm-adapted lichen in the temperate zone.Graphical abstract (Source: Molecular Phylogenetics and Evolution)
Source: Molecular Phylogenetics and Evolution - December 8, 2019 Category: Molecular Biology Source Type: research

Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae)
Publication date: Available online 5 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Florian Wagner, Tankred Ott, Maximilian Schall, Ulrich Lautenschlager, Robert Vogt, Christoph OberprielerAbstractDelineating species boundaries in a group of recently diverged lineages is challenging due minor morphological differences, low genetic differentiation and the occurrence of gene flow among taxa. Here, we employ traditional Sanger sequencing and restriction-site associated DNA (RAD) sequencing, to investigate species delimitation in the close-knit Moroccan daisy group around Rhodanthemum arundanum B.H.Wilcox...
Source: Molecular Phylogenetics and Evolution - December 6, 2019 Category: Molecular Biology Source Type: research

Cryptic ecological and geographic diversification in coral-associated nudibranchs
This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the gen...
Source: Molecular Phylogenetics and Evolution - December 6, 2019 Category: Molecular Biology Source Type: research

The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity
Publication date: Available online 6 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Nicolas Violaine, Fabre Pierre-Henri, Bryja Josef, Denys Christiane, Verheyen Erik, Missoup Alain-Didier, Olayemi Ayodeji, Katuala Pionus, Dudu Akaibe, Colyn Marc, Kerbis Peterhans Julian, Demos TerrenceAbstractWood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used comple...
Source: Molecular Phylogenetics and Evolution - December 6, 2019 Category: Molecular Biology Source Type: research

Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China
Publication date: Available online 4 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Zhuo Chen, Hanyu Li, Xiaofei Zhai, Yanjun Zhu, Yuxiao He, Qiuya Wang, Zhen Li, Jianping Jiang, Rongchuan Xiong, Xiaohong ChenAbstractUnderstanding the process of speciation and the factors driving the geographical distribution patterns of species is of great interest in ecology and evolutionary biology. Herein, we investigated the phylogeographic patterns, speciation, demographic history and genetic structure of the widespread endemic Odorrana graminea sensu lato in Southern China and adjacent areas. A total of 439 spe...
Source: Molecular Phylogenetics and Evolution - December 5, 2019 Category: Molecular Biology Source Type: research

Sympatric lineages in the Mantidactylus ambreensis complex of Malagasy frogs originated allopatrically rather than by in-situ speciation
Publication date: Available online 3 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Safidy M. Rasolonjatovo, Mark D. Scherz, Carl R. Hutter, Frank Glaw, Andolalao Rakotoarison, Jary H. Razafindraibe, Steven M. Goodman, Achille P. Raselimanana, Miguel VencesAbstractMadagascar's biota is characterized by a high degree of microendemism at different taxonomic levels, but how colonization and in-situ speciation contribute to the assembly of local species communities has rarely been studied in this island. Here we analyze the phylogenetic relationships of riparian frogs of the Mantidactylus ambreensis speci...
Source: Molecular Phylogenetics and Evolution - December 4, 2019 Category: Molecular Biology Source Type: research

Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis
Publication date: Available online 4 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): Ran Wei, Xian-Chun ZhangAbstractDespite progress in resolving the phylogeny of twinsorus ferns (Diplazium) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related clades, suggesting a classic case of rapid evolutionary radiation. Here, we investigated the deep phylogenetic relationships within Diplazium by sampling all major clades and using 51 plastid genomes (plastomes), of which 38 were newly sequenced with high-throughput sequencing technolo...
Source: Molecular Phylogenetics and Evolution - December 4, 2019 Category: Molecular Biology Source Type: research

Origin and evolution of the CYP4G subfamily in insects, cytochrome P450 enzymes involved in cuticular hydrocarbon synthesis
Publication date: Available online 2 December 2019Source: Molecular Phylogenetics and EvolutionAuthor(s): René FeyereisenAbstractThe large and diverse P450 (CYP) superfamily encodes enzymes with a wide spectrum of monooxygenase and related activities. Insect P450 enzymes of the CYP4G subfamily are known to catalyze the synthesis of cuticular hydrocarbons that serve multiple functions from desiccation resistance to chemical communication. These functions are essential for survival. In order to understand the evolution of insect CYP4G genes, 368 sequences from 24 insect orders and 167 species were mined and analyzed. ...
Source: Molecular Phylogenetics and Evolution - December 4, 2019 Category: Molecular Biology Source Type: research

Codon Use and Aversion is Largely Phylogenetically Conserved Across the Tree of Life
We examined each codon within each ortholog to determine the codon usage for each species. In total, 890 814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25 771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1 109x more likely to be congruent with species relations...
Source: Molecular Phylogenetics and Evolution - December 4, 2019 Category: Molecular Biology Source Type: research