Charles M. Francis

Identification of Birds through DNA Barcodes

Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10× average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

Comprehensive DNA barcode coverage of North American birds

DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.

Confronting collinearity: comparing methods for disentangling the effects of habitat loss and fragmentation

Estimating the relative importance of habitat loss and fragmentation is necessary to estimate the potential benefits of specific management actions and to ensure that limited conservation resources are used efficiently. However, estimating relative effects is complicated because the two processes are highly correlated. Previous studies have used a wide variety of statistical methods to separate their effects and we speculated that the published results may have been influenced by the methods used. We used simulations to determine whether, under identical conditions, the following 7 methods generate different estimates of relative importance for realistically correlated landscape predictors: residual regression, model or variable selection, averaged coefficients from all supported models, summed Akaike weights, classical variance partitioning, hierarchical variance partitioning, and a multiple regression model with no adjustments for collinearity. We found that different methods generated different rankings of the predictors and that some metrics were strongly biased. Residual regression and variance partitioning were highly biased by correlations among predictors and the bias depended on the direction of a predictor’s effect (positive vs. negative). Our results suggest that many efforts to deal with the correlation between amount and fragmentation may have done more harm than good. If confounding effects are controlled and adequate thought is given to the ecological mechanisms behind modeled predictors, then standardized partial regression coefficients are unbiased estimates of the relative importance of amount and fragmentation, even when predictors are highly correlated.

The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia.

Background Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning. Methodology and Principal Findings DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized. Conclusions DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.

LONG-TERM CHANGES IN SURVIVAL RATES OF LESSER SNOW GEESE'

Survival rates of adult and juvenile Lesser Snow Geese (Anser caerulescens caerulescens) were estimated based on hunter recoveries from over 80 000 geese banded between 1970 and 1988 at La Perouse Bay, near Churchill, Manitoba. Adult survival rate increased significantly from -78% in 1970 to nearly 88% in 1987. Similar increases in adult survival, although not significant, occurred between 1969 and 1979 at a second colony of Snow Geese at Cape Henrietta Maria in Northern Ontario. These increases coincided with a decline in the proportion of Snow Geese being shot each year on the flyways, suggesting that reduced mortality from hunting may be responsible for the increased sur- vival. In contrast, survival rates of fledglings over their first year decreased significantly from a mean of 60% in 1970 to -30% in 1987, despite the reduction in hunting pressure. This indicates that young geese have been suffering increasing rates of nonhunting mortality, most likely prior to leaving the breeding grounds or on their first autumn migration. Their increased mortality appears to be related to slower growth rates and reduced body size induced by deteriorating feeding conditions on the breeding grounds. This study shows that different processes can influence mortality rates at different stages of the life cycle. The long-term changes indicate that mean values of age-specific survival rates are not adequate to describe the dynamics of this population.

Molecular phylogenetic reconstructions identify East Asia as the cradle for the evolution of the cosmopolitan genus Myotis (Mammalia, Chiroptera)

Sequences of the mitochondrial cytochrome b (1140 bp) and nuclear Rag 2 (1148 bp) genes were used to assess the evolutionary history of the cosmopolitan bat genus Myotis, based on a worldwide sampling of over 88 named species plus 7 species with uncertain nomenclature. Phylogenetic reconstructions of this comprehensive taxon sampling show that most radiation of species occurred independently within each biogeographic region. Our molecular study supports an early divergence of species from the New World, where all Nearctic and Neotropical species plus a lineage from the Palaearctic constitute a monophyletic clade, sister to the remaining Old World taxa. The major Old World clade includes all remaining Eurasian taxa, most Oriental species, one Oceanian, and all Ethiopian species. Another lineage, including M. latirostris from Taiwan, appears at the base of these two major biogeographic clades and, because it bears nyctalodont molars, could be considered as a distinct genus. However, this molar configuration is also found in crown-group species, indicating that these dental characters are variable in the genus Myotis and may confound interpretation of the fossil record. Molecular datings suggest an origin of all recent Myotis in the early Miocene (about 21MYA with 95% highest posterior density interval 23-20MYA). This period was characterized by a global climatic cooling that reduced the availability of tropical habitats and favoured the development of more temperate vegetation. This sharp climatic change might have triggered the evolution of Myotis in the Northern continents, because Myotis ancestors seem to have been well adapted and successful in such temperate habitats. Ancestral area reconstructions based on the molecular phylogeny suggest that the eastern portion of the Asian continent was an important center of origin for the early diversification of all Myotis lineages, and involved relatively few subsequent transcontinental range expansions.

