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Assessment of genetic and morphological differentiation among populations of the Diederik Cuckoo Chrysococcyx caprius
Abstract
The Diederik Cuckoo Chrysococcyx caprius is an African species widely distributed south of the Sahara, which migrates seasonally between breeding and nonbreeding sites. It is currently unknown whether the species consists of a single panmictic population or if it is genetically structured. To investigate this, we analysed sequence variation in three mitochondrial and two nuclear gene regions in combination with morphological measurements in specimens from four localities. Phylogenetic relationships were estimated using maximum-likelihood methods and included samples of Klaas's Cuckoo Chrysococcyx klaas, Red-chested Cuckoo Cuculus solitarius, and African Cuckoo Cuculus gularis. Haplotype networks and analysis of molecular variance were used to characterise the spatial distribution of genetic diversity. A principal component analysis was performed to investigate morphological variation among localities. Molecular analysis identified two divergent mitochondrial lineages, which were found to occur in sympatry in one South African locality (Limpopo Province). The magnitude of divergence between versus within these lineages was low (0.4-1%) yet significant (F ST : 0.84-0.88). Lack of apparent phylogeographic structure provides support for the absence of physical barriers to gene flow in this species. The divergent mitochondrial lineages did not differ in morphological measurements. The emergence and persistence of shallow mitochondrial divergence among sympatric lineages in the Diederik Cuckoo could be linked to maternal divergence in host selection of these brood parasites-a hypothesis requiring additional data to be tested.
Évaluation de la différenciation génétique et morphologique parmi les populations de Diederik Cuckoo Chrysococcyx caprius Le coucou didric Chrysococcyx caprius est une espèce africaine largement répandue au sud du Sahara, qui migre de manière saisonnière entre les sites de reproduction et les sites de non-reproduction. On ignore actuellement si l'espèce consiste en une seule population panmictique ou si elle est génétiquement structurée. Pour étudier cette question, nous avons analysé la variation des séquences de trois régions de gènes mitochondriaux et deux régions de gènes nucléaires en combinaison avec des mesures morphologiques chez des spécimens provenant de quatre localités. Les relations phylogénétiques ont été estimées avec la méthode de maximum de vraisemblance (maximum likelihood) en incluant des échantillons de coucou de Klaas Chrysococcyx klaas, de coucou solitaire Cuculus solitarius et de coucou africain Cuculus gularis. Des réseaux d'haplotypes et une analyse de la variance moléculaire (AMOVA) ont été utilisés pour caractériser la distribution spatiale de la diversité génétique. Une analyse en composantes principales a été réalisée pour étudier les variations morphologiques entre les localités. L'analyse moléculaire a permis d'identifier deux lignées mitochondriales divergentes, qui se rencontrent en sympatrie dans une localité d'Afrique du Sud (Limpopo). L'ampleur de la divergence entre ces lignées et à l'intérieur de celles-ci est faible (0,4-1%), mais significative (FST: 0,84-0,88). L'absence de structure phylogéographique confirme l'absence de barrières physiques au flux génétique chez cette espèce. Les lignées mitochondriales divergentes ne diffèrent pas dans les mesures morphologiques. L'émergence et la persistance de lignées mitochondriales divergentes entre des lignées sympatriques du coucou de Diederik pourraient être liées à une divergence maternelle dans la sélection des hôtes de ces parasites de couvée-une hypothèse qui nécessite des données supplémentaires pour être testée.
... The Diederik cuckoo is still classified as monotypic and results from detailed molecular study revealed no evidence of an emerging subspecies level divide between different populations based on neutral genomic markers and mitochondrial DNA (Smith et al., 2023). ...
... Samples were partitioned based on subspecies, sex, migration timing and location. Sex was determined by molecular methods as previously described (Smith et al., 2023) and 21 males and nine females were assayed. Furthermore, samples were partitioned into birds who experienced increased activity early or late during their annual breeding cycles. ...
... With the exception of the Adcyap1 gene in the Southern population, tests of equilibrium showed no significant deviations which is indicative that allele frequencies may stay the same between generations (Hedrick, 1987) in the Northern ranges with some evidence of differentiation happening in the South; consistent with previous phylogenetic studies in this species using nuclear markers and mitochondrial DNA (Smith et al., 2023). A recent review on clock genes in migrating birds (Le Clercq, Bazzi, et al., 2023e;Le Clercq, Bazzi, et al., 2023f) found similar patterns of low heterozygosity and high homozygosity for populations in equilibrium for the Clock gene and higher heterozygosity for Adcyap1. ...
The Diederik cuckoo, Chrysococcyx caprius, is a small Afrotropical bird in the family Cuculidae. It is taxonomically related to 13 other species within the genus Chrysococcyx and is migratory in sub‐Saharan Africa. It has a unique breeding behaviour of being a brood parasite: Breeding pairs lay their eggs in the nests of a host species and hatchlings expel the eggs of the host species. The aim of the present study was to investigate diversity in two circadian clock genes, Clock and Adcyap1, to probe for a relationship between genetic polymorphisms and their role in circannual timing and habitat selection (phenology) in intra‐African migrants. DNA extracted from blood was used for the PCR amplification and sequencing of clock genes in 30 Diederik cuckoos. Three alleles were detected for Clock with similar genotypes between individuals from the Northern and Southern breeding ranges while 10 alleles were detected for Adcyap1, having shorter alleles in the North and longer alleles in the South. Population genetic analyses, including allele frequency and zygosity analysis, showed distinctly higher frequencies for the most abundant Clock allele, containing 10 polyglutamine repeats, as well as a high degree of homozygosity. In contrast, all individuals were heterozygous for Adcyap1 and alleles from both regions showed distinct differences in abundance. Comparisons between both clock genes and phenology found several phenotypic correlations. This included evidence of a relationship between the shorter alleles and habitat selection as well as a relationship between longer alleles and timing. In both instances, evidence is provided that these effects may be sex‐specific. Given that these genes drive some of the synchronicity between environments and the life cycles of birds, they provide valuable insight into the fitness of species facing global challenges including climate change, urbanisation and expanding agricultural practices.
