The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present CLUMPAK (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, CLUMPAK identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software CLUMPP. Next, CLUMPAK identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in CLUMPP and simplifying the comparison of clustering results across different K values. CLUMPAK incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. CLUMPAK, available at http://clumpak.tau.ac.il, simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.

/pdf/clumpak-a-program-for-identifying-clustering-modes-and-4ljqxgdc53.pdf

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K

Motivation Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files. Results We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported. Availability and implementation PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.

High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(13)00231-0.pdf

Genome sequencing and population genomics in non-model organisms.

http://labs.icb.ufmg.br/lbem/aulas/pg/pdf/liu14c_popgenomBear.pdf

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

/pdf/population-genomics-of-populus-trichocarpa-identifies-4lmre9hf8m.pdf

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

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.

/pdf/whole-genome-sequencing-of-giant-pandas-provides-insights-3ycjqwy51q.pdf

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

The carnivoran giant panda has a specialized bamboo diet, to which its alimentary tract is poorly adapted. Measurements of daily energy expenditure across five captive and three wild pandas averaged 5.2 megajoules (MJ)/day, only 37.7% of the predicted value (13.8 MJ/day). For the wild pandas, the mean was 6.2 MJ/day, or 45% of the mammalian expectation. Pandas achieve this exceptionally low expenditure in part by reduced sizes of several vital organs and low physical activity. In addition, circulating levels of thyroid hormones thyroxine (T4) and triiodothyronine (T3) averaged 46.9 and 64%, respectively, of the levels expected for a eutherian mammal of comparable size. A giant panda–unique mutation in the DUOX2 gene, critical for thyroid hormone synthesis, might explain these low thyroid hormone levels. A combination of morphological, behavioral, physiological, and genetic adaptations, leading to low energy expenditure, likely enables giant pandas to survive on a bamboo diet.

/pdf/exceptionally-low-daily-energy-expenditure-in-the-bamboo-d9jxsnynmi.pdf

Exceptionally low daily energy expenditure in the bamboo-eating giant panda

Serosurvey of selected viruses in captive giant pandas (Ailuropoda melanoleuca) in China.

INTRODUCTION The goal of the giant panda ex situ breeding programme is to produce healthy, genetically diverse and reproductively sound offspring. However, reproduction in this species has been poor, in part, due to lack of male libido or aggressive behaviours towards conspecific females. Although giant panda breeding facilities have made progress in producing more surviving young, only about 29% of captive male giant pandas have ever sired offspring (Lindburg et al ., 1998), and most of these males were wild born. Of the 104 giant pandas in the ex situ population in China in 1996 (at the time of the first masterplanning meeting in China; Zheng et al ., 1997; see also Chapter 2), there were 33 adult males of reproductive age (6–26 years old). Only five (15.2%) had ever mated naturally and sired young. This was the main reason for ‘male reproduction’ being a primary target of the Biomedical Survey conducted under the umbrella of the Conservation Breeding Specialist Group (CBSG) (see Chapter 2). We had three goals, the first being to measure the presence or absence of any obvious physiological or anatomical abnormalities. The second was to learn more about species reproductive biology, specifically comparing males of different ages, successful versus unsuccessful breeders and wild-born versus captive born. Our approach also allowed a third opportunity: studies that would enhance our understanding on how better to use male gametes (sperm) to advance genetic management (see Chapter 21). In this case, our focus was on: sperm morphology and acrosomal integrity; testes development during the breeding season; […]

Jinguo Zhang

Papers

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

Exceptionally low daily energy expenditure in the bamboo-eating giant panda

Serosurvey of selected viruses in captive giant pandas (Ailuropoda melanoleuca) in China.

Giant Pandas: Male reproductive biology in giant pandas in breeding programmes in China