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Planting date, row configuration, and seeding rate are three critical factors in obtaining maximum soybean [Glycine max (L.) Merr.] grain yield and can vary based on soil texture. Therefore, two studies were conducted at the Delta Research and Extension Center in Stoneville, MS. The first study was conducted from 2019 to 2021 and sought to determine the effects of planting date (optimal and delayed 21 days), and row configuration (single‐, twin‐, and triple‐row) on soybean growth, development, and grain yield. The second study was conducted in 2021 with three site‐years to determine the effects of seeding rate (130,000, 180,000, and 220,000 seeds acre−1) in a triple‐row configuration on soybean grain yield compared to a single‐row configuration at 130,000 seeds acre−1 on two soil textures (silt loam and clay). Both studies were repeated on silt loam and clay soil textures in every site‐year. In the first study, the optimal planting date increased soybean grain yield regardless of soil texture. On both soil textures, twin‐ and single‐row configuration yields were equivalent, but triple‐row configuration reduced soybean grain yield up to 9%. Similarly, triple‐row configuration reduced soybean density and height at R3 and R8 growth stages. In the second study, increasing triple‐row configuration soybean seeding rate by at least 38% provided similar soybean grain yields to a single‐row configuration at 130,000 seeds acre−1. These data indicate that triple‐row soybean planting configurations do have some benefits, but that future research should focus on equipment limitations experienced in the current research.Plain Language Summary: Planting date, row configuration, and seeding rate decisions do not occur in a vacuum and must be influenced by other variables such as soil texture and tillage practices. Therefore, two studies were conducted in Stoneville, MS, from 2019 to 2021 at Mississippi State University's Delta Research and Extension Center to evaluate the effects of planting date and row configuration (single, twin, or triple row on a single 40‐inch‐wide seedbed) on two soil textures (silt loam and clay) on soybean yield. Regardless of soil texture, single‐ and twin‐row configurations produced equivalent yields while triple‐row configurations reduced soybean grain yield at a standard seeding rate. When the seeding rate was increased at least 38% on clay soil, triple‐row configurations yielded greater than single‐row configurations. These data indicate that triple‐row configurations in a raised seedbed environment are a possibility, but more research is needed to overcome limitations associated with current equipment. [ABSTRACT FROM AUTHOR]

One of the major constraints to profitable soybean [Glycine max (L.) Merr.] production is yield losses caused by disease. The mid-southern region of the United States typically experiences environmental conditions that are conducive to disease development, particularly during later reproductive growth stages. It is common for producers in this region to apply fungicides at the beginning of pod development (R3 growth stage; development of pods 3/16 inches long). Producers often question if establishing crops in different row patterns would alter the yield response to prophylactic fungicide applications. Producers also seek answers regarding the yield and grain quality responses to fungicide applications across different row patterns. However, limited data exist to determine if fungicide applications influence the responses of soybean’s yield and grain quality between different row spacings. The objective of this research was to evaluate soybean’s growth, development, yield, and grain quality across various row spacings, planting dates, and prophylactic fungicide application programs in the absence of disease. These data support that early-planted soybean had greater yield than later-planted soybean. No interactions were observed among row spacing, planting date, and fungicide product with respect to yield. Independently, no yield differences were observed regardless of the row spacing or the fungicide product. Regarding quality, soybean planted later resulted in fewer total damaged soybean kernels. These data suggest that row spacing and planting date may not influence soybean’s yield response to prophylactic fungicide. Furthermore, these data also suggest that prophylactic fungicide during pod development may not influence the subsequent grain quality. [ABSTRACT FROM AUTHOR]

