Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny.

Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari-specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non-monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.

A systematic review of the subfamily Syringophilinae (Acari: Syringophilidae) of the Nearctic region. Part 1: quill mites associated with passerines (Aves: Passeriformes).

Quill mites belonging to the subfamily Syringophilinae Lavoipierre, 1953 associated with the Nearctic passeriform birds are revised. All of the 49 known species, which are grouped in seven genera, are recorded. Among them, four new species are described: Syringophiloidus audubioni sp. nov. from Spizella breweri (Cassini) (Emberizidae), Syringophilopsis catesbyi sp. nov. from Vireo olivaceus (Linnaeus) (Vireonidae), S. wilsoni sp. nov. from Pheucticus melanocephalus (Swainson) (Cardinalidae), and S. bartrami sp. nov. from Spizella passerina (Bechstein) (Emberizidae). The species Syringophilopsis hylocichlae Clark, 1964 syn. nov. is synonymized with Syringophilopsis turdus (Fritsch, 1958), and Syringophiloidus zonotrichia syn. nov. is synonymized with Betasyringophiloidus seiuri (Clark, 1964) comb. nov. Six species are recorded from the Nearctic region for the first time: Syringophiloidus delichonum Bochkov, 2001, S. glandarii (Fritsch, 1958), S. weiszii Skoracki et al., 2001, S. bombycillae Skoracki, 2002, Syringophilopsis mimidus Sikora et al., 2011, and Torotrogla merulae Skoracki et al., 2000. Data on Nearctic syringophiline species, their hosts and distribution are summarized and the keys to all species are constructed.

A review of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Prostigmata: Syringophilidae).

The fauna of quill mites of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Cheyletoidea: Syringophilidae) is comprehensively revised. All of 78 known species, which are grouped into 11 genera, are examined and diagnosed or redescribed. Data on picobiine hosts and distribution are summarized, including new host and locality records. The following new species are described: Charadriineopicobia apricaria sp. nov. ex Pluvialis apricaria (Linnaeus) (Charadriiformes: Charadriidae) from France, Neopicobia pari sp. nov. ex Periparus venustulus Swinhoe (type host) (Passeriformes: Paridae) from China, Parus major Linnaeus (Paridae) from Macedonia and Finland, and Poecile varius Temminck and Schlegel (Paridae) from Japan, Picobia magellani sp. nov. ex Scytalopus magellanicus (Gmelin) (Passeriformes: Rhinocryptidae) from Colombia, Picobia lonchura sp. nov. ex Lonchura leucogastra (Blyth) (Passeriformes: Estrildidae) from Indonesia, Picobia makoli sp. nov. ex Xiphocolaptes promeropirhynchus (Lesson) (Passeriformes: Furnariidae) from Colombia. The species Picobia polonica Skoracki, Magowski and Dabert, 2001 syn. nov. is a junior synonym of C. khulkhaskhani Kivganov and Sharafat, 1995. The following new combinations are proposed: Neopicobia ictericus (Skoracki and Glowska, 2010) comb. nov., Rafapicobia brotogeris (Fain, Bochkov and Mironov, 2000) comb. nov., and Rafapicobia ramphastos (Fain, Bochkov and Mironov, 2000) comb. nov. Keys to the all picobiine genera and species are presented, along with a check-list of picobiine species and their hosts.

Coevolutionary patterns and diversification of avian malaria parasites in African sunbirds (Family Nectariniidae).

The coevolutionary relationships between avian malaria parasites and their hosts influence the host specificity, geographical distribution and pathogenicity of these parasites. However, to understand fine scale coevolutionary host-parasite relationships, robust and widespread sampling from closely related hosts is needed. We thus sought to explore the coevolutionary history of avian Plasmodium and the widespread African sunbirds, family Nectariniidae. These birds are distributed throughout Africa and occupy a variety of habitats. Considering the role that habitat plays in influencing host-specificity and the role that host-specificity plays in coevolutionary relationships, African sunbirds provide an exceptional model system to study the processes that govern the distribution and diversity of avian malaria. Here we evaluated the coevolutionary histories using a multi-gene phylogeny for Nectariniidae and avian Plasmodium found in Nectariniidae. We then assessed the host-parasite biogeography and the structuring of parasite assemblages. We recovered Plasmodium lineages concurrently in East, West, South and Island regions of Africa. However, several Plasmodium lineages were recovered exclusively within one respective region, despite being found in widely distributed hosts. In addition, we inferred the biogeographic history of these parasites and provide evidence supporting a model of biotic diversification in avian Plasmodium of African sunbirds.

