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Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution. [ABSTRACT FROM AUTHOR]

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma , and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome. [ABSTRACT FROM AUTHOR]

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest. [ABSTRACT FROM AUTHOR]

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest. [ABSTRACT FROM AUTHOR]

Local habitats shape animal vocalizations through selection to improve transmission of signals to receivers. This process can be variable, however, when landscapes are changing continuously due to urbanization or other factors. Studies have shown that some birds alter the frequency, amplitude and structure of their songs in urban habitats. Because songbirds learn their songs from other individuals, this cultural transmission can result in substantial change over time. Urban bird populations may therefore show rapid shifts in song form and variation may result from the combined or interacting effects of time and anthropogenic habitat change. In this study, we used historic and recent song recordings to investigate changes in spotted towhee (Pipilo maculatus) songs over 45 years across an urban-to-rural gradient in northern California. We found that pre-trill and trilled song parts covaried differently with urban development at the two time-points, with more change occurring in trill phrases than pre-trills. Additionally, we found that birds in 1970 adjusted trills in urban areas by raising maximum frequencies and broadening bandwidths, while birds in 2015 narrowed song bandwidths by decreasing maximum frequencies in more urban areas. These results did not fit our prediction that urbanization would have a consistent effect on song at two time-points. We suggest that habitat, cultural evolution and cultural drift can act on song elements in complicated ways that vary over time. [ABSTRACT FROM AUTHOR]

Species delimitation requires a broad assessment of population-level variation using multiple lines of evidence, a process known as integrative taxonomy. More specifically, studies of species limits must address underlying questions of what limits the distribution of populations, how traits vary in association with different environments, and whether the observed trait differences may lead to speciation through reproductive isolation. While genomic data have revolutionized the process of delimiting species, such data should be analyzed along with phenotypic, behavioral, and ecological traits that shape individuals across geographic and environmental space. The integration of multiple traits promotes taxonomic stability and should be a major guiding principle for species delimitation. Equally important, however, is thorough geographic sampling to adequately represent population-level variation--both in allopatry and across putative contact zones. We discuss the importance of both of these factors in the context of species concepts and traits and present different examples from birds that illustrate criteria for species delimitation. In addition, we review a decade of proposals for species-level taxonomic revisions considered by the American Ornithological Society's North American Classification Committee, and summarize the basis for decisions on whether to split or lump species. Finally, we present recommendations and discuss challenges (specifically permits, time, and funding) for species delimitation studies. This is an exciting time to be studying species delimitation in birds: many species-level questions remain, and methodological advances along with increased access to data enable new approaches to studying age-old problems in avian taxonomy. [ABSTRACT FROM AUTHOR]

Three distinct Canada jay (Perisoreus canadensis) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species' range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species. [ABSTRACT FROM AUTHOR]

Bell's and Sagebrush sparrows (Artemisiospiza belli and A. nevadensis) are phenotypically and genetically distinct, but data have yielded contradictory findings for A. belli subspecies. Disjunct populations of A. b. canescens from the San Joaquin Valley and Mojave Desert are phenotypically indistinguishable but diagnosable from Coast Range A. b. belli. However, San Joaquin Valley A. b. canescens shares allozymes and mitochondrial DNA (mtDNA) with A. b. belli whereas Mojave Desert A. b. canescens is genetically distinct. Furthermore, Great Basin A. nevadensis is closer in mtDNA to non-desert A. belli subspecies than to Mojave Desert A. b. canescens, with which it contacts across an aridland transition. We assessed concordance of song with genetics and phenotype for these taxa, and also analysed songs and mtDNA for A. b. clementeae which is endemic to arid San Clemente Island off the coast of southern California. Songs of open, arid habitat populations (A. nevadensis, A. b. canescens, A. b. clementeae) are consistently more similar to each other than they are to songs of coastal A. b. belli. We examined bioclimatic and land cover conditions to understand the basis for these patterns across ecoregions, and discuss the effect of the acoustic environment on song. [ABSTRACT FROM AUTHOR]

The article offers information on the 14th supplement of the 7th edition of the "Check-list of North American Birds" of the American Ornithologists' Union (AOU). Summaries of the decisions made by the union's Committee on Classification and Nomenclature-North and Middle America between May 15, 2013 to May 15, 2014 are included. The addition of the species Ciconia maguari and Phylloscopus collybita, including their habitat and distribution, to the changes in the supplement is also highlighted.

