Cytonuclear discordance in the crowned-sparrows, Zonotrichia atricapilla and Zonotrichia leucophrys.

The golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes between Z. atricapilla and Z. leucophrys, and investigate the relationships among Z. leucophrys subspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly of Z. atricapilla and Z. leucophrys using large panels of single nucleotide polymorphisms (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure within Z. leucophrys with two distinct clades. Altogether, our results indicate deeper divergences between Z. atricapilla and Z. leucophrys than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.

A genome-wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome.

The house sparrow is an important model species for studying physiological, ecological and evolutionary processes in wild populations. Here, we present a medium density, genome wide linkage map for house sparrow (Passer domesticus) that has aided the assembly of the house sparrow reference genome, and that will provide an important resource for ongoing mapping of genes controlling important traits in the ecology and evolution of this species. Using a custom house sparrow 10 K iSelect Illumina SNP chip we have assigned 6,498 SNPs to 29 autosomal linkage groups, based on a mean of 430 informative meioses per SNP. The map was constructed by combining the information from linkage with that of the physical position of SNPs within scaffold sequences in an iterative process. Averaged between the sexes; the linkage map had a total length of 2,004 cM, with a longer map for females (2,240 cM) than males (1,801 cM). Additionally, recombination rates also varied along the chromosomes. Comparison of the linkage map to the reference genomes of zebra finch, collared flycatcher and chicken, showed a chromosome fusion of the two avian chromosomes 8 and 4A in house sparrow. Lastly, information from the linkage map was utilized to conduct analysis of linkage disequilibrium (LD) in eight populations with different effective population sizes (Ne ) in order to quantify the background level LD. Together, these results aid the design of future association studies, facilitate the development of new genomic tools and support the body of research that describes the evolution of the avian genome.

Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair.

Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recently diverged passerine species pair (Passer domesticus and Passer hispaniolensis) using a combination of proteomic and comparative evolutionary genomic approaches. First, we characterized and compared the SF proteome of the two species, revealing consistencies with known aspects of SFP biology and function in other taxa, including the presence and diversification of proteins involved in immunity and sperm maturation. Second, using whole-genome resequencing data, we assessed patterns of genomic differentiation between house and Spanish sparrows. These analyses detected divergent selection on immunity-related SF genes and positive selective sweeps in regions containing a number of SF genes that also exhibited protein abundance diversification between species. Finally, we analyzed the molecular evolution of SFPs across 11 passerine species and found a significantly higher rate of positive selection in SFPs compared with the rest of the genome, as well as significant enrichments for functional pathways related to immunity in the set of positively selected SF genes. Our results suggest that selection on immunity pathways is an important determinant of passerine SF composition and evolution. Assessing the role of immunity genes in speciation in other recently diverged taxa should be prioritized given the potential role for immunity-related proteins in reproductive incompatibilities in Passer sparrows.

Moult-related reduction of aerobic scope in passerine birds.

It is well established that the nutrient and energy requirements of birds increase substantially during moult, but it is not known if these increased demands affect their aerobic capacity. We quantified the absolute aerobic scope of house and Spanish sparrows, Passer domesticus and P. hispaniolensis, respectively, before and during sequential stages of their moult period. The absolute aerobic scope (AAS) is the difference between maximum metabolic rate (MMR) during peak locomotor activities and minimum resting metabolic rate (RMRmin), thus representing the amount of aerobic power above that committed to maintenance needs available for other activities. As expected, RMRmin increased over the moult period by up to 40 and 63% in house and Spanish sparrows, respectively. Surprisingly, the maximum metabolic rates also decreased during moult in both species, declining as much as 25 and 38% compared with pre-moult values of house and Spanish sparrows, respectively. The concurrent changes in RMRmin and MMR during moult resulted in significant decreases in AAS, being up to 32 and 47% lower than pre-moult levels of house and Spanish sparrows, respectively, during moult stages having substantial feather replacement. We argue that the combination of reduced flight efficiency due to loss of wing feathers and reduced aerobic capacity places moulting birds at greater risk of predation. Such performance constraints likely contribute to most birds temporally separating moult from annual events requiring peak physiological capacity such as breeding and migration.

Influence of the Agricultural Conservation Easement Program wetland practices on winter occupancy of Passerellidae sparrows and avian species richness.

