Fine-scale population genetic structure in a fission-fusion society

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations — especially of social mammals — with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants ( Loxodonta africana ), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (Φ_ST = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.     

Large mitochondrial DNA differences between morphologically similar Penaeid shrimp.

Sequencing of mtDNA fragments amplified with the polymerase chain reaction is used to examine genetic differences between species of Penaeid shrimp. The data show surprisingly high genetic differences among morphologically and ecologically similar species. Differences at silent sites between subgenera of shrimp are larger than between families of mammals. Between genera, Penaeid shrimp are more divergent than some orders of mammals. Because taxonomic differences are defined on morphological grounds, these results imply that the rates of molecular versus morphological evolution in shrimp are different than in mammals. Perhaps mtDNA evolution is accelerated in shrimp, or perhaps stabilizing selection over a long time period has reduced rates of morphological change. For Penaeid shrimp, morphological similarity can mask large genetic differences.     

中国兽类遗传与进化研究进展与展望

中国兽类物种丰富,且具有150个特有种。本文综述了60年来中国兽类遗传与进化的研究进展,内容涵盖系统发育关系重建、遗传多样性评估、种群遗传结构、适应性进化以及趋同进化的分子机制。本文重点概述了食肉目（大、小熊猫）、有蹄类、翼手目、灵长目、小型兽类以及海兽类等重要类群的研究进展,为中国兽类的物种保护提供了重要资料。另外,本文还对中国兽类遗传与进化研究未来的研究方向提出几点建议,包括运用各种组学技术、筛选新型遗传标记和候选基因（调控序列）、结合表观遗传学并借助进化发育生物学研究方法,以期全面深入地理解中国兽类分类地位、起源以及特异表型产生和独特适应的发育遗传学机制等,进而实现“天人合一”保护生物学的新理念和新愿景。     

Bloodlines: mammals,leeches, and conservation in southern Asia

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to find mammals in a given area. While these invertebrate-parasite-derived DNA (iDNA) methods are promising, most of the leech species utilized for this type of survey remain unevaluated, notwithstanding that their diversity varies substantially. Here we examine approximately 750 individual leech specimens in the genus Haemadipsa across a large range in southern Asia (Bangladesh, Cambodia, and China), specifically reviewing the diversity of mammals they feed on and their own genetic structuring. Leeches were found to feed on a considerable variety of mammals, corroborating prior studies. Additionally, leeches were found to have fed both on bats and on birds, neither of which has previously been recorded with this method. The genetic structuring of the leeches themselves revealed 15 distinct clades of which only two precisely corresponded to previously characterized species, indicating that much work is needed to finalize classifications in this genus. Most importantly, with regards to mammal conservation, leeches in these clades appear to feed on a broad range of mammals.     

Of "mice" and mammals: utilizing classical inbred mice to study the genetic architecture of function and performance in mammals

The house mouse is one of the most successful mammals and the premier research animal in mammalian biology. The classical inbred strains of house mice have been artificially modified to facilitate identification of the genetic factors underlying phenotypic variation among these strains. Despite their widespread use in basic and biomedical research, functional and evolutionary morphologists have not taken full advantage of inbred mice as a model for studying the genetic architecture of form, function, and performance in mammals. We illustrate the potential of inbred mice as a model for mammalian functional morphology by examining the genetic architecture of maximum jaw-opening performance, or maximum gape, across 21 classical inbred strains. We find that variation in maximum gape among these strains is heritable, providing the first evidence of a genetic contribution to maximum jaw-opening performance in mammals. Maximum gape exhibits a significant genetic correlation with body size across strains, raising the possibility that evolutionary increases in size frequently resulted in correlated increases in maximum gape (within the constraints of existing craniofacial form) during mammalian evolution. Several craniofacial features that influence maximum gape share significant phenotypic and genetic correlations with jaw-opening ability across these inbred strains. The significant genetic correlations indicate the potential for coordinated evolution of craniofacial form and jaw-opening performance, as hypothesized in several comparative analyses of mammals linking skull form to variation in jaw-opening ability. Functional studies of mammalian locomotion and feeding have only rarely examined the genetic basis of functional and performance traits. The classical inbred strains of house mice offer a powerful tool for exploring this genetic architecture and furthering our understanding of how form, function, and performance have evolved in mammals.     