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Niche divergence or conservatism and phenotypic adaptation are important in lineage diversification. We used mitochondrial DNA ( mtDNA), morphology and ecological niche models to examine these processes in three subspecies of Sage Sparrow ( Artemisiospiza belli belli, A. b. canescens and A. b. nevadensis) that breed in bioclimatically diverse ecoregions in western North America. Overall, mtDNA and morphology are congruent with subspecies, ecoregion and bioclimatic niche. Niche divergence, rather than niche conservatism, accompanied by phenotypic adaptation, is associated with lineage diversification between subspecies. This diversification has occurred with and without physical barriers or accompanying genetic divergence. Populations of A. b. canescens are divided by a montane barrier into two bioclimatic regions ( San Joaquin Valley, Mojave Desert), where they are indistinguishable phenotypically, but show distinctive genetic patterns. Although there is no physical barrier between A. b. canescens in the San Joaquin Valley and A. b. belli in the Coast Ranges, these populations occupy different bioclimatic niches and are phenotypically, but not genetically, diagnosable. Niche overlap is greatest between A. b. canescens from the Mojave Desert and A. b. nevadensis from the Great Basin, yet these subspecies maintain distinctive phenotypes and mtDNA, even in local secondary contact and sympatry. Palaeoclimatic niche models for the Last Glacial Maximum ( c. 21 000 bp) and the Last Interglacial ( c. 120 000 bp) suggest that ecoregionally distinct populations of Artemisiospiza belli experienced different Pleistocene range fluctuations and glacial refugia, with temporal niche conservatism. Populations probably reached their current distributions as favourable climates and habitats expanded after the last glaciation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••-••. [ABSTRACT FROM AUTHOR]

ABSTRACT Introduction. Type 1 diabetic women may be affected by sexual dysfunction, mainly due to peripheral vascular disease. Aim. To determine whether daily tadalafil 5 mg is effective in type 1 premenopausal women affected by sexual genital arousal disorder. Method. Thirty-three volunteers were enrolled in a 12-week daily tadalafil 5 mg prospective study. Main Outcome Measures. The efficacy of daily tadalafil 5 mg on sexual genital arousal (primary end point), and desire, orgasm, enjoyment and frequency of sexual activity, and genital pain (secondary end points) were assessed (i) subjectively by the Short Personal Experiences Questionnaire; and (ii) objectively by translabial color Doppler sonography of clitoral blood flow. Moreover, the Short Form-36 questionnaire was used to assess Quality of Life (QoL). Results. Thirty-two women completed the study. Women reported a QoL improvement at the 12th week follow-up ( P < 0.05). Tadalafil improved the experience of sexual genital arousal, and orgasm, sexual enjoyment, satisfaction by frequency of sexual activity, and frequency of sexual thoughts or fantasies ( P < 0.05). Finally, dyspareunia decreased with respect to baseline ( P < 0.001). After tadalafil administration, the mean peak systolic velocity increased and the mean diastolic velocity decreased from baseline ( P < 0.001). Moreover, the mean resistance index and the mean pulsatility index were significantly higher compared with baseline values ( P < 0.001). Conclusions. Daily tadalafil 5 mg treatment seems to improve subjective sexual aspects and could be used to treat genital arousal disorder of premenopausal women with type 1 diabetes. The limits of the study were the small sample and the lack of a placebo control group. Caruso S, Cicero C, Romano M, Lo Presti L, Ventura B, and Malandrino C. Tadalafil 5 mg daily treatment for type 1 diabetic premenopausal women affected by sexual genital arousal disorder. J Sex Med 2012;9:2057-2065. [ABSTRACT FROM AUTHOR]

Range limits and secondary contact zones often occur at ecotones between major associations of habitat and climate. Therefore, understanding processes that limit sympatry between species in such areas provides an important framework for testing biogeographic and evolutionary hypotheses. Theoretical and empirical work has shown that the evolution of species borders is influenced by a complexity of factors, including gene flow from central to peripheral populations and the ability of species to adapt locally to environmental conditions. However, few studies have used bioclimatic models, combined with molecular and morphological data, to predict geographic range limits in the context of gene flow across a secondary contact zone. In this study, I applied these methods to test specific hypotheses about barriers to sympatry between closely related species where they approach and contact each other. Specifically, I examined the importance of historical isolation, local adaptation, and symmetry of gene flow in limiting sympatry and range expansion of ecologically distinct species across environmental gradients. Molecular (mitochondrial DNA, allozymes), morphological, and bioclimatic data were obtained for two avian sibling species (Baeolophus inornatus and B. ridgwayi) that exist in recent, narrow secondary contact in northern California. These species are broadly allopatric and occupy rangewide associations of oak and pinyon-juniper woodlands, respectively, although B. inornatus also inhabits mixed or juniper woodlands locally. Patterns of molecular variation generally were congruent with morphological and bioclimatic data, and support prior evidence for a history of isolation, adaptation, and divergence in distinctive, species-specific vegetation-climate associations. However, molecular and morphological clines fall east of the limit of oaks, and individuals of B. inornatus in this juniper-associated contact zone experience bioclimates that are more... [ABSTRACT FROM AUTHOR]

