Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative ...definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayr's definition, as necessary properties of species. On the other hand, the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayr's popular species definition are commonly confused under the name "the biological species concept," they are more or less clearly distinguished in Mayr's early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr. Definitions of the species category that identify a particular contingent property of metapopulation lineages (including intrinsic reproductive isolation) as a necessary property of species reduce the number of metapopulation lineages that are to be recognized taxonomically as species, but they cause conflicts among alternative species definitions and compromise the status of the species as a basic category of biological organization.
Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high‐throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic ...DNA from dried and fluid‐preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target‐capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin‐fixed tissues. We designed capture probes based on double‐digest restriction‐site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture‐based samples clustered together, but RADseq samples did not cluster with corresponding capture‐based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin‐fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.
Fossorial Origin of the Turtle Shell Lyson, Tyler R.; Rubidge, Bruce S.; Scheyer, Torsten M. ...
CB/Current biology,
07/2016, Letnik:
26, Številka:
14
Journal Article
Recenzirano
Odprti dostop
The turtle shell is a complex structure that currently serves a largely protective function in this iconically slow-moving group 1. Developmental 2, 3 and fossil 4–7 data indicate that one of the ...first steps toward the shelled body plan was broadening of the ribs (approximately 50 my before the completed shell 5). Broadened ribs alone provide little protection 8 and confer significant locomotory 9, 10 and respiratory 9, 11 costs. They increase thoracic rigidity 8, which decreases speed of locomotion due to shortened stride length 10, and they inhibit effective costal ventilation 9, 11. New fossil material of the oldest hypothesized stem turtle, Eunotosaurus africanus 12 (260 mya) 13, 14 from the Karoo Basin of South Africa, indicates the initiation of rib broadening was an adaptive response to fossoriality. Similar to extant fossorial taxa 8, the broad ribs of Eunotosaurus provide an intrinsically stable base on which to operate a powerful forelimb digging mechanism. Numerous fossorial correlates 15–17 are expressed throughout Eunotosaurus’ skeleton. Most of these features are widely distributed along the turtle stem and into the crown clade, indicating the common ancestor of Eunotosaurus and modern turtles possessed a body plan significantly influenced by digging. The adaptations related to fossoriality likely facilitated movement of stem turtles into aquatic environments early in the groups’ evolutionary history, and this ecology may have played an important role in stem turtles surviving the Permian/Triassic extinction event.
•Recently discovered stem turtles indicate the shell did not evolve for protection•Adaptation related to digging was the initial impetus in the origin of the shell•Digging adaptations facilitated the movement of turtles into aquatic environments•Fossoriality likely helped stem turtles survive the Permian/Triassic extinction
The origin of the turtle shell is a major evolutionary transition whose initial function was unknown. Lyson et al. present a strongly supported idea that a burrowing ecology and adaptations related to digging favored the initial transformations on the road to the modern turtle shell. Only later was the shell coopted for protection.
The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and ...methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.
Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has ...been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses.
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little ...research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post‐colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor‐poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.
Abstract
Recent biological discoveries have changed our understanding of the distribution and evolution of neotropical biotas. In the Brazilian Atlantic Forest, the discovery of closely related ...species isolated on distant mountains has led to the hypothesis that the ancestors of montane species occupied and dispersed through lowland regions during colder periods. This process may explain the distribution of an undescribed Anolis lizard species that we recently discovered at a montane site in the Serra dos Órgãos National Park, a popular tourist destination close to the city of Rio de Janeiro. To investigate whether this species is closely related to other Atlantic Forest montane anoles, we implement phylogenetic analyses and divergence time estimation based on molecular data. We infer the new species nested within the Dactyloa clade of Anolis, forming a clade with A. nasofrontalis and A. pseudotigrinus, two species restricted to montane sites about 400 km northeast of Serra dos Órgãos. The new species diverged from its sister A. nasofrontalis around 5.24 mya, suggesting a cold-adapted lowland ancestor during the early Pliocene. Based on the phylogenetic results, we emend the definitions of the series taxa within Dactyloa, recognizing a clade containing the new species and several of its relatives as the nasofrontalis series. Lastly, we provide morphological data supporting the recognition of the new species and give it a formal scientific name. Future studies are necessary to assess how park visitors, pollutants, and shrinking montane habitats due to climate change will affect this previously overlooked anole species.
Display omitted
► The Dactyloa clade is inferred with strong support. ► Five subclades are inferred: eastern, latifrons, Phenacosaurus, roquet and western. ► Each subclade is strongly supported and ...exhibits a coherent geographic range.
The Dactyloa clade, one of two major subgroups of mainland Anolis lizards, is distributed from Costa Rica to Peru, including the Amazon region and the southern Lesser Antilles. We estimated the phylogenetic relationships within Dactyloa based on mitochondrial (ND2, five transfer-RNAs, COI) and nuclear (RAG1) gene regions using likelihood and Bayesian methods under different partition strategies. In addition, we tested the monophyly of five previously recognized groups within Dactyloa. The data strongly support the monophyly of Dactyloa and five major clades: eastern, latifrons, Phenacosaurus, roquet and western, each of which exhibits a coherent geographic range. Relationships among the five major clades are less clear: support for basal nodes within Dactyloa is weak and some contradictory relationships are supported by different datasets and/or phylogenetic methods. Of the previously recognized subgroups within Dactyloa, only the roquet series consistently passed the topology tests applied. The monophyly of the aequatorialis, latifrons (as traditionally circumscribed) and punctatus series was strongly rejected, and the monophyly of Phenacosaurus (as traditionally circumscribed) yielded mixed results. The results of the phylogenetic analyses suggest the need for a revised taxonomy and have implications for the biogeography and tempo of the Dactyloa radiation.
The vagaries of history lead to the prediction that repeated instances of evolutionary diversification will lead to disparate outcomes even if starting conditions are similar. We tested this ...proposition by examining the evolutionary radiation of Anolis lizards on the four islands of the Greater Antilles. Morphometric analyses indicate that the same set of habitat specialists, termed ecomorphs, occurs on all four islands. Although these similar assemblages could result from a single evolutionary origin of each ecomorph, followed by dispersal or vicariance, phylogenetic analysis indicates that the ecomorphs originated independently on each island. Thus, adaptive radiation in similar environments can overcome historical contingencies to produce strikingly similar evolutionary outcomes.
PDF
