Per Alström

Uppsala University | UU · Department of Ecology and Genetics

Background Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene–Pleistocene boundary. Results Here we investigate the phylogenetic relationships of all species of Prunellidae usin...

Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of four Emberiza species (Aves: Emberizidae...

The processes generating the earth’s montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypothese...

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the “black-and-white wagtails”, a group of five species in the songbird g...

The species complex comprising the rufous-naped lark Corypha africana, Sharpe’s lark Corypha sharpii, the red-winged lark Corypha hypermetra, the Somali long-billed lark Corypha somalica and Ash’s lark Corypha ashi encompasses 31 recognised taxa across sub-Saharan Africa, many of which are extremely poorly known and some not observed for decades. O...

Animals that colonize islands often undergo significant evolutionary changes in comparison with their continental counterparts as a response to specific island conditions. The pace of such changes can be relatively fast, which poses challenges in the evaluation of the taxonomic status of island taxa. The Japanese and Manchurian Bush Warbler species...

Larks (Alaudidae) constitute one of the avian families best adapted to xeric environments, having colonized a wide suite of open habitats including deserts. Although their highest diversity is in Africa, larks occur on all non-polar continents. We tested whether larks exhibit exceptional and/or correlated shifts in the tempos of speciation and ecol...

Simple Summary The distributions of many birds show a northward expansion in response to climate change. Brownish-flanked Bush Warbler (Horornis fortipes) is such a species, whose distribution expanded from 35° N to 40° N during the past decade. In this study, we documented the distribution of the newly established populations of this species and f...

The Buff-bellied Pipit Anthus rubescens comprises two allopatric subspecies groups: A. r. rubescens and A. r. alticola in North America and A. [r.] japonicus in north-east Asia. Despite their great morphological resemblance in breeding plumage, most individuals can be assigned to one or the other subspecies group in non breeding plumage. Allopatric...

Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the "black-and-white wagtails", a group of five species in the songbird g...

Song is considered to play an important role in the maintenance of prezygotic reproductive isolation between closely related songbird species. Therefore, song-mixing in a contact zone between closely related species is often considered as evidence of hybridization. The Sichuan Leaf Warbler Phylloscopus forresti and the Gansu Leaf Warbler P. kansuen...

The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and lar...

Is the Sand Lark Alaudala raytal krishnakumarsinhji a valid taxon?

The seasonal migration of birds is a fascinating natural wonder. Avian migratory behavior changes are common and are likely a polygenic process, as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotat...

The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts over the past two decades, there is still no comprehensive and well-resolved species-level phylogeny for Muscicapidae. Here we present a supermatrix phylogeny that includes all 50 currently recog...

Morphology has been a leading taxonomic guiding light to systematists for the last couple of hundred years. However, the genetic and – more recently – genomic revolution have produced numerous demonstrations of erroneous classifications that were based on labile morphological traits. We used thousands of genome‐wide markers to shed light on evoluti...

We describe the discovery of a previously unknown population of Melodious Lark Mirafra cheniana from northern Tanzania and southern Kenya, some 2000 km north of what was previously thought to be its northern limit in central Zimbabwe. The identification of this population as M. cheniana is based primarily on analyses of mitochondrial DNA and song....

Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study, we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with...

Mountain biotas have considerable conservation and research importance, but the formation of montane communities remains incompletely understood. Study of Indo-Pacific island faunas has inspired two main hypotheses for the generation of montane diversity. The first posits that montane populations arise via direct colonization from other mountain ar...

Background Field studies from 2011 onwards have demonstrated the presence of a breeding population of Yellow Wagtails ( Motacilla flava ) in the Xinjiang Uygur Autonomous Region, China that is phenotypically distinct from known subspecies occurring in Asia. Here we describe the plumages and vocalisations of this population and discuss its taxonomic...

Identification of juvenile Baird's and White-rumped Sandpipers

Identification of Lanceolated Warbler Locustella lanceolata

Prinias (Cisticolidae: Prinia) are resident warblers of open areas across Africa and Asia and include many polytypic species whose species limits have not been seriously reevaluated recently. Based on an integrative taxonomic analysis of morphology, song, and mitochondrial DNA (mtDNA), we suggest that 2 species should be recognized in the Graceful...

Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships wit...

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 f...

Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens–Sand Lark A. raytal complex, which has an intricate taxonomi...

The eastern subspecies of Greater Short-toed Lark Calandrella brachydactyla dukhunensis has recently been considered a separate species, Calandrella dukhunensis, by several authors based on molecular data. We present supporting evidence for this treatment based on studies of morphology, vocalisations and song-flight, and also present new data on ot...