Farmers have been interested in using foliar‐applied nutrient products to increase soybean [Glycine max (L.) Merr.] yield since at least the 1970s, despite limited evidence that these products offer consistent yield increases when used prophylactically. Recently, interest in foliar fertilizer products for soybean production has been renewed, likely related to elevated soybean prices. Over the 2019 and 2020 growing seasons (46 site‐years), agronomists in 16 states collaborated to test six foliar nutrient treatments (commercial mixtures of macro‐ and micro‐nutrients) on soybean grain yield and composition. Soybean grain yield and composition differed among sites but not among foliar fertilizer treatments. Results show that prophylactic foliar fertilization is likely to decrease the profitability of soybean production. Foliar fertilizer products tested in this study and similar products should not be recommended to U.S. soybean farmers in the absence of visual symptoms of nutrient deficiency. Core Ideas: The tested prophylactic foliar fertilizers did not increase soybean yield.Foliar fertilizers did not change grain composition.Prophylactic foliar fertilizers tested decreased profitability. [ABSTRACT FROM AUTHOR]

Aim: Shaped by climate change and sea‐level rise, tidal salt marshes represent ephemeral systems that are home to only a few species. The dynamic ecological histories of these habitats, however, render it challenging to reconstruct the complete biogeographical histories of their endemic taxa. To better understand the evolutionary history of tidal marsh endemic sparrows, we employ genomic data to evaluate the timing and direction of tidal marsh colonization events and leverage these data to test a series of models describing the biogeographical history of our study taxa. Location: North America. Taxon: Ammospiza Sparrows. Methods: We sampled 54 individuals from the Ammospiza clade from freshwater and saltwater habitats. We sequenced whole genomes and generated a dataset containing 21 million SNPs. Detailed phylogenomic analyses were conducted to identify relationships between tidal marsh and freshwater species. These phylogenies were then used to date divergence times and reconstruct the biogeographical history of the clade as well as identify historic signals of introgression. Results: Phylogenies based on several million SNPs supported well‐resolved clades that correspond to all previous species designations. Demographic modelling within A. nelsoni provided further resolution into the subspecies topology. Phylogenetic and biogeographical reconstructions support a series of saltwater to freshwater colonization events, with some endemic taxa exhibiting associations with tidal marsh habitat over longer evolutionary time‐scales and some habitat transitions occurring as recently as 5,000 years ago. Main Conclusions: Biogeographical and phylogenomic reconstructions support an original freshwater origin of the Ammospiza sparrows currently inhabiting tidal marshes in North America. We also found strong evidence for a saltwater to freshwater transition in A. n. subvirgatus as opposed to the long hypothesized freshwater origin of this group. We conclude that the increased resolution from genomic data paired with an integrative framework of phylogenomic, demographic and biogeographical reconstructions is important for resolving evolutionary histories in complex and ephemeral environments. [ABSTRACT FROM AUTHOR]

We present comments on an article published by Confer et al. (Ecology and Evolution, 10, 2020). Confer et al. (2020) aggregate data from multiple studies of social pairing between Vermivora chrysoptera and V. cyanoptera, two wood warblers in the family Parulidae that hybridize extensively where they co‐occur. From analysis of these data, they conclude there is near‐complete reproductive isolation between these two species. In our reply, we show that this finding is not supported by other lines of evidence, and significant drawbacks of their study design preclude such strong conclusions. In our critique, we show that (a) coarse‐scale plumage classifications cannot be used to accurately estimate hybrid ancestry in Vermivora; (b) extra‐pair paternity is very high in Vermivora and is likely facilitating hybridization, yet was not considered by Confer et al. (2020), and we suggest this will have a substantial influence on the interpretation of reproductive isolation in the system; and (c) the central finding of strong total reproductive isolation is not compatible with the results of other long‐term studies, which demonstrate low isolation and high gene flow. We conclude with a more comprehensive interpretation of hybridization and reproductive isolation in Vermivora warblers. [ABSTRACT FROM AUTHOR]

Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome‐wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced‐representation genome sequencing of 17 winter‐season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few FST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype–environment associations we found that ~200 single‐nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome‐ and range‐wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide‐ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world‐wide local adaptation in these highly dispersive and invasive birds. [ABSTRACT FROM AUTHOR]

