Calibration of a molecular clock in tits (Paridae)—Do nucleotide substitution rates of mitochondrial genes deviate from the 2% rule?

The ABC-D of animal linguistics: are syntax and compositionality for real?

In several animal species, an alarm call (e.g. ABC notes in the Japanese tit Parus minor) can be immediately followed by a recruitment call (e.g. D notes) to yield a complex call that triggers a third behaviour, namely mobbing. This has been taken to be an argument for animal syntax and compositionality (i.e. the property by which the meaning of a complex expression depends on the meaning of its parts and the way they are put together). Several additional discoveries were made across species. First, in some cases, animals respond with mobbing to the order alarm-recruitment but not to the order recruitment-alarm. Second, animals sometimes respond similarly to functionally analogous heterospecific calls they have never heard before, and/or to artificial hybrid sequences made of conspecific and heterospecific calls in the same order, thus adding an argument for the productivity of the relevant rules. We consider the details of these arguments for animal syntax and compositionality and argue that, with one important exception (Japanese tit ABC-D sequences), they currently remain ambiguous: there are reasonable alternatives on which each call is a separate utterance and is interpreted as such ('trivial compositionality'). More generally, we propose that future studies should argue for animal syntax and compositionality by explicitly pitting the target theory against two deflationary analyses: the 'only one expression' hypothesis posits that there is no combination in the first place, for example just a simplex ABCD call; while the 'separate utterances' hypothesis posits that there are separate expressions (e.g. ABC and D), but that they form separate utterances and are neither syntactically nor semantically combined.

Demographic history and genomics of local adaptation in blue tit populations

Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (F_ST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (F_ST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

Phylogeny of the Eurasian Wren Nannus troglodytes (Aves: Passeriformes: Troglodytidae) reveals deep and complex diversification patterns of Ibero-Maghrebian and Cyrenaican populations

The Mediterranean Basin represents a Global Biodiversity Hotspot where many organisms show high inter- and intraspecific differentiation. Extant phylogeographic patterns of terrestrial circum-Mediterranean faunas were mainly shaped through Pleistocene range shifts and range fragmentations due to retreat into different glacial refugia. Thus, several extant Mediterranean bird species have diversified by surviving glaciations in different hospitable refugia and subsequently expanded their distribution ranges during the Holocene. Such a scenario was also suggested for the Eurasian Wren (Nannus troglodytes) despite the lack of genetic data for most Mediterranean subspecies. Our phylogenetic multi-locus analysis comprised 18 out of 28 currently accepted subspecies of N. troglodytes, including all but one subspecies which are present in the Mediterranean Basin. The resulting phylogenetic reconstruction dated the onset of the entire Holarctic radiation of three Nannus species to the early Pleistocene. In the Eurasian Wren, two North African subspecies represented separate basal lineages from the Maghreb (N. t. kabylorum) and from the Libyan Cyrenaica (N. t. juniperi), being only distantly related to other Mediterranean populations. Although N. troglodytes appeared to be paraphyletic with respect to the Nearctic Winter Wren (N. hiemalis), respective nodes did not receive strong statistical support. In contrast, paraphyly of the Ibero-Maghrebian taxon N. t. kabylorum was strongly supported. Southern Iberian populations of N. t. kabylorum did not clade with Maghrebian populations of the same subspecies but formed a sister clade to a highly diverse European clade (including nominate N. t. troglodytes and eight further taxa). In accordance with a pattern also found in other birds, Eurasian populations were split into a western clade (Europe, Caucasus) and an eastern clade (Central Asia, Sino-Himalayas, East Asia). This complex phylogeographic pattern revealed cryptic diversification in N. troglodytes, especially in the Iberio-Maghrebian region.

Pleistocene glacial cycles and physical barriers influence phylogeographic structure in Black-capped Chickadees (Poecile atricapillus), a widespread North American passerine

The nonmigratory Black-capped Chickadee (Poecile atricapillus (Linnaeus, 1766)) has a continent-wide distribution extending across large parts of North America. To investigate the phylogeographic structure and verify possible refugia during the last glacial maximum, we sequenced a 678 bp region of the mitochondrial control region from 633 Black-capped Chickadees at 35 sites across North America and performed paleoecological distribution modeling. Two genetically distinct groups were found using multiple analyses: one in Newfoundland (Canada) and a widespread continental group, with additional substructure evident in western continental populations. While gene flow is low throughout the range, it is especially low in peripheral populations. The Newfoundland population has remained isolated from continental populations for at least 65 000 years and contains a number of fixed nucleotide differences. Within the continental populations, Black-capped Chickadees are subdivided into Pacific Coast, Alaska (USA), southeast Rockies, and main-northeast groups consistent with late Pleistocene vicariance events. Evidence of secondary contact was identified between Pacific and main-northeast populations in northwest British Columbia (Canada) and between southeast Rockies and main-northeast groups in Montana (USA). Paleoecological distribution modeling predicted suitable habitat in Alaska, off the coast of Newfoundland, and several locations across the southern United States during the last glacial maximum, whereas suitable habitat during the last interglacial was more similar to the contemporary distribution.

Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) - phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation

Isolated islands and their often unique biota continue to play key roles for understanding the importance of drift, genetic variation and adaptation in the process of population differentiation and speciation. One island system that has inspired and intrigued evolutionary biologists is the blue tit complex (Cyanistes spp.) in Europe and Africa, in particular the complex evolutionary history of the multiple genetically distinct taxa of the Canary Islands. Understanding Afrocanarian colonization events is of particular importance because of recent unconventional suggestions that these island populations acted as source of the widespread population in mainland Africa. We investigated the relationship between mainland and island blue tits using a combination of Sanger sequencing at a population level (20 loci; 12 500 nucleotides) and next-generation sequencing of single population representatives (>3 200 000 nucleotides), analysed in coalescence and phylogenetic frameworks. We found (i) that Afrocanarian blue tits are monophyletic and represent four major clades, (ii) that the blue tit complex has a continental origin and that the Canary Islands were colonized three times, (iii) that all island populations have low genetic variation, indicating low long-term effective population sizes and (iv) that populations on La Palma and in Libya represent relicts of an ancestral North African population. Further, demographic reconstructions revealed (v) that the Canary Islands, conforming to traditional views, hold sink populations, which have not served as source for back colonization of the African mainland. Our study demonstrates the importance of complete taxon sampling and an extensive multimarker study design to obtain robust phylogeographical inferences.

Refugia, colonization and diversification of an arid-adapted bird: coincident patterns between genetic data and ecological niche modelling

Phylogeographical studies are common in boreal and temperate species from the Palaearctic, but scarce in arid-adapted species. We used nuclear and mitochondrial markers to investigate phylogeography and to estimate chronology of colonization events of the trumpeter finch Bucanetes githagineus, an arid-adapted bird. We used 271 samples from 16 populations, most of which were fresh samples but including some museum specimens. Microsatellite data showed no clear grouping according to the sampling locations. Microsatellite and mitochondrial data showed the clearest differentiation between Maghreb and Canary Islands and between Maghreb and Western Sahara. Mitochondrial data suggest differentiation between different Maghreb populations and among Maghreb and Near East populations, between Iberian Peninsula and Canary Islands, as well as between Western Sahara and Maghreb. Our coalescence analyses indicate that the trumpeter finch colonized North Africa during the humid Marine Isotope Stage 5 (MIS5) period of the Sahara region 125 000 years ago. We constructed an ecological niche model (ENM) to estimate the geographical distribution of climatically suitable habitats for the trumpeter finch. We tested whether changes in the species range in relation to glacial-interglacial cycles could be responsible for observed patterns of genetic diversity and structure. Modelling results matched with those from genetic data as the species' potential range increases in interglacial scenarios (in the present climatic scenario and during MIS5) and decreases in glacial climates (during the last glacial maximum, LGM, 21 000 years ago). Our results suggest that the trumpeter finch responded to Pleistocene climatic changes by expanding and contracting its range.

When east meets west: population structure of a high-latitude resident species, the boreal chickadee (Poecile hudsonicus)

The population genetic structure of northern boreal species has been strongly influenced both by the Quaternary glaciations and the presence of contemporary barriers, such as mountain ranges and rivers. We used a combination of mitochondrial DNA (mtDNA), nuclear microsatellites and spatial distribution modelling to study the population genetic structure of the boreal chickadee (Poecile hudsonicus), a resident passerine, and to investigate whether historical or contemporary barriers have influenced this northern species. MtDNA data showed evidence of eastern and western groups, with secondary admixture occurring in central Canada. This suggests that the boreal chickadee probably persisted in multiple glacial refugia, one in Beringia and at least one in the east. Palaeo-distribution modelling identified suitable habitat in Beringia (Alaska), Atlantic Canada and the southern United States, and correspond to divergence dates of 60-96 kya. Pairwise FST values for both mtDNA and microsatellites were significant for all comparisons involving Newfoundland, though mtDNA data suggest a more recent separation. Furthermore, unlike mtDNA data, nuclear data support population connectivity among the continental populations, possibly due to male-biased dispersal. Although both are significant, the isolation-by-distance signal is much stronger for mtDNA (r(2)=0.51) than for microsatellites (r(2)=0.05), supporting the hypothesis of male-biased dispersal. The population structure of the boreal chickadee was influenced by isolation in multiple refugia and contemporary barriers. In addition to geographical distance, physical barriers such as the Strait of Belle Isle and northern mountains in Alaska are restricting gene flow, whereas the Rocky Mountains in the west are a porous barrier.