A review of mites of the subfamily Picobiinae Johnston & Kethley, 1973 (Prostigmata: Syringophilidae) from North American birds.

The fauna of ectoparasitic mites of the subfamily Picobiinae (Acari: Syringophilidae) associated with birds of the North America is revised. A new genus, Charadriineopicobia n. g. is proposed for two quill mite species, Ch. calidris n. sp. from Calidris alba (Pallas) (Charadriiformes: Scolopacidae) and Ch. leucophaeus (Skoracki, Hendricks & Spicer, 2010) n. comb. from Leucophaeus atricilla Linnaeus (Charadriiformes: Laridae). The new genus differs from the closely related Neopicobia Skoracki, 2011 by the presence of one pair of setae in pseudanal series and by clearly discernible chambers in each lateral branch of the peritremes, in both sexes. Additionally, a new species of Picobia Haller, 1878, P. hylocichlae n. sp., parasitising Hylocichla mustelina (Gmelin) (Passeriformes: Turdidae), is described. The species of picobiine mites presently recorded from North America are summarised.

Cophylogeny of quill mites from the genus Syringophilopsis (Acari: Syringophilidae) and their North American passerine hosts.

Species of Syringophilopsis quill mites are found in the flight feathers of passerine birds. A phylogeny of species from this genus infecting North American passerines was inferred from the mitochondrial cytochrome oxidase I gene and the nuclear 28S ribosomal RNA gene. Based on the large genetic distance among lineages, the genus appears to be composed of several cryptic species. A reconciliation analysis of these mites and their avian hosts indicates a limited, but significant, degree of cophylogeny. However, strict cospeciation is not found to be occurring in this system.

Further investigations of the mite genus Syringophiloidus Kethley, 1970 (Acariformes: Syringophilidae) from North American passerines.

Four new syringophilid species of Syringophiloidus Kethley, 1970 are described from North American passerines: S. zonotrichia n. sp. from Zonotrichia albicolis (Gmelin) (Emberizidae) on Texas; S. jackowiaki n. sp. from Poecile carolinensis (Auduborn) (Paridae) in Texas; and S. xanthocephalus n. sp. from Xanthocephalus xanthocephalus (Bonaparte) (Icteridae) and S. agelaius n. sp. from Agelaius phoeniceus Linnaeus (Icteridae), both from Arizona. Spizella breweri (Cassin) (Emberizidae) from California is a new host for Syringophiloidus sialius Skoracki, Flannery & Spicer, 2009; and Melospiza lincolnii (Auduborn) (Emberizidae) from Texas and Vermivora ruficapilla (Wilson) (Parulidae) from California are new hosts for S. seiuri (Ckark, 1964). S. daberti Bochkov, Fain & Skoracki, 2004 from Passerina ciris Linnaeus (Cardinalidae) is recorded in the USA for the first time. A table with the host associations and distribution of all of the North American species of Syringophiloidus is given.

New species of parasitic quill mites of the genus Picobia (Acari: Syringophilidae: Picobiinae) from North American birds.

Five new species of the genus Picobia are described and illustrated: (1) P. leucophaeus sp. nov. from the Laughing Gull Leucophaeus atricilla L. (Charadriiformes: Laridae) from Texas; (2) P. troglodytes sp. nov. from the House Wren Troglodytes aedon Vieillot (Passeriformes: Troglodytidae) from California; (3) P. cardinalis sp. nov. from the Northern Cardinal Cardinalis cardinalis (L.) (Passeriformes: Cardinalidae) from Texas; (4) P. carpodacus sp. nov. from the Purple Finch Carpodacus purpureus (Gmelin) (Passeriformes: Fringillidae) from California; and (5) P. psaltriparus sp. nov. from the Bushtit Psaltriparus minimus (Townsend) (Passeriformes: Aegithalidae) from Texas. Two avian species from the family Picidae (Piciformes) are recorded as new hosts for P. dryobatis (Fritsch, 1958): the Downy Woodpecker Picoides pubescens (L.) from Texas and the Ladder-backed Woodpecker Picoides scalaris (Wagler) from California. Additionally, all named species of the genus Picobia with their host associations and distributions are summarized in tabular form.

Four new species of Aulonastus Kethley, 1970 (Acari: Syringophilidae) from North American passerines.

