Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes)

The evolutionary affinities within and among many groups of nine-primaried oscines remain unresolved. One such group is Sporophila, a large genus of New World tanager-finches. Our study focused particularly on clarifying the relationship between this genus and a closely related one, Oryzoborus, and on examining the phylogenetic affinities of the "capuchinos," a group of 11 Sporophila species that share a similar male plumage coloration pattern. Our phylogenetic analyses, based on 498 bp of mitochondrial DNA sequence, indicated that: (1) Oryzoborus is embedded within a well-supported clade containing all Sporophila species, which strongly suggests that both genera should be merged, (2) the species of capuchinos comprise a monophyletic group, implying that the plumage patterns common to all probably arose only once, and (3) the capuchinos clade is comprised of two sub-clades, one including two species that are distributed in northern South America and the other one containing eight species that are present south of the Amazon River. Mean sequence divergence among the southern capuchinos species was extremely low, suggesting a rapid radiation within the last half-million years that may be related to the high level of sexual selection present in the genus and might have been promoted by marine ingressions and egressions that occurred in some southern coastal regions of South America in the Late Pleistocene.     

Molecular phylogenetics of the clover genus (Trifolium--Leguminosae)

Trifolium, the clover genus, is one of the largest genera of the legume family. We conducted parsimony and Bayesian phylogenetic analyses based on nuclear ribosomal DNA internal transcribed spacer and chloroplast trnL intron sequences obtained from 218 of the ca. 255 species of Trifolium, representatives from 11 genera of the vicioid clade, and an outgroup Lotus. We confirm the monophyly of Trifolium, and propose a new infrageneric classification of the genus based on the phylogenetic results. Incongruence between the nrDNA and cpDNA results suggests five to six cases of apparent hybrid speciation, and identifies the putative progenitors of the allopolyploids T. dubium, a widespread weed, and T. repens, the most commonly cultivated clover species. Character state reconstructions confirm 2n=16 as the ancestral chromosome number in Trifolium, and infer a minimum of 19 instances of aneuploidy and 22 of polyploidy in the genus. The ancestral life history is hypothesized to be annual in subgenus Chronosemium and equivocal in subgenus Trifolium. Transitions between the annual and perennial habit are common. Our results are consistent with a Mediterranean origin of the genus, probably in the Early Miocene. A single origin of all North and South American species is hypothesized, while the species of sub-Saharan Africa may originate from three separate dispersal events.     

Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae)

Ainscough, B.J., Breinholt, J.W., Robison, H.W. & Crandall, K.A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). —Zoologica Scripta, 42, 306–316. The crayfish genus Fallicambarus contains 19 species of primary burrowing freshwater crayfish divided into two distinct subgenera. We test current hypotheses of the phylogenetic relationships among species within the genus as well as the monophyly of the genus. Our study samples all 19 species for five gene regions (both nuclear and mitochondrial) to estimate a robust phylogenetic hypothesis for the genus. We show that the genus is not a monophyletic group. The subgenus Creaserinus does fall out as a monophyletic group, but distinct from the subgenus Fallicambarus. The subgenus Fallicambarus appears to be monophyletic with the exception of the species Procambarus (Tenuicambarus) tenuis, which falls in the midst of this subgenus suggesting that it might be better classified as a Fallicambarus species. We also show that the species Fallicambarus fodiens is a species complex with distinct evolutionary lineages that are regionalized to different geographic areas.     

Molecular phylogenetics and evolution of the endemic Hawaiian genus Adenophorus (Grammitidaceae)

