Zhengwang Zhang

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae

Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups (“pheasants” and “partridges”) is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.

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.

Effect of geological vicariance on mitochondrial DNA differentiation in Common Pheasant populations of the Loess Plateau and eastern China.

Population differentiation within species can be stimulated by various geographic and climatic factors. In this study, we analyzed the population structure of the Common Pheasant (Phasianus colchicus) in the Loess Plateau and its adjacent eastern areas (named eastern China). We sequenced mitochondrial cytochrome b and control regions of 249 samples collected from 42 populations that covered the whole Loess Plateau and eastern China. Two groups (one containing populations 1-27 and the other populations 28-42) were identified using Analysis of Molecular Variance, Spatial Analysis of Molecular Variance, median-joining network analysis and maximum-parsimony analysis. The results demonstrated that although populations were distributed continuously throughout the study area, there was clear differentiation between populations. Geographically, population differentiation was sutured along the eastern edge of the Loess Plateau. The Migration Divergence (MDIV) analysis suggested that the two groups diverged at about 0.21 million years ago, which corresponded to a period when numerous large inland paleo-lakes greatly receded across the Loess Plateau during 0.25-0.20 million years before present (Ma BP). We inferred that the rapid recession of the Loess Plateau paleo-lakes caused dramatic shifts from a relatively humid climate, to one that was significantly more arid. Such severe climate transition combined with a dry-cold starting of one of multi-cycled climate fluctuations from warm-humid to dry-cold since about 0.24-0.22 Ma BP on the Loess Plateau may have been the impetus that effectively facilitated differentiation between different pheasant populations.

Explaining variation in brood parasitism rates between potential host species with similar habitat requirements

Host specialization evolved in many parasite-host systems. Evolution and maintenance of host specificity may be influenced by host life-history traits, active host selection by the parasite, and host anti-parasite strategies. The relative importance of these factors is poorly understood in situations that offer parasites a choice between hosts with similar habitat requirements. The common cuckoo Cuculus canorus is a generalist parasite on the species level, but individual females prefer particular host species. In reed beds of the Yellow River Delta, China, two potential hosts with similar nest characteristics, Oriental reed warblers Acrocephalus orientalis and reed parrotbills Paradoxornis heudei, breed in sympatry. We found that warblers were parasitized at much higher rates than parrotbills. Both hosts recognized and rejected non-mimetic model eggs well, indicating that they have been involved in an arms-race with cuckoos. Cuckoo eggs closely resembled warbler eggs, and such eggs were mostly accepted by warblers but rejected by parrotbills. Only warblers recognized adult cuckoos as a specific threat. Both hosts were equally good at raising cuckoo chicks. Low nest density, partial isolation by breeding time, small scale differences in nest and nest site characteristics, and high rejection rates of natural cuckoo eggs are likely cumulatively responsible for the low current parasitism rate in parrotbills. This study emphasizes the importance of integrating the study of general host life-history characteristics and specific anti-parasitism strategies of hosts across all breeding stages to understand the evolution of host specificity.

Molecular Evidence for Species Status of the Endangered Hainan Peacock Pheasant

Abstract The Hainan peacock pheasant is an endangered taxon found only on Hainan Island of China. Due to lack of detailed taxonomic studies, whether it is a subspecies of the grey peacock pheasant (Polyplectron bicalcaratum katsumatae) or a full species (Polyplectron katsumatae) remained unclear. We used molecular markers, including the complete mitochondrial cytochrome b gene and intron G of the nuclear ovomucoid gene, to reevaluate the taxonomy of the Hainan peacock pheasant. The results showed phylogeographic monophyly and large genetic distance between the Hainan peacock pheasant and the grey peacock pheasant. Sequence differences corroborated the species-level distinction between these two peacock pheasants, which were inferred to have diverged about 1.4±0.3 million years ago, near the time Hainan Island became separated from mainland China. Because the population density of the Hainan peacock pheasant is very low in its tropical forest on the island and the wild population is declining, it is now becoming severely endangered and should be ranked as the rarest species in the Order Galliformes in China. Our results increase the urgency of getting more morphological data to support the classification of the Hainan peacock pheasant as a distinct species and taking more conservation action immediately to protect this endangered island species.

Community-wide changes in intertaxonomic temporal co-occurrence resulting from phenological shifts

Global climate change is known to affect the assembly of ecological communities by altering species spatial distribution patterns, but little is known about how climate change may affect community assembly by changing species temporal co-occurrence patterns, which is highly likely given the widely observed phenological shifts associated with climate change. Here, we analyzed a 29-year phenological data set comprising community-level information on the timing and span of temporal occurrence in 11 seasonally occurring animal taxon groups from 329 local meteorological observatories across China. We show that widespread shifts in phenology have resulted in community-wide changes in the temporal overlap between taxa that are dominated by extensions, and that these changes are largely due to taxas altered span of temporal occurrence rather than the degree of synchrony in phenological shifts. Importantly, our findings also suggest that climate change may have led to less phenological mismatch than generally presumed, and that the context under which to discuss the ecological consequences of phenological shifts should be expanded beyond asynchronous shifts.