An Update of Wallace’s Zoogeographic Regions of the World

Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

Deep sympatric mitochondrial divergence without reproductive isolation in the common redstart Phoenicurus phoenicurus

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.

Profound climatic effects on two East Asian black-throated tits (Ave: Aegithalidae), revealed by ecological niche models and phylogeographic analysis

Although a number of studies have assessed the effects of geological and climatic changes on species distributions in East Asian, we still have limited knowledge of how these changes have impacted avian species in south-western and southern China. Here, we aim to study paleo-climatic effects on an East Asian bird, two subspecies of black-throated tit (A. c. talifuensis–concinnus) with the combined analysis of phylogeography and Ecological Niche Models (ENMs). We sequenced three mitochondrial DNA markers from 32 populations (203 individuals) and used phylogenetic inferences to reconstruct the intra-specific relationships among haplotypes. Population genetic analyses were undertaken to gain insight into the demographic history of these populations. We used ENMs to predict the distribution of target species during three periods; last inter-glacial (LIG), last glacial maximum (LGM) and present. We found three highly supported, monophyletic MtDNA lineages and different historical demography among lineages in A. c. talifuensis–concinnus. These lineages formed a narrowly circumscribed intra-specific contact zone. The estimated times of lineage divergences were about 2.4 Ma and 0.32 Ma respectively. ENMs predictions were similar between present and LGM but substantially reduced during LIG. ENMs reconstructions and molecular dating suggest that Pleistocene climate changes had triggered and shaped the genetic structure of black-throated tit. Interestingly, in contrast to profound impacts of other glacial cycles, ENMs and phylogeographic analysis suggest that LGM had limited effect on these two subspecies. ENMs also suggest that Pleistocene climatic oscillations enabled the formation of the contact zone and thus support the refuge theory.

Plumage patterns are good indicators of taxonomic diversity, but not of phylogenetic affinities, in Australian grasswrens Amytornis (Aves: Maluridae)

The grasswrens (Maluridae: Amytornis) are elusive songbirds from the arid zones of Australia. Although some other Australian bird genera are also largely restricted to arid regions, none show the level of localized taxonomic diversity seen in Amytornis. Furthermore, their cryptic plumage patterns provide excellent camouflage but make it difficult to determine whether shared patterns reflect phylogenetic relationships or adaptations to similar terrain. To resolve the systematics and patterns of ecological diversification within Amytornis, we here present the results of a phylogenetic analysis of mitochondrial and nuclear multi-locus data for all recognized species and most subspecies, using traditional concatenation-based methods as well as a coalescent-based species-tree approach. Phylogenetic patterns retrieved by the species-tree approach were highly congruent with traditional methods, although branch support was generally higher in concatenation-based analysis, suggesting that species-tree methods may furnish more conservative results. In terms of identifying taxonomic diversity there was good concordance between plumage-based assessments and DNA distances. The same concordance was not found when comparing plumage-based and DNA-based predictions of phylogenetic relationships. Four primary lineages were identified: (a) barbatus; (b) merrotsyi; (c) the textilis complex, purnelli, ballarae, goyderi and housei; and (d) woodwardi, dorotheae, and the striatus complex. There was no robust resolution of relationships between lineages. It appears that in Amytornis, plumage differentiation between discrete populations is taxonomically significant, and not greatly influenced by ecophenotypic variation. However, at the deeper phylogenetic level, similar suites of plumage characters may be phylogenetically uninformative because of homoplasy. The study reveals higher levels of taxonomic diversity in Amytornis than previously recognized, with many taxa being highly localized. Such extensive short range endemism is mainly encountered in poorly-dispersing invertebrates and is unique in Australian birds. The identification here of the additional restricted range taxa has important conservation implications.

Old divergences in a boreal bird supports long-term survival through the Ice Ages

Background

Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species.