Authentic DNA sequences are crucial for reliable evolutionary inference. Concerns about the identification of DNA sequences have been voiced several times in the past but few quantitative studies exist. Mitogenomes play important roles in phylogenetics, phylogeography, population genetics and DNA identification. However, the large number of mitogenomes being published routinely, often in brief data papers, has raised questions about their authenticity. In this study, we quantify problematic mitogenomes of birds and their re-usage in other papers. Of 1876 complete or partial mitogenomes of birds published until 1 January 2020, the authenticity of 1559 could be assessed with sequences of conspecifics. Of these, 78 (5.0%) were found to be problematic, including 45 curated reference sequences. Problems were due to misidentification (33), chimeras of two or three species (23), sequencing errors/numts (18), incorrect sequence assembly (1), mislabelling at GenBank but not in the final paper (2), or vice versa (1). The number of problematic mitogenomes has increased sharply since 2012. Worryingly, these problematic sequences have been re-used 436 times in other papers, including 385 times in phylogenies. No less than 53% of all mitogenomic phylogenies/networks published until 1 January 2020 included at least one problematic mitogenome. Problematic mitogenomes have resulted in incorrect phylogenetic hypotheses and proposals for unwarranted taxonomic revision, and may have compromised comparative analyses and measurements of divergence times. Our results indicate that a major upgrade of quality control measures is warranted. We propose a comprehensive set of measures that may serve as a new standard for publishing mitogenome sequences.
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
Unusual patterns of mtDNA diversity can reveal interesting aspects of a species’ biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next‐generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA‐based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus‐specific patterns.
Parasitism by diederik cuckoos Chrysococcyx caprius on their main southern African host, the red bishop bird Euplectes orix, was studied. Virtually all the cases of parasitism occurred where there were low densities of red bishop nests. Data from the present study were combined with published observations to show that the incidence of parasitism is much higher in small breeding colonies of red bishops than in large colonies. Aggression of red bishops towards diederiks is described. I suggest that diederik cuckoos cannot approach red bishop nests undetected where large concentrations of red bishops are found. High levels of brood failure in small red bishop colonies caused by brood parasitism may constitute a selective force for colonial breeding in this host species.In hierdie studie word parasitisme deur diedertk-koekoeke Chrysococcyx caprius op hulls belangrikste suider- Afrikaanse gasheer, die rooivink Euptectes orix, ondersoek. Bykans alle gevalle van parasitisme het voorgekom waar rooivinkneste in lae digthede voorgekomhet, Data uit hierdie studie is gekombineer met dié van ander outeurs en dui daaropdat broei-parasitisrnebaie hoër is by klein rooivink-broeikolonies as by groot kolonies. Aggressie van rooivinke teenoor diederikke word beskryf en dit skyn dat die koekoeke nie neste onopgemerk kan nader as daar baie rooivinke is nie. Hoe mortaliteit van rooivink-broeisels a.g.v. parasitisme in klein kolonies mag ’n bron wees waardeurdaar seleksie plaasvind vir koloniale broeigewoontes.
Background: The accurate delimitation of species is essential to numerous areas of biological research. An unbiased assessment of the diversity, including the cryptic diversity, is of particular importance for the below ground fauna, a major component of global biodiversity. On the British Isles, the epigeic earthworm Lumbricus rubellus, which is a sentinel species in soil ecotoxicology, consists of two cryptic taxa that are differentiated in both the nuclear and the mitochondrial (mtDNA) genomes. Recently, several deeply divergent mtDNA lineages were detected in mainland Europe, but whether these earthworms also constitute cryptic species remains unclear. This information is important from an evolutionary perspective, but it is also essential for the interpretation and the design of ecotoxicological projects. In this study, we used genome-wide RADseq data to assess the reproductive isolation of the divergent mitochondrial lineages of L. rubellus that occur in sympatry in multiple localities in Central Europe.
Results: We identified five divergent (up to 16% net p-distance) mitochondrial lineages of L. rubellus in sympatry. Because the clustering of the RADseq data was according to the population of origin and not the mtDNA lineage, reproductive isolation among the mtDNA lineages was not likely. Although each population contained multiple mtDNA lineages, subdivisions within the populations were not observed for the nuclear genome. The lack of fixed differences and sharing of the overwhelming majority of nuclear polymorphisms between localities, indicated that the populations did not constitute allopatric species. The nucleotide diversity within the populations was high, 0.7-0.8%.
The merger of formerly isolated lineages is hypothesized to occur in vertebrates under certain conditions. However, despite many demonstrated instances of introgression between taxa in secondary contact, examples of lineage mergers are rare. Preliminary mtDNA sequencing of a Malagasy passerine, Xanthomixis zosterops (Passeriformes: Bernieridae), indicated a possible instance of merging lineages. We tested the hypothesis that X. zosterops lineages are merging by comparing mtDNA sequence and microsatellite data, as well as mtDNA sequence data from host-specific feather lice in the genus Myrsidea (Phthiraptera: Menoponidae). Xanthomixis zosterops comprises four deeply divergent, broadly sympatric, cryptic mtDNA clades that likely began diverging approximately 3.6 million years ago. Despite this level of divergence, the microsatellite data indicate that the X. zosterops mtDNA clades are virtually panmictic. Three major phylogroups of Myrsidea were found, supporting previous allopatry of the X. zosterops clades. In combination, the datasets from X. zosterops and its Myrsidea document a potential merger of previously allopatric lineages that likely date to the Pliocene. This represents the first report of sympatric apparent hybridization among more than two terrestrial vertebrate lineages. Further, the mtDNA phylogeographic pattern of X. zosterops, namely the syntopy of more than two deeply divergent cryptic clades, appears to be a novel scenario among vertebrates. We highlight the value of gathering multiple types of data in phylogeographic studies to contribute to the study of vertebrate speciation.