Oriental reed warbler (Acrocephalus orientalis) nest defence behaviour towards brood parasites and nest predators

Brood parasites and predators pose different threats to passerines that may favour the evolution of enemy-specific defence strategies. Furthermore, potential sex-specific variation in parental investment may be manifested in differences between male and female nest defence behaviour. We investigated these hypotheses in Oriental reed warblers ( Acrocephalus orientalis), by recording sex- and stage-specific (nests with eggs or nestlings) responses to stuffed dummies placed at their nests. Warblers showed the highest level of aggression to the co-occurring parasite, the common cuckoo ( Cuculus canorus), colour morph (grey), but showed reluctance to mob or attack the co-occurring nest predator, the magpie ( Pica pica). There was a sex difference in rate of body attacks towards rufous morph common cuckoo, sparrowhawk ( Accipiter nisus) (locally absent parasite and predator, respectively) and the spotted dove ( Streptopelia chinensis) (locally present, harmless species), with females showing better ability to distinguish between these species than males.

Was the exposed continental shelf a long-distance colonization route in the ice age? The Southeast Asia origin of Hainan and Taiwan partridges.

Research on island biotas has greatly contributed to the development of modern evolutionary and biogeographic theories. Until now, most studies have suggested that continental islands received their biotas directly from the adjacent mainland. However, only a few studies have indicated that species on continental islands might originate from other distantly non-adjacent regions. Here, we used the hill partridges (genus Arborophila) that are widely distributed in the southwest and southeast China mainland, Indochina, Hainan and Taiwan islands to test whether species on continental islands might originate from distant regions rather than the adjacent mainland. Based on molecular phylogenies inferred from three mitochondrial fragments and three nuclear introns, together with ancestral area reconstruction, we found that the ancestors of the endemic Hainan and Taiwan partridges (A. ardens and A. crudigularis) likely originated from Indochina, rather than the nearby southeast China mainland. The divergence time estimates demonstrate that their ancestors likely colonized Hainan and Taiwan islands using the long exposed continental shelf between Indochina, Hainan and Taiwan islands during glacial periods, which had not been demonstrated before. Thus, integrating distribution data with phylogenetic information can shed new lights on the historical biogeography of continental islands and surrounding mainland regions.

Coupling Genetic and Species Distribution Models to Examine the Response of the Hainan Partridge (Arborophila ardens) to Late Quaternary Climate

Understanding the historical dynamics of animal species is critical for accurate prediction of their response to climate changes. During the late Quaternary period, Southeast Asia had a larger land area than today due to lower sea levels, and its terrestrial landscape was covered by extensive forests and savanna. To date, however, the distribution fluctuation of vegetation and its impacts on genetic structure and demographic history of local animals during the Last Glacial Maximum (LGM) are still disputed. In addition, the responses of animal species on Hainan Island, located in northern Southeast Asia, to climate changes during the LGM are poorly understood. Here, we combined phylogeographic analysis, paleoclimatic evidence, and species distribution models to examine the response of the flightless Hainan Partridge (Arborophila ardens) to climate change. We concluded that A. ardens survived through LGM climate changes, and its current distribution on Hainan Island was its in situ refuge. Range model results indicated that A. ardens once covered a much larger area than its current distribution. Demographic history described a relatively stable pattern during and following the LGM. In addition, weak population genetic structure suggests a role in promoting gene flow between populations with climate-induced elevation shifts. Human activities must be considered in conservation planning due to their impact on fragmented habitats. These first combined data for Hainan Partridge demonstrate the value of paired genetic and SDMs study. More related works that might deepen our understanding of the responses of the species in Southeast Asia to late Quaternary Climate are needed.

Characterization of nine microsatellite loci for a globally vulnerable species, Reeves’s Pheasant (Syrmaticus reevesii)

Reeves’s Pheasant, Syrmaticusxa0reevesii, is an endemic species of China. Due to habitat loss, poaching and human disturbance, its wild population has been decreased drastically and it is listed as a globally vulnerable species by IUCN/BirdLife/WPA (IUCN 2008). Here, we report nine new polymorphic microsatellite markers isolated from the Reeves’s Pheasant. The number of alleles per locus varies between four and fourteen, with expected heterozygosity ranging from 0.349–0.776 (nxa0xa0=xa090). These polymorphic loci provide a valuable tool for future population studies that relate to the conservation of this pheasant.