Wetlands enrolled in the Agricultural Conservation Easement Program (ACEP) are established as a means of restoring wetland ecosystems and wildlife habitat on private, agricultural land. In West Virginia, USA, ACEP wetlands have never been evaluated to determine how they function as wildlife habitat in comparison to other available wetland habitat in the state. We measured the wintering occupancy of Passerellidae species and apparent avian species richness on ACEP wetlands and a set of reference wetlands located on public land in West Virginia to evaluate if ACEP wetlands are being used similarly by avian species to other available wetland habitat in the state. Apparent avian species richness and the occupancy probability of four Passerellidae species-song sparrows (Melospiza melodia), dark-eyed juncos (Junco hyemalis), swamp sparrows (Melospiza georgiana), and white-throated sparrows (Zonotrichia albicollis)-did not differ between ACEP and reference sites. In addition to other vegetative and habitat associations for each species, dark-eyed junco occupancy was negatively correlated with wetland size while swamp sparrow occupancy and apparent avian species richness were positively associated with wetland size. These results indicate that ACEP wetlands are providing winter avian habitat as well as another source of wetland habitat in the state. Maintaining and expanding ACEP wetlands in West Virginia would continue to provide wetland systems in areas that are otherwise lacking these habitats.

Host migration strategy and blood parasite infections of three sparrow species sympatrically breeding in Southeast Europe.

Mobile hosts like birds occupy a wide array of habitats in which they encounter various vector and parasite faunas. If the infection probability for vector-borne parasites varies among seasons and biomes, a migratory life can critically influence the infections of a host. The growing body of literature on avian blood parasites suggests that host migrations do not only influence prevalence of infection but can also evoke higher infection intensities and increased parasite diversity in migrant compared to resident host species. We investigated the prevalence, intensity and diversity of Plasmodium and Haemoproteus infections in three closely-related and sympatrically breeding sparrow species with different migration strategies ranging from residential house sparrow and partially migratory tree sparrow to the obligate migratory Spanish sparrow. With a prevalence of 49%, the migratory Spanish sparrows were significantly less frequently infected than the resident house sparrows (82%). The partially migratory tree sparrow showed an intermediate prevalence of 60%. The parasitaemias were similar in all three host species and indicated mostly chronic but also few acute infections. While we found Plasmodium parasites in all three sparrow species, only Spanish sparrows were infected with Haemoproteus parasites in our study. With nine clearly identified parasite lineages in our study and the highest number of lineages per infected individuals (i.e. relative diversity), Spanish sparrows harboured the most diverse parasite fauna. Our results suggest that migration strategies can affect Plasmodium and Haemoproteus infections of sparrows resulting in a lower parasite prevalence and higher parasite diversity in migratory hosts-at least during our host's breeding period. A general scope for all annual cycle periods and across various bird taxa remains to be elucidated.

Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer).

BACKGROUND: The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. RESULTS: The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. CONCLUSIONS: Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non-classical MHC-I genes, and that the evolutionary origin of these genes predate the split of the three investigated sparrow species 7 million years ago. Because only the classical MHC-I genes are involved in antigen presentation, the function of different MHC-I genes should be considered in future ecological and evolutionary studies of MHC-I in sparrows and other songbirds.

The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae).

The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot. We studied the biogeography and systematics of two closely related genera of sparrows (Passerellidae): Melozone and Aimophila. Collectively, this group is distributed from the southwestern United States and southward as far as central Costa Rica. We sampled 81 individuals of 8 Melozone and 2 Aimophila species, from 19 localities distributed throughout their ranges. We reconstructed phylogenetic relationships and time-calibrated species trees using multilocus sequence data comprised of one mitochondrial gene and five nuclear genes. We conducted an ancestral area reconstruction analysis to determine the probability of ancestral range at each divergent event. Despite analyzing six loci, we were unable to obtain a fully resolved phylogenetic tree. We recovered four main lineages: lineage 1 includes four Melozone species distributed north of Isthmus of Tehuantepec (M. albicollis, M. crissalis, M. aberti, M. fusca); lineage 2 includes three Melozone species distributed south of the Isthmus of Tehuantepec (M. biarcuata, M. cabanisi, M. leucotis); lineage 3 lineage consists of a single species endemic to the Pacific coast of Mexico (M. kieneri); and lineage 4 includes the more widely distributed sparrows in the genus Aimophila. Our analyses suggest that these genera probably originated during the late Miocene in the Madrean Highlands of southern Mexico. We identified dispersal as the prevalent cause of speciation in this clade with most lineages dispersing to their current distributions from southern Mexico either to the north following a developing and expanding Madro-Tertiary flora, or to the south across the Isthmus of Tehuantepec. A similar pattern of dispersal from this biogeographic region has been reported in other taxa including fishes, reptiles, and birds. Our results reveal that the four lineages identified represent geographically coherent and ecologically similar assemblages of taxa. Finally, when our genetic results are considered, along with apparent differences in morphology and song, the allopatric forms M. b. cabanisi and M. l. occipitalis warrant recognition as biological species.