The need for profitable soybean [Glycine max (L.) Merr.] production practices grows as input costs rise and profit margins decline. In the mid‐southern United States, a prophylactic fungicide application at the initiation of pod development (R3 growth stage) is a common practice to protect yield potential in soybean. Experiments were conducted during 2017 and 2018 to determine optimal fungicide application timing in the absence of disease, while assessing multiple fungicide options and the resulting impact on soybean yield, quality, and partial return. Fungicide treatments included azoxystrobin as Quadris (Syngenta Crop Protection), azoxystrobin + difenoconazole as Quadris Top SBX (Syngenta Crop Protection), and the combination of fluxapyroxad + pyraclostrobin as Priaxor (BASF) and tetraconazole as Domark 230ME (Gowan). Fungicides were applied in single applications at R3 (three‐sixteenth‐inch long pod development), R4 (three‐fourth inch long pod development), R5 (beginning seed), or R6 (completely developed seed) growth stages or as two applications applied at R3 and again at R5. Based on results, soybean treated with Quadris Top SBX or Priaxor + Domark 230ME produced greater yield than non‐treated soybean. The growth stage when fungicides were applied did not influence soybean yield, confirming the value of current management strategies while also allowing flexibility in the application timing in situations that warrant application during later growth stages. These data suggest an application of Quadris Top SBX to soybean can protect yield while resulting in partial return at a market price of at least US$8.00 bu−1. Adoption of prophylactic, multiplemode of action fungicide applications during fruiting development may sustain yields and improve net returns. Core Ideas: Timing of fungicide application did not affect soybean grain yield.Multiplemode of action fungicides improved soybean yield compared to no fungicide application.Application of fungicides increased overall seed mass, thus increasing yield.Quadris Top SBX generated the highest partial return at a selling price of US$8.00 per bushel. [ABSTRACT FROM AUTHOR]

Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent's most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range‐wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt‐marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced‐representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range‐wide persistence of similarly highly variable species. [ABSTRACT FROM AUTHOR]

Determining the effects of timing and intensity of physical damage in cotton (Gossypium hirsutum L.) grown in the Mid‐South could improve management decisions and insurance adjustments after weather‐ or wildlife‐related crop damage has occurred. Research was conducted to quantify the effects of time of damage and intensity of damage on early‐ and late‐maturing cotton varieties in the Mid‐South. Cultivar selection affected plant height at first bloom, first bloom + 4 wk, and harvest (p ≤.0008), and number of nodes at first bloom + 4 wk and harvest (p ≤.0372). The interaction of intensity of damage by time of damage had an effect on plant height and number of nodes at pinhead square, first bloom, first bloom + 4 wk, and at harvest (p ≤.0001), where reductions in plant height ranged from 20 to 57% and the number of nodes were reduced by 12–64% as damage increased when compared to the untreated check. Damage intensity by time of damage interaction affected lint turnout, lint yield, micronaire, fiber length, and fiber strength (p ≤.0391). Reductions in lint yield (11–70%), lint turnout (2–6%), and micronaire (3–8%) were observed. Increases of 3 and 2% in fiber length and fiber strength, respectively, were also observed at eight node removal at pinhead square. Overall, as the intensity of damage increased, lint yield declined regardless of growth stage, therefore it should be expected to have yield loss where damage has occurred in cotton. [ABSTRACT FROM AUTHOR]

Temperatures that vary spatially and temporally over the soybean growing areas affect soybean seed yield and quality. Five day/night temperature, 21/13, 25/17, 29/21, 33/25, and 37/29°C, effects on total biomass, yield, and seed quality parameters were investigated on indeterminate (Asgrow AG5332, AG) and determinate (Progeny P5333RY, PR) soybean cultivars. The cultivar × temperature interaction was significant for total biomass, seed yield, protein, oil, palmitic acid, oleic acid, linolenic acid, raffinose, and stachyose. Quadratic functions best described the response of yield to temperature, where the optimum temperature for maximum yield was 26°C for AG, and 23°C for PR. Temperature affected all seed quality parameters in both cultivars. Seed protein concentration was slightly higher at the two lower and higher temperatures than at 29/21°C. Seed oil concentration increased with temperature up to 26°C for AG and 25°C for PR and declined at higher temperatures. Palmitic acids showed quadratic responses to temperature with a significant interaction between cultivars, while stearic acid showed a similar quadratic response in both cultivars. Oleic acid increased with increasing temperature while linolenic and linoleic acids declined linearly with temperature. Sucrose concentration declined with an increase in temperature in both the cultivars. Raffinose and stachyose concentrations in the two cultivars responded differently to temperature and declined with increasing temperature. The effects of temperature on yield and seed quality that are described in this research can be used to improve crop growth models and the management of soybean under climate change. [ABSTRACT FROM AUTHOR]