Four new species belonging to Aulonastus Kethley, 1970 (Acari: Prostigmata: Syringophilidae), which are found inside the quills of body feathers of North American passerines (Aves: Passeriformes), are described and figured: A. emberizicus n. sp. from Ammodramus savanarum (Gmelin) (Emberizidae) (type-host) in Texas, Zonotrichia atricapilla (Gmelin) (Emberizidae) in California and Passerculus sandwichensis (Gmelin) (Emberizidae) in Texas; A. euphagus n. sp. from Euphagus cyanocephalus (Wagler) (Icteridae) in California; A. pirangus n. sp. from Piranga ludoviciana (Wilson) (Cardinalidae) in California; and A. sturnellus n. sp. from Sturnella magna (Linnaeus) (Icteridae) in Texas. A key to females of the known species of Aulonastus is presented.

A supermatrix-based molecular phylogeny of the family Drosophilidae.

The genus Drosophila is diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny for Drosophila and related genera. The genus Drosophila as currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genus Drosophila is paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenus Sophophora, which includes Drosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the Hawaiian Drosophila, the genus Scaptomyza, and the virilis-repleta radiation. The second contains the immigrans-tripunctata radiation as well as the genera Hirtodrosophila (except Hirtodrosophila duncani), Mycodrosophila, Zaprionus and Liodrosophila. We argue that these results support a taxonomic revision of the genus Drosophila.

Mites of the genus Torotrogla (Prostigmata: Syringophilidae) from North American passerines.

Five new quill mite species of the genus Torotrogla Kethley, 1970 (Acari: Syringophilidae) are described from North American passerines: T. aphelocoma sp.n. from Aphelocoma californica (Corvidae) and T. cardinalis sp.n. from Cardinalis cardinalis (Cardinalidae) in Texas; and T. coccothraustes sp.n. from Coccothraustes vespertinus (Fringillidae), T. cyanocitta sp.n. from Cyanocitta stelleri (Corvidae), and T. piranga sp.n. from Piranga ludoviciana (Thraupidae) in California. A key to females of all known Torotrogla spp. and a table with their host associations and distributions are given.

Quill mites of the genus Syringophilopsis Kethley, 1970 (Acari: Syringophilidae) from North American birds.

Seven mite species belonging to the genus Syringophilopsis Kethley, 1970 (Acari: Prostigmata: Cheyletoidea) are recorded from 10 passeriform host species from the USA. Three new species are described and illustrated: Syringophilopsis polioptilus sp. n. from Polioptila caerulea (Linnaeus) (Polioptilidae); S. empidonax sp. n. from Empidonax hamrnmondii (Vesey) and Empidonax wrightii Baird (Tyrannidae); and S. sialiae sp. n. from Sialia mexicana Swainson (Turdidae). In addition, records of new hosts are given: Turdus migratorius Linnaeus (Turdidae) for Syringophilopsis turdus (Fritsch, 1958); three tyrannid species (Tyrannidae), Myiarchus crinitus (Linnaeus), M. cinerascens (Lawrence) and Tyrannus verticalis Say for S. tyranni Bochkov et Galloway, 2004; Euphagus cyanocephalus (Wagler) (Icteridae) for S. elongatus (Ewing, 1911); and two parulid species (Parulidae), Dendroica graciae Baird and Wilsonia pusilla (Wilson) for S. dendroicae Bochkov et Galloway, 2001. All known species of the genus Syringophilopsis from the Nearctic Region are summarized in tabular form. Syringophilopsis porzanae Bochkov et Galloway, 2004 is reassigned to the genus Ascetonmylla Kethley, 1970.

Phylogenetic relationships within an endemic group of Malagasy 'assassin spiders' (Araneae, Archaeidae): ancestral character reconstruction, convergent evolution and biogeography.

The phylogenetic relationships in an endemic group of Malagasy 'assassin spiders' (Araneae, Archaeidae: Eriauchenius) called the gracilicollis group, are inferred from mitochondrial 12S, 16S and COI DNA sequence data. Archaeid spiders of Madagascar have evolved varying degrees of elongation in the cephalic area. These molecular data support the monophyly of the gracilicollis group. The evolution of the cephalic area is examined by performing an ancestral character reconstruction on this character, which reveals that the cephalic area is elongating independently. The biogeography of the gracilicollis group reveals an east-west split of the clade on Madagascar.

Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion.

