Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI “barcoding” primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. “V” stratified by depth, and “A” differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.     

New insights into the molecular phylogeny and taxonomy of mormyrids (Osteoglossiformes,Actinopterygii) in northern East Africa

Based on morphological data and analysis of mitochondrial cytochrome b gene and nuclear (S7 intron 1) DNA sequences, the phylogenetic relationships of all Pollimyrus species known from the Omo‐Turkana enclosed basin and Nile system below the Murchison Falls were solved. A mormyrid “Pollimyrus” petherici is distantly related to all other studied Pollimyrus species and clusters together with Cyphomyrus species forming with the later a monophyletic group. Moreover, the West African (but not the Congo River) populations of Cyphomyrus psittacus, the type species of the genus, seem to be conspecific to C. petherici. That is, the range of the genus Cyphomyrus is extended toward the Nile and Omo‐Turkana basins. This genus belongs to the large clade widely distributed in sub‐Saharian Africa and characterized by the presence of a chin appendage. Significance of this character for mormyrid phylogeny is discussed. Two distinct lineages of Pollimyrus occurring sympatrically in the White Nile tributaries and previously reported as the light and dark forms of Pollimyrus isidori together with five other congeneric species studied form a monophyletic group. The light form apparently represents P. isidori distributed in the Nile system downstream of the Murchison Falls and West Africa; the dark‐colored form (designated as Pollimyrus “D”) represents a distinct phylogenetic lineage inhabiting both the Omo‐Turkana and the White Nile basin. Morphological and ecological data suggest that this form may be conspecific to East African Pollimyrus nigricans or most probably represents a new species.     

MITOCHONDRIAL PHYLOGEOGRAPHY OF THE LAND SNAIL ALBINARIA IN CRETE: LONG-TERM GEOLOGICAL AND SHORT-TERM VICARIANCE EFFECTS

The land snail genus Albinaria exhibits an extreme degree of morphological differentiation in Greece, especially in the island of Crete. Twenty-six representatives of 17 nominal species and a suspected hybrid were examined by sequence analysis of a PCR-amplified mitochondrial DNA fragment of the large rRNA subunit gene. Maximum parsimony and neighbor-joining phylogenetic analyses demonstrate a complex pattern of speciation and differentiation and suggest that Albinaria species from Crete belong to at least three distinct monophyletic groups, which, however, are not monophyletic with reference to the genus as a whole. There is considerable variation of genetic distance within and among “species” and groups. The revealed phylogenetic relations do not correlate well with current taxonomy, but exhibit biogeographical coherence. Certain small- and large-scale vicariance events can be traced, although dispersal and parapatric speciation may also be present. Our analysis suggests that there was an early and rapid differentiation of Albinaria groups across the whole of the range followed by local speciation events within confined geographical areas.     

The molecular phylogeny of the sea star Echinaster (Asteroidea: Echinasteridae) provides insights for genus taxonomy

In this study, we used sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and 16S rRNA, and one nuclear gene, 28S rRNA, to test the monophyly of the sea star genus Echinaster, and understand the phylogenetic relationships among species and subgenera within this genus. Phylogenetic analyses based on Bayesian inference and maximum likelihood methods revealed three clades with high values of genetic divergence among them (K2P distances for COI over 23%). One of the clades grouped all Echinaster (Othilia) species, and the other two clades included Echinaster (non‐Othilia) species and Henricia species, respectively. Although the relationships among Henricia, Othilia, and Echinaster could not be completely clarified, the Othilia clade was a well‐supported group with shared diagnostic morphological characters. Moreover, the approximately unbiased test applied to the phylogenetic reconstruction rejected the hypothesis of the genus Echinaster as a monophyletic group. According to these results, we suggest the revalidation of Othilia as a genus instead of a subgenus within Echinaster. Our study clarifies important points about the phylogenetic relationships among species of Echinaster. Other important systematic questions about the taxonomic classification of Echinaster and Henricia still remain open, but this molecular study provides bases for future research on the topic.     