AGE-RELATED DIFFERENCES IN BODY MASS AND RATES OF MASS GAIN OF PASSERINES DURING AUTUMN MIGRATORY STOPOVER

Abstract Age-related differences in stopover ecology of migrant songbirds are poorly understood. We compared body mass, fat scores, and rates of mass gain of adults and immatures of 52 species of birds during autumn migration stopover at Long Point, Ontario, Canada, on the north shore of Lake Erie. Mean body mass of adults was greater than that of immatures in the majority of species with a detectable difference, but the average difference across species was only 1%. Fat scores were also higher for adults in many species, suggesting that mass differences were due to differences in condition rather than body size. Mean rate of mass gain, estimated from changes in body mass of first captures over the course of the day, did not differ significantly between adults and immatures of most species. However, the power to detect differences was low. Averaged across species (n = 117 903 birds), the estimated rate of mass gain for adults was 10% higher than that for immatures, but with 95% confidence limits ranging from 12% lower to 32% higher. The observed differences in body mass could be produced by a small difference in rate of mass gain. Small differences in body mass and rate of mass gain between immatures and adults could indicate that young passerines rapidly develop similar foraging skills to those of adults, or that young birds are not particularly disadvantaged at Long Point either because of good food supply, or because there is little need to accumulate large amounts of fat in the early stages of migration. Diferencias Dadas por la Edad en la Masa Corporal y la Tasa de Aumento de Masa de Aves Paserinas durante Escalas Migratorias Otoñales Resumen. La ecología de las aves canoras migratorias de diferentes edades en sus sitios de descanso es poco conocida. Comparamos la masa corporal, los niveles de grasa y la tasa de aumento de masa de adultos e inmaduros de 52 especies de aves durante escalas migratorias otoñales en la costa norte del Lago Erie, Long Point, Ontario, Canadá. La masa corporal de los adultos fue superior a la de los inmaduros en la mayoría de las especies, pero en promedio esta diferencia fue sólo del 1% para todas las especies. Los niveles de grasa también fueron mayores en adultos de muchas especies, lo que sugiere que las diferencias en masa se debieron a diferencias en la condición física y no al tamaño corporal de las aves. La tasa media de aumento de masa, estimada a partir de cambios en la masa corporal de las primeras capturas en el curso del día, no difirió significativamente entre adultos e inmaduros para la mayoría de las especies, pero el poder de la prueba estadística para detectar diferencias fue bajo. Promediada para todas las especies (n = 117 903 aves), la tasa estimada de aumento de masa para los adultos fue superior en un 10% a la de los inmaduros, pero con intervalos de confianza del 95% fluctuando entre un mínimo de 12% y 32%. Las diferencias observadas en masa corporal pudieron ser producidas por una pequeña diferencia en las tasas de aumento de masa. Las pequeñas diferencias en la masa corporal y la tasa de aumento de masa entre inmaduros y adultos podrían indicar que las aves jóvenes desarrollan habilidades de forrajeo similares a las de los adultos rápidamente o que las aves jóvenes no están particularmente en desventaja en Long Point ya sea porque el alimento es abundante o porque no es necesario acumular grandes cantidades de grasa en las primeras etapas de la migración.

CHANGES IN SURVIVAL RATES OF LESSER SNOW GEESE WITH AGE AND BREEDING STATUS

Survival rates of Lesser Snow Geese (Chen caerulescens caerulescens) were ex- amined based on recoveries and recaptures of about 350,000 geese banded at breeding colonies in northern Canada, at migration stopover points in the Dakotas and Missouri, and on the wintering grounds in Louisiana and Texas. First-year survival rates for goslings banded on the breeding grounds varied from 10 to 70% of adult survival rates. Much of the juvenile mortality occurred on the breeding grounds or early on the first migration. Young geese that reached migration stopovers or the wintering grounds were more vulnerable to hunters than adults, but had only slightly lower survival rates than adults. Greater vulnerability and lower survival continued through the second year of life, even though yearlings do not breed. In contrast, older birds that did not breed, or failed early in a nesting attempt, were much less vulnerable to hunters in the following hunting season than successful breeding adults, but did not appear to have higher survival as a result. Geese captured for the first time as breeding adults had slightly lower survival rates than geese that had been recaptured at the colony at least once, suggesting experienced breeders have higher survival. Although there was some evidence that older birds were slightly more vulnerable to hunters, there were no signs of any changes in survival rate with age in older geese, indicating that senescence, if it affects survival, does not do so for at least the first 10 to 15 years of age. With current hunting levels, less than 5% of Lesser Snow Geese are likely to live beyond this age. Our study demonstrates a variety of statistical methods for testing hypotheses about age-specific survival using both recovery and recapture data, even when the data do not permit estimation of the exact survival rates. Received 13 May 1991, accepted 13 January 1992.

