Waves of genomic hitchhikers shed light on the evolution of gamebirds (Aves: Galliformes)

Background  

The phylogenetic tree of Galliformes (gamebirds, including megapodes, currassows, guinea fowl, New and Old World quails, chicken, pheasants, grouse, and turkeys) has been considerably remodeled over the last decades as new data and analytical methods became available. Analyzing presence/absence patterns of retroposed elements avoids the problems of homoplastic characters inherent in other methodologies. In gamebirds, chicken repeats 1 (CR1) are the most prevalent retroposed elements, but little is known about the activity of their various subtypes over time. Ascertaining the fixation patterns of CR1 elements would help unravel the phylogeny of gamebirds and other poorly resolved avian clades.     

Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae)

? Premise of the study: The mint family (Lamiaceae) is the sixth largest family of flowering plants, with the tribe Mentheae containing about a third of the species. We present a detailed perspective on the evolution of the tribe Mentheae based on a phylogenetic analysis of cpDNA and nrDNA that is the most comprehensive to date, a biogeographic set of analyses using a fossil-calibrated chronogram, and an examination of staminal evolution. ? Methods: Data from four cpDNA and two nrDNA markers representing all extant genera within the tribe Mentheae were analyzed using the programs BEAST, Lagrange, S-DIVA, and BayesTraits. BEAST was used to simultaneously estimate phylogeny and divergence times, Lagrange and S-DIVA were used for biogeographical reconstruction, and BayesTraits was used to infer staminal evolution within the tribe. ? Key results: Currently accepted subtribal delimitations are shown to be invalid and are updated. The Mentheae and all five of its subtribes have a Mediterranean origin and have dispersed to the New World multiple times. The vast majority of New World species of subtribe Menthinae are the product of a single dispersal event in the mid-late Miocene. At least four transitions from four stamens to two stamens have occurred within Mentheae, once in the subtribe Salviinae, once in the subtribe Lycopinae, and at least twice in the subtribe Menthinae. ? Conclusions: Worldwide cooling trends probably played a large role in the diversification and present day distribution of the tribe Mentheae. Additional work is needed to ascertain relationships within some Mentheae genera, especially in the subtribe Menthinae.     

Increased taxon and character sampling reveals novel intergeneric relationships in the Cracidae (Aves: Galliformes)

The Cracidae is one of the most endangered bird families in the World. Several studies have been published recently on the evolution and conservation of cracids. Phylogenetic analyses using a fragment of 661 bp of the mitochondrial cytochrome b gene for 39 different species of cracids corroborated most relationships found in previous studies. The present work attempts to refine the former phylogenetic hypothesis by increasing taxon sampling and combining molecular with osteological, integumentary and behavioural characters using Maximum Parsimony (MP) and Bayesian analyses. We present both separate and combined total evidence analyses with our molecular data, 152 osteological and 74 integumentary + behavioural characters. While supporting most aspects of the molecular-based hypotheses, the tree based on the combined matrix suggests several modifications of the generic composition for each of the two subfamilies: Penelopinae and Cracinae, and supports the merging of the genera Pipile with Aburria and Mitu with Pauxi . These results suggest that increased taxon and character sampling from a diversity of sources may be at least as important as increased sampling of only one type. Besides, of a total of 891 characters we had 437 parsimony-informative sites (almost half of the analyzable sites) proving the efficiency of a total-evidence approach.     

Molecular phylogenetics and biogeography of Neotropical piping guans (Aves: Galliformes): Pipile Bonaparte, 1856 is synonym of Aburria Reichenbach, 1853

The Cracidae are Neotropical galliform birds with 11 genera currently recognized. To investigate the questioned validity of Pipile Bonaparte, 1856 and the monotypic Aburria Reichenbach, 1853 as separate genera, we gathered data from 2727 bp of mitochondrial DNA (cytochrome b, ND2 and control region) and 151 osteological characters. Our phylogenetic analyses of DNA sequences indicated that Aburria aburri is embedded within Pipile. Also, genetic distances between Aburria and any Pipile species are equivalent to the distances estimated for other congeneric cracid species, which genus status is not doubtful. Although the osteological characters do not have phylogenetic signal to solve the phylogenetic relationships at species level, five synapomorphies were found for Aburria and Pipile. Therefore, we suggest that Pipile should be merged with Aburria, which is the oldest described genus. We estimated that speciation in this group occurred in the Plio-Pleistocene, concordant with other birds, primates and rodents that have similar geographic distribution, and proposed a diversification hypothesis based on the occurrence of sea transgressions and the formation of the Amazon Lagoon. Therefore, we conclude that these palaeogeographic events may have contributed to Neotropical taxa diversification to a greater extent than previously suspected.     