In order to maximise breeding success in a seasonally fluctuating environment animals breed during periods of increased resource abundance and avoid times of resource constraint. In tropical savannahs, variation in resources in time and space is dependent on the amplitude of the rains and their predictability. We quantified the degree to which tropical savannah birds have concentrated their breeding around predicted periods of increased food availability coincident with rainfall. We used the proportion of adults caught with brood patches and/or the juvenile-to-adult ratio in 25 species of small savannah bird which were caught over a 10-year period in Nigeria, West Africa, to assess the degree to which there were clear seasonal peaks in breeding activity. We found two-thirds of species bred in all seasons (68 %), but that most species showed distinct seasonal peaks (96 %) in the timing of their breeding. Over one-half of species (60 %) varied the timing of their breeding across the years. Granivorous species bred later than insectivorous and frugivorous species, which probably indicates synchronisation with their respective peak abundance in food type. Overall we found distinct seasonal peaks in breeding effort (i.e. breeding seasons), and this is most likely in response to changing resource availability brought about by seasonal rainfall. We also demonstrated the potential utility of using brood patches to test for patterns in breeding in multi-species long-term datasets.
Mitochondrial DNA usually shows low sequence variation within and high sequence divergence among species, which makes it a useful marker for phylogenetic inference and DNA barcoding. A previous study on the common redstart (Phoenicurus phoenicurus) revealed two very different mtDNA haplogroups (5% K2P distance). This divergence is comparable to that among many sister species; however, both haplogroups coexist and interbreed in Europe today. Herein, we describe the phylogeographic pattern of these lineages and test hypotheses for how such high diversity in mtDNA has evolved. We found no evidence for mitochondrial pseudogenes confirming that both haplotypes are of mitochondrial origin. When testing for possible reproductive barriers, we found no evidence for lineage-specific assortative mating and no difference in sperm morphology, indicating that they are not examples of cryptic species, nor likely to reflect the early stages of speciation. A gene tree based on a short fragment of cytochrome c oxidase subunit 1 from the common redstart and 10 other Phoenicurus species, showed no introgression from any of the extant congenerics. However, introgression from an extinct congeneric cannot be excluded. Sequences from two nuclear introns did not show a similar differentiation into two distinct groups. Mismatch distributions indicated that the lineages have undergone similar demographic changes. Taken together, these results confirm that deeply divergent mitochondrial lineages can coexist in biological species. Sympatric mtDNA divergences are relatively rare in birds, but the fact that they occur argues against the use of threshold mtDNA divergences in species delineation.
A problem frequently faced by researchers involved in collecting tissues for DNA isolation is the preservation of samples in the field prior to and during their transportation to the laboratory. Prevention of DNA degradation is usually achieved through freezing. As this is not always practical, we have tested the efficiency of chemical solutions containing high concentrations of salts (e.g., NaCl, EDTA, and diaminocyclohexanetetraacetate) and detergent at preserving DNA in bird tissue and blood samples stored at ambient temperature for extended periods of time. For blood samples, we recommend the use of a buffer that lyses the cells and nuclei and contains 0.01 M Tris, 0.01 M NaCl, 0.01 M EDTA, and 1% n-lauroylsarcosine, pH 7.5. Tissue samples are best preserved as small pieces in a saline solution made of 20% dimethyl sulfoxyde, 0.25 M EDTA, saturated with NaCl, pH 8.0. DNA extracted from samples preserved in these solutions for up to 24 weeks was compared with DNA recovered from tissue samples stored at -70-degrees-C and blood samples at -70 and -20-degrees-C. Yields were similar, averaging 300-mu-g/0.2 g of tissue and 500-mu-g/50-mu-L of blood. Quality of DNA in terms of fragment size, ability to be cut by restriction enzymes, and ability to hybridize to radioactive probes was also similar between cryopreserved and chemically preserved samples. Yields of DNA recovered from tissue samples preserved in 70% ethanol for 6 or 11 weeks was very low and significant degradation was observed. We have also examined how DNA contained in crude avian blood samples withstands freeze-thaw cycles. We found normal yields and no significant degradation of DNA in samples that experienced up to six cycles. We encourage field researchers who refrain from preserving tissue samples because of logistical problems, such as transporting liquid nitrogen containers in the field, to consider using these solutions. Both solutions can also facilitate exchanges of samples between laboratories, and they form an alternative to storage of samples at -70-degree-C for laboratories and museums with limited access to deep-freezing facilities.
An estimated 19% of the world's 9,856 extant bird species are migratory, including some 1,600 species of land- and waterbirds. In 2008, 11% of migratory land- and waterbirds were classed by BirdLife International as threatened or near-threatened on the IUCN Red List. Red List indices show that these migrants have become more threatened since 1988, with 33 species deteriorating and just six improving in status. There is also increasing evidence of regional declines. Population trend data show that more Nearctic–Neotropical migrants have declined than increased in North America since the 1980s, and more Palearctic–Afrotropical migrants breeding in Europe declined than increased during 1970–2000. Reviews of the status of migratory raptors show unfavourable conservation status for 51% of species in the African–Eurasian region (in 2005), and 33% of species in Central, South and East Asia (in 2007). Land-use change owing to agriculture is the most frequently cited threat affecting nearly 80% of all threatened and near-threatened species. However, while agricultural intensification on the breeding grounds is often proposed as the major driver of declines in Palearctic–Afrotropical migrants, some species appear to be limited by the quantity and quality of available habitat in non-breeding areas, notably the drylands of tropical Africa. Forest fragmentation in breeding areas has contributed to the declines of Nearctic–Neotropical migrants with deforestation in non-breeding areas another possible factor. Infrastructure development including wind turbines, cables, towers and masts can also be a threat. Over-harvesting and persecution remain serious threats, particularly at key migration locations. Climate change is affecting birds already, is expected to exacerbate all these pressures, and may also increase competition between migratory and non-migratory species. The conservation of migratory birds thus requires a multitude of approaches. Many migratory birds require effective management of their critical sites, and Important Bird Areas (IBAs) provide an important foundation for such action; however to function effectively in conserving migratory species, IBAs need to be protected and the coherence of the network requires regular review. Since many migratory species (c. 55%) are widely dispersed across their breeding or non-breeding ranges, it is essential to address the human-induced changes at the wider landscape scale, a very considerable challenge. Efforts to conserve migratory birds in one part of the range are less effective if unaddressed threats are reducing these species' populations and habitats elsewhere. International collaboration and coordinated action along migration flyways as a whole are thus key elements in any strategy for the conservation of migratory birds.
Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact:
peter@biomatters.com
Parasites that exploit multiple hosts often experience diversifying selection for host-specific adaptations. This can result in multiple strains of host specialists coexisting within a single parasitic species. A long-standing conundrum is how such sympatric host races can be maintained within a single parasitic species in the face of interbreeding among conspecifics specializing on different hosts. Striking examples are seen in certain avian brood parasites such as cuckoos, many of which show host-specific differentiation in traits such as host egg mimicry. Exploiting a Zambian egg collection amassed over several decades and supplemented by recent fieldwork, we show that the brood parasitic Greater Honeyguide Indicator indicator exhibits host-specific differentiation in both egg size and egg shape. Genetic analysis of honeyguide eggs and chicks show that two highly divergent mitochondrial DNA lineages are associated with ground- and tree-nesting hosts, respectively, indicating perfect fidelity to two mutually exclusive sets of host species for millions of years. Despite their age and apparent adaptive diversification, however, these ancient lineages are not cryptic species; a complete lack of differentiation in nuclear genes shows that mating between individuals reared by different hosts is sufficiently frequent to prevent speciation. These results indicate that host specificity is maternally inherited, that host-specific adaptation among conspecifics can be maintained without reproductive isolation, and that host specificity can be remarkably ancient in evolutionary terms.
DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and
features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number
of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene
flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical
outputs for an easy visualization of results.
Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.
The common cuckoo Cuculus canorus is divided into host-specific races (gentes). Females of each race lay a distinctive egg type that tends to match the host's eggs, for instance, brown and spotted for meadow pipit hosts or plain blue for redstart hosts. The puzzle is how these gentes remain distinct. Here, we provide genetic evidence that gentes are restricted to female lineages, with cross mating by males maintaining the common cuckoo genetically as one species. We show that there is differentiation between gentes in maternally inherited mitochondrial DNA, but not in microsatellite loci of nuclear DNA. This supports recent behavioural evidence that female, but not male, common cuckoos specialize on a particular host, and is consistent with the possibility that genes affecting cuckoo egg type are located on the female-specific W sex chromosome. Our results also support the ideas that common cuckoos often switched hosts during evolution, and that some gentes may have multiple, independent origins, due to colonization by separate ancestral lineages.
The cuckoos are the most variable birds in social behavior and parental care: a few cuckoos are among the most social of all birds and rear their young in a common nest; most cuckoos are caring parents that rear their own young with some females laying a few eggs in the nests of others; while many cuckoo species are brood parasites who leave their eggs in the nests of other birds to rear, with their young maturing to kill their foster nestmates. In The Cuckoos, Robert B. Payne presents a new evolutionary history of the family based on molecular genetics, and uses the family tree to explore the origins and diversity of their behaviour. He traces details of the cuckoos’ biology to their original sources, includes descriptions of previously unpublished field observations, and reveals new comparisons of songs showing previously overlooked cuckoo species. Lavishly illustrated with specially commissioned colour plates and numerous maps, halftones, and line drawings, The Cuckoos provides the most comprehensive and up-to-date account of this family yet available.
The evolutionary, ecological and behavioral questions posed by obligate brood parasites are among the most intriguing of all contemporary ornithological topics. Avian brood parasites lay their eggs in the nests of other birds and may be a major contributing factor driving several species of songbirds to near extinction. As one of the first books to present a comprehensive overview of this fascinating phenomenon, this work discusses the comparative biology and co-evolutionary adaptations exhibited by the five families of birds that engage in such behavior. Several chapters dealing with the comparative biology of both intraspecific and interspecific brood parasites, are followed by individual accounts of all known species—nearly 100 altogether, primarily cowbirds and cuckoos. Some of the more remarkable behavioral and structural adaptations of these birds include egg mimicry, juvenile mimicry, elimination by starvation or actual attack of other nestlings or host eggs, and even the learning and partial mimicry of host song traits. An extended glossary, a list of Latin names, 400 literature citations and range maps of all parasitic species discussed are also included. Detailed line drawings by the author enhance this synthesis of biological and ecological information.
Significance
Validating an almost century-old hypothesis, we show that a critical host-specific adaptation in a brood-parasitic bird, mimicry of host egg coloration, is maternally inherited, allowing mothers to transmit specialized mimicry to their daughters irrespective of the father’s host species. This genetic architecture, however, is a double-edged sword for parasites: the loss of recombination and heterozygosity as sources of evolutionary novelty likely constrains the parasite from mimicking the full range of color polymorphisms that hosts have evolved as an escalated defense against parasitism. This important tradeoff of asexual inheritance may have relevance for understanding coevolution in other host–parasite systems.