Canadian Estimate of Bird Mortality Due to Collisions and Direct Habitat Loss Associated with Wind Turbine Developments

We estimated impacts on birds from the development and operation of wind turbines in Canada considering both mortality due to collisions and loss of nesting habitat. We estimated collision mortality using data from carcass searches for 43 wind farms, incorporating correction factors for scavenger removal, searcher efficiency, and carcasses that fell beyond the area searched. On average, 8.2 ± 1.4 birds (95% C.I.) were killed per turbine per year at these sites, although the numbers at individual wind farms varied from 0 26.9 birds per turbine per year. Based on 2955 installed turbines (the number installed in Canada by December 2011), an estimated 23,300 birds (95% C.I. 20,000 28,300) would be killed from collisions with turbines each year. We estimated direct habitat loss based on data from 32 wind farms in Canada. On average, total habitat loss per turbine was 1.23 ha, which corresponds to an estimated total habitat loss due to wind farms nationwide of 3635 ha. Based on published estimates of nest density, this could represent habitat for ~5700 nests of all species. Assuming nearby habitats are saturated, and 2 adults displaced per nest site, effects of direct habitat loss are less than that of direct mortality. Installed wind capacity is growing rapidly, and is predicted to increase more than 10-fold over the next 10-15 years, which could lead to direct mortality of approximately 233,000 birds / year, and displacement of 57,000 pairs. Despite concerns about the impacts of biased correction factors on the accuracy of mortality estimates, these values are likely much lower than those from collisions with some other anthropogenic sources such as windows, vehicles, or towers, or habitat loss due to many other forms of development. Species composition data suggest that < 0.2% of the population of any species is currently affected by mortality or displacement from wind turbine development. Therefore, population level impacts are unlikely, provided that highly sensitive or rare habitats, as well as concentration areas for species at risk, are avoided. RESUME. Nous avons evalue les impacts de la construction et de l’operation de parcs eoliens sur les oiseaux au Canada en considerant la mortalite attribuable tant aux collisions qu’a la perte d’habitat de nidification. Nous avons estime la mortalite par collision a partir de donnees provenant de la recherche de carcasses dans 43 parcs eoliens, et avons inclus des facteurs de correction tenant compte de l’efficacite des observateurs, de la persistance des carcasses et du fait qu’elles pouvaient se trouver a l’exterieur de l’aire couverte par les recherches. En moyenne, 8,2 ± 1,4 oiseaux (IC a 95 %) ont ete tues par eolienne par annee dans ces parcs, quoique ce nombre a varie de 0 a 26,9 oiseaux par eolienne par annee lorsque les parcs ont ete pris individuellement. Fonde sur 2 955 eoliennes construites (bilan en decembre 2011 au Canada), nous estimons que 23 300 oiseaux (IC a 95 % = 20 000 a 28 300) seraient tues a la suite de collisions avec les eoliennes chaque annee. Nous avons ensuite estime la perte directe d’habitat a partir de donnees de 32 parcs eoliens au Canada. En moyenne, la perte d’habitat par turbine s’elevait a 1,23 ha, ce qui equivaut a 3 635 ha d’habitat perdu au profit d’eoliennes dans l’ensemble du Canada. Selon des estimations de densite de nids publiees, une quantite d’habitat de cet ordre pourrait contenir 5 700 nids, toutes especes confondues. En presumant que les milieux voisins sont satures et que deux adultes sont deplaces par site de nidification, les effets de la perte d’habitat directe sont moins importants que ceux qui sont attribuables a la mortalite directe. Or, la puissance eolienne installee augmente rapidement et on prevoit qu’elle se multipliera par plus de dix d’ici 10 a 15 ans, ce qui pourrait se traduire par la mortalite directe d’environ 233 000 oiseaux/annee et le deplacement de 57 000 couples. Malgre les preoccupations quant aux impacts des biais des facteurs de correction sur la precision des estimations de la mortalite, ces valeurs sont vraisemblablement moins elevees que celles calculees pour les collisions avec d’autres sources anthropiques comme les fenetres, les vehicules ou les tours, ou encore celles associees a la perte d’habitat attribuable a de nombreuses autres formes de developpement. Les donnees sur la composition specifique indiquent que < 0,2 % des populations, peu importe l’espece, est en realite touchee par la mortalite ou le deplacement Canadian Wildlife Service Avian Conservation and Ecology 8(2): 10 http://www.ace-eco.org/vol8/iss2/art10/ occasionne par le developpement eolien. Ainsi, les repercussions sur le plan des populations sont peu probables, pourvu que les milieux tres sensibles ou rares, de meme que les aires de concentration d’especes en peril soient evites.

Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity

Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.