Yibo Hu

Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation

The panda lineage dates back to the late Miocene and ultimately leads to only one extant species, the giant panda (Ailuropoda melanoleuca). Although global climate change and anthropogenic disturbances are recognized to shape animal population demography their contribution to panda population dynamics remains largely unknown. We sequenced the whole genomes of 34 pandas at an average 4.7-fold coverage and used this data set together with the previously deep-sequenced panda genome to reconstruct a continuous demographic history of pandas from their origin to the present. We identify two population expansions, two bottlenecks and two divergences. Evidence indicated that, whereas global changes in climate were the primary drivers of population fluctuation for millions of years, human activities likely underlie recent population divergence and serious decline. We identified three distinct panda populations that show genetic adaptation to their environments. However, in all three populations, anthropogenic activities have negatively affected pandas for 3,000 years.

Black and white and read all over: the past, present and future of giant panda genetics

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high‐profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation.

Giant panda scent-marking strategies in the wild: role of season, sex and marking surface

Scent marking entails significant energetic and opportunity costs that demand efficiency. Signal detection theory offers a theoretical framework that generates testable hypotheses regarding where animals should place scent signals in the environment in a way that maximizes their probability of detection by target receivers while minimizing costs of production and distribution. Solitary and reliant on chemical communication, the giant panda, Ailuropoda melanoleuca, offers an interesting model to test these ideas. We studied scent-marking patterns in wild giant pandas in the Foping Nature Reserve by surveying areas containing a high density of scent posts. Pandas did not deploy scent marks randomly in this environment, but targeted trees with specific characteristics that promoted signal persistence, range and/or likelihood of detection. Variables affecting selection of scent-marking sites included bark roughnesss, presence of moss on the tree trunk, tree diameter and distance to the trail. That pandas should be efficient with their use of chemosignals comes as no surprise, as mounting evidence is suggesting that many aspects of giant panda life history are constrained by their energetically poor diet. We also found seasonal and sex differences in marking patterns, indicating a role for scent marking in reproduction and competition. Males scent-marked throughout the year, whereas females scent-marked predominantly during the mating season, suggesting functional differences in scent marking between the sexes.

Giant Pandas Are Not an Evolutionary cul-de-sac: Evidence from Multidisciplinary Research

The giant panda (Ailuropoda melanoleuca) is one of the worlds most endangered mammals and remains threatened by environmental and anthropogenic pressure. It is commonly argued that giant pandas are an evolutionary cul-de-sac because of their specialized bamboo diet, phylogenetic changes in body size, small population, low genetic diversity, and low reproductive rate. This notion is incorrect, arose from a poor understanding or appreciation of giant panda biology, and is in need of correction. In this review, we summarize research across morphology, ecology, and genetics to dispel the idea, once and for all, that giant pandas are evolutionary dead-end. The latest and most advanced research shows that giant pandas are successful animals highly adapted to a specialized bamboo diet via morphological, ecological, and genetic adaptations and coadaptation of gut microbiota. We also debunk misconceptions around population size, population growth rate, and genetic variation. During their evolutionary history spanning 8 My, giant pandas have survived diet specialization, massive bamboo flowering and die off, and rapid climate oscillations. Now, they are suffering from enormous human interference. Fortunately, continued conservation effort is greatly reducing impacts from anthropogenic interference and allowing giant panda populations and habitat to recover. Previous ideas of a giant panda evolutionary cul-de-sac resulted from an unsystematic and unsophisticated understanding of their biology and it is time to shed this baggage and focus on the survival and maintenance of this high-profile species.

Ecological niche modeling of the sympatric giant and red pandas on a mountain-range scale

Habitat use and separation between the two sympatric species, the giant panda and the red panda, have been primary causes of coexistence at the fine scale. In this paper, we addressed the question of coexistence between species in space. By Ecological Niche Factor Analysis, we calculated species-specific habitat requirements, built habitat suitability maps and examined interspecific differences in spatial niche parameters. According to the ENFA scores, suitable habitats in the giant and red panda are surrounded by high-altitude, and are rich in conifer forest. Compared with the giant panda, however, the red panda rather preferred sparse forests, and normally colonized far from village and road. Despite similar narrow niche breadth for both pandas, difference of niche overlap indices implied that the width of environmental niche of red pandas almost completely encompasses that of the giant panda. We, therefore, suggest that differences in use of ecological niche variables may contribute to coexistence of the sympatric species in space. Based on highly suitable locations of the sympatric species maps, most official reserves appear to be poorly located or are too small, and new reserves are recommended to be established in the central part of core habitats in the Liangshan Mountains.