Recent studies of the phylogeny of several groups of native Hawaiian vascular plants have led to significant insights into the origin and evolution of important elements of the Hawaiian flora. No groups of Hawaiian pteridophytes have been subjected previously to rigorous phylogenetic analysis. We conducted a molecular phylogenetic analysis of the endemic Hawaiian fern genus Adenophorus employing DNA sequence variation from three cpDNA fragments: rbcL, atpbeta, and the trnL-trnF intergenic spacer (IGS). In the phylogenetic analyses we employed maximum parsimony and Bayesian inference. Bayesian phylogenetic inference often provided stronger support for hypothetical relationships than did nonparametric bootstrap analyses. Although phylogenetic analyses of individual DNA fragments resulted in different patterns of relationships among species and varying levels of support for various clades, a combined analysis of all three sets of sequences produced one, strongly supported phylogenetic hypothesis. The primary features of that hypothesis are: (1) Adenophorus is monophyletic; (2) subgenus Oligadenus is paraphyletic; (3) the enigmatic endemic Hawaiian species Grammitis tenella is strongly supported as the sister taxon to Adenophorus; (4) highly divided leaf blades are evolutionarily derived in the group and simple leaves are ancestral; and, (5) the biogeographical origin of the common ancestor of the Adenophorus-G. tenella clade remains unresolved, although a neotropical origin seems most likely.     

Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.     

Review of the Capitellidae (Annelida, Polychaeta) from the Eastern Tropical Pacific region, with notes on selected species

The main objective of this work is to contribute to the taxonomic knowledge of the species of Capitellidae reported for the Eastern Tropical Pacific. This catalogue includes the original name of each species, new names, synonymies, type localities, the museum or institution where the type material is deposited, revision of the material reported for the region by different authors, new examined material, previous reports from other regions of the world, and comments on systematics and distributions. The catalogue lists 43 species in 19 genera. Of these, 6 species were erroneously recorded for the region (Decamastus gracilis Hartman, 1963; Decamastus nudus Thomassin, 1970; Mastobranchus variabilis Edwing, 1984; Notomastus aberans Day, 1957; Notomastus americanus Day, 1973; Notomastus latericeus Sars, 1851) and 5 species are found here to be questionable records for the Eastern Tropical Pacific (Capitella capitata (Fabricius, 1780); Dasybranchus glabrus Moore, 1909; Decamastus lumbricoides Grube, 1878; Notomastus lineatus Claparède, 1870 and Notomastus tenuis Moore, 1909).     

Molecular phylogenetics and evolutionary analysis of body shape in the genus Cyrtonus (Coleoptera, Chrysomelidae)

The leaf beetle genus Cyrtonus Latreille, 1829 (Chrysomelidae, Chrysomelinae) is a species-rich genus subendemic to the Iberian Peninsula, with only a few species in the neighbouring France and Morocco. All the species are wingless and preferentially inhabiting mountainous areas. The taxonomic knowledge of this group is extremely poor and its systematics almost inexistent. Here, we analyse and characterize with a morphometric analysis one promising systematic trait, the adult body profile, distinguishing between elongated and rounded shapes. Although the monophyly of the genus is not contentious, we test for it using mitochondrial rrnl sequences and the chrysomeline homologous sequences available in GenBank. In addition, four genetic markers, two mitochondrial and two nuclear are used to produce a phylogenetic hypothesis for half the species within the genus and to analyse the evolution of shape, summarized as two continuous variables, length and width, and their ratio. These traits covary significantly with the phylogeny, showing a strong phylogenetic association: elongated species appear to constitute a clade within a paraphyletic assemblage of rounded species. In addition, the mitochondrial DNA tree is used to test for constant rate of evolution in this marker and is calibrated using both biogeographical evidence and the standard insect mitochondrial average substitution rate. This molecular clock hypothesis is used to date the age of speciation events on the phylogeny, reconstructing the origin of the genus in the Middle Miocene, with a relatively constant speciation rate until the end of the Pliocene and an apparent increase in this rate in the Pleistocene, possibly associated with the effect of dramatic climatic changes in this period. Finally, the high systematic value of shape profile in Cyrtonus is discussed, arguing the absence of evidence relating it to adaptation.     