Phylogenetics of barbets (Aves: Piciformes) based on nuclear and mitochondrial DNA sequence data

A combination of nuclear (beta-fibrinogen intron 7; 938 bp) and mitochondrial (cytochrome b; 1045 bp) DNA sequence data analyzed with model-based phylogenetic methods yields a hypothesis of barbet and toucan relationships supported by high Bayesian posterior probabilities and several synapomorphic indels in the nuclear intron data. The basal topology differs from previous morphology and mitochondrial DNA sequence based hypotheses, but is consistent with DNA-DNA hybridization results. The mitochondrial DNA sequence data provide resolution at the tips of the tree, but when analyzed alone, yield a different basal topology than the combined data. However, the basal nodes in the mitochondrial-based tree have little statistical support. Combined data analysis produced strong statistical support at basal nodes and a relatively simple geographic structure. Barbets from each of the three tropical regions are monophyletic, but the Old World barbets are paraphyletic. The African and New World clades are sister taxa, and the Asian clade is basal. This geographic structure indicates that similarities in plumage, voice, and behavior between Gymnobucco and Calorhamphus are convergent. The data are not conclusive, but suggest paraphyly of the New World barbets. Only 4% of the Bayesian posterior distribution unites Semnornis with the other New World barbets.     

Historical biogeography of tits (Aves: Paridae, Remizidae)

Tits (Aves: Paroidea) are distributed all over the northern hemisphere and tropical Africa, with highest species numbers in China and the Afrotropic. In order to find out if these areas are also the centers of origin, ancestral areas were reconstructed based on a molecular phylogeny. The Bayesian phylogenetic reconstruction was based on sequences for three mitochondrial genes and one nuclear gene. This phylogeny confirmed most of the results of previous studies, but also indicated that the Remizidae are not monophyletic and that, in particular, Cephalopyrus flammiceps is sister to the Paridae. Four approaches, parsimony- and likelihood-based ones, were applied to derive the areas occupied by ancestors of 75?% of the extant species for which sequence data were available. The common ancestor of the Paridae and the Remizidae inhabited tropical Africa and China. The Paridae, as well as most of its (sub)genera, originated in China, but Baeolophus originated in the Nearctic and Cyanistes in the Western Palearctic. Almost all biogeographic reconstruction methods produced similar results, but those which consider the likelihood of the transition from one area to another should be preferred.     

Phylogeny,character evolution,and classification of Selaginellaceae(lycophytes)

Selaginella is the largest and most taxonomically complex genus in lycophytes.The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes.Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions(74% increase of the earlier largest sampling) representing ca.300 species to infer a new phylogeny.The evolution of 10 morphological characters is studied in the new phylog...     

Phylogeny, character evolution, and classification of Sapotaceae (Ericales)

We present the first cladistic study of the largely tropical family Sapotaceae based on both morphological and molecular data. The data were analyzed with standard parsimony and parsimony jackknife algorithms using equally and successive weighted characters. Sapotaceae are confirmed to constitute two main evolutionary lineages corresponding to the tribes Isonandreae‐Mimusopeae‐Sideroxyleae and Chrysophylleae‐Omphalocarpeae. The Sideroxyleae are monophyletic, Isonandreae are polyphyletic as presently circumscribed, and as suggested by the analyses, the subtribe Mimusopeae‐Mimusopinae has evolved within the Mimusopeae‐Manilkarinae, which hence is also paraphyletic. Generic limits must be altered within Sideroxyleae with the current members Argania, Nesoluma and Sideroxylon. Argania cannot be maintained at a generic level unless a narrower generic concept is adopted for Sideroxylon. Nesoluma cannot be upheld in a narrow or broad generic concept of Sideroxylon. The large tribe Chrysophylleae circumscribes genera such as Chrysophyllum, Pouteria, Synsepalum, and Xantolis, but the tribe is monophyletic only if the taxa from Omphalocarpeae are also included. Neither Chrysophyllum nor Pouteria are monophyletic in their current definitions. The results indicate that the African taxa of Pouteria are monophyletic and distinguishable from the South American taxa. Resurrection of Planchonella, corresponding to Pouteria section Oligotheca, is proposed. The African genera Synsepalum and Englerophytum form a monophyletic group, but their generic limits are uncertain. Classification of the Asian genus Xantolis is particularly interesting. Morphology alone is indecisive regarding Xantolis relationships, the combined unweighted data of molecules and morphology indicates a sister position to Isonandreae‐Mimusopeae‐Sideroxyleae, whereas molecular data alone, as well as successive weighted combined data point to a sister position to Chrysophylleae‐Omphalocarpeae. An amended subfamily classification is proposed corresponding to the monophyletic groups: Sarcospermatoideae (Sarcosperma), Sapotoideae (Isonandreae‐Mimusopeae‐Sideroxyleae) and Chrysophylloideae (Chrysophylleae‐Omphalocarpeae), where Sapotoideae circumscribes the tribes Sapoteae and Sideroxyleae as well as two or three as yet unnamed lineages. Morphological characters are often highly homoplasious and unambiguous synapomorphies cannot be identified for subfamilies or tribes, which we believe are the reason for the variations seen between different classifications of Sapotaceae. © The Willi Hennig Society 2005.     