Subspecies delineation amid phenotypic, geographic and genetic discordance in a songbird.

Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and salt marsh (Ammodramus caudacutus) sparrow complex, a group with populations that span considerable geographic distributions and a habitat gradient. We evaluated genetic structure among and within five putative subspecies of A. nelsoni and A. caudacutus using a reduced-representation sequencing approach to generate a panel of 1929 SNPs among 69 individuals. Although we detected morphological differences among some groups, individuals sorted along a continuous phenotypic gradient. In contrast, the genetic data identified three distinct clusters corresponding to populations that inhabit coastal salt marsh, interior freshwater marsh and coastal brackish-water marsh habitats. These patterns support the current species-level recognition but do not match the subspecies-level taxonomy within each species-a finding which may have important conservation implications. We identified loci exhibiting patterns of elevated divergence among and within these species, indicating a role for local selective pressures in driving patterns of differentiation across the complex. We conclude that this evidence for adaptive variation among subspecies warrants the consideration of evolutionary potential and genetic novelty when identifying conservation units for this group.

Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality.

The Saffron-billed Sparrow (Arremon flavirostris) complex occurs in the undergrowth of deciduous woodlands and forests from the Andes of Bolivia and northern Argentina to Paraguay and southern, mid-western and interior eastern Brazil. Currently four subspecies are recognized: A. f. flavirostris, A. f. polionotus, A. f. devillii and A. f. dorbignii. We review the taxonomy of this complex by analyzing coloration and morphometrics of a series of 234 skins, and by comparing 101 sound recordings. Our results suggest that under both the Phylogenetic and Biological Species Concept, three species should be recognized in this complex: A. flavirostris, A. polionotus and A. dorbignii. On the other hand, A. devillii should be considered a junior synonym of A. polionotus since these two have no constant differences in morphology and vocalization. These species are diagnosable by their coloration characters, but not by morphometrics. Vocalizations are useful in diagnosing A. flavirostris from A. dorbignii, but do not diagnose A. polionotus from the others. We show that part of the previous taxonomic confusion can be attributed to variation in back color of adult and immature A. polionotus. Finally, we comment on the recently located holotype of A. flavirostris, which was believed to be lost, and its type locality.

The evolution of highly variable immunity genes across a passerine bird radiation.

To survive, individuals must be able to recognize and eliminate pathogens. The genes of the major histocompatibility complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognized by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next-generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian motion in the species studied, that is following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary 'bursts'. By characterizing MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation.

Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species.

We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.

The mitochondrial genome of white Java sparrow (Padda oryzivora).

The complete mitochondrial genome of Padda oryzivora (Estrildidae, Passeriformes) was sequenced. It is 16 817 bp in length, with an AT content of 54.72%, including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and 1 control region. Phylogenetic analysis demonstrated that the Java sparrow is a close relative of zebrafinch (Taeniopygia guttata) within the same family. These results are desired to provide molecular data for species taxonomy and further phylogenetic studies of passerines.

Complete mitochondrial genome of the Onychostruthus taczanowskii (Aves, Passeridae) and its phylogenetic analysis.

The complete mitochondrial genome sequence of Onychostruthus taczanowskii consisted 16 917 bp, the genome harbored the same gene order with that of other birds, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 non-coding control region. The all tRNAs formed typical cloverleaf secondary structures, except tRNA(Ser (AGN)) and tRNA(Phe). The control region was located between tRNA(Glu) and tRNA(Phe) with 1310 bp in length, which consist of three domains: highly variable domain I, central conserved domain II and conserved sequence domain III. According to the phylogenetic analysis, Onychostruthus taczanowskii had a closer relationship with Pyrgilauda ruficollis, and Passer montanus were sister to them.

A microsatellite-based linkage map for song sparrows (Melospiza melodia).

Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.

Analysis of plumage, morphology, and voice reveals species-level differences between two subspecies of Prevost's Ground-sparrow Melozone biarcuata (Prévost and Des Murs) (Aves: Emberizidae).