We compared sequences from two mitochondrial DNA (mtDNA) genes (ND2, ND3) in Savannah Sparrows (Passerculus sandwichensis; n = 112) sampled from Baja California (five sites), coastal Sonora and the continental range (eight sites). Populations from Baja California, San Diego and Sonora formed a clade within which there was no phylogeographic structure; this clade merits species status (Passerculus rostratus). The other clade, consisting of phenotypically “typical” savannah sparrows, should be classified as P. sandwichensis. Among the typical sparrows, there was no phylogeographic structure, although two major clades were discovered. Representatives of each of the two main clades occurred at most sampling localities, excluding Suisan Bay, California and Sable Island, Nova Scotia, Canada. Haplotypes found on Sable Island, representing the “Ipswich Sparrow,” were not distinctive, thereby failing to support species status for this taxon. On Isla San Benito, a single haplotype was found, which also occurred in other Mexican localities. The results for Sable Island and Isla San Benito show that size and plumage coloration can evolve rapidly.
Variación en ADN Mitocondrial, Límites entre Especies y Evolución Rápida de la Coloración del Plumaje y el Tamaño en Passerculus sandwichensis
Resumen. En este estudio comparamos secuencias de dos genes mitocondriales (ND2 y ND3) entre individuos de la especie Passerculus sandwichensis (n = 112) muestreados en Baja California (5 sitios), la costa de Sonora y el rango de distribución continental (8 sitios). Las poblaciones de Baja California, San Diego y Sonora formaron un clado, al interior del cual no existió estructura filogeográfica; este clado merece estatus de especie (Passerculus rostratus). El otro clado, conformado por individuos fenotípicamente “típicos”, debe clasificarse como P. sandwichensis. Entre los individuos típicos no existió estructura filogeográfica, aunque se descubrieron dos clados principales. Individuos representativos de cada uno de estos dos clados se encontraron en la mayoría de las localidades, excepto Suisan Bay, California y Sable Island, Nova Scotia. Los haplotipos encontrados en Sable Island, correspondientes al “gorrión de Ipswich” no fueron distintivos, lo que no apoya el estatus de especie para este taxón. En Isla San Benito se encontró un solo halpotipo, el cual también se encontraba en otras localidades mexicanas. Los resultados de Sable Island e Isla San Benito muestran que el tamaño y la coloración del plumaje pueden evolucionar rápidamente.
A new intergeneric hybrid manakin is characterized using morphological characters and mitochondrial and nuclear DNA sequences. Many morphological traits suggest the bird is intermediate between Ilicura militaris and Chiroxiphia caudata. Sequences of the maternally inherited mitochondrial ND2 gene demonstrate the female parent to be Chiroxiphia caudata, and the nuclear beta-fibrinogen intron 5 sequences can not eliminate Chiroxiphia and Ilicura as parents. Therefore, DNA sequence data lead to the conclusion that Ilicura is the male parent of this unusual bird. This study is important because it highlights the significance of using multiple character systems in diagnosing unusual bird specimens.
Significance
Biologists believe that a major mass extinction is happening in the tropics. Destruction of forests is a key reason. However, there are no solid predictions of the percentage of species that will go extinct as more and more forests are disturbed. This paper provides estimates based on extrapolating the respective numbers of species in disturbed and undisturbed habitats. It uses a large global database of species inventories at particular sites. Trees and 10 groups of animals are analyzed. All the disturbed habitats put together include 41% fewer species than the undisturbed forests. This proportion varies among groups but is always substantial. Furthermore, disturbed local communities are dominated by widespread species such as rats and electric ants.
A major requirement of a good data analysis is flexibility. If your data changes, or you discover something that makes you rethink your basic assumptions, you need to be able to easily change many plots at once. The main inhibitor of flexibility is code duplication. If you have the same plotting statement repeated over and over again, you’ll have to make the same change in many different places. Often just the thought of making all those changes is exhausting! This chapter will help you overcome that problem by showing you how to program with ggplot2.
Maternal inheritance via the female-specific W chromosome was long ago proposed as a potential solution to the evolutionary enigma of co-existing host-specific races (or 'gentes') in avian brood parasites. Here we report the first unambiguous evidence for maternal inheritance of egg colouration in the brood-parasitic common cuckoo Cuculus canorus. Females laying blue eggs belong to an ancient (∼2.6 Myr) maternal lineage, as evidenced by both mitochondrial and W-linked DNA, but are indistinguishable at nuclear DNA from other common cuckoos. Hence, cuckoo host races with blue eggs are distinguished only by maternally inherited components of the genome, which maintain host-specific adaptation despite interbreeding among males and females reared by different hosts. A mitochondrial phylogeny suggests that blue eggs originated in Asia and then expanded westwards as female cuckoos laying blue eggs interbred with the existing European population, introducing an adaptive trait that expanded the range of potential hosts.
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level.
Here, we present popart , an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production.
popart also provides a platform for the implementation and distribution of new network‐based methods – we describe one such new method, integer neighbour‐joining .
The software is open source and freely available for all major operating systems.
We constructed a molecular phylogeny of 15 species of cuckoos using mitochondrial DNA sequences spanning 553 nucleotide bases of the cytochrome b gene and 298 nucleotide bases of the ND2 gene. A parallel analysis for the cytochrome b gene including published sequences in the Genbank database was performed. Phylogenetic analyses of the sequences were done using parsimony, a sequence distance method (Fitch-Margoliash), and a character-state method which uses probabilities (maximum likelihood). Phenograms support the monophyly of three major clades: Cuculinae, Phaenicophaeinae and Neomorphinae-Crotophaginae. Clamator, a strictly parasitic genus traditionally included within the Cuculinae, groups together with Coccyzus (a nonobligate parasite) and some nesting cuckoos. Tapera and Dromococcyx, the parasitic cuckoos from the New World, appear as sister genera, close to New World cuckoos: Neomorphinae and Crotophaginae. Based on the results, and being conscious that a more strict resolution of the relationships among the three major clades is required, we postulate that brood parasitism has a polyphyletic origin in the Cuculiformes, with parasite species being found within the three defined clades. Evidence suggests that species within each clade share a common parasitic ancestor, but some show partial or total loss of brood parasitic behaviour.