Checklist of the ants (Hymenoptera,Formicidae) of the Solomon Islands and a new survey of Makira Island

The intent of this paper is to facilitate future research of the Solomon Islands ant fauna by providing the first comprehensively researched species inventory in over 75 years. The species list presented here includes the names of all ant species recorded from the islands that are available in the literature together with specimen records from several museum collections and new records from our 2008 Makira field expedition. All the names of described species presented are valid in accordance with the most recent Formicidae classification. In total, the checklist is composed of 237 species and subspecies (including 30 morphospecies) in 59 genera representing nine subfamilies. We report that the recent field expedition added 67 new species records to Makira and 28 new species records to the Solomon Islands. Our research recovered species occurrence records for 32 individual islands and five island groups. The five islands with the highest number of recorded species are: Makira (142 spp.), Guadalcanal (107 spp.), Malaita (70 spp.), Santa Isabel (68 spp.), and Rennell (66 spp.). Based on our results, we discuss the taxonomic composition of the archipelago’s ant fauna, which islands are most in need of additional sampling, and the importance of establishing biodiversity baselines before environmental threats such as the invasive ant Wasmannia auropunctata cause irrevocable harm to the native biodiversity.     

Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca)

Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five segments), 12S rRNA, cytochrome c oxidase subunit I, histone H3 and elongation factor 1alpha. The alignment has a combined length of 3995 base positions for 36 taxa, comprising 29 Caenogastropoda representing all of its major lineages and seven outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. The results generally support monophyly of Caenogastropoda and Hypsogastropoda (Caenogastropoda excepting Architaenioglossa, Cerithioidea and Campanilioidea). Within Hypsogastropoda, maximum likelihood and Bayesian analyses identified a near basal clade of nine or 10 families lacking an anterior inhalant siphon, and Cerithiopsidae s.l. (representing Triphoroidea), where the siphon is probably derived independently from other Hypsogastropoda. The asiphonate family Eatoniellidae was usually included in the clade but was removed in one Bayesian analysis. Of the two other studied families lacking a siphon, the limpet-shaped Calyptraeidae was associated with this group in some analyses, but the tent-shaped Xenophoridae was generally associated with the siphonate Strombidae. The other studied hypsogastropods with an anterior inhalant siphon include nine families, six of which are Neogastropoda, the only traditional caenogastropod group above the superfamily-level with strong morphological support. The hypotheses that Neogastropoda are monophyletic and that the group occupies a derived position within Hypsogastropoda are both contradicted, but weakly, by the molecular analyses. Despite the addition of large amounts of new molecular data, many caenogastropod lineages remain poorly resolved or unresolved in the present analyses, possibly due to a rapid radiation of the Hypsogastropoda following the Permian-Triassic extinction during the early Mesozoic.     

Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizations

Abstract A molecular phylogenetic study of Bystropogon L'Her. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution.     

Molecular phylogenetics of the sexually deceptive orchid genus Ophrys (Orchidaceae) based on nuclear and chloroplast DNA sequences.

We present a phylogenetic analysis of the major lineages of the sexually deceptive orchid genus Ophrys based on nuclear ribosomal (nr) DNA (internal transcribed spacer region) and noncoding chloroplast (cp) DNA (trnL-trnF region) sequences. Sequence divergence within and among major Ophrys lineages was low for both nrDNA and cpDNA sequences. Separate analyses resulted in similar but poorly resolved trees. An incongruence length difference test revealed that nrDNA and cpDNA data sets were not incongruent. A combined analysis resulted in a better-resolved phylogenetic hypothesis of relationships among the major Ophrys lineages. Our data strongly support a division of Ophrys into two groups. These groups do not correspond to the earlier proposed sections Euophrys and Pseudophrys and are thus in conflict with traditional classifications. Our results support a well-resolved monophyletic group that contains the geographically widespread O. bombyliflora, O. speculum, O. tenthredinifera, and the O. fusca-lutea lineage. Relationships in the other group are poorly resolved. Based on our observations that taxa with identical sequences at presumably rapidly evolving loci clearly differ in floral morphology, we hypothesize that the diversity in the genus Ophrys is the result of a recent radiation in this orchid lineage.     

