Ancestral Pattern Research Articles

A rapid rate of sex-chromosome turnover and non-random transitions in true frogs

The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the ‘hot-potato’ model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.

The palaeontological record of the Anthropocene

Most species on planet Earth have specific ecological ranges. In the near surface of the oceans, planktonic foraminifera define water masses that are warm in the tropics, and cold in polar regions. Tropical rainforests have trees and animals that are distinct from those in warm temperate or cold temperate zones. The fauna and flora of Australia are distinct from those of the Americas. These natural patterns, defined by factors such as latitudinal changes in surface temperature and rainfall, or geographical isolation, have evolved over millions, sometimes tens of millions of years. Now this natural pattern is being overprinted by the actions of a single species, Homo sapiens, which has made the whole Earth its ecological range, and some parts of nearby space too. The human ancestral pattern of gradually increasing impact on the Earth can be traced in the stratigraphic record for nearly 3 million years, and in its later and more pervasive phases may serve to help define a biostratigraphical signal for the Anthropocene Epoch.

Dental homologies and evolutionary transformations in Caviomorpha (Hystricognathi, Rodentia): new data from the Paleogene of Peruvian Amazonia

ABSTRACTDental homologies and evolutionary transformations within caviomorph rodents have long been disputed. Here, we participate in these debates in providing new insights from the dental morphology of Paleogene caviomorphs from Peruvian Amazonia (Contamana and Shapaja). Their analyses and comparisons with many hystricognaths allow (1) to generalize some hypotheses previously proposed about occlusal morphology of caviomorph cheek teeth, and (2) to propose new ones. In caviomorphs, the third crest of upper teeth would correspond either to a mesoloph or to a mesolophule or to a combination of both. The transformation from a pentalophodont pattern to a tetralophodont pattern would be explained by the disappearance of the metaloph. Likewise, the transformation from a tetralophodont pattern to a trilophodont pattern is observed by the loss of the third crest. A direct transformation from a pentalophodont pattern to a trilophodont pattern is also observed. Concerning lower teeth, discrepancies of homologies are centered on the mesial cristids, which can be notably distinguished depending on their compositions and connections with other structures. The ancestral patterns of caviomorph lower molars and dp4s were likely tetralophodont and pentalophodont, respectively. However, schemes with five and four (even three) transverse cristids cannot be ruled out for the two loci, respectively.

Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea

Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78–144 Mya).

Hunter-gatherer diets and human behavioral evolution

Human behavior and physiology evolved under conditions vastly different from those which most humans inhabit today. This paper summarizes long-term dietary studies conducted on contemporary hunter-gatherer populations (sometimes referred to as foragers). Selected studies for the most part that use evolutionary theoretical perspectives and data collection methods derived from the academic field of human behavioral ecology, which derives relatively recently from the fields of evolutionary biology, ethology, population biology and ecological anthropology. I demonstrate how this body of research illuminates ancestral patterns of food production, consumption and sharing, infant feeding, and juvenile subsistence contributions in hunter-gatherer economies. Insights from hunter-gatherer studies are then briefly discussed within the context of better-studied human populations that are Westernized, Educated, Industrialized, Rich, and Democratic (WEIRD).

Is Amazonia a ‘museum’ for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae)

The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the ‘cradle’ or ‘museum’ model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth.

Morphological integration in the gorilla, chimpanzee, and human neck.

Although integration studies are important to understand the evolution of organisms' traits across phylogenies, vertebral integration in primates is still largely unexplored. Here we describe and quantify patterns of morphological integration and modularity in the subaxial cervical vertebrae (C3-C7) in extant hominines incorporating the potential influence of size. Three-dimensional landmarks were digitized on 546 subaxial cervical vertebrae from 141 adult individuals of Gorilla gorilla, Pan troglodytes, and Homo sapiens. Integration and modularity, and the influence of size effects, were quantified using geometric morphometric approaches. All subaxial cervical vertebrae from the three species show a strong degree of integration. Gorillas show the highest degree of integration; conversely, humans have the lowest degree of integration. Analyses of allometric regression residuals show that size is an important factor promoting integration in gorillas, with lesser influence in chimpanzees and almost no effect in humans. Results point to a likely ancestral pattern of integration in non-human hominines, whereby the degree of integration decreases from cranial to caudal positions. Humans deviate from this pattern in the cranialmost (C3) and, to a lesser extent, in the caudalmost (C7) vertebrae, which are less integrated. These differences can be tentatively related to the emergence of bipedalism due to the presence of modern human-like C3 in australopiths, which still preserve a more chimpanzee-like C7.

