Habitat‐driven diversification,hybridization and cryptic diversity in the Fork‐tailed Drongo (Passeriformes: Dicruridae: Dicrurus adsimilis)

Species complexes of widespread African vertebrates that include taxa distributed across different habitats are poorly understood in terms of their phylogenetic relationships, levels of genetic differentiation and diversification dynamics. The Fork‐tailed Drongo (Dicrurus adsimilis) species complex includes seven Afrotropical taxa with parapatric distributions, each inhabiting a particular bioregion. Various taxonomic hypotheses concerning the species limits of the Fork‐tailed Drongo have been suggested, based largely on mantle and upperpart coloration, but our understanding of diversity and diversification patterns remains incomplete. Especially given our lack of knowledge about how well these characters reflect taxonomy in a morphologically conservative group. Using a thorough sampling across Afrotropical bioregions, we suggest that the number of recognized species within the D. adsimilis superspecies complex has likely been underestimated and that mantle and upperpart coloration reflects local adaptation to different habitat structure, rather than phylogenetic relationships. Our results are consistent with recent phylogeographic studies of sub‐Saharan African vertebrates, indicating that widespread and often morphologically uniform species comprise several paraphyletic lineages, often with one or more of the lineages being closely related to phenotypically distinct forms inhabiting a different, yet geographically close, biome.     

Multiple transisthmian divergences,extensive cryptic diversity,occasional long‐distance dispersal,and biogeographic patterns in a marine coastal isopod with an amphi‐American distribution

Excirolana braziliensis is a coastal intertidal isopod with a broad distribution spanning the Atlantic and Pacific tropical and temperate coasts of the American continent. Two separate regional studies (one in Panama and one in Chile) revealed the presence of highly genetically divergent lineages, implying that this taxon constitutes a cryptic species complex. The relationships among the lineages found in these two different regions and in the rest of the distribution, however, remain unknown. To better understand the phylogeographic patterns of E. braziliensis, we conducted phylogenetic analyses of specimens from much of its entire range. We obtained DNA sequences for fragments of four mitochondrial genes (16S rDNA, 12S rDNA, COI, and Cytb) and also used publicly available sequences. We conducted maximum likelihood and Bayesian phylogenetic reconstruction methods. Phylogeographic patterns revealed the following: (1) new highly divergent lineages of E. braziliensis; (2) three instances of Atlantic–Pacific divergences, some of which appear to predate the closure of the Isthmus of Panama; (3) the distributional limit of highly divergent lineages found in Brazil coincides with the boundary between two major marine coastal provinces; (4) evidence of recent long‐distance dispersal in the Caribbean; and (5) populations in the Gulf of California have closer affinities with lineages further south in the Pacific, which contrasts with the closer affinity with the Caribbean reported for other intertidal organisms. The high levels of cryptic diversity detected also bring about challenges for the conservation of this isopod and its fragile environment, the sandy shores. Our findings underscore the importance of comprehensive geographic sampling for phylogeographic and taxonomical studies of broadly distributed putative species harboring extensive cryptic diversity.     

Climatic niche evolution in Smilacaceae (Liliales) drives patterns of species diversification and richness between the Old and New World

Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the striking disparity in species richness between Asia and the Americas remain poorly understood. Here, we synthesize global phylogenetic and macroecological data on the diversification of Smilacaceae, deciphering potential drivers underlying the species diversity pattern biased toward Asia. We compiled global distributions of all Smilacaceae species, and reconstructed the biogeographic history and niche evolution using a new time-calibrated phylogeny (eight genes, 135 species). Integrating these data sets, we estimated evolutionary histories and diversification rates for each region, and tested correlations among species diversification, niche evolution, and niche divergence. Smilacaceae probably originated during the Late Cretaceous/Early Palaeocene and began to diversify in middle to low latitudes in Central America and Eurasia during the Late Eocene. Both the Old and New World clades exhibited a steady, albeit slight, increase of species diversification from the Late Eocene to Early Miocene. However, the Old World clade experienced an abrupt increase in net diversification during the Late Miocene. Our findings also revealed that species diversification rates were positively correlated with ecological niche evolution and niche divergence. Niche shifts and climatic niche evolution since the Middle Miocene played crucial roles in species diversification dynamics within Smilacaceae. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.     

Recent population declines in Afro‐Palaearctic migratory birds: the influence of breeding and non‐breeding seasons

Aim

Recent, rapid population declines in many Afro‐Palaearctic migratory bird species have focussed attention on changing conditions within Africa. However, processes influencing population change can operate throughout the annual cycle and throughout migratory ranges. Here, we explore the evidence for impacts of breeding and non‐breeding conditions on population trends of British breeding birds of varying migratory status and wintering ecology.

Location

Great Britain (England & Scotland).

Methods

Within‐ and between‐species variation in population trends is quantified for 46 bird species with differing migration strategies.

Results

Between 1994 and 2007, rates of population change in Scotland and England differed significantly for 19 resident and 15 long‐distance migrant species, but were similar for 12 short‐distance migrant species. Of the six long‐distance migrant species that winter in the arid zone of Africa, five are increasing in abundance throughout Britain. In contrast, the seven species wintering in the humid zone of Africa are all declining in England, but five of these are increasing in Scotland. Consequently, populations of both arid and humid zone species are increasing significantly faster in Scotland than England, and only the English breeding populations of species wintering in the humid zone are declining.

Main conclusions

Population declines in long‐distance migrants, especially those wintering in the humid zone, but not residents or short‐distance migrants suggest an influence of non‐breeding season conditions on population trends. However, the consistently less favourable population trends in England than Scotland of long‐distance migrant and resident species strongly suggest that variation in the quality of breeding grounds is influencing recent population changes. The declines in humid zone species in England, but not Scotland, may result from poorer breeding conditions in England exacerbating the impacts of non‐breeding conditions or the costs associated with a longer migration, while better conditions in Scotland may be buffering these impacts.

     

Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids‐adapted clade of cichlids from the Congo River

The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double‐digest restriction‐associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage‐specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD‐Seq data in understanding diversification processes operating both below and above the species level.     

Island theory, matrix effects and species richness patterns in habitat fragments

Island biogeography theory, created initially to study diversity patterns on islands, is often applied to habitat fragments. A key but largely untested assumption of this application of theory is that landscape matrix species composition is non‐overlapping with that of the islands. We tested this assumption in successional old field patches in a closely mowed matrix, and because our patches are appropriately viewed as sets of contiguous habitat units we studied patterns of species richness per unit area. Previous studies at our site did not find that diversity patterns on patch ‘islands’ conformed to predictions of island biogeography theory. Our results indicate that when matrix species are removed from the patch samples, diversity patterns conform better to theory. We suggest that classical island theory remains an appropriate tool to study diversity patterns in fragmented habitats, but that allowances should be made for spill‐over colonization of ‘islands’ from the ‘sea’.     

Marphysa (Eunicidae,polychaete, Annelida) species of the Sanguinea group from Australia,with comments on pseudo‐cryptic species

The genus Marphysa is widely collected for bait by recreational fishermen in Australia, and yet the number of species remains unresolved. A new species is described together with additional information on a previously described species. This study reveals that while species of Marphysa superficially resemble one another, detailed studies on the distribution of different types of chaetae along the body, together with molecular studies, uncover species which may co‐occur. Correct identification is critical for management of these largely intertidal species. This study also highlights the increasing awareness of the presence of pseudo‐cryptic species in polychaetes.     

Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection

The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model‐testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species‐specific and related to life‐history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification.