Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments

Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations along a latitudinal gradient (54.9 - 63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, likely reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.

Learning to Diversify for Ensembling of An Amount of Classifiers

Not only common man but also intelligent machine always merge all available decisions to solve problems. However, given an amount of learned classifiers, how to select and combine diverse classifiers for machine is still a grand challenge in the literature for decades of history. In this paper, we introduce a novel approach for classifier ensemble, learning to diversify, which learns to adaptively combine classifiers by considering both accuracy and diversity. Specifically, our approach, learning to diversify via weighted kernels, performs classifier combination by optimizing a direct but simple criterion: maximizing ensemble accuracy and adaptive diversity simultaneously by minimizing a loss function. Given a measure formulation, the diversity is calculated with weighted kernels, i.e., the diversity is measured on the component classifiers’ outputs which are kernelized and weighted. Moreover, we propose an iterative training algorithm for weights optimization, where this loss function is iteratively minimized by estimating the kernel weights in conjunction with the classifier weights. Extensive experiments on a variety of classification benchmark datasets show that the proposed approach consistently outperforms state-of-the-art ensembles.

Mutations in coral soma and sperm imply lifelong stem cell differentiation

In many animals, the germline differentiates early in embryogenesis, so only mutations that accumulate in germ cells are inherited by offspring. Exceptions to this developmental process may indicate that other mechanisms have evolved to limit the effects of deleterious mutation accumulation. Stony corals are animals that can live for hundreds of years and have long been thought to produce gametes from somatic tissue. To clarify conflicting evidence about germline-soma distinction in corals, we sequenced high coverage, full genomes with technical replicates for parent coral branches and their sperm pools. We identified single nucleotide variants (SNVs) unique to each parent branch, then checked if each SNV was shared by the respective sperm pool: 26% of post-embryonic SNVs were shared by the sperm and 74% were not. We also identified germline SNVs, those that present in the sperm but not in the parent. These data suggest that self-renewing stem cells in corals differentiate into germ and soma throughout the adult life of the colony, with SNV rates and patterns differing markedly in stem, soma, and germ lineages. In addition to informing germline evolution, these insights inform how corals may generate adaptive diversity necessary in the face of global climate change.

Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

Review of congruence between global crop wild relative hotspots and centres of crop origin/diversity

Crop wild relatives (CWR) are important sources of adaptive diversity for plant breeding programmes. This paper aims to investigate the extent to which the centres of crop origin/diversity are congruent with areas of high CWR diversity. We established the predicted potential CWR distributions for 1,425 CWR species related to 167 crops using 334,527 known distribution locations and generated a global CWR hotspot map. This was then compared to the centres of origin/diversity proposed by Vavilov (amended by Hawkes); Zeven and Zhukovsky’s mega gene centres, Harlan’s centres and non-centres of crop domestication; and crop domestication areas identified using current archaeological evidence proposed by Purugganan and Fuller. Greatest congruence between the global CWR hotspots and other concepts was found with the concept proposed by Vavilov and amended by Hawkes, but there remained significant differences between the CWR hotspots and Vavilov’s concept. This paper concludes that all four centre concepts reviewed have some overlap with CWR diversity but that Vavilov’s original concept has the closest geographic coincidence with CWR hotspots. With the benefit of significant additional global datasets to those used by Vavilov, we were able to suggest amendments to his concept, adding further centres based on CWR hotspots in west and east USA, West Africa, South-east Brazil and Australia. As a result of this study more precise targeting of CWR and crop landrace can be implemented in future, aiding global food and nutritional security.

Alternative Adaptation Strategy during the Paleolithic–Neolithic Transition: Potential Use of Aquatic Resources in the Western Middle Yangtze Valley, China

The middle Yangtze Valley is an important region for studying the origin of rice agriculture. Archaeological remains of rice have been found in sites such as Pengtoushan and Bashidang as early as 8000 years ago. However, we know little about the adaptive diversity in this region as research has mostly focused on rice cultivation. With the help of new discoveries, this paper explores another adaptation behavior pattern that emphasizes the utilization of aquatic resources in the western part of the Jianghan Plain during the Paleolithic–Neolithic transition. Although the sea level was continuously rising with the warming process of early Holocene, the lakes that later became widely distributed were still in formation, thus not available for human utilization in the middle Yangtze Valley. However, most notably, the amelioration of the environment was producing a sort of new niche: utilizing aquatic resources became possible at least in parts of this region. A case study from the Guanzhou Site, based on lithics, suggests there were increasing demands for the utilization of aquatic resources. The study proposes that at least two different adaptation strategy changes occurred in the western Jianghan Plain during the Paleolithic–Neolithic transition, i.e., rice agriculture or complex hunting–gathering. These strategies represent adaptations to the different ecological conditions at the crossroads of habitat types.

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs

Sex chromosomes form once recombination is halted between the X and Y chromosomes. This loss of recombination quickly depletes Y chromosomes of functional content and genetic variation, which is thought to severely limit their potential to generate adaptive diversity. We examined Y diversity in Poecilia parae, where males occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph utilizes different complex reproductive strategies, and differ dramatically from each other in color, body size, and mating behavior. Remarkably, morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, each of which encodes the complex male morph characteristics. Using linked-read sequencing on multiple P. parae females and males of all five morphs from natural populations, we found that the genetic architecture of the male morphs evolved on the Y chromosome long after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs revealed that although the Ys of the three minor morphs that differ predominantly in color are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behavior. Taken together, our results reveal the extraordinary ability of evolution to overcome the constraints of recombination loss to generate extreme diversity resulting in five discrete Y chromosomes that control complex reproductive strategies.Significance StatementThe loss of recombination on the Y chromosome is thought to limit the adaptive potential of this unique genomic region. Despite this, we describe an extraordinary case of Y chromosome adaptation in Poecilia parae. This species contains five co-occurring male morphs, all of which are Y-linked, and which differ in reproductive strategy, body size, coloration, and mating behavior. The five Y-linked male morphs of P. parae evolved after recombination was halted on the Y, resulting in five unique Y chromosomes within one species. Our results reveal the surprising magnitude to which non-recombining regions can generate adaptive diversity and have important implications for the evolution of sex chromosomes and the genetic control of sex-linked diversity.