Cross-sectional properties of the lower limb long bones in the Middle Pleistocene Sima de los Huesos sample (Sierra de Atapuerca, Spain)

The recovery to date of three complete and five partial femora, seven complete tibiae, and four complete fibulae from the Atapuerca Sima de los Huesos site provides an opportunity to analyze the biomechanical cross-sectional properties in this Middle Pleistocene population and to compare them with those of other fossil hominins and recent modern humans.We have performed direct comparisons of the cross-sectional geometric parameters and reduced major axis (RMA) regression lines among different samples. We have determined that Atapuerca Sima de los Huesos (SH) fossils have significantly thicker cortices than those of recent modern humans for the three leg bones at all diaphyseal levels, except that of the femur at 35% of biomechanical length. The SH bones are similar to those of Neandertals and Middle Pleistocene humans and different from Homo sapiens in their diaphyseal cross-sectional shape and strength parameters.When standardized by estimated body size, both the SH and Neandertal leg bones have in general greater strength than those of H. sapiens from the early modern (EMH), Upper Paleolithic (UP), and recent populations (RH). The Sima de los Huesos human leg bones have, in general terms, an ancestral pattern similar to that of Pleistocene humans and differing from H. sapiens.

Evolutionary negative allometry of orthopteran hind femur length is a general phenomenon

1. Body size influences the way that organisms both perform their locomotor activities and perceive their environment. Allometry of insect legs with respect to body size is affected by many factors such as ontogenetic constraints and natural selection. Negative allometry, positive allometry, or isometry could result from different mechanisms influencing leg length and locomotion performance. 2. We tested three main models of hind femur length allometry (natural selection for jumping performance, ontogenetic constraint, and the size-grain model) in Orthoptera, a Polyneopteran order with large size range and high habitat and lifestyle diversification. We used a data set of 1549 species including members of both suborders, Ensifera and Caelifera, and many representative families using a Linear Mixed Model approach, and Reduced Major Axis and Ordinary Least Squares regression to explore evolutionary interspecific allometry in this order. 3. Our results showed a generalized trend of negative allometry (leg length decreases with body size increase) at the ordinal, subordinal, and familial levels, contrary to the expectations of the size-grain model and supporting our main hypothesis of a common ancestral developmental pattern regulating leg negative allometry in Orthoptera. 4. The conservation of a common hind leg allometric pattern in Orthoptera provides a basic framework to study adaptation of hind limbs to different habitats and lifestyles, and has important implications for the analysis of ecogeographic and evolutionary rules.

Transfusion Support of Minority Patients: Extended Antigen Donor Typing and Recruitment of Minority Blood Donors

One of the most important and persistent complications of blood transfusion is red blood cell (RBC) alloimmunization. When a patient is exposed to RBC antigens that differ from their own they can form alloantibodies to these foreign antigens. Blood group antigens are highly conserved and follow ancestral patterns of inheritance that may demonstrate population restriction. Minority populations who require chronic transfusion are at particularly high risk of alloimmunization when the blood donor population does not share the same ancestral background, resulting in exposure to non-self RBC antigens. It is incumbent on blood collectors to support patients with risk factors for alloimmunization as well as patients who have already formed alloantibodies. Increasing utilization of RBC genotyping may represent an opportunity to improve access to RBC units from donors that match the extended RBC phenotype of all possible patients.

Ancestral kinship patterns substantially reduce the negative effect of increasing group size on incentives for public goods provision

Numerous theories on the evolution of altruistic in-group beneficial behavior in humans exist. Many of these abstract away from the effects of kinship on incentives for public goods provision, though. Here, a simple model is devised that illustrates how genetic relatedness changes the incentive structure of that paradigmatic game which is conventionally used to model and experimentally investigate collective action problems: the linear public goods game. Using recent anthropological data sets on relatedness in contemporary hunter-gatherer and horticulturalist societies the parameters of the model are estimated. It turns out that the kinship patterns observed in these societies substantially reduce the negative effect of increasing group size on incentives for public goods provision. It is suggested, therefore, that renewed attention should be given to inclusive fitness theory in the context of public goods provision also in sizable groups.

The Palmar and Plantar Anatomy of Dromiciops gliroides Thomas, 1894 (Marsupialia, Microbiotheria) and its Relationship to Australian Marsupials

The monito del monte Dromiciops gliroides Thomas, 1894, is a marsupial endemic to the temperate rainforests of Argentina and Chile. Studies on its phylogenetic relationships show the species is more closely related to Australian marsupials than to any other American taxon. The study of the palmar and plantar anatomy in this species through direct observation of more than 86 specimens and comparisons with American and Australian marsupials show the pattern of D. gliroides is derived from the ancestral mammalian pattern. Dromiciops gliroides show the presence of a single palmar/plantar pad in the position of interdigital pad 1 and the lack of a thenar pad (or the complete fusion between both pads), a pattern that appears closer to some Australian diprotodont marsupials. Also shared with several Australian marsupials is the transverse orientation of pad ridges, a condition that is not shared with most arboreal/scansorial American marsupials (e.g., Caluromys spp., Marmosa spp., Marmosops spp.).

Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction.

Most modern mammals, including strictly diurnal species, exhibit sensory adaptations to nocturnal activity that are thought to be the result of a prolonged nocturnal phase or 'bottleneck' during early mammalian evolution. Nocturnality may have allowed mammals to avoid antagonistic interactions with diurnal dinosaurs during the Mesozoic. However, understanding the evolution of mammalian activity patterns is hindered by scant and ambiguous fossil evidence. While ancestral reconstructions of behavioural traits from extant species have the potential to elucidate these patterns, existing studies have been limited in taxonomic scope. Here, we use an extensive behavioural dataset for 2,415 species from all extant orders to reconstruct ancestral activity patterns across Mammalia. We find strong support for the nocturnal origin of mammals and the Cenozoic appearance of diurnality, although cathemerality (mixed diel periodicity) may have appeared in the late Cretaceous. Simian primates are among the earliest mammals to exhibit strict diurnal activity, some 52-33 million years ago. Our study is consistent with the hypothesis that temporal partitioning between early mammals and dinosaurs during the Mesozoic led to a mammalian nocturnal bottleneck, but also demonstrates the need for improved phylogenetic estimates for Mammalia.

Did saber-tooth kittens grow up musclebound? A study of postnatal limb bone allometry in felids from the Pleistocene of Rancho La Brea.

Previous studies have demonstrated that the Pleistocene saber-toothed cat Smilodon fatalis had many forelimb adaptations for increased strength, presumably to grapple with and subdue prey. The Rancho La Brea tar pits yield large samples of juvenile limb bones forming a growth series that allow us to examine how Smilodon kittens grew up. Almost all available juvenile limb bones were measured, and reduced major axis fits were calculated to determine the allometric growth trends. Contrary to expectations based on their robust limbs, Smilodon kittens show the typical pattern of growth found in other large felids (such as the Ice Age lion, Panthera atrox, as well as living tigers, cougars, servals, and wildcats) where the limb grows longer and more slender faster than they grow thick. This adaptation is thought to give felids greater running speed. Smilodon kittens do not grow increasingly more robust with age. Instead, they start out robust and follow the ancestral felid growth pattern, while maintaining their robustness compared to other felids. Apparently, the growth of felid forelimbs is highly canalized and their ontogeny is tightly constrained.

Deep time perspective on turtle neck evolution: chasing the Hox code by vertebral morphology

The unparalleled ability of turtle neck retraction is possible in three different modes, which characterize stem turtles, living side-necked (Pleurodira), and hidden-necked (Cryptodira) turtles, respectively. Despite the conservatism in vertebral count among turtles, there is significant functional and morphological regionalization in the cervical vertebral column. Since Hox genes play a fundamental role in determining the differentiation in vertebra morphology and based on our reconstruction of evolutionary genetics in deep time, we hypothesize genetic differences among the turtle groups and between turtles and other land vertebrates. We correlated anterior Hox gene expression and the quantifiable shape of the vertebrae to investigate the morphological modularity in the neck across living and extinct turtles. This permitted the reconstruction of the hypothetical ancestral Hox code pattern of the whole turtle clade. The scenario of the evolution of axial patterning in turtles indicates shifts in the spatial expression of HoxA-5 in relation to the reduction of cervical ribs in modern turtles and of HoxB-5 linked with a lower morphological differentiation between the anterior cervical vertebrae observed in cryptodirans. By comparison with the mammalian pattern, we illustrate how the fixed count of eight cervical vertebrae in turtles resulted from the emergence of the unique turtle shell.

Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates.

Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ∼350 million years. Thus, we show that traits involved in local-scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems.

Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity

Recent genomic studies of both ancient and modern indigenous people of the Americas have shed light on the demographic processes involved during the first peopling. The Pacific Northwest Coast proves an intriguing focus for these studies because of its association with coastal migration models and genetic ancestral patterns that are difficult to reconcile with modern DNA alone. Here, we report the low-coverage genome sequence of an ancient individual known as "Shuká Káa" ("Man Ahead of Us") recovered from the On Your Knees Cave (OYKC) in southeastern Alaska (archaeological site 49-PET-408). The human remains date to ∼10,300 calendar (cal) y B.P. We also analyze low-coverage genomes of three more recent individuals from the nearby coast of British Columbia dating from ∼6,075 to 1,750 cal y B.P. From the resulting time series of genetic data, we show that the Pacific Northwest Coast exhibits genetic continuity for at least the past 10,300 cal y B.P. We also infer that population structure existed in the late Pleistocene of North America with Shuká Káa on a different ancestral line compared with other North American individuals from the late Pleistocene or early Holocene (i.e., Anzick-1 and Kennewick Man). Despite regional shifts in mtDNA haplogroups, we conclude from individuals sampled through time that people of the northern Northwest Coast belong to an early genetic lineage that may stem from a late Pleistocene coastal migration into the Americas.

Long-Distance Range Expansion and Rapid Adjustment of Migration in a Newly Established Population of Barn Swallows Breeding in Argentina

When bird populations spread, long-distance pioneering populations are often backfilled by a more slowly advancing front [1-3]. The Barn Swallow Hirundo rustica, a globally distributed passerine [4, 5], expanded its breeding range an exceptional 7,000km when it began breeding 35 years ago in its regular wintering range in Argentina [6], subsequently expanding over 500km from its starting point [7-11]. Trans-hemispheric breeding attempts have occurred previously in related swallows [12-14], but only this colonization has lasted. Comparative studies of birds show a remarkable diversity in patterns of change in migratory habits [15-21], and these Argentine-breeding swallows might retain ancestral patterns, breeding in Argentina but returning to North America for the austral winter. Feather isotopes from these birds are consistent with the alternative possibility that they migrate no farther than northern South America [22]. Because isotopic patterns cannot definitively distinguish these alternatives, we pursued a solar geolocator study [23, 24] to do so. Data from nine tagged birds show conclusively that Barn Swallows breeding in Argentina have rapidly changed their movements to migrate no farther north in austral winter than northern South America. The phenology of the annual cycles of molt, migration, and breeding for these Argentine-breeding swallows have all shifted by about 6months, and we suggest that stimulatory day lengths and the proliferation of nesting substrates facilitated their colonization.

Hierarchical and accusative alignment of Verbal Person Marking in Trans-Himalayan

Abstract Verbal Person Marking is a neglected feature of Trans-Himalayan (Sino-Tibetan) languages. TH systems are of great typological interest, showing both canonical versions and unusual variations of both hierarchical and accusative alignment. The predominant and ancestral pattern is hierarchical, but we also see innovative accusative patterns. Canonical hierarchical and accusative systems do occur, but a majority of VPM systems of both alignments show variations on the basic patterns. Hierarchical systems sometimes develop means to index both participants in a transitive configuration rather than only the higher. Accusative systems frequently develop secondary O indexation for SAP arguments, and sometimes move further in the direction of hierarchical patterning. Thus Trans-Himalayan offers a wealth of examples of VPM systems, which deserve greater attention from the field of typology.

Evolution of the hypercarnivorous dentition in mammals (Metatheria, Eutheria) and its bearing on the development of tribosphenic molars.

One major innovation of mammals is the tribosphenic molar, characterized by the evolution of a neomorphic upper cusp (=protocone) and a lower basin (=talonid) that occlude and provide shearing and crushing functions. This type of molar is an evolutionarily flexible structure that enabled mammals to achieve complex dental adaptations. Among carnivorous mammals, hypercarnivory is a common trend that evolved several times among therians (marsupials, placentals, and stem relatives). Hypercarnivory involves an important simplification of the carnassial molar pattern from the ancestral tribosphenic molar pattern, with the modification of the triangular tooth crown, and the loss of several cusps and cuspids typical of the tribosphenic molar. These losses confer to the molars of the hypercarnivorous mammals a plesiomorphic/paedomorphic morphology that resembles more the earliest mammaliaforms than the earliest therians. Here, we demonstrate that the modification of the molar morphology is fully explained by a patterning cascade mode of cusp development. Contrary to what was previously proposed, our study concludes that the metaconid (mesiolingual cusp of lower molars, associated with a puncturing function) does not influence cusp development of the talonid (distal crushing heel of lower molars). Moreover, it provides a new example of how heterochronic changes were crucial to the evolution of mammal dentition. To overcome the difficulty of applying behavioral or ecological definitions of diets to fossil animals, we characterize hypercarnivorous dentitions on the basis of the molar morphology and more particularly on the loss or retention of crushing structures, each dentition resulting from adaptations to a distinct ecomorphotype. Despite repeated and convergent evolution of hypercarnivorous forms, hypercarnivory appears as a highly constrained specialization (i.e., "dead end") that is unlikely to evolve back to omnivorous dentition, especially when the crushing structures are lost.