The Long-tailed Rosefinch Carpodacus sibiricus breeds in two widely disjunct areas in East Asia. Five subspecies are usually recognized. The plumage differences between different subspecies groups within C. sibiricus are notable, suggesting it may actually comprise more than one species. However, proper taxonomic assessment has not been carried out...

We re‐evaluated the taxonomy of the Striated Prinia Prinia crinigera‐Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age‐related, geographic, and taxon‐specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses focused on...

The taxonomy of the Lesser/Asian Short‐toed Lark Alaudala rufescens–cheleensis complex has been debated for decades, mainly because of minor morphological differentiation among the taxa within the complex, and different interpretations of the geographical pattern of morphological characters among different authors. In addition, there have been few...

Aim The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we ai...

Aim Variation in species diversity among different geographical areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions, and a long time available for the...

We present a revised taxonomy of Estrildidae based on the first time-calibrated phylogeny of the family Estrildidae estimated from a data set including the majority of the species, and all genera except the monospecific Paludipasser, using two mitochondrial and five nuclear markers. We find that most differences in current taxonomy reflect alternat...

Talk "Identification of Eastern vagrants to Britain" given at Birdfair, Rutland Water Aug 2019. Audio recording of talk is available at: https://britishbirds.co.uk/rspb-bb-birders-lecture/

In biological systems, biological diversity often displays a rapid turn-over across elevations. This defining feature has made mountains classic systems for studying the spatial variation in diversity. Because patterns of elevational diversity can vary among lineages and mountain systems it remains difficult to extrapolate findings from one montane...

We used the mitochondrial control region and ND2 and ATP8+6 genes (c. 2900 bp), an intron in the CHD1Z gene on the Z-chromosome (c. 550 bp) and non-molecular (mainly morphological) data to reconstruct the phylogeny of nearly all of the least-inclusive nominal taxa in the avian genus Motacilla (wagtails). All three data sets are incongruent, althoug...

Phylogeographic analyses of the genus Eremophila (Horned Lark E. alpestris and Temminck’s Lark E. bilopha) were carried out based on the mitochondrial cytochrome b and ND2 genes. Four primary lineages with para-/allopatric distributions were identified: (1) a Qinghai–Tibetan–Himalayan lineage; (2) a North African and Middle Eastern lineage; (3) a n...

In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by 'speciation reversal' or by mitochondrial capture through genet...

Diversification of avifaunas associated with savannah and steppes appear to correlate with open habitats becoming available as a result of the spreading of C4 grasses, starting in the Miocene. Few comparative analyses exist for families for which all species are predominantly adapted to these habitats. One such group is Laniidae (Passeriformes), wh...

Taxa classified as subspecies may in fact be cryptic species. We assessed the taxonomic status of the Blue‐throated Flycatcher Cyornis rubeculoides complex in India, which consists of several forms with similar plumages and song. We used mitochondrial and nuclear DNA, plumage traits, and detailed song analysis to ascertain the taxonomic status of t...

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncert...

Despite the ongoing taxonomic revolution incorporating multiple species delimitation methods, knowledge gaps persist in the taxonomy of comparatively well-studied animal groups such as birds. Morphologically cryptic species risk slipping under the conservation radar, as they get mistakenly united with other species. Here, we employed six to 11 voca...

Background: The White-browed Shortwing (Brachypteryx montana) is widespread from the central Himalayas to the southeast Chinese mainland and the island of Taiwan, the Philippines and Indonesia. Multiple subspecies are recog- nised, and several of these have recently been suggested to be treated as separate species based on differences in morphology...

As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespre...

DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and “song babblers”), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using m...

The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not be...

The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide t...

identification of pipits in Indian Subcontinent. Available on YouTube (with songs and calls): https://www.youtube.com/watch?v=Jc5CgsfEDXs&t=13s

Identification of vagrant leaf warblers (Phylloscopus spp.) to Europe. Available on YouTube (with songs and calls): https://www.youtube.com/watch?v=gA04atLT8i8&t=21s

This talk was given for the Dutch Birding Association in 2016, and presents some interesting and surprising results from studies of the evolution of passerine birds. The talk is available on YouTube: https://www.youtube.com/watch?v=yaBXqldwIQo

Previous studies have suggested that bird populations in East Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitoc...

Generally, genotypes and phenotypes are expected to be spatially congruent, however, in widespread species complexes with few barriers to dispersal, multiple contact zones, and limited reproductive isolation, discordance between phenotypes and phylogeographic groups is more probable. Wagtails (Aves: Motacilla) are a genus of birds with striking plu...

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based...

Aspects of bird song have been shown to correlate with morphological and ecological features, including beak and body size, and habitat. Here we study evolution of song length and song frequency among 30 species belonging to the Cettiidae. Frequency is negatively correlated with body size, and song length increases with latitude. Although migration...