Narrow endemics on coastal plains: Miocene divergence of the critically endangered genus Avellara (Compositae)

Critically endangered species representing ancient, evolutionarily isolated lineages must be given priority when allocating resources for conservation projects. Sound phylogenetic analyses and divergence time estimations are required to detect them, and studies on their population genetics, ecological requirements and breeding system are needed to understand their evolutionary history and to design efficient conservation strategies. Here we present the paradigmatic case of Avellara, a critically endangered monotypic genus of Compositae inhabiting a few swamps in the west–southwest Iberian coastal plains. Our phylogenetic and dating analyses based on nuclear (ITS) and plastid (matK) DNA sequences support a Miocene (>8.6 Ma) divergence between Avellara and closely related genera, resulting in marked morphological and ecological differentiation. We found alarmingly low levels of genetic diversity, based on AFLPs and plastid DNA sequences, and confirmed the prevalence of clonal reproduction. Species distribution modelling suggested a large macroclimatically suitable area for Avellara in the western Iberian Peninsula, but its apparently narrow microecological requirements restrict its distribution to peatlands with low‐mineralised waters. Although five populations have been recorded from Spain and Portugal in the past, its current distribution may be reduced to only one population, recurrently found in the last decade but threatened by herbivory and habitat degradation. All this confirms the consideration of Avellara as a threatened species with high phylogenetic singularity, and makes it a flagship species for plant conservation in both Spain and Portugal that should be given priority in the design of in situ and ex situ conservation programmes.     

Introgression and selection shaped the evolutionary history of sympatric sister‐species of coral reef fishes (genus: Haemulon)

Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister‐species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site‐associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister‐species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174–0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.     

Patterns of natural selection on morphology of male and female collared flycatchers (Ficedula albicollis)

Natural selection may act in different directions among years, life stages, or classes of individuals. Fluctuating selection of this kind is potentially an important mechanism by which additive genetic variation for quantitative traits is maintained, and can prevent populations reaching local adaptive peaks. We analysed natural selection acting on three morphological traits of male and female collared flycatchers via both fecundity and survival, using 15 years' data from a large isolated population on Godand, Sweden. We particularly investigated variation in the direction and magnitude of selection acting: (1) among years over the study period; (2) on different life stages and (3) the consistency of observed patterns of selection with sexual size dimorphism (SSD) in this population. We found little evidence of natural selection on these traits over the study period. Evidence for directional, stabilizing and disruptive selection was found for some year-trait combinations, but these patterns were inconsistent with respect to both the magnitude and form of selection found. Consequently, our results, based on the detailed analysis of natural selection in a large wild population over a period of 15 years, provide evidence for the common assumption that forces of selection acting on quantitative traits are generally weak. They are also consistent with the suggestion that environmental stability is an important determinant of the degree to which organisms fit their environment.     

Molecular phylogenetics provides a novel hypothesis of chromosome evolution in Neotropical fishes of the genus Potamorhina (Teleostei,Curimatidae)

Potamorhina includes the largest species in the Neotropical fish family Curimatidae. They perform long-distance migrations in large schools and represent relative importance for regional fisheries in South American lowlands. A morphology-based phylogenetic study recognized five species and proposed interspecific phylogenetic relationships mostly based on osteology, squamation, and morphology of the gasbladder. Subsequent cytogenetic studies revealed extreme variability in diploid numbers and other cytomolecular structures and hypothesized multiple events of chromosome rearrangements with centric fissions followed by reversed fusions. However, neither the taxonomic revision and phylogeny nor the cytogenetic hypothesis of chromosome evolution in Potamorhina was tested using molecular phylogenetic approaches. Here, we use mitochondrial and nuclear DNA sequences to delimit species of Potamorhina with an extensive sampling across the Amazon basin and use phylogenetic methods to test prior hypothesis of multiple events of chromosome rearrangements during the evolution of the genus. Phylogenetic and species delimitation methods clearly support the presence of five species but reveal novel interspecific relationships allowing a reinterpretation of the morphological characters relative to the number of vertebrae, caudal peduncle pigmentation, and modifications in the gasbladder chambers. With the new phylogenetic arrangement, we propose a novel hypothesis of occurrence of a single chromosome fission in the lineage of P. latior followed by an extraordinary event that involved more than 20 chromosome-pair fissions during the evolution of the ancestor of P. altamazonica and P. squamoralevis. This novel hypothesis represents a simpler and more conceivable explanation for the achievement of these elevated chromosome numbers during the evolution of Potamorhina.     

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla)

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.