Ancestral Lineage Research Articles

Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa.

The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5–3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.

Traveling Ode of the Faqir: Song Transmission & Spiritual Genealogies in a Sufi Community

Traveling Ode of the Faqir: Song Transmission & Spiritual Genealogies in a Sufi Community Youssef Carter “Bismi ilayy may jog di kañ, In the name of Allah, I stand to praise, Sangue bi Cheikh Arouna Faye, the noble Sheikh Arona Faye Seutou Mame Samba, am na ndam, The grandson of grandpa Samba, He has [victory], Yalla buur sagali gnonam.” May Allah brighten his family and entourage Am Na Ndam(“He has victory”) is a Wolof tribute song that primarily honors the work of Shaykh Arona Faye Al‐Faqir , a modern‐day Senegalese marabout considered by his students to be a penultimate religious scholar and spiritual teacher/ guide. According to his followers, he has inherited his knowledge of attaining righteousness from his late uncle and founder of the Mustafawiyy Sufi Order, Shaykh Mustafa Gueye Haydar (1926–1989). The song was composed in Thiés, Senegal by men loosely affiliated with the Order and honors the Shaykh's ancestral line while weaving together multiple network locations in the Mustafawiyy Order such as Senegal, Gambia, Spain, and the USA. While the singers do not travel abroad to praise the mission of Shaykh Arona Faye, the song itself was recorded and shared digitally across the Atlantic where it was copied onto compact discs that would be distributed from the zawiyah of Moncks Corner, South Carolina to other locations throughout the network such as Philadelphia, Washington D.C., and to various families located along the eastern seaboard who are affiliated with the Mustafawiyy Order. Shaykh Arona Faye lectures his students and family members about Islam in Thiès, Senegal, 2015. Photo by Youssef Carter Embedded within the lyrics of Am Na Ndamis a prayer for Shaykh Arona Faye's continued success and long life. There is a way in which the song has traveled across water, along roads, and from house to house as its listeners, many who do not speak Wolof, hum its catchy melody and simultaneously allow for the embedded supplication to be uttered through audio speakers—both stationary and mobile. Throughout the song's journeys, its lyrics tell the story of a Senegalese Muslim man who has crossed the Atlantic in order to guide those who follow on the journey toward God. Here, I emphasize the manner in which Wolof cultural performance informs a Sufic interpretation of religious practice in order to shed light upon the varying ways that uses of language, ideas about lineage in relation to self, and West African Muslim tradition become expressed through song and shared throughout a diasporic Muslim network. I suggest that through looking in depth at the exchange and transmission of this tribute song, we can better identify the precise manner by which religious observances, particularly those of (African‐ and Anglo‐) American Muslims, are rerouted and indigenized into Senegambian traditions. Thus, I use lyrics as primary source, informed by ethnographic observation, to analyze the manner in which place, religion, and lineage emerge through a song composed in the Wolof language and meanwhile radiates outward to the entirety of a diasporic spiritual community. The intent here is to open up questions about travel, memory, and diaspora as they pertain to African and American Muslims in the context of a Senegalese Islamic tradition. Some questions that drive this analysis are: how does the CD itself operate as a medium for religious and cultural continuities? What is significant about this song's journey in particular? What can this song's journey tell us about diaspora—namely African and American Muslim mobilities? What can it tell us about transnational religious networks? What can it offer regarding intersections between the two? I first heard this song while sitting in the living room of an elder South Carolinian woman whom I would come to affectionately know as “Umm Aisha (Mother Aisha),” an African American Muslimah and wife of Shaykh Arona Faye [a somewhat petite Senegalese man whose voice projects far beyond his physical frame and has a penchant for snazzy dress and the color red]. Umm Aisha's quaint house is situated in a quiet suburban neighborhood in the sleepy, blue‐collar town of Moncks Corner—about a 45‐minute drive northwest of Charleston. There I sat with other students as...

Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0–1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms.

