(Mol Phylogenet Evol[TA])
- Phylogenetic analysis of two Plectus mitochondrial genomes (Nematoda: Plectida) supports a sister group relationship between Plectida and Rhabditida within Chromadorea. [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 13
- Plectida is an important nematode order with species that occupy many different biological niches. The order includes free-living aquatic and soil-dwelling species, but its phylogenetic position has ...
Plectida is an important nematode order with species that occupy many different biological niches. The order includes free-living aquatic and soil-dwelling species, but its phylogenetic position has remained uncertain. We sequenced the complete mitochondrial genomes of two members of this order, Plectus acuminatus and Plectus aquatilis and compared them with those of other major nematode clades. The genome size and base composition of these species are similar to other nematodes; 14,831 and 14,372 bp, respectively, with AT contents of 71.0% and 70.1%. Gene content was also similar to other nematodes, but gene order and coding direction of Plectus mtDNAs were dissimilar from other chromadorean species. P. acuminatus and P. aquatilis are the first chromadorean species found to contain a gene inversion. We reconstructed mitochondrial genome phylogenetic trees using nucleotide and amino acid datasets from 87 nematodes that represent major nematode clades, including the Plectus sequences. Trees from phylogenetic analyses using maximum likelihood and Bayesian methods depicted Plectida as the sister group to other sequenced chromadorean nematodes. This finding is consistent with several phylogenetic results based on SSU rDNA, but disagrees with a classification based on morphology. Mitogenomes representing other basal chromadorean groups (Araeolaimida, Monhysterida, Desmodorida, Chromadorida) are needed to confirm their phylogenetic relationships.
- Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences. [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 13
- In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD)...
In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined. Lampreys, along with hagfishes, are cyclostomata (jawless fishes), which is a sister group of gnathostomata (jawed vertebrates). Although those results suggested that one gene was orthologous to the gnathostome RHCG genes, we did not identify clear orthologues for other genes. In this study, therefore, we identified three novel cDNA sequences that belong to the RH gene family using de novo transcriptome analysis of another cyclostome: the brown hagfish (Eptatretus atami). We also determined the nucleotide sequences for the RHBG and RHCG genes in a red stingray (Dasyatis akajei), which belongs to the cartilaginous fishes. The phylogenetic tree showed that two brown hagfish genes, which were probably duplicated in the cyclostome lineage, formed a cluster with the gnathostome RHAG genes, whereas another brown hagfish gene formed a cluster with the gnathostome RHCG genes. We estimated that the RH genes had a higher evolutionary rate than the RHAG, RHBG, and RHCG genes. Interestingly, in the RHBG genes, only the bird lineage showed a higher rate of nonsynonymous substitutions. It is likely that this higher rate was caused by a state of relaxed functional constraints rather than positive selection nor by pseudogenization.
- Phylogenetic relationships of Mediterranean and North-East Atlantic Cantharidinae and notes on Stomatellinae (Vetigastropoda: Trochidae). [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 13
- The subfamily Cantharidinae Gray, 1857 (Trochoidea: Trochidae) includes 23 recognized genera and over 200 known living species. These marine top shell snails are microphagous grazers that generally l...