Core Ideas: A sensor threshold of –90 kPa resulted in net returns that were $142/acre greater than the producer standard.A sensor threshold of –90 kPa increased IWUE at least 61% relative to ‐50 and ‐130 kPa thresholds.Neither increasing nor decreasing the threshold as a function of growth stage improved yield relative to a season‐long threshold of –90 kPa. The Mississippi River Valley Alluvial Aquifer (MRVAA) is declining at a rapid rate due to withdrawal for agricultural irrigation. This research was conducted to develop a sensor‐based irrigation threshold for cotton (Gossypium hirsutum L.) that maximizes net returns and irrigation water use efficiency (IWUE). The effects of irrigation based on growth stage (full season, emergence to first bloom, first bloom to peak bloom, and peak bloom to first cracked boll) and irrigation threshold (non‐irrigated, –50 kPa, –90 kPa, and –130 kPa) on cotton lint yield, net returns above irrigation costs, and IWUE were evaluated on a Leeper silty clay loam (fine, smectitic, nonacid, thermic Vertic Epiaquepts). Net returns above irrigation costs were $142/acre greater when the threshold was maintained at –90 kPa rather than –50 kPa (p < 0.0001). Maintaining the threshold at –90 kPa also increased IWUE at least 61% relative to the –50 and –130 kPa thresholds (p < 0.0001). Neither increasing nor decreasing the threshold as a function of growth stage improved yield relative to a season–long threshold of –90 kPa (p = 0.5460). Our data indicate that yield, net returns above irrigation costs, and IWUE are maximized by maintaining a season‐long threshold of –90 kPa. Adoption of this technique could reduce agriculture withdrawal from the MRVAA and thus improve its sustainability. [ABSTRACT FROM AUTHOR]

Abstract: Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150–600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade‐offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy‐wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD‐seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost‐ and time‐efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated. [ABSTRACT FROM AUTHOR]

Abstract: Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority. [ABSTRACT FROM AUTHOR]

Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced-representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans. [ABSTRACT FROM AUTHOR]

Lake Tanganyika, Africa's oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes. [ABSTRACT FROM AUTHOR]

With its large size, complex topography and high number of avian endemics, Hispaniola appears to be a likely candidate for the in situ speciation of its avifauna, despite the worldwide rarity of avian speciation within single islands. We used multilocus comparative phylogeography techniques to examine the pattern and history of divergence in 11 endemic birds representing potential within-island speciation events. Haplotype and allele networks from mitochondrial ND2 and nuclear intron loci reveal a consistent pattern: phylogeographic divergence within or between closely related species is correlated with the likely distribution of ancient sea barriers that once divided Hispaniola into several smaller paleo-islands. Coalescent and mitochondrial clock dating of divergences indicate species-specific response to different geological events over the wide span of the island's history. We found no evidence that ecological or topographical complexity generated diversity, either by creating open niches or by restricting long-term gene flow. Thus, no true within-island speciation appears to have occurred among the species sampled on Hispaniola. Divergence events predating the merging of Hispaniola's paleo-island blocks cannot be considered in situ divergence, and postmerging divergence in response to episodic island segmentation by marine flooding probably represents in situ vicariance or interarchipelago speciation by dispersal. Our work highlights the necessity of considering island geologic history while investigating the speciation-area relationship in birds and other taxa. [ABSTRACT FROM AUTHOR]