Dull plumages prevail among parasitic birds. Parasitic cuckoos are significantly less brightly marked than are nesting cuckoos. Dull parasitic birds are less readily seen and recognized by hosts, and dull plumages also appease the hosts by absence of releasers of aggressive behavior. Inconspicuousness and appeasement increase the vulnerability of hosts to the brood parasites. The dull juvenal plumages in some parasitic birds may have been incorporated into the adult communication signals by neoteny. Evidence of neoteny among brood parasites includes prolonged retention of juvenal plumage, juvenal-adult-like species pairs, and the retention of juvenal-like incomplete skull ossification throughout adult life. Polymorphism and an unusual degree of variation in plumage are adaptations in parasitic cuckoos which reduce the probability of recognition by hosts. Polymorphism in Cuculus canorus and other parasitic cuckoos is considered to be the result of apostatic selection for deviant phenotypes. Polymorphism of cuckoo eggs is mimetic, and the tendency for the eggs of Chrysococcyx caprius to be laid in nests with matching eggs is statistically significant. Aggressive mimicry which deceives host species occurs in all stages of the life cycle of parasitic birds but mainly during the period of host parental care.
There is a high degree of concordance among the patterns of geographic size variation in birds in the eastern and central United States. This is demonstrated for 12 species by assuming that wing length measurements are an indicator of body size on the intraspecific level, and by arranging the data in the form of a grid of means of wing lengths for sample areas. Maps giving isophenetic lines for wing length indicate gradually increasing size clines northward and westward from Florida in the Hairy Woodpecker (Dendrocopos villosus), Dowy Woodpecker (Dendrocopos pubescens), Blue Jay (Cyanocitta cristata), Carolina Chickadee (Parus carolinensis), White-breasted Nuthatch (Sitta carolinensis), and Eastern Meadowlark (Sturnella Magna). In each case there is a trend for larger (or longer-winged) birds to extend southward in the Appalachian Mountains and for smaller (or shorter-winged) birds to extend northward in the Mississippi River valley. Maps made by a computer and automatic plotter using contour intervals of 0.5 mm of mean wing length for the Downy Woodpecker, for male White-breasted Nuthatches, and for female Blue Jays show that, in addition to the patter just mentioned, relatively longer-winged birds extend southward in the interior highlands of Arkansas, and relatively shorter-winged birds extend northward up other river valleys. These subtle relationships between intraspecific size variation and topographic features suggest that the link between the two phenomena may be precise adaptations to even minor climatic gradients. The relationship between these findings and the subspecies concept is discussed. Correlation coefficients for the patter of variation in the Downy Woodpecker with seasonal and annual wet-bulb temperature, vapor pressure, and absolute humidity were all either equal to or higher than correlations with dry-bulb temperature. Since these variables reflect the combined effects of temperature and humidity, the obvious indication is that size variation is more closely related to this combination than to temperature alone. Additional correlations using the mean wing length data for seven other species confirmed that wet-bulb temperature patterms are more closely related to bird size than either dry-bulb temperature patters or latitude. These relationship can be expressed numerically as regressions of mean wing length on either annual wet-bulb temperature or mean annual total heat per pound of air. Since increased evaporation at high altitudes and in arid areas accentuates the depression of a wet-bulb thermometer, my hypothesis may partially account for several cases of size variation in birds cited by others as disturbing exceptions to Bergmann's ecogeographic rule. Sections of a translation of Bergmann's paper published in 1847 are given. The biological mechanisms by which these relationships are maintainted are unknown, and the wide range of tolerance by birds to diurnal and seasonal temperature variations tends to mask them. If the well-established inverse relationship between weight and metabolic rate per gram of homeotherms is operative on the intraspecific level, the relationships can be discussed in terms of avenues of heat loss and of energy budget equations.
Macdonald, M. A. 1980. Observations on the Diederik Cuckoo in southern Ghana. Ostrich 51:75-79.Casual observations were made on the Diederik Cuckoo Chrysococcyx caprius at Cape Coast in southern Ghana from 1975 to 1978. The Diederik was largely separated from its three congeners (Kiaas's, Emerald and Yellowthroated Cuckoos) by habitat. Most food was taken from or close to the ground, and consisted mainly of caterpillars or similar larvae. Diederiks were almost absent from the area during September and October. The main host colony of Ploceus weavers was attended by up to five males and three females simultaneously during the wet season. Apparent laying attempts observed between March and July are described. Usually the female removed a host egg and spent between 3 and 9 s in the nest. The Spottedbacked Weaver Ploceus cucullalus was recorded as a biological host. The contrast between the social systems described from southern Africa and that found at Cape Coast is discussed and a link with the social systems of their hosts is suggested.
Craig, A. J. F. K. 1982. Breeding success of a Red Bishop colony. Ostrich 53982–188.In Natal, South Africa, breeding success of Red Bishops at the same colony in two successive seasons was very low. Heavy rainfall and predation were equally important sources of mortality in the first season, while predation alone was the major source of nest loss in the second season. The influence of predation on populations of breeding birds is discussed.
Birds in the northern hemisphere usually increase mass reserves in response to seasonal low temperatures and shorter day length that increase foraging unpredictability and so starvation risk. In the lowland tropics, relatively low temperatures and short day lengths are absent and so the risk of starvation may be reduced, leading to much smaller seasonal effects on mass. Nevertheless, other factors such as high temperatures and water and food availability may vary greatly between tropical wet and dry seasons, leading to variable starvation risk and seasonal mass effects. Using data collected from 47 species of birds caught over a 10-year period in a tropical savannah region in West Africa we tested for seasonal variation in mass in response to a predictable, strongly seasonal tropical climate. Many species (91%) showed seasonal variation in mass, and this was often in a clear annual pattern that was constant across the years. Many species (89%) varied their mass in response to seasonally predictable rainfall. Annual variation in mass was also important (45% of species). Relatively few species (13%) had a seasonal pattern of mass variation that varied between years. Feeding guild or migratory status was not found to affect seasonal or annual mass variation. Seasonal mass change was on average 8.1% across the 21 species with a very large sample size and was comparable with both northern and southern temperate species. Our study showed that biologically significant consistent seasonal mass variation is common in tropical savannah bird species, and this is most likely in response to changing resource availability brought about by seasonal rainfall and the interrupted foraging response due to the constraints of breeding.