Phylogeny and biogeography of Oriolidae (Aves: Passeriformes)

Understanding oscine passerine dispersal patterns out of their Australian area of origin is hampered by a paucity of robust phylogenies. We constructed a molecular phylogeny of the oscine family, Oriolidae, which is distributed from Australia through to the Old World. We used the phylogeny to assess direction and timing of dispersal and whether dispersal can be linked with the well‐documented movements of geological terranes in the Indonesian Archipelago. We sampled 29 of 33 species of Oriolidae from fresh tissue and from toe pads from museum specimens, and examined two nuclear introns and two mitochondrial genes. Model‐based phylogenetic analyses yielded strong support for clades that generally mirrored classical systematics. Biogeographical analyses and divergence time estimates demonstrated that the family originated in the Australo‐Papuan region from where it dispersed first to Asia and then onwards to Africa and the Philippines before back‐colonising Asia and the Indonesian archipelago. Thus, contrary to several other avian families in the region, Oriolidae represents a sequential dispersal pattern from Australia to Africa via Asia. However, it is noteworthy that the Pacific islands and archipelagos remain uncolonised and that members inhabiting Wallacea are recent colonisers suggesting that Oriolidae are poorly adapted to island life.     

Phylogenetics and biogeography of Mascarene angraecoid orchids (Vandeae, Orchidaceae)

The large angraecoid orchid clade (subtribe Angraecinae sensu lato) has undergone extensive radiation in the western Indian Ocean, which includes Africa, Madagascar, and a number of Indian Ocean islands, such as the Mascarene Archipelago. To investigate systematics and biogeography of these Mascarene orchids, phylogenetic relationships were inferred from four plastid DNA regions, trnL intron, trnL-F intergenic spacer, matK gene, and rps16 intron. Parsimony and Bayesian analyses provided identical sets of relationships within the subtribe; the large genus Angraecum as currently circumscribed does not form an exclusive clade. Bonniera, an endemic genus to Reunion, is shown to be embedded in part of Angraecum. Evidence from our research supports the main origin of Mascarene Angraecinae from Madagascar, and although there were many independent colonizations, only a few of the lineages radiated within the Mascarene Archipelago.     

Reappraisal of early Miocene rails (Aves,Rallidae) from central France: diversity and character evolution

In Europe, Miocene rails (Aves, Rallidae) are quite abundant, but their phylogenetic placement in the context of recent forms has remained elusive. Rails from the early Miocene of the Saint‐Gérand‐le‐Puy area in central France were first described in the 19th century, and currently, only two species are recognized, namely Palaeoaramides christyi and Paraortygometra porzanoides. Our examination of the material however suggests the presence of four, likely coeval, species of rail from these deposits. Palaeoaramides eximius, previously synonymized with Palaeoaramides christyi, is here shown to probably be a distinct species, and a previously unrecognized rail, Baselrallus intermedius gen. et sp. nov., is described. To find out how these fossil rails are related to modern Rallidae, we compared them with an extensive sample of extant rails and identified plesiomorphic and derived features for crown group Rallidae. Our assessment does not support a particularly close relationship of either Palaeoaramides to Aramides or Paraortygometra to Crex (Ortygometra), and overall, these fossil rails are more primitive than previously assumed. Based on our observations of the morphology of the previously undescribed humerus of Palaeoaramides, we show this taxon to be outside crown group Rallidae, and perhaps closely related to the early Oligocene taxon Belgirallus. On the other hand, Paraortygometra porzanoides bears a resemblance to recent flufftails (Sarothrura spp.) in some elements, but whether it can be included in a clade together with flufftails is uncertain.     

