The lacrimal/ectethmoid region of waterfowl (Aves, Anseriformes): Phylogenetic signal and major evolutionary patterns.

Waterfowl (Aves, Anseriformes) constitute an ancient global radiation, and understanding the pattern and timing of their evolution requires a well-corroborated phylogeny including extant species and fossils. Following the molecular advances in avian systematics, however, morphology has often been held as misleading, yet congruence with molecular data has been shown to vary considerably among different skeletal parts. Here, we explore phylogenetic signal in discrete characters of the lacrimal/ectethmoid region of waterfowl, which is highly variable among species and constitutes a rich source of data. We do so by combining cladistic and multivariate approaches, and using phylogenetic comparative methods. We quantitatively recognize three major morphological types among lacrimal bones, and discuss homoplasy and potential synapomorphies of major clades using a molecular backbone tree. Our results clearly indicate that the lacrimal bone carries substantial phylogenetic signal and could be of systematic value at different levels of the phylogeny of waterfowl, feeding the exploration of other regions of the skull with this combined approach.

Virome heterogeneity and connectivity in waterfowl and shorebird communities.

Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.

Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species.

The highly repetitive DNA sequence of centromeric heterochromatin is an effective molecular cytogenetic marker for investigating genomic compartmentalization between macrochromosomes and microchromosomes in birds. We isolated four repetitive sequence families of centromeric heterochromatin from three Anseriformes species, viz., domestic duck (Anas platyrhynchos, APL), bean goose (Anser fabalis, AFA), and whooper swan (Cygnus cygnus, CCY), and characterized the sequences by molecular cytogenetic approach. The 190-bp APL-HaeIII and 101-bp AFA-HinfI-S sequences were localized in almost all chromosomes of A. platyrhynchos and A. fabalis, respectively. However, the 192-bp AFA-HinfI-L and 290-bp CCY-ApaI sequences were distributed in almost all microchromosomes of A. fabalis and in approximately 10 microchromosomes of C. cygnus, respectively. APL-HaeIII, AFA-HinfI-L, and CCY-ApaI showed partial sequence homology with the chicken nuclear-membrane-associated (CNM) repeat families, which were localized primarily to the centromeric regions of microchromosomes in Galliformes, suggesting that ancestral sequences of the CNM repeat families are observed in the common ancestors of Anseriformes and Galliformes. These results collectively provide the possibility that homogenization of centromeric heterochromatin occurred between microchromosomes in Anseriformes and Galliformes; however, homogenization between macrochromosomes and microchromosomes also occurred in some centromeric repetitive sequences.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans.

Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans (Cygnus atratus) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage (C. sumnerensis, Pouwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction.

Recombinant Turkey Herpesvirus-AI Vaccine Virus Replication in Different Species of Waterfowl.

Waterfowl play a key role in the epidemiology of the H5N1 subtype of highly pathogenic avian influenza (HPAI) virus; therefore, efficient immunization of domesticated ducks and geese to maximize the impact of other control measures is of great importance. A recombinant (r)HVT-AI, expressing the HA gene of a clade 2.2 H5N1 HPAI strain had been developed and proved to be efficient against different clades of H5N1 HPAI virus in chickens after a single vaccination at 1 day old and could provide long-term immunity. We investigated whether rHVT-AI applied at 1 day old is able to replicate in different species and crossbreeds of ducks and in geese with the aim of collecting data on the possible application of rHVT-AI vaccine in different species of waterfowl for the control of H5N1 HPAI. We tested the possible differences among different waterfowl species, i.e., between geese (Anser anser, domesticated greylag goose), Muscovy ducks (Cairina moschata forma domestica), Pekin ducks (Anas platyrhynchos forma domestica), and mule ducks (Muscovy duck × Pekin duck), in their susceptibility to support the replication of rHVT-AI. Vaccine virus replication was followed by real-time PCR in spleen, bursa, and feather tip samples. Humoral immune response to vaccination was tested using the hemagglutination inhibition (HI) test and H5-specific commercial ELISA. Significant differences among the different waterfowl species regarding the rate of rHVT-AI replication was detected that were not reflected by the same difference in the immune response to vaccination. Replication of the rHVT-AI vaccine was very limited in Pekin ducks, somewhat better in mule ducks, and the vaccine virus was replicating significantly better in Muscovy ducks and geese, reaching 100% detectability at certain time points after administration at 1 day old. Results indicated that the vaccine virus could establish different levels of persistent infection in these species of waterfowl. No humoral immune response could be detected either by HI test or ELISA during the tested postvaccination period (5 wk).