The migrant Diederik Cuckoo Chrysococcyx caprius was studied on a 72–acre area near the Klein Jukskei River near Johannesburg from 1955–1958. The birds first arrive in early October, after which the males take up territories and call continually until February; subsequent calls up to April are probably made by young birds.
Courtship displays, which involve courtship feeding, and egg-laying follow the birds' arrival by about a month. The Red Bishop Euplectes orix was the species most commonly parasitized, with smaller equal numbers of Cape Sparrows Passer melanurus and Masked Weavers Ploceus velatus. The cuckoos' eggs differ according to the host species and in two cases hatched between ten and 14 days after laying. The chicks normally evict their hosts' offspring on the second or third day after hatching. The fledging period appears to be roughly 19–20 days, and there is a period of post-fledging care lasting between 17 and 38 days, during which the chicks are fed different foods by different host species (grass seeds by bishops; insects of different sizes by weavers and sparrows).
The fact that the eggs and the calls of the chicks vary according to their host species suggest the existence of three separate host-specific strains in this area. The incidence of brood parasitism in Red Bishops' nests varied from 7–50% and averaged 25%.
A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from 13 currently recognized species of
the midwater deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae) and three gonostomatid outgroup taxa. Phylogenetic analyses using maximum parsimony and maximum
likelihood methods were performed on unambiguously aligned, combined sequences (803 bp) of the two genes. The resultant tree
topologies from the two methods were congruent, being robust and supported by various tree statistics, enabling the evolutionary
history ofCyclothone to be described in detail. The molecular phylogeny demonstrated striking inconsistencies with previously proposed “natural
groups”, although the latter could be confidently refuted by the molecular data. The most significant characteristic of the
evolutionary history ofCyclothone was the independent acquisition of an apomorphic depth habitat from the relatively ancestral, lower mesopelagic habitat,
by each of three major distinct lineages that had diverged earlier in their evolution. Moreover, such macroevolutionary habitat
shifts had been necessarily accompanied by morphological and ecological novelties, presumably originating from paedomorphosis.
Repeated evolution of such changes strongly suggests ontogenetic plasticity inCyclothone which could enable these fishes to acquire larval-like, simple organization of body structure. Such a body plan could help
them subsist in food-poor surroundings and regulate reproductive variables that take advantage of increasing larval survival
toward shallower depths. Recent speciation events, on the contrary, have produced contemporary sister species of allopatric
(or microallopatric) distributions, but few morphological and ecological differences. Even if remarkable miniaturization has
occurred, such as in the Mediterranean endemicC. pygmaea, it had to have been a simple truncation of ancestral species' ontogeny without attendance of any discernible paedomorphic
features. On the basis of the fossil record, geological history of the Mediterranean region, and ectotherm molecular divergence
rate, it was estimated thatCyclothone radiation had already started in the early-middle Miocene (17–20 million years ago).
Mitochondria and Wolbachia are maternally inherited genomes that exhibit strong linkage disequilibrium in many organisms. We surveyed Wolbachia infections in 187 specimens of the fig wasp species, Ceratosolen solmsi, and found an infection prevalence of 89.3%. DNA sequencing of 20 individuals each from Wolbachia-infected and -uninfected subpopulations revealed extreme mtDNA divergence (up to 9.2% and 15.3% in CO1 and cytochrome b, respectively) between infected and uninfected wasps. Further, mtDNA diversity was significantly reduced within the infected group. Our sequencing of a large part of the mitochondrial genome from both Wolbachia-infected and -uninfected individuals revealed that high sequence divergence is common throughout the mitochondrial genome. These patterns suggest a partial selective sweep of mitochondria subsequent to the introduction of Wolbachia into C. solsmi, by hybrid introgression from a related species.
Cuckoo eggs are renowned for their mimicry of different host species, leading to the evolution of host-specific races (or 'gentes') defined by egg colour and pattern. This study aims to test the prediction that another property of parasitic eggs, namely shell strength, might also have experienced divergent selection within cuckoo species. Host races of the common cuckoo Cuculus canorus encountering stronger host rejection have thicker-shelled eggs than those parasitising less discriminating species, as expected if egg strengthening discourages host rejection. Moreover, in the diederik cuckoo Chrysococcyx caprius, eggshell thickness was correlated across cuckoo gentes and host species, as expected if eggshell strength has been involved in coevolutionary interactions. This is the first report of host-specific differences in cuckoo egg properties other than colour and pattern and lends correlational support to the hypothesis that the strong eggshells of brood parasites are an adaptation to reduce host rejection.
The Meliphagoidea comprises the largest radiation of Australasian passerines. Here we present the first detailed molecular phylogenetic analysis of its families and genera, particularly the Acanthizidae, using sequences from nine gene regions including both mitochondrial and nuclear DNA. Our results support some suggested relationships but challenge other groupings, particularly in Meliphagidae and Acanthizidae. Maluridae is sister to all other members of the superfamily. With appropriate taxon sampling and multilocus data, we provide the first strong molecular evidence supporting earlier recognition of bristlebirds, Dasyornis, as a separate family, Dasyornithidae. We further clarify its position as sister to Acanthizidae+Pardalotidae+Meliphagidae. Pardalotidae is sister to Acanthizidae, and thus its retention as a separate family is arbitrary. The meliphagid genus Lichenostomus is polyphyletic. We find no support for the current subfamily structure within Acanthizidae but recognise a clade that includes members of the subfamily Sericornithinae excluding Oreoscopus and Acanthornis. Subfamily Acanthizinae is paraphyletic. Surprisingly, the Tasmanian island endemic Acanthornis magna of mesic habitats is sister to the Aphelocephala whitefaces of mainland Australian xeric zones. This is one of several unexpected alignments of taxa as sisters that probably reflects the age of the Meliphagoidea. We find no evidence for separate radiations of New Guinean and Australian members of the Meliphagoidea.