Genetic evidence for sex-biased dispersal in resident bottlenose dolphins (Tursiops aduncus)

In most mammals males usually disperse before breeding, while females remain in their natal group or area. However, in odontocete cetaceans behavioural and/or genetic evidence from populations of four species indicate that both males and females remain in their natal group or site. For coastal resident bottlenose dolphins field data suggest that both sexes are philopatric to their natal site. Assignment tests and analyses of relatedness based on microsatellite markers were used to investigate this hypothesis in resident bottlenose dolphins, Tursiops aduncus, from two small coastal populations of southeastern Australia. Mean corrected assignment and mean relatedness were higher for resident females than for resident males. Only 8% of resident females had a lower probability than average of being born locally compared to 33% of resident males. Our genetic data contradict the hypothesis of bisexual philopatry to natal site and suggest that these bottlenose dolphins are not unusual amongst mammals, with females being the more philopatric and males the more dispersing sex.     

Evolution of Mammalian Sex Chromosomes: Cooperation of Genetic and Epigenetic Factors

The X and Y chromosomes of mammals, which significantly differ in structure and genetic composition, are thought to originate from a pair of autosomes. During evolution of sex chromosomes in placental mammals, the degradation of the Y chromosome and inactivation spreading along the X chromosome occurred gradually and in concert. Thus, at the molecular level, the genetic and epigenetic factors interacted toward greater differentiation of the X/Y pair. In this review, in context of a comparison permitting to trace this evolutionary pathway, we consider the structural features of mammalian sex chromosomes focusing on the X-chromosomal genes and the unique epigenetic mechanism of their regulation. Possible causes and consequences of the genes escaping X inactivation and aspects of molecular mechanism of X-chromosome inactivation are discussed. A number of hypotheses are considered on evolutionary relationships of X-chromosome inactivation and other molecular processes in mammals.     

Evolution of mammalian sex chromosomes: cooperation of genetic and epigenetic factors

The X and Y chromosomes of mammals, which significantly differ in structure and genetic composition, are thought to originate from a pair of autosomes. During evolution of sex chromosomes in placental mammals, the degradation of the Y chromosome and inactivation spreading along the X chromosome occurred gradually and in concert. Thus, at the molecular level, the genetic and epigenetic factors interacted toward greater differentiation of the X/Y pair. In this review, in context of a comparison permitting to trace this evolutionary pathway, we consider the structural features of mammalian sex chromosomes focusing on the X-chromosomal genes and the unique epigenetic mechanism of their regulation. Possible causes and consequences of the genes skipping inactivation and aspects of molecular mechanism of X-chromosome inactivation are discussed. A number of hypotheses are considered on evolutionary relationships of X-chromosome inactivation and other molecular processes in mammals.     

丰富环境对社会行为的影响及其生物学研究进展

哺乳动物大脑伴随个体从出生到成熟,衰老、死亡处于动态发展中,受到先天遗传因素和后天环境因素影响。其中遗传因素相对易于作为共性或特征进行研究,但是后天环境复杂多变。环境因素影响大脑对认知、情感、社会交往等行为的调控,其影响程度和机制尚未完全清楚,本文就丰富环境对大鼠社会行为影响研究进展做概要介绍。     

Genetic anomalies associated with Cerion hybrid zones: the origin and maintenance of new electromorphic variants called hybrizymes

Natural hybrid zones involving the West Indian pulmonate land snail Cerion are characterized by the occurrence, in low to moderate frequencies, of allozymes that are unique to interspecific hybrid zones. As such electrophoretically detected genetic anomalies have also been reported in hybrid zones involving mammals, birds, reptiles, amphibians, and insects this appears to be a general phenomenon. These unexpected allozymes are inappropriately called 'rare alleles' and the term hybrizyme is introduced. The origins of hybrizymes are discussed in terms of suppressor-mutation systems, transposon-induced hybrid dysgenesis and intragenic recombination, but available evidence will not resolve this issue. Similarly, it is not clear whether the relatively high frequencies of particular hybrizymes are due to selection or genetic drift or some combination of these agents. Finally, the evolutionary significance of hybrizymes and the possible role of hybridization in introducing new genetic variation into populations are discussed.     