Influenza A Viruses from Overwintering and Spring-Migrating Waterfowl in the Lake Erie Basin, United States.

Influenza A virus (IAV) surveillance in migratory waterfowl in the United States has primarily occurred during late summer and the autumn southern migration. Data concerning the presence and ecology of IAVs in waterfowl during winter and spring seasons in the U.S. northern latitudes have been limited, mainly due to limited access to waterfowl for sampling. The southwestern Lake Erie Basin is an important stopover site for waterfowl during migration periods, and over the past 28 years, 8.72% of waterfowl sampled in this geographic location have been positive for IAV recovery during summer and autumn (June-December). To gain a better understanding of influenza A viral dynamics in waterfowl populations during winter and spring migration (February through April), cloacal swabs were collected from overwintering and spring-migrating waterfowl in Ohio and Michigan in 2006, 2007, 2013, and 2014. A total of 740 cloacal swabs were collected and tested using virus isolation in embryonating chicken eggs, resulting in the recovery of 33 (4.5%) IAV isolates. The influenza A isolates were recovered from eight waterfowl species in the order Anseriformes. Antigenically, the IAV isolates represent 15 distinct hemagglutinin (HA) and neuraminidase (NA) combinations, with seven (21%) of the isolates reported as mixed infections based on antigenic HA subtyping, NA subtyping, or both. This effort demonstrates the presence of antigenically diverse IAV in waterfowl during overwintering and spring migration at northern latitudes in the United States, thereby contributing to the understanding of the maintenance of diversity among waterfowl-origin IAVs.

Antigenic Characterization of H3 Subtypes of Avian Influenza A Viruses from North America.

Besides humans, H3 subtypes of influenza A viruses (IAVs) can infect various animal hosts, including avian, swine, equine, canine, and sea mammal species. These H3 viruses are both antigenically and genetically diverse. Here, we characterized the antigenic diversity of contemporary H3 avian IAVs recovered from migratory birds in North America. Hemagglutination inhibition (HI) assays were performed on 37 H3 isolates of avian IAVs recovered from 2007 to 2011 using generated reference chicken sera. These isolates were recovered from samples taken in the Atlantic, Mississippi, Central, and Pacific waterfowl migration flyways. Antisera to all the tested H3 isolates cross-reacted with each other and, to a lesser extent, with those to H3 canine and H3 equine IAVs. Antigenic cartography showed that the largest antigenic distance among the 37 avian IAVs is about four units, and each unit corresponds to a 2 log 2 difference in the HI titer. However, none of the tested H3 IAVs cross-reacted with ferret sera derived from contemporary swine and human IAVs. Our results showed that the H3 avian IAVs we tested lacked significant antigenic diversity, and these viruses were antigenically different from those circulating in swine and human populations. This suggests that H3 avian IAVs in North American waterfowl are antigenically relatively stable.

One Decade of Active Avian Influenza Wild Bird Surveillance in Belgium Showed a Higher Viroprevalence in Hunter-Harvested Than in Live-Ringed Birds.

Active monitoring of avian influenza (AI) viruses in wild birds was initiated in Belgium in 2005 in response to the first highly pathogenic avian influenza (HPAI) H5N1 outbreaks occurring in Europe. In Belgium, active wild bird surveillance that targeted live-ringed and hunter-harvested wild birds was developed and maintained from 2005 onward. After one decade, this program assimilated, analyzed, and reported on over 35,000 swabs. The 2009-2014 datasets were used for the current analysis because detailed information was available for this period. The overall prevalence of avian influenza (AI) in samples from live-ringed birds during this period was 0.48% whereas it was 6.12% in hunter-harvested samples. While the ringing sampling targeted a large number of bird species and was realized over the years, the hunting sampling was mainly concentrated on mallard (Anas platyrhynchos) during the hunting season, from mid-August to late January. Even when using just AI prevalence for live-ringed A. platyrhynchos during the hunting season, the value remained significantly lower (2.10%) compared to that detected for hunter-harvested mallards. One explanation for this significant difference in viroprevalence in hunter-harvested mallards was the game restocking practice, which released captive-bred birds in the wild before the hunting period. Indeed, the released game restocking birds, having an AI-naïve immune status, could act as local amplifiers of AI viruses already circulating in the wild, and this could affect AI epidemiology. Also, the release into the wild of noncontrolled restocking birds might lead to the introduction of new strains in the natural environment, leading to increased AI presence in the environment. Consequently, the release of naïve or infected restocking birds may affect AI dynamics.

Waterbird Susceptibility to Avian Cholera at Hayward Marsh, California, USA.