Testing adaptive regime shifts for range size evolution of endemic birds of China

In this brief report, adaptive regime shifts for the range size evolution of the endemic birds of China were identified. Four models with different biological meanings were tested and compared through maximum likelihood models, including the Brownian motion model, one global optimal range size model for all lineages in the phylogeny, two optimal regime model of range sizes for lineages with large and small range sizes (OU2), and three optimal regime model in which an additional regime is added to the ancestral lineages. The results of model evaluation and comparison using the maximum likelihood technique show that over 48 endemic taxa, two optimal regimes (the OU2 model) were observed for bird lineages with large and small range sizes in the country. The possible reasons for such an observation were outlined accordingly, including the different evolutionary times, which were subjected to different historical and geological conditions, heterogeneous environmental conditions, and complex climatic fluctuations. Overall, the range size evolution of the endemic taxa was subjected to multiple selective stresses. For future implications, more studies are desired to provide a holistic view of the evolution and divergence of endemic taxa.

RNA structure replaces the need for U2AF2 in splicing.

RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.

Do hybrid‐origin polyploid amphibians occupy transgressive or intermediate ecological niches compared to their diploid ancestors?

AbstractAimSpeciation can either proceed as gradual divergence, mostly in allopatry or parapatry, or by duplication of chromosome sets: polyploidization. Hybrid‐origin or allopolyploidization is an important mechanism of hybrid speciation with strong, although often incomplete, postzygotic reproductive barriers between the polyploid hybrid and its diploid parents. Allopolyploids often present novel phenotypes that exceed the ranges of their ancestral lineages, leading to the hypothesis that niche shifts could be supportive of hybrid speciation. Although polyploidy is phylogenetically widespread in animals, ecological niches of diploid ancestral and derived allopolyploids have been rarely comparatively examined. Here, we do so for five species of Palaearctic green toads (Bufo viridis subgroup), involving three ploidy levels.LocationCentral Asia, High Asia.MethodsWe gathered distributional records of genotyped toads, covering the whole range of the five toad species. We then used similarity and equivalency tests and examined whether bioclimatic (Grinellian) niches of allopolyploids are intermediate to those of the extant diploid relatives of their ancestral forms or whether they are transgressive (beyond those of both ancestors).ResultsWe found evidence for both transgressive and conservative niches in allopolyploids. Allotetraploids (Bufo pewzowi, B. oblongus) showed transgressive niche evolution; they inhabited environments that were harsher (more arid and with colder winters) than both of their parental species. In contrast, the allotriploid B. baturae exhibited a conserved niche, similar to an ancestral lineage that provided two‐thirds of its hybrid genome. For most comparisons, niches of extant diploid ancestral lineages were significantly different from each other.Main conclusionWe conclude that allopolyploidization in amphibians leads potentially but not a necessarily to transgressive niche evolution, and may facilitate hybrid speciation by allowing newly formed hybrids to colonize novel habitats and thus escape their parental lineages.

Cloning, expression of, and evidence of positive selection for, the prolactin receptor gene in Chinese giant salamander (Andrias davidianus).

Prolactin receptor (PRLR) is a protein associated with reproduction in mammals and with osmoregulation in fish. In this study, the complete length of Chinese giant salamander Andrias davidianus prolactin receptor (AD-prlr) was cloned. Andrias davidianus prlr expression was high in the kidney, pituitary, and ovary and low in other examined tissues. The AD-prlr levels were higher in ovary than in testis, and increased in ovaries with age from 1 to 6 years. To determine effect of exogenous androgen and aromatase inhibitor on AD-prlr expression, methyltestosterone (MT) and letrozole (LE) were injected, resulting in decreased AD-prlr in both brain and ovary, with MT repressing prlr transcription more rapidly than did LE. The molecular evolution of prlr was assessed, and found to have undergone a complex evolution process. The obranch-site test detected four positively selected sites in ancestral lineages prior to the separation of mammals and birds. Fourteen sites underwent positive selection in ancestral lineages of birds and six were positively selected in amphibians. The site model showed that 16, 7, and 30 sites underwent positive selection in extant mammals, amphibians, and birds, respectively. The positively selected sites in amphibians were located outside the transmembrane domain, with four in the extracellular and three in the intracellular domain, indicating that the transmembrane region might be conserved and essential for protein function. Our findings provide a basis for further studies of AD-prlr function and molecular evolution in Chinese giant salamander. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 707-719, 2015. © 2015 Wiley Periodicals, Inc.