An adaptation in one lineage (e.g. predators) may change the selection pressure on another lineage (e.g. prey), giving rise to a counter-adaptation. If this occurs reciprocally, an unstable runaway escalation or 'arms race' may result. We discuss various factors which might give one side an advantage in an arms race. For example, a lineage under strong selection may out-evolve a weakly selected one (' the life-dinner principle'). We then classify arms races in two independent ways. They may be symmetric or asymmetric, and they may be interspecific or intraspecific. Our example of an asymmetric interspecific arms race is that between brood parasites and their hosts. The arms race concept may help to reduce the mystery of why cuckoo hosts are so good at detecting cuckoo eggs, but so bad at detecting cuckoo nestlings. The evolutionary contest between queen and worker ants over relative parental investment is a good example of an intraspecific asymmetric arms race. Such cases raise special problems because the participants share the same gene pool. Interspecific symmetric arms races are unlikely to be important, because competitors tend to diverge rather than escalate competitive adaptations. Intraspecific symmetric arms races, exemplified by adaptations for male-male competition, may underlie Cope's Rule and even the extinction of lineages. Finally we consider ways in which arms races can end. One lineage may drive the other to extinction; one may reach an optimum, thereby preventing the other from doing so; a particularly interesting possibility, exemplified by flower-bee coevolution, is that both sides may reach a mutual local optimum; lastly, arms races may have no stable and but may cycle continuously. We do not wish necessarily to suggest that all, or even most, evolutionary change results from arms races, but we do suggest that the arms race concept may help to resolve three long-standing questions in evolutionary theory.
By using the polymerase chain reaction to amplify and sequence 178 bp of a rapidly evolving region of the mtDNA genome (segment I of the control region) from 81 individuals, approximately 11% of the variation present in the lesser snow goose Chen caerulescens caerulescens L. mitochondrial genome was surveyed. The 26 types of mtDNA detected formed two distinct mitochondrial clades that differ by an average of 6.7% and are distributed across the species range. Restriction analysis of amplified fragments was then used to assign the mtDNA of an additional 29 individuals to either of these clades. Within one major clade, sequence among mtDNAs was concordant with geographic location. Within the other major clade the degree of sequence divergence among haplotypes was lower and no consistent geographic structuring was evident. The two major clades presumably result from vicariant separation of lesser snow geese during the Pleistocene.
There is abundant geographic variation in both morphology and gene frequency in most species. The extent of geographic variation
results from a balance of forces tending to produce local genetic differentiation and forces tending to produce genetic homogeneity.
Mutation, genetic drift due to finite population size, and natural selection favoring adaptations to local environmental conditions
will all lead to the genetic differentiation of local populations, and the movement of gametes, individuals, and even entire
populations--collectively called gene flow--will oppose that differentiation. Gene flow may either constrain evolution by
preventing adaptation to local conditions or promote evolution by spreading new genes and combinations of genes throughout
a species' range. Several methods are available for estimating the amount of gene flow. Direct methods monitor ongoing gene
flow, and indirect methods use spatial distributions of gene frequencies to infer past gene flow. Applications of these methods
show that species differ widely in the gene flow that they experience. Of particular interest are those species for which
direct methods indicate little current gene flow but indirect methods indicate much higher levels of gene flow in the recent
past. Such species probably have undergone large-scale demographic changes relatively frequently.
Surveys of mitochondrial DNA (mtDNA) variation in macaque monkeys have revealed extremely high levels of intraspecific divergence among haplotypes. One consistent pattern that has emerged from these studies is that divergent haplotypes are geographically segregated so that sampling a few matrilines from a given region shows them to be identical, or a closely related subset of haplotypes. Geographically structured mtDNA variation has also been commonly observed in other taxa. In this study, haplotype variation and distribution are studied in detail within a local population of toque macaques. The results show that highly divergent haplotypes, differing by 3.1% in their nucleotide sequences, coexist in this population and that they may be spatially segregated even on this micro-geographic scale. Furthermore, these differences are maintained between social groups that exchange male migrants, and thus nuclear genes, frequently.
The exploitation of a new host by a parasite may result in host-race formation or speciation. A brood parasitic bird, the common cuckoo, is divided into host races, each characterized by egg mimicry of different host species. Microsatellite DNA markers were used to examine cuckoo mating patterns and host usage in an area where a new host has been recently colonized. Female cuckoos show strong host preferences, but individual males mate with females that lay in the nests of different hosts. Female host specialization may lead to the evolution of sex-linked traits such as egg mimicry, even though gene flow through the male line prevents completion of the speciation process.
For most of the past century, prehistorians have had to rely on the fossil and archaeological records in order to reconstruct the past. In the last few decades, this evidence has been substantially supplemented from classical human genetics. More recently, phylogenetic analyses of DNA sequences that incorporate geographical information have provided a high-resolution tool for the investigation of prehistoric demographic events, such as founder effects and population expansions. These events can be dated using a molecular clock when the mutation rate and founder haplotypes are known. We have previously applied such methods to sequence data from the mitochondrial DNA control region, to suggest that most extant mitochondrial sequences in western Europe have a local ancestry in the Early Upper Palaeolithic, with a smaller proportion arriving from the Near East in the Neolithic. Here, we describe a cladistic notation for mitochondrial variation and expand upon our earlier analysis to present a more detailed portrait of the European mitochondrial record.
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.