Predation and other factors currently limiting New Zealand forest birds

Holdaway (1989) described three phases of historical extinctions and declines in New Zealand avifauna, the last of which (Group III, declining 1780?1986) was associated with European hunting, habitat clearance, and predation and competition from introduced European mammals. Some forest bird species have continued to decline since 1986, while others have increased, usually after intensive species-specific research and management programmes. In this paper, we review what is known about major causes of current declines or population limitation, including predation, competition for food or another resource, disease, forest loss, and genetic problems such as inbreeding depression and reduced genetic variation. Much experimental and circumstantial evidence suggests or demonstrates that predation by introduced mammals remains the primary cause of declines and limitation in remaining large native forest tracts. Predation alone is generally sufficient to explain the observed declines, but complex interactions between factors that vary between species and sites are likely to be the norm and are difficult to study. Currently, the rather limited evidence for food shortage is mostly circumstantial and may be obscured by interactions with predation. Climate and food supply determine the number of breeding attempts made by herbivorous species, but predation by introduced mammals ultimately determines the outcome of those attempts. After removal of pest mammals, populations are apparently limited by other factors, including habitat area, food supply, disease or avian predators. Management of these, and of inbreeding depression in bottlenecked populations, is likely to assist the effectiveness and resilience of management programmes. At the local or regional scale, however, forest area itself may be limiting in deforested parts of New Zealand. Without predator management, the number of native forest birds on the New Zealand mainland is predicted to continue to decline.     

哺乳动物毛色调控机制及其适应性进化研究进展

哺乳动物类群呈现出的丰富毛色是引人注目的一种生物现象,是研究和理解哺乳动物适应性进化的理想模型之一。哺乳动物的毛色多态在躲避天敌、捕食、求偶及抵御紫外线等方面都具有重要作用。哺乳动物毛发的色素化过程由体内黑色素的数量、质量和分布状况所决定。黑色素的形成过程复杂,包括黑素细胞的分化、成熟,黑素体等细胞器的形态发生及黑色素在黑素细胞中的合成代谢和转运等过程;而在细胞色素化的每个阶段/时相都伴随着一些重要功能基因的参与,并通过基因之间的相互作用形成了黑色素生物代谢的复杂调控网络,进而形成不同的毛色有助于哺乳动物适应不同生存环境。对哺乳动物不同毛色形成机制的探究一直以来都是遗传学及进化生物学的重要研究领域和聚焦热点。本文综述了哺乳动物毛色色素化过程的主要分子机制以及毛色适应性进化的遗传基础,以期为哺乳动物毛色多态及其适应性进化的分子机制研究提供参考。     

Genetic analysis of the cytoplasmic dynein subunit families

Cytoplasmic dyneins, the principal microtubule minus-end-directed motor proteins of the cell, are involved in many essential cellular processes. The major form of this enzyme is a complex of at least six protein subunits, and in mammals all but one of the subunits are encoded by at least two genes. Here we review current knowledge concerning the subunits, their interactions, and their functional roles as derived from biochemical and genetic analyses. We also carried out extensive database searches to look for new genes and to clarify anomalies in the databases. Our analysis documents evolutionary relationships among the dynein subunits of mammals and other model organisms, and sheds new light on the role of this diverse group of proteins, highlighting the existence of two cytoplasmic dynein complexes with distinct cellular roles.     

Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies

Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor 1 gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (Y chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals.     

Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome

Interference among loci subject to selection (the Hill-Robertson effect) may considerably reduce levels of adaptation and variability in genomic regions that lack recombination. Y- or W chromosomes are particularly vulnerable to such effects, since they represent large, non-recombining blocks of genetic material. In birds, the W chromosome and mitochondrial genomes are both maternally transmitted, and hence fail to recombine with each other, whereas in mammals the Y chromosome is paternally transmitted. We show here that mitochondrial DNA sequence diversity is reduced in non-ratite birds compared with mammals. After considering possible confounding factors, such as differences in generation times, mutation rates and demography, we conclude that Hill-Robertson effects associated with the W chromosome provide the most likely explanation for this difference.     