The timing of origin of modern North American bird species in relation to Pleistocene glaciations has long been the topic of significant discussion and disagreement. Recently, Klicka and Zink (1997) and Avise and Walker (1998) enlivened this debate by using calibrated molecular distance values to estimate timing of speciations. Here we use new molecular studies to test their conclusions. Molecular distance values for 39 pairs of proven sister species, 27 of which are based on new data, alter the currently perceived pattern that avian species splits occurred mainly in the Pliocene and early-mid-Pleistocene. Mitochondrial DNA divergence values for this set of taxa showed a skewed distribution pointing toward relatively young speciation times, in contrast to the pattern presented by Klicka and Zink (1997) for 35 sister plus non-sister species pairs. Our pattern was not significantly different from that of Avise and Walker (1998) for "intraspecific phylogroups," some of which are species. We conclude that the entire Pleistocene, including the last two glacial cycles (<250,000 years ago), was important in speciations of modern North American birds. A substantial number of speciations were both initiated and completed in the last 250,000 years. Simultaneously, many taxa began to diverge in the Pleistocene but their speciations are not yet complete (per Avise and Walker 1998). The suggestion that durations of speciations average two million years is probably a substantial overestimate. [ABSTRACT FROM AUTHOR]

Investigates the different species of the Least Tern in North America. Identification of the different species; Where do these species nest; Information on the category in which the subspecies should be assessed; Sex differences between the birds; Methodology used to carry out the investigation; Results of the investigation.

Comments on studies focusing on the tempo of avian diversification. Hypotheses about late Pleistocene origins for North American songbirds; Agreement on the importance of a null model in hypothesis testing; Use of differential selection of species pairs in the analysis in explaining research discrepancies.

ABSTRACT Introduction. To date, women may use flexible oral contraceptive (OC) regimens. Aim. The aim of this study was to evaluate the quality of sexual life of healthy women on continued-regimen OCs. Methods. Fifty women (age range 18-38) were enrolled. The Female Sexual Function Index (FSFI) and the Short Form-36 (SF-36) questionnaires were used to investigate, respectively, sexual behavior and the quality of life (QoL) of women on OC for 72 days with a 4-day hormone-free interval, for two cycles. Both the FSFI and the SF-36 were administered before starting OC intake, at the first (72-82 days) and the second (144-154 days) follow-ups. Main Outcome Measure. The main outcomes are the FSFI and the SF-36 questionnaires. Results. The FSFI score obtained at the first follow-up detected a worsening with respect to baseline score ( P < 0.05). The score obtained at the second follow-up detected an improvement with respect to both the baseline and the first follow-up total scores ( P < 0.05). QoL improved at the first follow-up only as regards body pain ( P < 0.05), and at the second follow-up as regards: physical role, body pain, general health, vitality, and social function ( P < 0.05). Conclusions. The use of continued-regimen OCs is able to improve the sexual behavior and the QoL of women. Caruso S, Malandrino C, Cicero C, Ciancio F, Cariola M, and Cianci A. Quality of sexual life of women on oral contraceptive continued-regimen: Pilot study. J Sex Med **;**:**-**. [ABSTRACT FROM AUTHOR]

Introduction In mammals, the effects of ovarian steroids influence sexual behavior. In humans, there are a few studies that take into account if ovulation occurs. Aim The study aims to investigate if a woman's sexuality changes during the week and over the menstrual cycle, and if so, in what way. Methods This is a prospective cohort study; 1,957 heterosexual women were involved over the period January 2004- December 2011. Two subgroups were taken into consideration, women having a partner and singles. Main Outcome Measure Sexual interview and the Female Sexual Function Index and Female Sexual Distress Scale questionnaires were used to exclude women with sexual dysfunction. Women with ovulation confirmed by sonography were enrolled. Women were given diary cards on which to report their daily sexual activity. Serum concentrations of estradiol, progesterone, total testosterone, sex hormone binding globulin, and free androgen index were measured during the follicular, periovular, and luteal phase of the menstrual cycle. Results One thousand one hundred eighty women (age range 18-40 years) were included in the analyses. Of them, 925 had a heterosexual relationship and 255 were single. Women with a partner had more sexual activity during the weekend, while the singles had a constant sexual activity over the week. The sexual activity of singles was higher during the ovulatory phase and lower during menses than that of the women with a partner. A linear correlation between sexual activity and androgenic hormonal profile during the menstrual cycle in women with and without a partner was observed. Conclusions Ovarian steroids modulate a woman's sexual activity. This aspect was more evident in singles than in women having a partner, in which a variety of nonhormonal factors can have a role. Caruso S, Agnello C, Malandrino C, Lo Presti L, Cicero C, and Cianci S. Do hormones influence women's sex? Sexual activity over the menstrual cycle. J Sex Med 2014;11:211-221. [ABSTRACT FROM AUTHOR]