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We describe 15 polymorphic microsatellite loci from the white-ruffed manakin Corapipo altera, a common understory bird of Neotropical lowland and montane evergreen forests from eastern Honduras to northwestern Colombia. These markers were developed in order to assess population structure and genetic diversity in a fragmented landscape, and to study gene flow between forest fragments. Primers were tested on a population of 159 individuals from the Coto Brus region of southwestern Costa Rica. We found between four and 23 alleles per locus, and observed heterozygosities ranging from 0.23 to 0.93. [ABSTRACT FROM AUTHOR]

The simple geographic structure of island systems often makes them tractable for studies of the patterns and processes of biological diversification. The Calyptophilus chat-tanagers of Hispaniola are of general evolutionary interest because their multiple lineages might have arisen on a single island, of conservation concern because several isolated populations are nearly extinct, and taxonomically ambiguous because they have been variously lumped or split into one to four species. To explore the context of diversification of the seven extant Calyptophilus populations, we conducted a multilocus coalescent analysis based on sequences of mitochondrial ND2 and three nuclear intron loci. We then compared patterns of phylogeographic genetic variation with the morphological differences that distinguish these populations. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by a large magnitude of nucleotide divergence. Intron structure largely paralleled the geographic grouping pattern of the mitochondrial DNA (mtDNA), but these groups were only reciprocally monophyletic at one of the three introns. Also, the magnitude of between-group divergence was much lower in the introns than mtDNA genealogies. Multilocus coalescent analyses inferred a nonzero divergence time between these two major geographic groups, but suggested that they have experienced a low level of gene flow. All four markers showed substantial allele sharing within each of the two groups, demonstrating that many now separated montane populations do not have long histories of isolation. Considered in concert, our multilocus phylogeographic reconstructions support the recognition of two species within the Calyptophilus complex, and raise the possibility that these taxa differentiated prior to the fusion of the two palaeo-islands that form present-day Hispaniola. [ABSTRACT FROM AUTHOR]

In the socially monogamous barn swallow, previous studies of individuals in the European subspecies Hirundo r. rustica have shown that a male's tail streamer length is under strong sexual selection and is positively associated with several measures of reproductive success, including a low probability of being cuckolded by other males. The prominence of these results has led to subsequent experimental and correlational investigations of individuals in the phenotypically divergent subspecies H. r. erythrogaster in North America, where it has been shown that male tail streamer length is not as strongly associated with reproductive success as in European populations. We examined relationships between male tail streamer length and patterns of: (1) social mate selection and reproductive success, and (2) extra-pair paternity in 265 progeny of 53 social fathers within a New York barn swallow population. Although tail streamers in this population were sexually dimorphic, male tail streamer length did not predict patterns of mate selection, seasonal reproductive success, or extra-pair paternity. Moreover, in contrast to the strong positive relationships between paternity and male streamer length in European populations, summarized in this paper, we found no positive relationship between a male's paternity of young in the nest he is attending and his tail streamer length in our study population in New York. Our results further corroborate recent suggestions that the function of sexual signals varies geographically in this species, although we await additional experimental analyses on streamer lengths to understand the maintenance of sexual dimorphism in this trait. [ABSTRACT FROM AUTHOR]

