A multi-gene approach reveals a complex evolutionary history in the Cyanistes species group

The impact of geographic isolation and host shifts on population divergence of the rare cicada Subpsaltria yangi

The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130-0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.

Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Parallel evolution can be expected among closely related taxa exposed to similar selective pressures. However, parallelism is typically stronger at the phenotypic level, while genetic solutions to achieve these phenotypic similarities may differ. For polygenic traits, the availability of standing genetic variation (i.e., heterozygosity) may influence such genetic nonparallelism. Here, we examine the extent to which high-elevation adaptation is parallel-and whether the level of parallelism is affected by heterozygosity-by analyzing genomes of 19 Paridae species distributed across East Asia with a dramatic east-west elevation gradient. We find that western highlands endemic parids have consistently lower levels of heterozygosity-likely the result of late-Pleistocene demographic contraction-than do parids found exclusively in eastern lowlands, which remained unglaciated during the late Pleistocene. Three widespread species (east to west) have high levels of heterozygosity similar to that observed in eastern species, although their western populations are less variable than eastern ones. Comparing genomic responses to extreme environments of the Qinghai-Tibet Plateau, we find that the most differentiated genomic regions between each high-elevation taxon and its low-elevation relative are significantly enriched for genes potentially related to the oxygen transport cascade and/or thermogenesis. Despite no parallelism at particular genes, high similarity in gene function is found among comparisons. Furthermore, parallelism is not higher in more heterozygous widespread parids than in highland endemics. Thus, in East Asian parids, parallel functional response to extreme elevation appears to rely on different genes, with differences in heterozygosity having no effect on the degree of genetic parallelism.

Common patterns in the molecular phylogeography of western palearctic birds: a comprehensive review

A plethora of studies have offered crucial insights in the phylogeographic status of Western Palearctic bird species. However, an overview integrating all this information and analyzing the combined results is still missing. In this study, we compiled all published peer-reviewed and grey literature available on the phylogeography of Western Palearctic bird species. Our literature review indicates a total number of 198 studies, with the overwhelming majority published as journal articles (n = 186). In total, these literature items offer information on 145 bird species. 85 of these species are characterized by low genetic differentiation, 46 species indicate genetic variation but no geographic structuring i.e. panmixia, while 14 species show geographically distinct lineages and haplotypes. Majority of bird species inhabiting the Western Palearctic display genetic admixture. The glaciation cycles in the past few million years were pivotal factors in shaping this situation: during warm periods many species expanded their distribution range to the north over wide areas of Eurasia; whereas, during ice ages most areas were no longer suitable and species retreated to refugia, where lineages mixed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10336-021-01893-x.

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.

The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone

BACKGROUND

A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses.

RESULTS

ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids.

CONCLUSIONS

Isolation for 2.4 Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.

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.

Genetic, morphological, and acoustic evidence reveals lack of diversification in the colonization process in an island bird

Songbirds with recently (i.e., early Holocene) founded populations are suitable models for studying incipient differentiation in oceanic islands. On such systems each colonization event represents a different evolutionary episode that can be studied by addressing sets of diverging phenotypic and genetic traits. We investigate the process of early differentiation in the spectacled warbler (Sylvia conspicillata) in 14 populations separated by sea barriers from three Atlantic archipelagos and from continental regions spanning from tropical to temperate latitudes. Our approach involved the study of sexual acoustic signals, morphology, and genetic data. Mitochondrial DNA did not provide clear population structure. However, microsatellites analyses consistently identified two genetic groups, albeit without correspondence to subspecies classification and little correspondence to geography. Coalescent analyses showed significant evidence for gene flow between the two genetic groups. Discriminant analyses could not correctly assign morphological or acoustic traits to source populations. Therefore, although theory predicting that in isolated populations genetic, morphological, or acoustic traits can lead to radiation, we have strikingly failed to document differentiation on these attributes in a resident passerine throughout three oceanic archipelagos.

Pronounced fixation, strong population differentiation and complex population history in the Canary Islands blue tit subspecies complex

Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.

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.

Comment on Gohli et al. (2013): "Does promiscuity explain differences in levels of genetic diversity across passerine birds?"

Gohli et al. (2013) report a positive relationship between genetic diversity and promiscuity across passerine birds, and suggest that female promiscuity acts as a form of balancing selection, maintaining differences in genetic variation across species. This is an interesting hypothesis, but the enormous variation in genetic diversity present within species is not taken into account in their analyses. This, combined with a small sample size at several levels, makes the relationship between genetic diversity and promiscuity very difficult to interpret. Demonstrating that species-level differences in genetic diversity (if they occur at all) are affected by promiscuity would require a far more comprehensive study than is presently possible.

Multilocus phylogeography (mitochondrial, autosomal and Z-chromosomal loci) and genetic consequence of long-distance male dispersal in Black-throated tits (Aegithalos concinnus)

Multilocus data from the different genomes are essential to understand the phylogeographic history of species, particularly when a species has the male-biased dispersal pattern. Although Black-throated tits (Aegithalos concinnus) are socially monogamous and cooperatively breeding birds, limited observational data suggested that males may have the ability of long-distance dispersal. We have previously detected three highly supported mitochondrial populations within two subspecies of Black-throated tits (A. c. concinnus and A. c. talifuensis). Here, we used several genetic markers with different inheritance patterns to gain insights about their phylogeographic history. Phylogenetic and individual-based Bayesian analysis showed weak geographical structure amongst nuclear sequences (autosomal and Z-chromosomal loci). Coalescent analysis revealed high levels of gene flow among mitochondrial populations, even between allopatric populations. These results strongly suggested that male-biased gene flow was responsible for the discordant cytonuclear phylogeographic patterns. Consistent with expectation on the genetic consequence of long-distance male dispersal, mantel tests revealed a significant pattern of isolation by distance for mitochondrial sequences, but failed to provide a similar pattern for nuclear genes within a continuous population; female Black-throated tits showed a stronger but not significantly different relationship of isolation by distance than males when using mitochondrial DNA alone. We discussed the contribution of male juveniles with delayed dispersal to the non-significantly different IBD patterns between sexes. Our results using multilocus genetic data revealed aspects of the complex evolutionary history of Black-throated tits and the important role of long-distance male dispersal in the population structuring.

Extensive introgressive hybridization within the northern oriole group (Genus Icterus) revealed by three-species isolation with migration analysis

Until recently, studies of divergence and gene flow among closely-related taxa were generally limited to pairs of sister taxa. However, organisms frequently exchange genes with other non-sister taxa. The “northern oriole” group within genus Icterus exemplifies this problem. This group involves the extensively studied hybrid zone between Baltimore oriole (Icterus galbula) and Bullock's oriole (I. bullockii), an alleged hybrid zone between I. bullockii and black-backed oriole (I. abeillei), and likely mtDNA introgression between I. galbula and I. abeillei. Here, we examine the divergence population genetics of the entire northern oriole group using a multipopulation Isolation-with-Migration (IM) model. In accordance with Haldane's rule, nuclear loci introgress extensively beyond the I. galbula–I. bullockii hybrid zone, while mtDNA does not. We found no evidence of introgression between I. bullockii and I. abeillei or between I. galbula and I. abeillei when all three species were analyzed together in a three-population model. However, traditional pairwise analysis suggested some nuclear introgression from I. abeillei into I. galbula, probably reflecting genetic contributions from I. bullockii unaccounted for in a two-population model. Thus, only by including all members of this group in the analysis was it possible to rigorously estimate the level of gene flow among these three closely related species.