Phylogeny and phylogeography of the Mediterranean species of the parasitic ant genus <Emphasis Type="Italic">Chalepoxenus</Emphasis> and its <Emphasis Type="Italic">Temnothorax</Emphasis> hosts

We analysed the phylogenetic and phylogeographic relationships of four Mediterranean species of the rare slave-making ant genus Chalepoxenus and eleven of its about 20 Temnothorax host species by sequencing the mitochondrial Cytochrome Oxidase I and II genes. Neighbour-Joining, Maximum Parsimony and Bayesian analyses based on 1320 bp indicate that the genus Chalepoxenus constitutes a monophylum. In all three analyses, C. kutteri from Southwest Europe and the workerless, “degenerate slavemaker” C. brunneus from North Africa form a monophyletic group. C. muellerianus and C. tauricus, distributed in Southern Europe and Ukraine, respectively, form a monophylum in the Neighbour-Joining and the Maximum Parsimony analysis. In our limited set of only 11 of several hundred Temnothorax species, T. flavicornis forms the sister group of Chalepoxenus. Our study further indicates paraphyly of the genus Temnothorax with respect to Chalepoxenus. Moreover, the results suggest that speciation in this slave-making genus is possibly caused by the formation of host races as different Chalepoxenus species use different hosts, and some samples seem to cluster by host species rather than by geographical distance. Received 5 September 2006; revised 17 March 2007; accepted 23 March 2007.     

Species‐specific mitochondrial gene rearrangements in biting midges and vector species identification

Abstract Partial mitochondrial gene sequences of 16 Culicoides species were determined to elucidate phylogenetic relations among species and to develop a molecular identification method for important virus vector species. In addition, the analysis found mitochondrial gene rearrangement in several species. Sequences of the mitochondrial genome region, cox1–trnL2–cox2 (1940–3785 bp) of 16 Culicoides and additional sequences were determined in some species, including whole mitochondrial genome sequences of Culicoides arakawae. Nine species showed common organization in this region, with three genes cox1–trnL2–cox2 and a small or no intergenic region (0–30 bp) between them. The other seven species showed translocation of tRNA and protein‐coding genes and/or insertion of AT‐rich non‐coding sequences (65–1846 bp) between the genes. The varied gene rearrangements among species within a genus is very rare for mitochondrial genome organization. Phylogenetic analyses based on the sequences of cox1+cox2 suggest a few clades among Japanese Culicoides species. No relationships between phylogenetic closeness and mitochondrial gene rearrangements were observed. Sequence data were used to establish a polymerase chain reaction tool to distinguish three important vector species from other Culicoides species, for which classification during larval stages is not advanced and identification is difficult.     

Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data

We studied the phylogenetic history of opossum shrimps of the genus Mysis Latreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long‐debated question of the origin of the non‐marine (continental) taxa in the genus, i.e., “glacial relicts” in circumpolar postglacial lakes and “arctic immigrants” in the Caspian Sea. A simultaneous analysis of the data sets gave a single tree supporting monophyly of all continental species, as well as monophyly of the taxa from circumpolar lakes and from the Caspian Sea. A clade of three circumarctic marine species was sister group to the continental taxa, whereas Atlantic species had more distant relationships to the others. Small molecular differentiation among the morphologically diverse endemic species from the Caspian Sea suggested their recent speciation, while the phenotypically more uniform “glacial relict” species from circumpolar lakes (Mysis relicta group) showed deep molecular divergences. For the length‐variable ITS2 region both direct optimization and a priori alignment procedures gave similar topologies, although the former approach provided a better overall resolution. In terms of partitioned Bremer support (PBS), mitochondrial protein coding genes provided the largest contribution (83%) to the total tree resolution. This estimate however, appears to be partly spurious, due to the concerted inheritance of mitochondrial characters and probable cases of introgression or ancestral polymorphism. © The Willi Hennig Society 2005.     

Molecular phylogeny and divergence time of the water penny genus Eubrianax (Coleoptera: Psephenidae) in Japan

The phylogenetic relationships among the Japanese members of the genus Eubrianax (Coleoptera: Psephenidae) were examined using the mitochondrial cytochrome oxidase subunit I (COI) gene and nuclear 28S rRNA gene sequences. Based on the molecular phylogeny as well as morphological features, the species status of Eubrianax brunneicornis Nakane, 1952 was proposed. The phylogenetic analyses recovered monophyly of the previously proposed pellucidus species group with four Japanese species, whereas a single Japanese species of the granicollis group was included in the lineage of the ramicornis group with five Japanese species. The divergence times of the species were estimated by dating the phylogenetic tree against the fossil record and a molecular clock based on the COI gene. The divergence of the Japanese species was inferred to have occurred during the Pliocene epoch.     

A multilocus phylogeny of the fish genus Poeciliopsis: Solving taxonomic uncertainties and preliminary evidence of reticulation

The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, that is, concatenated (also known as super‐matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans‐Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north–south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US‐Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by “breakdown” of an asexual hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome‐wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.     

An updated classification for the hyper-diverse genus Corydalis (Papaveraceae: Fumarioideae) based on phylogenomic and morphological evidence

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent “series”. Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five “series”, 25 sections and one “series” are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.     