We characterized past avian cholera outbreaks in waterbirds at Hayward Marsh, California, US. In 2013, we surveyed populations and determined the presence of disease using several diagnostic methods, including behavioral and physical observations, field necropsy, and bacterial culture. We compiled this information with data from previous outbreaks from 1990-2012 to compare waterbird abundance to various measures of mortality, including percentage of mortality and percentage of difference between abundance and mortality by species. We suggest that Ruddy Duck ( Oxyura jamaicensis ) have consistently suffered greater mortality from this disease than have other species at this site.

Taxonomic and Geographic Bias in Conservation Biology Research: A Systematic Review of Wildfowl Demography Studies.

Demographic data are important to wildlife managers to gauge population health, to allow populations to be utilised sustainably, and to inform conservation efforts. We analysed published demographic data on the world's wildfowl to examine taxonomic and geographic biases in study, and to identify gaps in knowledge. Wildfowl (order: Anseriformes) are a comparatively well studied bird group which includes 169 species of duck, goose and swan. In all, 1,586 wildfowl research papers published between 1911 and 2010 were found using Web of Knowledge (WoK) and Google Scholar. Over half of the research output involved just 15 species from seven genera. Research output was strongly biased towards 'high income' countries, common wildfowl species, and measures of productivity, rather than survival and movement patterns. There were significantly fewer demographic data for the world's 31 threatened wildfowl species than for non-threatened species. Since 1994, the volume of demographic work on threatened species has increased more than for non-threatened species, but still makes up only 2.7% of total research output. As an aid to research prioritisation, a metric was created to reflect demographic knowledge gaps for each species related to research output for the species, its threat status, and availability of potentially useful surrogate data from congeneric species. According to the metric, the 25 highest priority species include thirteen threatened taxa and nine species each from Asia and South America, and six from Africa.

Complete mitochondrial genome of Cygnus cygnus (Aves, Anseriformes, Anatidae).

In this study, the complete mitochondrial genome of Cygnus cygnus (Aves, Anseriformes, Anatidae) was sequenced. The genome, consisting of 16 724 base pairs (bp), encoded 13 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a control region (CR). Two rRNA genes for 12S rRNA (991 bases) and 16S rRNA (1608 bases) are located between tRNA-Phe and tRNA-Leu (UUR) and divided by the tRNA-Val. The CR, of 1156 bp in length, is located between tRNA-Glu and tRNA-Phe. The overall base composition of C. cygnus is G + C: 47.2%, A + T: 52.8%, apparently with a slight AT bias. Phylogenetic analysis showed that the C. cygnus was closed to Cygnus columbianus.

Phylogenetic studies of two Anas platyrhynchos (Anatini: Anatinae) in Hunan province of China based on complete mitochondrial DNA sequences.

In this study, we cloned and sequenced the complete mitochondrial DNAs of Chinese duck, Anas platyrhynchos, population from two different areas of Hunan province in China. The Anas platyrhynchos breed Linwu duck (LW) sample was taken from the Linwu county of Chenzhou city, and the Anas platyrhynchos breed Youxian duck (YX) sample was taken from the Youxian county of Zhuzhou city. The lengths of their complete mitochondrial genome were 16,604 bp (LW) and 16,606 bp (YX), respectively. The organization of the two Anas platyrhynchos breed mitochondrial genomes was similar to those reported from other duck mitochondrial genomes. Phylogenetic analyses using N-J computational algorithms showed that the analyzed species are divided into four major clades: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Also, the Linwu duck and Youxian duck have highly similar phylogenetic relationship.

A likelihood-based approach for assessment of extra-pair paternity and conspecific brood parasitism in natural populations.

Genotypes are frequently used to assess alternative reproductive strategies such as extra-pair paternity and conspecific brood parasitism in wild populations. However, such analyses are vulnerable to genotyping error or molecular artefacts that can bias results. For example, when using multilocus microsatellite data, a mismatch at a single locus, suggesting the offspring was not directly related to its putative parents, can occur quite commonly even when the offspring is truly related. Some recent studies have advocated an ad-hoc rule that offspring must differ at more than one locus in order to conclude that they are not directly related. While this reduces the frequency with which true offspring are identified as not directly related young, it also introduces bias in the opposite direction, wherein not directly related young are categorized as true offspring. More importantly, it ignores the additional information on allele frequencies which would reduce overall bias. In this study, we present a novel technique for assessing extra-pair paternity and conspecific brood parasitism using a likelihood-based approach in a new version of program cervus. We test the suitability of the technique by applying it to a simulated data set and then present an example to demonstrate its influence on the estimation of alternative reproductive strategies.