Results

In a sample of 113 individuals from 18 populations we identified 42 haplotypes of the mitochondrial cytochrome b gene, which separated into three clades: A - Alaska and mainland Eurasia (except Kamchatka); B - Kamchatka, Sakhalin and Hokkaido; and C - Honshu, Shikoku and Kyushu (i.e. Japan except Hokkaido). The oldest split among these clades, between A/B and C, is estimated to have taken place sometime between the mid Pliocene and early Pleistocene, and the second divergence, between clades A and B, in the early to mid Pleistocene. Within all of the three main clades, there are signs of population expansion.

Conclusions

The Arctic Warbler separated into three main clades in close succession around the Pliocene/Pleistocene border, with the two northern clades diverging last. All three clades probably experienced population bottlenecks during the Pleistocene as a result of range shifts and contractions, but nevertheless survived and maintained their integrities. Several other clades of Northeastern Palearctic birds are noted to have diversified during the Pliocene. In contrast, avian species or phylogroups presently occupying formerly glaciated North American ground are generally younger. The differences between these regions could be due to slower speciation rates in the Eastern Palearctic due to less fragmentation of forest habitats during glacial periods, or to longer survival of Eastern Palearctic clades as a result of less severe conditions in that region compared to northern North America. Several other Palearctic organisms show concordant biogeographical patterns to that of the Arctic Warbler, indicating common causes of their diversifications.

Phylogeny of long-tailed tits and allies inferred from mitochondrial and nuclear markers (Aves: Passeriformes, Aegithalidae)

In this paper we provide a molecular phylogeny based on three mitochondrial and three nuclear markers for all long-tailed tit species of the genus Aegithalos including several doubtful subspecies (17 taxa) plus three close allies of SE Asian Leptopoecile and North American Psaltriparus. Genus Aegithalos is divided into three major clades, two of them showing only minor differentiation. Separation of two mitchondrial haploytpe clusters in the N Palearctic Long-tailed Tit, Ae. caudatus, was dated back to the Late Pleistocene, however, descendants from both lineages underwent a rapid post-Pleistocene range expansion and largely mixed over the entire distribution area. The Chinese populations of the glaucogularis subspecies group represent a slightly earlier Pleistocene split from the Ae. caudatus clade. Genetic differentiation among several doubtful SE Asian species taxa on the sister clade of the latter N Palearctic/Chinese clade matches the intraspecific differentiation within Ae. caudatus. Unexpectedly, cytochrome-b distances among Himalayan Ae. iouschistos (including the subspecies bonvaloti from China and sharpei from Myanmar) and the Chinese endemic Ae. fuliginosus range at approximately 0.5% and apparently all these extant populations separated only very recently during late Pleistocene times, too. W Himalayan Ae. niveogularis clearly appeared as the sister species of the latter taxon assemblage. Unlike the two latter major clades, Ae. concinnus shows strong intraspecific differentiation with cyt-b distances as high as 6% among two Himalayan populations of ssp. iredalei, ssp. manipurensis from Myanmar and a fourth lineage from SW and SC China including ssp. talifuensis and nominate concinnus. A sister-group relationship between all Ae. concinnus and Ae. leucogenys was strongly supported. N American bushtits of genus Psaltriparus represent the sister clade to Palearctic genus Aegithalos, including a clear split between the minimus and the plumbeus subspecies group which was again dated back to Pleistocene times. The two tit-warbler species of genus Leptopoecile are strongly differentiated from one another and represent an early split from the Aegithalidae tree.

High mitogenomic evolutionary rates and time dependency

Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

BACKGROUND

During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.

RESULTS

A phylogenetic analysis of cytochrome b third-codon position confirms that the mitochondrial DNA mutation rate is quite variable in birds, passerines being the fastest evolving order. On average, mitochondrial DNA evolves slower in birds than in mammals of similar body size. This result is in agreement with the longevity hypothesis, and contradicts the hypothesis of a metabolic rate-dependent mutation rate. Birds show no footprint of adaptive selection on cytochrome b evolutionary patterns, but no link between direct estimates of population size and cytochrome b diversity. The mutation rate is the best predictor we have of within-species mitochondrial diversity in birds. It partly explains the differences in mitochondrial DNA diversity patterns observed between mammals and birds, previously interpreted as reflecting Hill-Robertson interferences with the W chromosome.

CONCLUSION

Mitochondrial DNA diversity patterns in birds are strongly influenced by the wide, unexpected variation of mutation rate across species. From a fundamental point of view, these results are strongly consistent with a relationship between species maximal longevity and mitochondrial mutation rate, in agreement with the mitochondrial theory of ageing. Form an applied point of view, this study reinforces and extends the message of caution previously expressed for mammals: mitochondrial data tell nothing about species population sizes, and strongly depart the molecular clock assumption.