The pterolichoid feather mites (Acarina, Astigmata) of the Megapodiidae (Aves, Galliformes)

The pterolichoid feather mites of megapodes are reviewed. Named taxa are briefly discussed and most are figured. The Pterolichidae (Pterolichinae) are: Ascetohchus Perez & Atyeo, three species; Echinozonus Atyeo & Perez, six species; Pereziella Atyeo, two species; and Phycoferus Atyeo & Perez, two species. New pterolichine taxa, with the type species listed first, include: Botryaspis cordiforma gen. et sp.n. and B. cordata gen. et sp.n.; Cycloprotarsus lineatus gen. et sp.n., C. centralis gen. et sp.n. and C. monacrotrichus gen. et sp.n.; Eurypterolichus gen.n. for Pterolichus navicula comb.n. Trouessart & Neumann and E. coniger gen. et sp.n.; Goniodurus gen.n. for Pterolichus ( Pseudalloptes ) quadratus comb.n. Trouessart and G. bilobatus gen. et sp.n.; Haptepigynus gen.n. for Pterolichus ( Pseudalloptes ) tridentiger comb.n. Trouessart and H. holonotus gen. et sp.n.; Heliaspis ventralis gen. et sp.n.; Leipobius ocellatus gen. et sp.n.; Maleolichus maleo gen. et sp.n.; Mayracarus gen.n. for Pterolichus (P.) tritilobus comb.n. Trouessart; Megapodobius arcuatus gen. et sp.n. and M. striatus gen. et sp.n.; Oxygynurus brevissimus gen. et sp.n., O. longicaulis gen. et sp.n., O. mediocaulis gen. et sp.n. and O. parvicaulis gen. et sp. n.; Prionoturus amembranatus gen. et sp. n.; Talegallobius bidentatus gen. et sp.n.; and Tanysomacarus imperfectus gen. et sp.n. and T. brachymeles gen. et sp.n. A new taxon of the Thoracosathesidae is: Thoracosathes caudiculata sp.n. Keys are provided and host- commensal associations are discussed. All taxa are restricted to the Megapodiidae. Cheylabis fuscina Trouessart is assigned to Pereziella and has as a synonym P. dupilcata Atyeo.     

Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae)

The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.     

Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae)

? Premise of the study: The recognition of monophyletic genera for groups that have high levels of homoplastic morphological characters and/or conflicting results obtained by different studies can be difficult. Such is the case in the grammitid ferns, a clade within the Polypodiaceae. In this study, we aim to resolve relationships among four clades of grammitid ferns, which have been previously recovered either as a polytomy or with conflicting topologies, with the goal of circumscribing monophyletic genera. ? Methods: The sampling included 89 specimens representing 61 species, and sequences were obtained for two genes (atpB and rbcL) and four intergenic spacers (atpB-rbcL, rps4-trnS, trnG-trnR, and trnL-trnF), resulting in a matrix of 5091 characters. The combined data set was analyzed using parsimony, likelihood, and Bayesian methods. Ninety-six morphological characters were optimized onto the generated trees, using the parsimony method. ? Key results: Lellingeria is composed of two main clades, the L. myosuroides and the Lellingeria s.s. clades, which together are sister to Melpomene. Sister to all three of these is a clade with two species of the polyphyletic genus Terpsichore. In the L. myosuroides clade, several dispersal events occurred between the neotropics, Africa, and the Pacific Islands, whereas Lellingeria s.s. is restricted to the neotropics, with about 60% of its diversity in the Andes. ? Conclusions: Overall, our results suggest that Lellingeria is monophyletic, with two clades that are easily characterized morphologically and biogeographically. Morphological characters describing the indument are the most important to define the clades within the ingroup. A small clade, previously considered in Terpsichore, should be recognized as a new genus.     

Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and Chloroplast DNA restriction site character sets

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character sets, one representing variation in 364 mapped and cladistically informative restriction sites from all regions of the chloroplast genome, the other representing variation in 42 informative “structural characters.” The structural character set includes morphological, anatomical, chromosomal, and biochemical features, plus structural features of the chloroplast genome. The taxon sample comprises 75 exemplar taxa, including 72 representatives of Poaceae and one representative of each of three related families (Flagellariaceae, Restionaceae, and Join-villeaceae);Flagellaria served as the outgroup for the purpose of cladogram rooting. Among the grasses, 24 tribes and all 16 subfamilies of grasses recognized by various modern authors were sampled. Transformations of structural characters are mapped onto the phylogenetic hypotheses generated by the analysis, and interpreted with respect to biogeography and the evolution of wind pollination in the grass family. A major goal of the study was to test the monophyly of several putatively natural groups, including Bambusoideae, Pooideae, Arundinoideae, and the “PACC clade” (the latter comprising subfamilies Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to analyze the phylogenetic structure within these groups and others. Several genera of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, andStreptochaeta) also were included, with the goal of determining their phylogenetic affinities. The two character sets were analyzed separately, and a simultaneous analysis of the combined matrices also was conducted. The combined data set also was analyzed using homoplasy-implied weights. Among major results of the combined unweighted analysis were resolution of a sister-group relationship betweenJoinvillea and Poaceae; resolution of a clade comprisingAnomochloa andStreptochaeta as the sister of all other grasses, withPharus the next group to diverge from the lineage that includes all remaining grasses; and resolution of other taxa often assigned to Bambusoideae s.l. (includingEhrharta and Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within which is nested a clade that consists ofBrachyelytrum, the PACC clade (includingAmphipogon), and Pooideae (including Brachypodieae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). Within the PACC clade,Aristida is identified as the sister of all other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each resolved as monophyletic, the latter two being sister-groups; and the remaining Arundinoid elements constitute a paraphyletic group within which are nested these three subfamilies. Within the Pooideae, four “core tribes” (Bromeae, Hordeeae [i.e., Triticeae], Agrostideae [i.e., Aveneae], andPoeae, the latter includingSesleria) are resolved as a monophyletic group that is nested among the remaining elements of the subfamily (Brachypodieae, Meliceae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). A second principal goal of the analysis was to identify structural synapomorphies of clades. Among the synapomorphies identified for some of the major clades are the following: gain of a 6.4 kb inversion in the chloroplast genome inJoinvillea and the grasses; reduction to 1 ovule per pistil, gain of a lateral “grass-type” embryo, and gain of an inversion around the gene trnT in the chloroplast genome in the grasses; loss of arm cells in the clade that consists ofBrachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain ofPanicum- type endosperm starch grains in the clade that comprises Centothecoideae and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two alternative placements of Pooideae among other groups). These findings are consistent with an origin and early diversification of grasses as forest understory herbs, followed by one or more radiations into open habitats, concomitant with multiple origins of C₄ photosynthesis and specialization for wind pollination.     

On the classification, evolution and biogeography of terrestrial haemadipsoid leeches (Hirudinida: Arhynchobdellida: Hirudiniformes)

A scourge of tropical and subtropical jungles, bloodfeeding terrestrial leeches of Haemadipsidae have long confused systematists and defied sensible biogeographic interpretation. The family Haemadipsidae usually includes problematic taxa that neither fit the typical IndoPacific distribution of the group, nor properly match diagnostic characters used to define the family. Historically, four additional families-Xerobdellidae, Diestecostomatidae Mesobdellidae and Nesophilaemonidae-have occasionally been recognized for New World and European representatives, though agreement on the composition of those families has not been consistent. Here, we expand the phylogenetic sampling of non-IndoPacific (among other) genera to include Meso American Diestecostoma species and Nesophilaemon skottsbergii from the Juan Fernandez Archipelago in order to critically assess prior hypotheses in a molecular phylogenetic analysis of arhynchobdellid leeches. The result, based on nuclear 18S rDNA and 28S rDNA and mitochondrial COI indicates that there are two distantly related lineages of bloodfeeding terrestrial leeches. The otherwise monophyletic family Haemadipsidae is found to exclude species of Xerobdella, Mesobdella and Diestecostoma. Xerobdellidae is formally resurrected to accommodate species of those three genera. Morphological characteristics corroborate the distinction of Haemadipsidae and Xerobdellidae on the basis of sexual and nephridial characters. Idiobdella seychellensis belongs in Haemadipsidae notwithstanding its lacking respiratory auricles. Nesophilaemon skottsbergii too is in Haemadipsidae notwithstanding its geographic proximity to the xerobdellid Mesobdella gemmata. The characters used to define haemadipsoid families are reevaluated. Feeding preferences and biogeographic patterns are also examined.