Evidence of genetic monogamy in the lemur Indri (Indri indri)

Monogamy is a rare strategy among mammals but relatively common among primates. The study of the evolution of monogamy in mammals and primates is lacking empirical studies that assess the relationship between a pair‐living social organization and genetic monogamy. Sexual or genetic monogamy can only be assessed by performing molecular analyses and investigating rates of extra‐pair paternity (EPP). Studying the occurrence of EPP can provide valuable insights into reproductive strategies and their adaptive value. The indri is a pair‐living primate that lives in stable groups. Their social units are composed of the reproductive pair and up to four more individuals, but extra‐pair copulation (EPC) can occur. This raises the question of whether this event may or may not lead to EPP. Here, we investigated whether a pair‐living social organization corresponds to genetic monogamy in indris (Indri indri). We analyzed the paternity of 12 offspring from seven pairs using a set of six microsatellite loci on fecal samples (mean number of alleles 11.7 ± 1.8 (mean ± standard deviation). We found that in 92% of cases the genetic profile of the offspring matched the paired male of the group for all the loci considered. In the only case of paternity mismatch, the paternity assignment remained inconclusive. Our results show that I. indri genetic monogamy is the norm and supports the hypothesis that pair‐living social organization is associated with low EPP rate. Also, our results are in contrast with the hypothesis of infertility as a reason to engage in EPC for this species.     

Hearing Aid for Vertebrates via Multiple Episodic Adaptive Events on Prestin Genes

Auditory detection is essential for survival and reproduction of vertebrates, yet the genetic changes underlying the evolution and diversity of hearing are poorly documented. Recent discoveries concerning prestin, which is responsible for cochlear amplification by electromotility, provide an opportunity to redress this situation. We identify prestin genes from the genomes of 14 vertebrates, including three fishes, one amphibian, one lizard, one bird, and eight mammals. An evolutionary analysis of these sequences and 34 previously known prestin genes reveals for the first time that this hearing gene was under positive selection in the most recent common ancestor (MRCA) of tetrapods. This discovery might document the genetic basis of enhanced high sound sensibility in tetrapods. An investigation of the adaptive gain and evolution of electromotility, an important evolutionary innovation for the highest hearing ability of mammals, detects evidence for positive selections on the MRCA of mammals, therians, and placentals, respectively. It is suggested that electromotility determined by prestin might initially appear in the MRCA of mammals, and its functional improvements might occur in the MRCA of therian and placental mammals. Our patch clamp experiments further support this hypothesis, revealing the functional divergence of voltage-dependent nonlinear capacitance of prestin from platypus, opossum, and gerbil. Moreover, structure-based cdocking analyses detect positively selected amino acids in the MRCA of placental mammals that are key residues in sulfate anion transport. This study provides new insights into the adaptation and functional diversity of hearing sensitivity in vertebrates by evolutionary and functional analysis of the hearing gene prestin.     

Genetic consequences of group living in Mongolian gerbils

Social behavior can shape the local population genetic structure of mammals. Group living can increase pairwise genetic relatedness of mammals at a local level but differentiate the genetic structure at a population level through offspring philopatry and nonrandom mating. Our study aimed to test the hypothesis that social groups of Mongolian gerbils (Meriones unguiculatus) would consist of genetically related individuals due to offspring philopatry and would have distinct genetic structures because of restricted gene flow among social groups and nonrandom mating. We genotyped 327 wild gerbils, live captured from 28 social groups in Inner Mongolia, China, using nine microsatellite loci. The within-group pairwise genetic relatedness coefficient averaged 0.28 ± 0.14 (standard deviation), whereas the average pairwise genetic relatedness coefficient of the whole gerbil population was 0.0 ± 0.2. Additionally, the value of the global F statistic (F(st)) was 0.21, suggesting a substantial genetic differentiation among social groups of Mongolian gerbils. The Bayesian clustering divided the 327 gerbils into 23 distinct genetic clusters. Therefore, our results show that high within-group genetic relatedness and among-group genetic differentiation are the genetic consequences of group living in social mammals because of restricted gene flow, female philopatry, and nonrandom mating within social groups.