MOLECULAR PHYLOGENY AND REVISION OF THE GENUS NETRIUM (ZYGNEMATOPHYCEAE,STREPTOPHYTA): NUCLEOTAENIUM GEN. NOV.1

Nuclear‐encoded SSU rDNA, chloroplast LSU rDNA, and rbcL genes were sequenced from 53 strains of conjugating green algae (Zygnematophyceae, Streptophyta) and used to analyze phylogenetic relationships in the traditional order Zygnematales. Analyses of a concatenated data set (5,220 nt) established 12 well‐supported clades in the order; seven of these constituted a superclade, termed “Zygnemataceae.” Together with genera (Zygnema, Mougeotia) traditionally placed in the family Zygnemataceae, the “Zygnemataceae” also included representatives of the genera Cylindrocystis and Mesotaenium, traditionally placed in the family Mesotaeniaceae. A synapomorphic amino acid replacement (codon 192, cysteine replaced by valine) in the LSU of RUBISCO characterized this superclade. The traditional genera Netrium, Cylindrocystis, and Mesotaenium were shown to be para‐ or polyphyletic, highlighting the inadequacy of phenotypic traits used to define these genera. Species of the traditional genus Netrium were resolved as three well‐supported clades each distinct in the number of chloroplasts per cell, their surface morphology (structure and arrangement of lamellae) and the position of the nucleus or nuclear behavior during cell division. Based on molecular phylogenetic analyses and synapomorphic phenotypic traits, the genus Netrium has been revised, and a new genus, Nucleotaenium gen. nov., was established. The genus Planotaenium, also formerly a part of Netrium, was identified as the sister group of the derived Roya/Desmidiales clade and thus occupies a key position in the evolutionary radiation leading to the most species‐rich group of streptophyte green algae.     

Mitogenomes provide insights into the phylogeny and evolution of brittle stars (Echinodermata,Ophiuroidea)

Ophiuroidea is the most speciose of all classes of Echinoderma. It is an important component in benthic ecosystems, occurring in almost all ecological niches of modern seas. To date, the phylogeny and complete evolutionary history of the ophiuroids have not yet been fully resolved. In this study, we sequenced the complete mitochondrial genomes (mitogenomes) of Ophiothrix (Ophiothrix) exigua and two deep-sea species Histampica sp. CS049 and Ophioplinthaca sp. M5261. These two deep-sea ophiuroids displayed reversed strand-compositional bias and rearranged gene orders. Thirteen distinct patterns of mitochondrial gene order among ophiuroid mitogenomes were detected, with two gene order newly found in Ophiuroidea. Our data supported the gene order found in all sampled Ophiuridae as the most likely ancestral order of all Ophiuroidea. To improve phylogenetic accuracy based on nucleotide differences, two different criteria were used for the analyses: (i) nucleotide sequence from all codon positions (PCG₁₂₃); (ii) the NTE method (“Neutral Transitions Excluded”) for ameliorating the misleading effects of a reverse strand bias in the data. The two methods confirmed the polyphyly of the orders Ophiacanthida and Amphilepidia. At family and genus level, Ophiuridae, Ophionotus and Ophioplinthus were not monophyletic. The most notable exception was that the NTE phylogeny showed low variation of branch length. NTE dataset generated younger age for most lower-level nodes than that from PCG123 dataset. All analyses suggested that the ophiuroids radiation occurred around the Permian–Triassic mass extinction event, and the divergence time of the deep-sea lineages was during the Cretaceous.     

THE INTERFACE BETWEEN PHYLOGENETICS AND POPULATION GENETICS: INVESTIGATING GENE TREES,SPECIES TREES,AND POPULATION DYNAMICS IN THE PHYLLOPHAGA FRATERNA SPECIES GROUP

This study uses traditional and contemporary phylogenetic and population genetic analyses to assess the causes of discordance (i.e., lineage sorting and introgression) among mitochondrial and nuclear gene trees for a clade of eastern North American scarab beetles (fraterna species group, genus Phyllophaga). I estimated gene trees using individual and combined analysis of one mitochondrial and two nuclear loci in MrBayes , and inferred a species tree using a hierarchical coalescent approach based on all loci in the program Best . Because hybridization violates the assumptions of Best , I tested for introgression by comparing species monophyly between the mitochondrial and nuclear gene trees based on the prediction that cytoplasmic genomes introgress more readily than nuclear genomes. Haplotype exclusivity was identified using Bayesian tests of monophyly and the genealogical sorting index. I used the results of the phylogenetic analyses and monophyly tests to develop an explicit hypothesis of introgression that could be tested in the program IMa. Results from these analyses provided evidence for introgression across clades within the fraterna group. The tiered analytical approach used in this study demonstrated how the use of multiple methods can identify when assumptions are violated and methods are prone to yield misleading results.     