The ultimate goal of comparative phylogeographical analyses is to infer processes of diversification from contemporary geographical patterns of genetic diversity. When such studies are employed across diverse groups in an array of communities, it may be difficult to discover common evolutionary and ecological processes associated with diversification. In order to identify taxa that have responded in a similar fashion to historical events, we conducted comparative phylogeographical analyses on a phylogenetically and ecologically limited set of taxa. Here, we focus on a group of squamate reptiles (snakes and lizards) that share similar ecological requirements and generally occupy the same communities in the western USA. At a gross level, deep genetic division in Contia tenuis, Diadophis punctatus, Elgaria multicarinata, the Charina bottae complex, and Lampropeltis zonata are often concordant in the Transverse Ranges, the Monterey Bay and Sacramento-San Joaquin Delta region, and the southern Sierra Nevada in California. Molecular clock estimates suggest that major phyletic breaks within many of these taxa roughly coincide temporally, and may correspond to important geological events. Furthermore, significant congruence between the phylogeographies of E. multicarinata and L. zonata suggests that the succession of vicariance and dispersal events in these species progressed in concert. Such congruence suggests that E. multicarinata and L. zonata have occupied the same communities through time. However, across our entire multi-taxon data set, the sequence of branching events rarely match between sympatric taxa, indicating the importance of subtle differences in life history features as well as random processes in creating unique genetic patterns. Lastly, coalescent and noncoalescent estimates of population expansion suggest that populations in the more southerly distributed clades of C. tenuis, D. punctatus, E. multicarinata, and L. zonata have been stable, while populations in more northerly clades appear to have recently expanded. This concerted demographic response is consistent with palaeontological data and previous phylogeographical work that suggests that woodland habitat has become more restricted in southern California, but more widespread in the North during Holocene warming. Future phylogeographical work focusing on allied and ecologically associated taxa may add insight into the ecological and evolutionary processes that yield current patterns of genetic diversity.

Dracula ant phylogeny as inferred by nuclear 28S rDNA sequences and implications for ant systematics (Hymenoptera: Formicidae: Amblyoponinae).

Ants are one of the most ecologically and numerically dominant families of organisms in almost every terrestrial habitat throughout the world, though they include only about 1% of all described insect species. The development of eusociality is thought to have been a driving force in the striking diversification and dominance of this group, yet we know little about the evolution of the major lineages of ants and have been unable to clearly determine their primitive characteristics. Ants within the subfamily Amblyoponinae are specialized arthropod predators, possess many anatomically and behaviorally primitive characters and have been proposed as a possible basal lineage within the ants. We investigate the phylogenetic relationships among the members of the subfamily, using nuclear 28S rDNA sequence data. Outgroups for the analysis include members of the poneromorph and leptanillomorph (Apomyrma, Leptanilla) ant subfamilies, as well as three wasp families. Parsimony, maximum likelihood, and Bayesian analyses provide strong support for the monophyly of a clade containing the two genera Apomyrma+Mystrium (100% bpp; 97% ML bs; and 97% MP bs), and moderate support for the monophyly of the Amblyoponinae as long as Apomyrma (Apomyrminae) is included (87% bpp; 57% ML bs; and 76% MP bs). Analyses did not recover evidence of monophyly of the Amblyopone genus, while the monophyly of the other genera in the subfamily is supported. Based on these results we provide a morphological diagnosis of the Amblyoponinae that includes Apomyrma. Among the outgroup taxa, Typhlomyrmex grouped consistently with Ectatomma, supporting the recent placement of Typhlomyrmex in the Ectatomminae. The results of this present study place the included ant subfamilies into roughly two clades with the basal placement of Leptanilla unclear. One clade contains all the Amblyoponinae (including Apomyrma), Ponerinae, and Proceratiinae (Poneroid clade). The other clade contains members from subfamilies Cerapachyinae, Dolichoderinae, Ectatomminae, Formicinae, Myrmeciinae, and Myrmicinae (Formicoid clade).

Molecular phylogeny of songbirds (Passeriformes) inferred from mitochondrial 16S ribosomal RNA gene sequences.

Phylogenetic relationships among the families of passerine birds have been the subject of many debates. These relationships have been investigated by using a number of different character sets, including morphology, proteins, DNA-DNA hybridization, and mitochondrial DNA gene sequences. Our objective was to examine the phylogenetic relationships of a set of passerine songbirds (Oscines) and to test the taxonomic relationships proposed by. We sequenced 1403 aligned bases encompassing the mitochondrial transfer-RNA-Valine and 16S ribosomal RNA genes in 27 species from 14 families (including a Suboscine outgroup). Our results differ in significant ways from the superfamily designations of Sibley and Ahlquist by questioning the monophyly of the Sylvioidea and by placing the Regulidae in the Corvoidea.

A phylogenetic analysis of the emberizid sparrows based on three mitochondrial genes.