We currently have only a partial understanding of how phylogenetic relationships relate to patterns of community structure, in part because, for most groups of organisms, we do not know the extent to which ecological similarity results from common ancestry. Associations between phylogenetic relatedness and local community structure are particularly interesting for groups in which many species that span a gradient of phylogenetic divergence occur in potential sympatry. We explored the relationship between evolutionary relatedness and current species co-occurrence among the North American wood-warblers (Aves: Parulidae), a group of songbirds known both for its species diversity and for exhibiting high levels of sympatry at breeding sites. Species co-occurrences were derived from North American Breeding Bird Survey transects comprising 160 000 census points distributed across North America. The nested point-within-transect structure of this survey provides an unusual opportunity to remove larger-scale geographical effects on local community composition and thereby consider patterns of co-occurrence only among regionally sympatric pairs of species. We indexed evolutionary relatedness among all pairs of taxa by genetic distances based on long mitochondrial DNA protein-coding sequences. Most regionally sympatric taxon pairs rarely co-occur at local sites, and the most closely related never exhibit high local co-occurrences, as predicted if past or present competitive effects are strongest for these recently separated lineages. Quantile regression shows that, for a subset of taxa, local co-occurrence does increase with time since common ancestry, and that this apparent relaxation of competitive exclusion is strongest for distantly related species that have differentiated in fundamental ecological and behavioral traits, such as terrestrial vs. arboreal foraging. Comparisons against a null model of species co-occurrence further demonstrate that these patterns occur against a background of phylogenetic niche conservatism: across all phylogenetic distances, sympatric species co-occurred at higher rates than expected by chance, a pattern that might stem from a tendency by these species to show conservatism in their selection of similar general habitat types. Considered in concert, these analyses suggest the simultaneous mediation of local community structure by the ecological similarity of closely related species and by trait divergence among a subset of more distant lineages. [ABSTRACT FROM AUTHOR]

The impact of founder events on levels of genetic variation in natural populations remains a topic of significant interest. Well-documented introductions provide a valuable opportunity to examine how founder events influence genetic diversity in invasive species. House finches ( Carpodacus mexicanus) are passerine birds native to western North America, with the large eastern North American population derived from a small number of captive individuals released in the 1940s. Previous comparisons using amplified fragment length polymorphism (AFLP) markers found equivalent levels of diversity in eastern and western populations, suggesting that any genetic effects of the founder event were ameliorated by the rapid growth of the newly established population. We used an alternative marker system, 10 highly polymorphic microsatellites, to compare levels of genetic diversity between four native and five introduced house finch populations. In contrast to the AFLP comparisons, we found significantly lower allelic richness and heterozygosity in introduced populations across all loci. Three out of five introduced populations showed significant reductions in the ratio of the number of alleles to the allele size range, a within-population characteristic of recent bottlenecks. Finally, native and introduced populations showed significant pairwise differences in allele frequencies in every case, with stronger isolation by distance within the introduced than native range. Overall, our results provide compelling molecular evidence for a founder effect during the introduction of eastern house finches that reduced diversity levels at polymorphic microsatellite loci and may have contributed to the emergence of the Mycoplasma epidemic which recently swept the eastern range of this species. [ABSTRACT FROM AUTHOR]

The Vitelline Warbler Dendroica vitellina is endemic to the Cayman Islands and Swan Islands in the West Indies. This study examined the phylogenetic affinities of the Vitelline Warbler and assessed mitochondrial differentiation among the three Cayman Island populations. Species-level phylogenetic analyses based on 3639 nucleotides of mitochondrial DNA (mtDNA) sequence were used to place the Vitelline Warbler in the larger Dendroica radiation. These analyses confirmed that the Vitelline Warbler is the sister taxon of the Prairie Warbler Dendroica discolor, a species that breeds in continental North America. The magnitude of mitochondrial differentiation between these sister taxa (2.4%) supports their current classification as separate taxonomic species. Additional comparisons based on the 1041-nucleotide NDII gene sequence from 26 Vitelline Warblers provided evidence of within-species genetic structure. NDII haplotypes from Grand Cayman vs. Cayman Brac/Little Cayman differed by 6–10 nucleotide substitutions, and no haplotypes were shared among these island groups, supporting the current separation of the Cayman Island populations into two subspecies. These patterns support the biogeographical scenario that the Vitelline Warbler was derived from a mainland population of the Prairie Warbler. This may have occurred due to a loss of migration in ancestral populations or from over-water dispersal of a mainland resident population. [ABSTRACT FROM AUTHOR]