Spirometra species from Asia: Genetic diversity and taxonomic challenges

Despite considerable controversy concerning the taxonomy of species within the genus Spirometra, human sparganosis and spirometrosis mainly in Asia and Europe has long been confidently ascribed to Spirometra erinaceieuropaei. Recently, the mitochondrial genomes of purported “S. erinaceieuropaei”, “Spirometra decipiens” and “Spirometra ranarum” from Asia have been determined. However, it has been pointed out that the morphological criteria used for identifying these species are unsuitable and thus these identifications are questionable. In the present study, therefore, Spirometra samples from Asia were re-examined based on mitochondrial cytochrome c oxidase subunit 1 gene sequences and the identification of these species was discussed. Haplotype network and phylogenetic analyses revealed that: i) two distinct Spirometra species, Type I and Type II, are present in Asia and neither of which is close to likely European “S. erinaceieuropaei”; ii) Type I is genetically diverse and widely distributed, however Type II is known so far from Japan and Korea; iii) “S. decipiens” and “S. ranarum” reported from Asia are conspecific with Type I; iv) Type I is probably conspecific with Spirometra mansoni, and Type II may represent an undescribed species.     

Sequence-based species delineation and molecular phylogenetics of the transitional Nearctic–Neotropical grasshopper genus Taeniopoda (Orthoptera,Romaleidae)

Taeniopoda is a genus of grasshoppers currently represented by 12 species distributed from southern USA to Panama, with most of them occurring along the transitional Nearctic–Neotropical region in central and southern Mexico. Despite being a small group of conspicuous, colourful species, the systematics of Taeniopoda has been largely neglected, including its phylogenetic affinity with the morphologically similar, monotypic genus Romalea. Here, we assessed the species limits in 11 of the species of Teniopoda based on two mitochondrial (mt) markers (COI, cyt b). Phylogenetic relationships were reconstructed adding two nuclear gene markers (28S, H3). A relaxed molecular clock analysis was performed based on the mt markers. We detected nuclear mt paralogues (numts) and the probable introgression of T. tamaulipensis mtDNA in specimens of T. eques from central Mexico. Between six and 14 species of Taeniopoda were delimited by the sequence-based approaches performed (COI divergence with thresholds of 1 and 2%; General Mixed Yule-Coalescent (GMYC) model). The GMYC and 1% threshold analyses with COI were more congruent with the currently recognized morphology-based taxonomy with 10 and 11 putative species, respectively. Four of these species were regarded as ‘stable’, since they were supported by at least one of the molecular analyses and by diagnostic morphological features. The species-based phylogeny recovered Taeniopoda as paraphyletic with respect to the monotypic genus Romalea. Three morphologically and geographically congruent major clades were recovered, two with species having a considerably elevated pronotal crest and one with its members having it less elevated. The origin and subsequent diversification of Taeniopoda were estimated to occur from the mid and late Miocene to Pliocene, respectively. The current species diversity in Taeniopoda was estimated to occur during the Pleistocene, which was probably influenced by the climatic oscillations that occurred during this period and the uplift of mountain ranges in Central America.     

The blood alga: phylogeny of Haematococcus (Chlorophyceae) inferred from ribosomal RNA gene sequence data

The status of the green algal genera Haematococcus and Stephanosphaera has been a source of debate among algal systematists. A phylogenetic alliance between Haematococcus (sensu lato) and the colonial Stephanosphaera was affirmed by earlier molecular phylogenetic investigations. Although the data suggested that the genus Haematococcus may not be a monophyletic group, taxon sampling limited the scope of any potential taxonomic revision. Results from new molecular phylogenetic analyses of data from the 18S and 26S rRNA genes support the establishment of a separate genus, Balticola, as originally proposed by Droop in 1956. Haematococcus remains as a valid genus, with H. pluvialis as its only member. The monotypic status of H. pluvialis is supported both by molecular phylogenetic analyses of the ribosomal RNA genes and assessments of molecular evolution in the ITS2 sequences of H. pluvialis strains. The near-complete absence of compensatory base changes in a sequence-structure analysis of the highly variable ITS2 gene from more than 40 geographically diverse isolates of H. pluvialis corroborates the unity of the species inferred from molecular phylogenetic analyses of 18S and 26S rRNA gene sequence data.     

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well‐supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time‐frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.