Previous molecular phylogenetic studies have examined the taxonomic relationships among a number of typical emberizid sparrow genera. To help clarify these relationships, we sequenced a 1673 base pair fragment for the complete sequence of three mitochondrial genes: adenosine triphosphatase (Atp8 and Atp6) and cytochrome oxidase subunit III (COIII) for 38 sparrow species, along with Passerina amoena (Cardinalidae) and Piranga ludoviciana (Thraupidae) which were selected as the outgroups. Our analysis confirms the monophyly of traditional genera such as Junco, Melospiza, and Zonotrichia. Although Calcarius and Plectrophenax are often thought to be putative emberizids, all our analyses placed these genera basal to all other sparrows examined. As observed with Calcarius, Spizella did not form a monophyletic group, with S. arborea being the sister-taxon to Passerella iliaca. Our analyses also suggest that Aimophila ruficeps is probably more closely related to the "brown towhees" (Pipilo aberti, P. crissalis, and P. fuscus) than its putative congeners. The genus Ammodramus was also not monophyletic, since it appears that Passerculus sandwichensis is more closely related to A. henslowii and A. leconteii then either one is related to its congener A. savannarum. Finally, our analyses exhibited other unsuspected associations, such as the sister-taxon relationships between Amphispiza bilineata and the Chondestes grammacus/Calamospiza melanocorys clade, and Amphispiza belli and Pooecetes gramineus.

Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle.

Little is known about what determines patterns of host association of horizontally transmitted parasites over evolutionary timescales. We examine the evolution of associations between mushroom-feeding Drosophila flies (Diptera: Drosophilidae), particularly in the quinaria and testacea species groups, and their horizontally transmitted Howardula nematode parasites (Tylenchida: Allantonematidae). Howardula species were identified by molecular characterization of nematodes collected from wild-caught flies. In addition, DNA sequence data is used to infer the phylogenetic relationships of both host Drosophila (mtDNA: COI, II, III) and their Howardula parasites (rDNA: 18S, ITS1; mtDNA: COI). Host and parasite phylogenies are not congruent, with patterns of host association resulting from frequent and sometimes rapid host colonizations. Drosophila-parasitic Howardula are not monophyletic, and host switches have occurred between Drosophila and distantly related mycophagous sphaerocerid flies. There is evidence for some phylogenetic association between parasites and hosts, with some nematode clades associated with certain host lineages. Overall, these host associations are highly dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared breeding sites and large potential host ranges of the nematodes.

EVOLUTION OF MULTIPLE KINDS OF FEMALE SPERM-STORAGE ORGANS IN DROSOPHILA.

Females of all species belonging to the family Drosophilidae have two kinds of sperm-storage organs: paired spherical spermathecae and a single elongate tubular seminal receptacle. We examined 113 species belonging to the genus Drosophila and closely allied genera and describe variation in female sperm-storage organ use and morphology. The macroevolutionary pattern of organ dysfunction and morphological divergence suggests that ancestrally both kinds of organs stored sperm. Loss of use of the spermathecae has evolved at least 13 times; evolutionary regain of spermathecal function has rarely if ever occurred. Loss of use of the seminal receptacle has likely occurred only once; in this case, all descendant species possess unusually elaborate spermathecae. Data further indicate that the seminal receptacle is the primary sperm-storage organ in Drosophila. This organ exhibits a pattern of strong correlated evolution with the length of sperm. The evolution of multiple kinds of female sperm-storage organs and the rapidly divergent and correlated evolution of sperm and female reproductive tract morphology are discussed.

PHYLOGENETIC EXAMINATION OF FEMALE INCORPORATION OF EJACULATE IN DROSOPHILA.

Males of some invertebrate species transfer large ejaculates, and many of the substances contained therein are incorporated by females into their somatic and ovarian tissues. These incorporated substances are expected to be energetically costly for males to produce, but benefit males by enhancing their fertilization success and/or the viability of their offspring. A better understanding of the evolution and maintenance of this important reproductive strategy should come from phylogenetic examination. We therefore quantified the extent of ejaculate incorporation by females of 34 species of Drosophila. Substantive amounts of male-derived proteins were more frequently detected in female somatic tissue than in ovarian tissue. Substantive ejaculate incorporation by females was found to have arisen numerous times across the phylogeny and tended to be lineage specific in expression. The extent to which evolution of a nutritive function of the ejaculate may have been influenced by phylogenetic history in the genus Drosophila is discussed. Macroevolutionary relationships between the amount of ejaculate incorporated by females and other features of species' reproductive and life-history biology, including body size, sperm length, the formation of an insemination reaction in females, and sex-specific ages of reproductive maturity, also were examined after controlling for phylogenetic effects.