Melozone biarcuata (Prevost's Ground-sparrow) has traditionally been divided into two allopatric groups based on differences in vocalizations and plumage characteristics: M. b. cabanisi in Costa Rica and M. b. biarcuata/M. b. hartwegi in northern Central America. However, the relationship between these subspecies has not been studied using a modern taxonomic approach. In this study, our objective was to provide the first detailed taxonomic comparison between these three subspecies using an integrative multi-trait analysis. We analyzed morphometric features, qualitative plumage patterns, and quantitative plumage measurements using spectral reflectance from all three subspecies, and we analyzed vocalizations for subspecies M. b. biarcuata and M. b. cabanisi. Our results show that M. b. cabanisi can be readily distinguished from the two other subspecies on the basis of morphometrics (M. b. cabanisi are smaller), plumage patterns (M. b. cabanisi have different facial markings and plumage patches), color differences (M. b. cabanisi have plumage patches that differ in color and brightness), and vocalizations (M. b. cabanisi have songs and calls that are acoustically distinct from those of M. b. biarcuata). By contrast, the two northern subspecies M. b. biarcuata and M. b. hartwegi were very similar for most traits, supporting previous suggestions that the two northern subspecies should be considered a single subspecies. Our data reveal that the differentiation in phenotypic characteristics between M. b. cabanisi versus M. b. biarcuata and M. b. hartwegi is similar to that reported for other complexes of subspecies where species status has been recognized. We argue that M. b. cabanisi should be treated as a species separate from M. biarcuata and propose that it be called Melozone cabanisi, White-faced Ground-sparrow. Our findings will contribute to the conservation efforts of the White-faced Ground-sparrow, which is endemic to Costa Rica's Central Valley and Turrialba Valley, by bringing focus to conservation policies that preserve ground-sparrow habitat (thickets, shade coffee plantations, and young secondary forest).

Population genetics of seaside Sparrow (Ammodramus maritimus) subspecies along the gulf of Mexico.

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this "Gulf Coast" clade using microsatellite and mtDNA data. Results of Bayesian analyses (Structure, GeneLand) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. fisheri near Corpus Christi. The two subspecies along the northern Gulf Coast of Florida are significantly differentiated from both A. m. sennetti and A. m. fisheri, but are not distinct from each other. We found a weak signal of isolation by distance within A. m. fisheri, indicating this population is not entirely panmictic throughout its range. Although continued conservation concern is warranted for all populations along the Gulf Coast, A. m. fisheri appears to be more secure than the far smaller populations in south Texas and the northern Florida Gulf Coast. In particular, the most genetically distinct populations, those in Texas south of Corpus Christi, occupy unique habitats within a very small geographic range.

A new genus for the American Tree Sparrow (Aves: Passeriformes: Passerellidae).

The genus Spizella (Bonaparte) contains seven species of North American sparrows in the recently resurrected family Passerellidae (Bock 1994; Barker et al. 2013), formerly placed in the Emberizidae, and includes a few of the region's most common and familiar bird species. Spizella sparrows occupy more or less open habitats; most species are at least partially migratory and form small flocks when not breeding. On the basis of their similar morphology and behavior, they have long been treated as a natural group (Ridgway 1901; American Ornithologists' Union 1998). 

Range expansion of house sparrows (Passer domesticus) in Kenya: evidence of genetic admixture and human-mediated dispersal.

Introduced species offer an opportunity to study the ecological process of range expansions. Recently, 3 mechanisms have been identified that may resolve the genetic paradox (the seemingly unlikely success of introduced species given the expected reduction in genetic diversity through bottlenecks or founder effects): multiple introductions, high propagule pressure, and epigenetics. These mechanisms are probably also important in range expansions (either natural or anthropogenic), yet this possibility remains untested in vertebrates. We used microsatellite variation (7 loci) in house sparrows (Passer domesticus), an introduced species that has been spreading across Kenya for ~60 years, to determine if patterns of variation could explain how this human commensal overcame the genetic paradox and expresses such considerable phenotypic differentiation across this new range. We note that in some cases, polygenic traits and epistasis among genes, for example, may not have negative effects on populations. House sparrows arrived in Kenya by a single introduction event (to Mombasa, ~1950) and have lower genetic diversity than native European and introduced North American populations. We used Bayesian clustering of individuals (n = 233) to detect that at least 2 types of range expansion occurred in Kenya: one with genetic admixture and one with little to no admixture. We also found that genetic diversity increased toward a range edge, and the range expansion was consistent with long-distance dispersal. Based on these data, we expect that the Kenyan range expansion was anthropogenically influenced, as the expansions of other introduced human commensals may also be.

Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics.

The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15,250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species.