[Habitat use patterns of the Black Brant Branta bernicla nigricans (Anseriformes: Anatidae) in natural and artificial areas of Guerrero Negro, Baja California Sur, Mexico]. / Patrones de uso de sitios naturales y artificiales por Branta bernicla nigricans (Anseriformes: Anatidae) en Guerrero Negro, Baja California Sur, Mexico.

The Black Brant is a common inhabitant of the Western Artic American tundra, which migrates to Southern Pacific coasts during the winter season. Approximately, 31000 birds (31%) constitute the Mexican population of Brants at Guerrero Negro, Ojo de Liebre, and Exportadora de Sal lagoon complex; nevertheless, there is little information about the distribution patterns and zone usage. At Guerrero Negro Lagoon (GNL), Ojo de Liebre Lagoon (OLL, both natural sites), and at Exportadora de Sal (ESSA, artificial site) we determined by monthly censuses (from November 2006 to April 2007, 08:00-16:00h) and observed: (1) season and site effects on population structure (age groups), and (2) the tide level relationship with the abundance and proportion of feeding birds. Within a total of 150 observation hours and 98 birds, our results showed a general 0.68 proportion of adults, that was higher in winter than in spring. The statistics analysis showed no effects by site on the proportion of feeding birds, but we observed a temporal decrease at ESSA and at GNL. In contrast the proportion of feeding birds at OLL was constant. We observed an increase in the juveniles between winter and spring. This increase is related with the differential migration, which mentions that the juveniles are the last to leave the wintering area. In winter the relations of the tide level with the abundance of Brant were: direct at ESSA, inverse at OLL and no relation found at GNL. In spring, no relation was observed in the sites. The proportion of Brants feeding at OLL (the site with the higher abundance) was independent of the tide level. This is related with two possible behaviors of the geese: (1) they can move through the lagoon and take advantage of the tidal lag, which is up to four hours; and (2) they can modify their feeding strategies, more on floating eelgrass (Zostera marina).

Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae.

Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups ("pheasants" and "partridges") is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.

Patrones de uso de sitios naturales y artificiales por Branta bernicla nigricans (Anseriformes: Anatidae) en Guerrero Negro, Baja California Sur, México / Habitat use patterns of the Black Brant Branta bernicla nigricans (Anseriformes: Anatidae) in natural and artificial areas of Guerrero Negro, Baja California Sur, Mexico

The Black Brant is a common inhabitant of the Western Artic American tundra, which migrates to Southern Pacific coasts during the winter season. Approximately, 31 000 birds (31%) constitute the Mexican population of Brants at Guerrero Negro, Ojo de Liebre, and Exportadora de Sal lagoon complex; nevertheless, there is little information about the distribution patterns and zone usage. At Guerrero Negro Lagoon (GNL), Ojo de Liebre Lagoon (OLL, both natural sites), and at Exportadora de Sal (ESSA, artificial site) we determined by monthly censuses (from November 2006 to April 2007, 08:00-16:00h) and observed: (1) season and site effects on population structure (age groups), and (2) the tide level relationship with the abundance and proportion of feeding birds. Within a total of 150 observation hours and 98 birds, our results showed a general 0.68 proportion of adults, that was higher in winter than in spring. The statistics analysis showed no effects by site on the proportion of feeding birds, but we observed a temporal decrease at ESSA and at GNL. In contrast the proportion of feeding birds at OLL was constant. We observed an increase in the juveniles between winter and spring. This increase is related with the differential migration, which mentions that the juveniles are the last to leave the wintering area. In winter the relations of the tide level with the abundance of Brant were: direct at ESSA, inverse at OLL and no relation found at GNL. In spring, no relation was observed in the sites. The proportion of Brants feeding at OLL (the site with the higher abundance) was independent of the tide level. This is related with two possible behaviors of the geese: (1) they can move through the lagoon and take advantage of the tidal lag, which is up to four hours; and (2) they can modify their feeding strategies, more on floating eelgrass (Zostera marina).

En el complejo lagunar Guerrero Negro-Ojo de Liebre-Exportadora de Sal inverna el 31% de la población de Ganso de collar (Branta bernicla nigricans) que utiliza México (31 000 aves en promedio). Nosotros realizamos censos de punto mensuales (noviembre 2006 a abril 2007) en tres sitios para determinar: (1) los efectos de la época del año y del sitio en la estructura poblacional (grupos de edad) y (2) la relación del nivel de marea con la abundan- cia y la proporción de aves alimentándose. La proporción general de adultos fue de 0.68. Esta proporción fue mayor en invierno que en primavera. Por sitio en LGN y ESSA disminuyó y en LOL se mantuvo constante. El incremento de aves inmaduras entre el invierno y la primavera se relaciona con su partida primaveral tardía. La alimentación del Ganso de collar en LOL (el sitio de mayor abundancia) fue independiente del nivel de marea, lo que se puede relacionar con dos conductas: (1) que las aves se muevan a lo largo de la laguna, para aprovechar el desfase, de hasta cuatro horas en el nivel de marea o (2) que modifiquen sus estrategias de alimentación, para consumir el pasto flotante.

