Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

An Unbiased Molecular Approach Using 3′-UTRs Resolves the Avian Family-Level Tree of Life

Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life

Wing shape and environmental energy are associated with molecular evolutionary rates in a large avian radiation

Among the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with a proxy of metabolic demands imposed by flight (wing morphology) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found a strong positive association between molecular rates in genomic regions that can change the coded amino-acid with wing morphology, environmental temperature, and UV radiation. Strikingly, however, we did not find evidence of such associations with molecular rates at sites not impacting amino-acids. Our results suggest that the demands of flight and environmental energy primarily impact genome evolution by placing selective constraints, instead of being associated with basal mutation rates.

An extensive molecular phylogeny of weaverbirds (Aves: Ploceidae) unveils broad nonmonophyly of traditional genera and new relationships

The diverse Old World avian family Ploceidae (weaverbirds) presently comprises 117 species in 17 genera. Despite being a well-known bird group, the family has received incomplete attention in terms of molecular systematics; systematists have often focused on subclades, with the most extensive study to date covering <66% of recognized species. As a consequence, weaverbird taxonomy remains outdated, and phylogenetic relationships, particularly of the African Malimbus (previously Ploceus and Malimbus) clade, remains largely unresolved. Here, we sampled 109 weaver species (and numerous nominal subspecies), including 99 of the 103 recognized “typical weaverbird” taxa for an 8-gene dataset. Antique DNA techniques were used to extract DNA from study skins of 27 rare taxa not available in global tissue collections. The study included 32 species and 4 genera of ploceids previously unstudied phylogenetically. Our analyses supported monophyly of the family and identified 8 distinct clades. Our results conflict extensively with current taxonomy. We suggest that plumage traits and morphology exhibit high plasticity, such that phenotype does not always reflect phylogenetic relationships in weaverbirds. We recommend (1) uniting African-Ploceus, Malimbus, Anaplectes, and Notiospiza in Malimbus; (2) retaining the monotypic genus Pachyphantes; and (3) placing Brachycope with Euplectes. This study, the first near-species-level phylogeny for the family, lays a firm foundation for downstream studies of biogeography and character evolution.

Correlated patterns of genetic diversity and differentiation across an avian family

ABSTRACTComparative studies of genomic differentiation among independent lineages can provide insights into aspects of the speciation process, such as the relative importance of selection and drift in shaping genomic landscapes, the role of genomic regions of high differentiation, and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and divergence in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology, and migratory behavior, to ask whether similar genomic regions are important in the evolution of independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from 5 taxa and found that patterns of genetic diversity and divergence are highly similar among different stonechat taxa. We then asked if these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g., areas of low recombination). Consequently, studies employing genome scans to search for areas important in reproductive isolation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or facilitate local adaptation.

Mating system, male territoriality and agility as predictors of the evolution of sexual size dimorphism in hummingbirds (Aves: Trochilidae)

Male and female animals often exhibit differences in body size; this difference is known as sexual size dimorphism (SSD). Hummingbirds are an excellent model system to test functional hypotheses of SSD because they exhibit a wide range of body sizes and reproductive behaviour between the sexes. Here, using phylogenetic comparative methods, we tested whether mating system, male territoriality and agility predicted the evolution of SSD in this avian family. Our results first suggest that evolutionary increases in male-biased SSD are related to increases in lekking behaviour. Second, we found that male agility is positively related to increases in male biased-SSD albeit this is only likely to occur in males of territorial species. Finally, we found an allometric pattern for SSD consistent with Rensch’s rule that was not explained by our estimates of male competition and agility.