Historical biogeography of Reticulitermes termites (Isoptera: Rhinotermitidae) inferred from analyses of mitochondrial and nuclear loci

Termites of the genus Reticulitermes are ecologically and economically important wood-feeding social insects that are widespread in the Holarctic region. Despite their importance, no study has yet attempted to reconstruct a global time-scaled phylogeny of Reticulitermes termites. In this study, we sequenced mitochondrial (2096bp) and nuclear (829bp) loci from 61 Reticulitermes specimens, collected across the genus’ entire range, and one specimen of Coptotermes formosanus, which served as an outgroup. Bayesian and Maximum likelihood analyses conducted on the mitochondrial and nuclear sequences support the existence of four main lineages that span four global geographical regions: North America (NA lineage), western Europe (WE lineage), a region including eastern Europe and western Asia (EA+WA lineage), and eastern Asia (EA lineage). The mitochondrial data allowed us to clarify the phylogenetic relationships among these lineages. They were also used to infer a chronogram that was time scaled based on age estimates for termite fossils (including the oldest Reticulitermes fossils, which date back to the late Eocene–early Oligocene). Our results support the hypothesis that the extant Reticulitermes lineage first differentiated in North America. The first divergence event in the ancestral lineage of Reticulitermes occurred in the early Miocene and separated the Nearctic lineages (i.e., the NA lineages) from the Palearctic lineages (i.e., WE, EE+WA, and EA lineages). Our analyses revealed that the main lineages of Reticulitermes diversified because of vicariance and migration events, which were probably induced by major paleogeographic and paleoclimatic changes that occurred during the Cenozoic era. This is the first global and comprehensive phylogenetic study of Reticulitermes termites, and it provides a crucial foundation for studying the evolution of phenotypic and life-history traits in Reticulitermes. For instance, the phylogeny we obtained suggested that ‘asexual queen succession’, a unique reproductive system, independently evolved at least three times during the diversification of the genus.

Lobopodians

Lobopodians

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

BackgroundThere has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.Results Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman’s coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.Conclusions Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Characterization of NLR-A subfamily members in miiuy croaker and comparative genomics revealed NLRX1 underwent duplication and lose in actinopterygii.

The NOD-like receptors (NLRs, nucleotide-binding domain and leucine-rich repeat containing receptors) are a recently identified family of intracellular pathogen recognition receptors in vertebrates. Several subfamilies of NLRs have been characterized in mammals and implicated in immunity and apoptosis, but studies of NLRs in teleost species have been lacking. Here we analyzed three NLR-A subfamily members from miiuy croaker: NLRC3, NLRC5, and NLRX1. Structural analysis showed that miiuy croaker NLR-A subfamily members own the feature of 5'UTR intron which may influence their role in enhancing translation level. Comparative analysis revealed NLRX1 duplicated into NLRX1a and NLRX1b, then NLRX1a was lost in actinopterygii and NLRX1b formed NLRX1 that now we called. Simultaneously, molecular evolutionary analysis indicated that the ancestral lineages of NLRX1 in tetrapod and actinopterygii under positive selection pressure. The positively sites in actinopterygii are mainly located in NACHT domain which was the critical region for signal transduction, suggesting that the evolution of NLRX1 gene in the ancestor of actinopterygii is beneficial in immune response. Pathogens challenge demonstrated that the expressions of NLRC3 and NLRC5 in miiuy croaker were induced not only by Vibrio anguillarum but also by poly (I:C), whereas NLRX1 exhibited more sensitive response to bacteria than virus.

Cretaceous amber inclusions of Spain and Myanmar demonstrate early diversification and wide dispersal of Cephenniitae (Coleoptera: Staphylinidae: Scydmaeninae)

The taxonomic status of previously misplaced species of an ant-like stone beetle from Spanish amber (Albian) is clarified. Specimens of Kachinus magnificus (originally placed as incertae sedis within Scydmaenitae) were re-examined and their characters were found different from those of the type species of Kachinus from Myanmar amber. Consequently, Archeutheia gen. nov. is proposed to accommodate the Spanish species, resulting in Archeutheia magnifica comb. nov. Moreover, in a comprehensive phylogenetic analysis Archeutheia was placed as a sister group to extant Eutheia, within the tribe Eutheiini of Cephenniitae. A specimen of an undetermined genus from Myanmar amber clearly belonging in Cephenniini is also recorded. Both taxa represent the first definite Cretaceous Cephenniitae, a supertribe whose recent members are distributed on all continents but are especially diverse in the Oriental and East Palaearctic regions. This finding demonstrates a diversification of two presently most species-rich tribes of Cephenniitae already in Early Cretaceous. Archeutheia is strikingly similar to the extant species of Eutheia and Veraphis, showing male dimorphic characters (modified protrochanters) and antennal cavities characteristic of Palaearctic Eutheiini. This fact suggests a long morphological stability in the supertribe. A previously proposed hypothesis of an early presence of the Cephenniitae in the Northern Hemisphere is for the first time supported by the fossil record, and the palaeolocalities (western Europe and Southeast Asia) demonstrate a wide distribution of Cephenniitae in the Cretaceous and an early split of its ancestral lineage.

Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora).

Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.

African Lungfish Reveal the Evolutionary Origins of Organized Mucosal Lymphoid Tissue in Vertebrates

One of the most remarkable innovations of the vertebrate adaptive immune system is the progressive organization of the lymphoid tissues that leads to increased efficiency of immune surveillance and cell interactions. The mucosal immune system of endotherms has evolved organized secondary mucosal lymphoid tissues (O-MALT) such as Peyer's patches, tonsils, and adenoids. Primitive semi-organized lymphoid nodules or aggregates (LAs) were found in the mucosa of anuran amphibians, suggesting that O-MALT evolved from amphibian LAs ∼250 million years ago. This study shows for the first time the presence of O-MALT in the mucosa of the African lungfish, an extant representative of the closest ancestral lineage to all tetrapods. Lungfish LAs are lymphocyte-rich structures associated with a modified covering epithelium and express all IGH genes except for IGHW2L. In response to infection, nasal LAs doubled their size and increased the expression of CD3 and IGH transcripts. Additionally, de novo organogenesis of inducible LAs resembling mammalian tertiary lymphoid structures was observed. Using deep-sequencing transcriptomes, we identified several members of the tumor necrosis factor (TNF) superfamily, and subsequent phylogenetic analyses revealed its extraordinary diversification within sarcopterygian fish. Attempts to find AICDA in lungfish transcriptomes or by RT-PCR failed, indicating the possible absence of somatic hypermutation in lungfish LAs. These findings collectively suggest that the origin of O-MALT predates the emergence of tetrapods and that TNF family members play a conserved role in the organization of vertebrate mucosal lymphoid organs.

Tragic Spirits: Shamanism, Memory, and Gender in Contemporary Mongolia by Manduhai Buyandelger.

Manduhai Buyandelger’s Tragic Spirits engages the anthropological literature ofshamanism by drawing on a series of life histories of Buryat shamans and their clientsthat focuses on issues of power, gender, and memory in post-socialist Mongolia. In theintroduction, the author explains how the arrival of socialism in Mongolia resulted inthe forced forgetting of ancestral lineages crucial for determining the identity of spiritsthat bring misfortune to a family.

Molecular Systematics of theChrysobothris femorataSpecies Group (Coleoptera: Buprestidae)

The Chrysobothris femorata (Olivier) species group has expanded to 12 recognized species. Many of these species are sympatric, share larval host plants, and are difficult to reliably separate morphologically. This study investigated species limits and relationships among the recognized species occurring within the southeastern United States. Results are presented from phylogenetic analyses including several group members using sequences from cytochrome oxidase I (cox I) and arginine kinase (AK). Cox I analyses validated the monophyly of several Chrysobothris species outside of the C. femorata species group and recovered group members C. adelpha Harold, C. viridiceps Melsheimer, and C. wintu Wellso and Manley as monophyletic. However, cox I analyses yielded well supported nodes that rendered C. femorata Olivier, C. quadriimpressa Gory and Laporte, C. rugosiceps Melsheimer, and C. shawnee Wellso and Manley paraphyletic. AK sequences provided statistical support for monophyly of C. wintu and two well supported clades that rendered C. femorata and C. quadriimpressa paraphyletic. Imperfect taxonomy cannot totally account for this phenomenon. The observed pattern could be the result of ancestral polymorphism or lineage sorting, yet introgression of these C. femorata species group members is possible. Although observed results from these genes suggest potential taxonomic synonymization, such steps are premature. Greater understanding of interactions between group members as occurs within their overlapping geographies and host plants is needed. We suggest future molecular studies adopting a population genetics approach utilizing several nuclear genes or SNiPs acquired subsequent to a NextGen sequencing campaign.

Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea.

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.

Genetic diversity of fluorescent protein genes generated by gene duplication and alternative splicing in reef-building corals.

IntroductionReef-building corals (Scleractinia) exhibit various colors, of which fluorescent proteins (FPs) are a major determinant. Gene duplication is considered a major mechanism in the generation of the FP gene family and color diversity. Examining gene duplication events and subsequent evolution may improve our understanding of FP gene family diversity.ResultsWe isolated a novel FP gene family from one individual of Montipora sp., which we named monGFP (GFP gene from Montipora sp.). This gene family consists of at least four genes that produce at least six different cDNA sequences. The sequences were categorized into two types based on the length of cDNA; this difference is attributed to alternative splicing. Although the amino acid sequences were different, the emission spectra of the monGFP variants were nearly identical (518–521 nm). In addition to this gene family, we isolated ten paralogous AdiFP10 (Adi-Fluorescent protein-10 gene from Acropora digitifera) sequences from cDNA of two Acropora species, A. digitifera and A. tenuis. Based on our phylogenetic analysis, five sequences from A. digitifera and four sequences from A. tenuis appeared to be in a different cluster from AdiFP10, suggesting a new FP gene cluster. The FP sequences were likely to have been generated independently in each species or generated by gene duplications in the ancestral lineage of Acropora, followed by extensive gene conversion within each species.ConclusionOur results clarify a part of the diversification process of FP genes during the evolutionary history of Montipora and Acropora species. Our analyses of monGFP indicate that FPs translated from different splicing variants and gene copies have evolved without changes in the function of fluorescence, and gene copies have been evolved under purifying selection. On the other hand, AdiFP10 paralogs and other RFP genes in Acropora species may have diversified their functions. Identification of conserved and divergent modes of evolution after the duplication of FP genes may reflect variation in the biological roles of different FPs.Electronic supplementary materialThe online version of this article (doi:10.1186/s40851-015-0020-5) contains supplementary material, which is available to authorized users.

Modeling the 3D Geometry of the Cortical Surface with Genetic Ancestry

Knowing how the human brain is shaped by migration and admixture is a critical step in studying human evolution [1, 2], as well as in preventing the bias of hidden population structure in brain research [3, 4]. Yet, the neuroanatomical differences engendered by population history are still poorly understood. Most of the inference relies on craniometric measurements, because morphology of the brain is presumed to be the neurocranium's main shaping force before bones are fused and ossified [5]. Although studies have shown that the shape variations of cranial bones are consistent with populationhistory [6-8], it is unknown how much human ancestry information is retained by the human cortical surface. In our group's previous study, we found that area measures of cortical surface and total brain volumes of individuals of European descent in the United States correlate significantly with their ancestral geographic locations in Europe [9]. Here, we demonstrate that the three-dimensional geometry of cortical surface is highly predictive of individuals' genetic ancestry in West Africa, Europe, East Asia, and America, even though their genetic background has been shaped by multiple waves of migratory and admixture events. The geometry of the cortical surface contains richer information about ancestry than the areal variability of the cortical surface, independent of total brain volumes. Besidesexplaining more ancestry variance than other brain imaging measurements, the 3D geometry of the cortical surface further characterizes distinct regional patterns in the folding and gyrification of the human brain associated with each ancestral lineage.

Population genetic structure and colonization history of short ninespine sticklebacks (Pungitius kaibarae).

The contemporary distribution and genetic structure of a freshwater fish provide insight into its historical geodispersal and geographical isolation following Quaternary climate changes. The short ninespine stickleback, Pungitius kaibarae, is a small gasterosteid fish occurring in freshwater systems on the Korean Peninsula and in southeast Russia. On the Korean Peninsula, P. kaibarae populations are distributed in three geographically separated regions: the NE (northeast coast), SE (southeast coast), and a limited area in the ND (Nakdong River). In this study, we used mitochondrial loci and microsatellites to investigate the evolutionary history of P. kaibarae populations by assessing their pattern of genetic structure. Our analyses revealed a marked level of divergence among three regional populations, suggesting a long history of isolation following colonization, although ND individuals showed relatively higher genetic affinity to populations from SE than those from NE. The populations from NE showed a great degree of interpopulation differentiation, whereas populations from SE exhibited only weak genetic structuring. Upon robust phylogenetic analysis, P. kaibarae formed a monophyletic group with Russian P. sinensis and P. tymensis with strong node confidence values, indicating that P. kaibarae populations on the Korean Peninsula originated from the southward migration of its ancestral lineage around the middle Pleistocene.