The subfamily Cantharidinae Gray, 1857 (Trochoidea: Trochidae) includes 23 recognized genera and over 200 known living species. These marine top shell snails are microphagous grazers that generally live in shallow rocky shores and in macroalgae and seagrass beds of sub-tropical and temperate waters from the Central and Western Indo-Pacific biogeographic regions to the Mediterranean Sea and the Eastern Atlantic Ocean. Recent molecular phylogenetic studies revising the family Trochidae supported the monophyly of the subfamily Cantharidinae and its sister group relationship to the subfamily Stomatellinae. These studies and others has thus far mostly focused on Indo-Pacific members of the subfamily Cantharidinae whereas here, we investigated phylogenetic relationships among their counterparts from the Mediterranean Sea and the North-eastern (NE) Atlantic Ocean including 33 species of genera Gibbula, Jujubinus, Phorcus, Clelandella, and Callumbonella. The Mediterranean and NE Atlantic taxa were supplemented with 30 Indo-Pacific Cantharidinae species plus 19 members of the sister group subfamily Stomatellinae. Phylogenetic trees were constructed using Bayesian inference and maximum likelihood with two datasets comprised of partial sequences of four or six mitochondrial (cox1, rrnL, rrnS, and cob) and nuclear (28S rRNA and histone H3) genes. A clade comprised of all Mediterranean and NE Atlantic taxa was recovered with high support, but its sister group among the Indo-Pacific lineages could not be determined with confidence (although the assignment of "Trochus" kotschyi to Priotrochus could be rejected). Within the Mediterranean and NE Atlantic clade, genera Phorcus and Jujubinus were recovered as reciprocally monophyletic, and the deep-sea genera Clelandella and Callumbonella were placed with high support as sister to Jujubinus. However, the genus Gibbula as currently defined was not monophyletic and constituent species were divided into three major clades and two independent lineages. Phylogenetic relationships among Phorcus, Jujubinus (plus Clelandella and Callumbonella), and the different clades of Gibbula were not fully resolved but received higher support in the phylogenetic analyses based on six genes. A first approach to resolve phylogenetic relationships within Stomatellinae was conducted showing that the diversity of the subfamily is highly underestimated at present, and that Calliotrochus is possibly a member of this subfamily. A chronogram was reconstructed using an uncorrelated relaxed lognormal molecular clock and the origin of the Mediterranean and NE Atlantic clade was dated right after the Azolla phase in the Middle Eocene about 48 million years ago whereas diversification of major clades (genera) followed the eastern closure of the Tethys Ocean in the Middle Miocene about 14 million years ago.
- Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta). [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 12
- Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265...
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
- Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome. [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 11
- The study of processes driving diversification requires a fully sampled and well resolved phylogeny. Multilocus approaches to the study of recent diversification provide a powerful means to study the...
The study of processes driving diversification requires a fully sampled and well resolved phylogeny. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (Canaries, Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
- Phylogenomic analysis of yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae). [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 11
- The phylogenetic relationships among genera of the subfamily Vespinae (yellowjackets and hornets) remain unclear. Yellowjackets and hornets constitute one of the only two lineages of highly eusocial ...
The phylogenetic relationships among genera of the subfamily Vespinae (yellowjackets and hornets) remain unclear. Yellowjackets and hornets constitute one of the only two lineages of highly eusocial wasps, and the distribution of key behavioral traits correlates closely with the current classification of the group. The potential of the Vespinae to elucidate the evolution of social life, however, remains limited due to ambiguous genus-level relationships. Here, we address the relationships among genera within the Vespinae using transcriptomic (RNA-seq) data. We sequenced the transcriptomes of six vespid wasps, including three of the four genera recognized in the Vespinae, combined our data with publicly available transcriptomes, and assembled two matrices comprising 1,507 and 3,356 putative single-copy genes. The results of our phylogenomic analyses recover Dolichovespula as more closely related to Vespa than to Vespula, therefore challenging the prevailing hypothesis of yellowjacket (Dolichovespula + Vespula) monophyly. This suggests that traits such as large colony size and high paternity arose in the genus Vespula following its early divergence from the remaining vespine genera.
- Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity. [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 5; 106:241-253
- Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Onl...
Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Only eight species of Xenosaurus, one of them with five subspecies (X. grandis), have been formally described. However, species limits within Xenosaurus have never been examined using molecular data, and no complete phylogeny of the genus has been published. Here, we used ddRADseq data from all of the described and potentially undescribed taxa of Xenosaurus to investigate species limits, and to obtain a phylogenetic hypothesis for the genus. We analyzed the data using a variety of phylogenetic models, and were able to reconstruct a well-resolved and generally well-supported phylogeny for this group. We found Xenosaurus to be composed of four major, allopatric clades concordant with geography. The first and second clades that branch off the tree are distributed on the Atlantic slopes of the Sierra Madre Oriental and are composed of X. mendozai, X. platyceps, and X. newmanorum, and X. tzacualtipantecus and an undescribed species from Puebla, respectively. The third clade is distributed from the Atlantic slopes of the Mexican Transvolcanic Belt in west-central Veracruz south to the Pacific slopes of the Sierra Madre del Sur in Guerrero and Oaxaca, and is composed of X. g. grandis, X. rectocollaris, X. phalaroanthereon, X. g. agrenon, X. penai, and four undescribed species from Oaxaca. The last clade is composed of the four taxa that are geographically closest to the Isthmus of Tehuantepec (X. g. arboreus, X. g. rackhami, X. g. sanmartinensis, and an undescribed species from Oaxaca). We also utilized a variety of molecular species delimitation approaches, including analyses with GMYC, PTP, BPP, and BFD(∗), which suggested that species diversity in Xenosaurus is at least 30% higher than currently estimated.