THE PARASITES OF GIANT PANDAS: INDIVIDUAL-BASED MEASUREMENT IN WILD ANIMALS

There is a growing recognition of parasites as a significant factor in the successful conservation of endangered species. Determining parasite infection and load in free-ranging populations traditionally is done via necropsy or coproscopy. For studies of wild animals, fecal sample collection can result in bias because the individual identity of animals is unknown and multiple samples may be collected from the same individual, yet treated as unrelated samples. We studied parasite load in wild giant pandas (Ailuropoda melanoleuca) across six mountain ranges in China. Genetic identification was used to determine the exact number of individuals sampled. The parasite fauna consisted of five species, dominated by Baylisascaris shroederi. The pattern of statistical difference between mountains was artificially inflated when animal identity was not included in the model. Our results suggest that caution should be exercised in inferring patterns from comparative parasitologic studies when samples cannot be attributed to specific individuals. Using noninvasive genetic sampling to avoid such bias should form a standard tool in the management of endangered species and their parasites.

Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

Significance The giant panda and red panda are obligate bamboo-feeders that independently evolved from meat-eating ancestors and possess adaptive pseudothumbs, making them ideal models for studying convergent evolution. In this study, we identified genomic signatures of convergent evolution associated with bamboo eating. Comparative genomic analyses revealed adaptively convergent genes potentially involved with pseudothumb development and essential bamboo nutrient utilization. We also found that the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings provide insights into genetic mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet in both pandas and offer an example of genome-scale analyses for detecting convergent evolution. Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution. Limb development genes DYNC2H1 and PCNT have undergone adaptive convergence and may be important candidate genes for pseudothumb development. As evolutionary responses to a bamboo diet, adaptive convergence has occurred in genes involved in the digestion and utilization of bamboo nutrients such as essential amino acids, fatty acids, and vitamins. Similarly, the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings offer insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet.

Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA

Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence‐based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai‐Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above‐mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite‐based Bayesian clustering clearly identified three groups (Qionglai‐Liangshan, Xiaoxiangling and Gaoligong‐Tibet). A significant isolation‐by‐distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large‐scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai‐Tibetan Plateau, subspecies classification and conservation of red pandas are discussed.

Large-Scale Genetic Survey Provides Insights into the Captive Management and Reintroduction of Giant Pandas

The captive genetic management of threatened species strives to preserve genetic diversity and avoid inbreeding to ensure populations remain available, healthy, and viable for future reintroduction. Determining and responding to the genetic status of captive populations is therefore paramount to these programs. Here, we genotyped 19 microsatellite loci for 240 captive giant pandas (Ailuropoda melanoleuca) (∼64% of the captive population) from four breeding centers, Wolong (WL), Chengdu (CD), Louguantai (LGT), and Beijing (BJ), and analyzed 655 bp of mitochondrial DNA control region sequence for 220 of these animals. High levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers, indicating that the captive population is genetically healthy and deliberate further genetic input from wild animals is unnecessary. However, the LGT population faces a higher risk of inbreeding, and significant genetic structure was detected among breeding centers, with LGT-CD and WL-BJ clustering separately. Based on these findings, we highlight that: 1) the LGT population should be managed as an independent captive population to resemble the genetic distinctness of their Qinling Mountain origins; 2) exchange between CD and WL should be encouraged because of similar wild founder sources; 3) the selection of captive individuals for reintroduction should consider their geographic origin, genetic background, and genetic contribution to wild populations; and 4) combining our molecular genetic data with existing pedigree data will better guide giant panda breeding and further reduce inbreeding into the future.

Withered on the stem: is bamboo a seasonally limiting resource for giant pandas?

In response to seasonal variation in quality and quantity of available plant biomass, herbivorous foragers may alternate among different plant resources to meet nutritional requirements. Giant pandas (Ailuropoda melanoleuca) are reliant almost exclusively on bamboo which appears omnipresent in most occupied habitat, but subtle temporal variation in bamboo quality may still govern foraging strategies, with population-level effects. In this paper, we investigated the possibility that temporal variation in the quality of this resource is involved in population regulation and examined pandas’ adaptive foraging strategies in response to temporal variation in bamboo quality. Giant pandas in late winter and early spring consumed a less optimal diet in Foping Nature Reserve, as the availability of the most nutritious and preferred components and age classes of Bashania fargesii declined, suggesting that bamboo may be a seasonally limiting resource. Most panda mortalities and rescues occurred during the same period of seasonal food limitation. Our findings raised the possibility that while total bamboo biomass may not be a limiting factor, carrying capacity may be influenced by subtle seasonal variation in bamboo quality. We recommend that managers and policy-makers should consider more than just the quantity of bamboo in the understory and that carrying capacity estimates should be revised downward to reflect the fact that all bamboos are not equal.