Many migratory songbirds produce flight calls that vary, sometimes strikingly, among species in duration, frequency, modulation, and pattern, and little is known about what factors are responsible for this variation. Negative correlations between body mass or bill length and song frequencies are well documented in birds, but no studies have examined these associations for flight calls. We explored relationships between flight call and song frequencies and body mass or bill length in 33 species of wood-warblers. Phylogenetically controlled and uncontrolled analyses showed no significant relationship between body mass or bill length and flight call frequency; however, we found significant differences between flight call and song frequencies and a significant relationship between maximum frequencies of flight calls and songs. Our findings suggest that factors other than body mass and bill length are responsible for variation in flight call frequencies in wood-warblers. We suggest that different ecological and atmospheric properties might play important roles in selection for flight call frequencies. [ABSTRACT FROM AUTHOR]

For the past two decades, population declines in Neotropical migrant songbirds have been both a flagship conservation issue and the subject of intensive research initiatives. Nonetheless, the design of effective conservation measures for Neotropical migrants has been hindered by a lack of information on where and how migrant populations are regulated. This problem stems in large part from the difficulty of following individual long-distance migrants throughout their annual cycles. As a result, there has been increasing interest in using genetic markers to determine patterns of connectivity between particular breeding populations and overwintering regions. In species with geographically structured genetic variation during the breeding season, genetic markers can be used to determine the origin of migrating and overwintering individuals. This information on demographic connectivity could be then used to infer the locations or seasons contributing to population trends of currently unknown origin. To date, genetic markers (primarily mitochondrial DNA) have been used to survey only a few species of migratory songbirds, with varying success. To provide examples of the geographic scale at which mtDNA markers are likely to prove most relevant to Neotropical migrant conservation, we surveyed breeding-season variation in North American populations of three long-distance migrant taxa: the Yellow-breasted Chat (Icteria virens ), Common Yellowthroat (Geothlypis trichas ), and Nashville Warbler (Vermivora ruficapilla ). We then used this information to screen individuals sampled at overwintering sites in Mexico and Central America. Genetic structure was only found at the broadest continent-wide scale in all three species, which allowed us to assign overwintering individuals to eastern or western breeding lineages but did not allow us to assign overwintering individuals to breeding populations of origin on a finer scale suitable for assaying local demographic trends. Owing to mitochondrial homogeneity among widely separated breeding locations, mtDNA markers (especially when used alone) are unlikely to provide a panacea for the problem of interseasonal connectivity among migrant songbirds. [ABSTRACT FROM AUTHOR]

Recent natural and anthropogenic disturbances have endangered two of the three oriole species endemic to single islands in the Lesser Antilles. The ongoing eruption of the Soufriere Hills volcano may have doomed the Montserrat Oriole ( Icterus oberi), whereas high levels of nest parasitism by a cowbird threaten the Martinique Oriole ( I. bonana). These orioles and related Antillean and Central American forms have been considered part of the Icterus dominicensis superspecies complex, but the taxonomic status of the different Antillean island populations has been long debated. To investigate levels of evolutionary differentiation among threatened Lesser Antillean orioles, we analyzed 2507 nucleotides of protein-coding mitochondrial DNA (mtDNA) sequence from orioles on Martinique, Montserrat, St. Lucia ( I. laudabilis), Puerto Rico ( I. dominicensis dominicensis), Mexico ( I. d. prosthemelas), and three Icterus outgroup species. Phylogenetic analyses of the mtDNA data supported the monophyly of Antillean members of the I. dominicensis complex and identified a star-like pattern of relationship among them. Mitochondrial distances between the Antillean populations were large (4.5–5.8% nucleotide divergence) and suggested that the Lesser Antillean orioles have been isolated evolutionarily from one another since the late Pliocene. The oriole taxa on Montserrat, Martinique, and St. Lucia meet species criteria under the phylogenetic species concept and represent evolutionarily significant units. The impending extinction of the phylogenetically unique Montserrat oriole highlights the vulnerability of island endemics to habitat degradation followed by rare and unpredictable natural catastrophes. [ABSTRACT FROM AUTHOR]

Analyzes the habitat diversity in fauna species-area relationships in Lesser Antilles. Correlation of species richness with the island area; Differences in the biological traits of the different faunal groups; Impact of island-size-dependent extinction.