- Resolving incongruence: Species of hybrid origin in Columnea (Gesneriaceae). [Journal Article]
- MPMol Phylogenet Evol 2016 Oct 5; 106:228-240
- Speciation by hybridization has long been recognized among plants and includes both homoploid and allopolyploid speciation. The numbers of presumed hybrid species averages close to 11% and tends to b...
Speciation by hybridization has long been recognized among plants and includes both homoploid and allopolyploid speciation. The numbers of presumed hybrid species averages close to 11% and tends to be concentrated in a subset of angiosperm families. Recent advances in molecular methods have verified species of hybrid origin that had been presumed on the basis of morphology and have identified species that were not initially considered hybrids. Identifying species of hybrid origin is often a challenge and typically based on intermediate morphology, or discrepancies between molecular datasets. Discrepancies between data partitions may result from several factors including poor support, incomplete lineage sorting, or hybridization. A phylogenetic analysis of species in Columnea (Gesneriaceae) indicated significant incongruencies between the cpDNA and nrDNA datasets. Tests that examined whether one or both of the datasets had the phylogenetic signal to reject the topology of the alternate dataset (Shimodaira and Hasegawa [SH] and approximately unbiased [AU] tests) indicated significant differences between the topologies. Splitstree analyses also showed that there was support for the placement of the discrepant taxa in both datasets and that the combined data placed the putative hybrid species in an intermediate position between the two datasets. The genealogical sorting index (GSI) implied that coalescence in nrDNA had occurred in all species where more than a single individual had been sampled, but the GSI value was lower for the cpDNA of most of the putative hybrids, implying that these regions have not yet coalesced in these lineages despite being haploid. The JML test that evaluates simulated species pairwise distances against observed distances also implies that observed nrDNA data generate shorter distances than simulated data, implying hybridization. It is most likely that C. gigantifolia, C. rubriacuta, and C. sp. nov. represent a lineage from a hybrid ancestor, but C. moorei may be a more recent hybrid and may still be undergoing hybridization with sympatric species.
- Multiple colonisations of the Lake Malawi catchment by the genus Opsaridium (Teleostei: Cyprinidae). [Journal Article]
- MPMol Phylogenet Evol 2016 Sep 30
- It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern ha...
It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern has been established for many lineages, most notably cichlids, there are opportunities to further investigate the concept using phylogenies of congeneric endemic species within ancient lake catchments. The Lake Malawi catchment contains three river-spawning cyprinids of the genus Opsaridium, two of which are endemic. These species differ in body size, migratory behaviour and habitat use, but it has never previously been tested if these represent a monophyletic radiation, or have instead colonised the lake independently. We placed these species in a broader phylogeny of Opsaridium and the related genus Raiamas, including all known species from the river systems surrounding Lake Malawi. Our results suggest that each of the species has independently colonised the lake catchment, with all three taxa having well-defined sister taxa outside of the lake, and all sharing a common ancestor ∼14.9 million years ago, before the Lake Malawi basin started to form ∼8.6 million years ago. Additionally, the results strongly support previous observations that Opsaridium is not a monophyletic group, but instead contains Raiamas from the Congo drainage. Together these results are supportive of the concept that river fish faunas within African catchments are primarily assembled through a process of accumulation from independent origins, rather than within-catchment speciation and adaptive radiation. In light of these results we also suggest there is scope for a re-evaluation of systematics of both Opsaridium and Raiamas.
New Search Next
- Gene duplication and concerted evolution of mitochondrial DNA in crane species. [Journal Article]
- MPMol Phylogenet Evol 2016 Sep 28; 106:158-163
- The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA d...
The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication in cranes and investigate the molecular evolutionary features of crane mtDNA, we analyzed the gene organization and the molecular phylogeny of mtDNA from 13 crane species. We found that the mtDNA in 13 crane species shared a tandem duplicated region, which consists of duplicated sequence sets including cytochrome b (Cytb), NADH6, control region (CR) and three genes of tRNA. The gene order in the duplicated region was identical among all the 13 crane species, and the nucleotide sequences found within each individual showed high similarities. In addition, phylogenetic trees based on homologous sequences of CR and Cytb indicated the possibility of concerted evolution among the duplicated genes. The results suggested that the duplication event occurred in the common ancestor of crane species or some older ancestors.