Molecular tools for species and sex identification in the mixed-species flocks of bean geese and white-fronted geese.

Genetic studies on protected species can be difficult, particularly when they form a mixed-species flock with other species. The bean goose (Anser fabalis), which is internationally recognized as a threatened species, was observed to form overwintering foraging flocks with white-fronted goose (Anser albifrons) at agricultural lands to feed on the grains in Korea. Non-invasive samples such as feces and feather that are readily available in their foraging ground can be useful for understanding the structure and composition of populations, but they often require specific experimental conditions due to small amount or low quality of DNA. In this study, we designed sets of primers that would allow efficient molecular identification of species and sex of individuals of bean geese and white-fronted geese. Species-specific primers (WFG-F/BG-F and G-R), developed from ND2 region of mitochondrial DNA, produced PCR products with different sizes which allow easy species identification without further sequencing. Based on published CHD 1 sequences, we designed internal primers (Gsex-F and Gsex-R) for sex determination that can be used in nested PCR after applying P2/P8 primers, and our methods clearly showed high success rate of molecular sexing from non-invasive samples. These molecular tools open the possibilities for genetic studies using non-invasive samples collected from a mixed-species aggregation containing bean geese and white-fronted geese.

Complete mitochondrial genome of the Bewick's swan Cygnus columbianus bewickii (Aves, Anseriformes, Anatidae).

The mitochondrial genome of Bewick's swan Cygnus columbianus bewickii was completely sequenced and then the resultant data were compared with those of the whistling swan Cygnus columbianus columbianus. The complete mitochondrial genome sequence of C. c. bewickii was 16,727 bp in length and its gene arrangement pattern, gene content, and genome organization were identical to those of Cygnus species. The similarities of nucleotide and amino acid sequences between the two swans were 99.1% and 99.6%, respectively. Out of the 13 protein-coding genes and 2 rRNA genes, COIII showed the lowest nucleotide sequence similarity with 98.0%. On the other hand, in amino acid sequence similarities, both COII and ATP6 showed the lowest with 98.7% in common. The control region has the 97.8% nucleotide sequence similarity.

Estimating partial observability and nonlinear climate effects on stochastic community dynamics of migratory waterfowl.

1. Understanding the impact of environmental variability on migrating species requires the estimation of sequential abiotic effects in different geographic areas across the life cycle. For instance, waterfowl (ducks, geese and swans) usually breed widely dispersed throughout their breeding range and gather in large numbers in their wintering headquarters, but there is a lack of knowledge on the effects of the sequential environmental conditions experienced by migrating birds on the long-term community dynamics at their wintering sites. 2. Here, we analyse multidecadal time-series data of 10 waterfowl species wintering in the Guadalquivir Marshes (SW Spain), the single most important wintering site for waterfowl breeding in Europe. We use a multivariate state-space approach to estimate the effects of biotic interactions, local environmental forcing during winter and large-scale climate during breeding and migration on wintering multispecies abundance fluctuations, while accounting for partial observability (observation error and missing data) in both population and environmental data. 3. The joint effect of local weather and large-scale climate explained 31·6% of variance at the community level, while the variability explained by interspecific interactions was negligible (<5%). In general, abiotic conditions during winter prevailed over conditions experienced during breeding and migration. Across species, a pervasive and coherent nonlinear signal of environmental variability on population dynamics suggests weaker forcing at extreme values of abiotic variables. 4. Modelling missing observations through data augmentation increased the estimated magnitude of environmental forcing by an average 30·1% and reduced the impact of stochasticity by 39·3% when accounting for observation error. Interestingly however, the impact of environmental forcing on community dynamics was underestimated by an average 15·3% and environmental stochasticity overestimated by 14·1% when ignoring both observation error and data augmentation. 5. These results provide a salient example of sequential multiscale environmental forcing in a major migratory bird community, which suggests a demographic link between the breeding and wintering grounds operating through nonlinear environmental effects. Remarkably, this study highlights that modelling observation error in the environmental covariates of an ecological model can be proportionally more important than modelling this source of variance in the population data.