Ancestor-descendant Relationships Research Articles

Resolving the conflictive phylogenetic relationships of Oceanites (Oceanitidae: Procellariiformes) with the description of a new species

The family Oceanitidae, formerly considered a subfamily of Hydrobatidae, includes all the small storm-petrels of the southern hemisphere. The ancestor-descendent relationships and evolutionary history of one of its genera, Oceanites, have been partially studied, yielding contrasting results. We revised the phylogenetic relationships of this group using Bayesian inference (BI) based on new sequence data of the mitochondrial gene Cytb and linear morphological measurements of all species and five subspecies-level taxa in Oceanites, including a new taxon from the Chilean Andes. Our BI results show that the Oceanites genus is monophyletic and composed of four well-supported clades (posterior probability > 0.95): (1) chilensis; (2) exasperatus; (3) gracilis, pincoyae, and barrosi sp. nov.; and (4) oceanicus and galapagoensis. The species O. chilensis is a basal clade within Oceanites. According to our time-calibrated tree, the split between Oceanites and the other genera in Family Oceanitidae is estimated to be ~35.9 Mya, and the oldest divergence within Oceanites (the split between O. chilensis and other Oceanites) was dated to the early Miocene, around c. 21.3 Mya. The most probable geographic origin of Oceanites is the Southern Ocean. The morphological data suggest continuous size variation between Oceanites taxa, ranging from smallest in gracilis to largest in exasperatus. Based on our phylogenetic hypothesis, and morphological analyses, we suggest elevating to species status the taxa galapagoensis, chilensis, and exasperatus, and we describe a new taxon barrosi sp. nov., thus recognizing a total of seven species within the genus Oceanites.

Evolutionary relationships, hybridization and diversification under domestication of the locoto chile (Capsicum pubescens) and its wild relatives.

Patterns of genetic variation in crops are the result of multiple processes that have occurred during their domestication and improvement, and are influenced by their wild progenitors that often remain understudied. The locoto chile, Capsicum pubescens, is a crop grown mainly in mid-highlands of South-Central America. This species is not known from the wild and exists only as a cultigen. The evolutionary affinities and exact origin of C. pubescens have still not been elucidated, with hypotheses suggesting its genetic relatedness and origin to two wild putative ancestral Capsicum species from the Central Andes, C.eximium and C. cardenasii. In the current study, RAD-sequencing was applied to obtain genome-wide data for 48 individuals of C. pubescens and its wild allies representing different geographical areas. Bayesian, Maximum Likelihood and coalescent-based analytical approaches were used to reconstruct population genetic patterns and phylogenetic relationships of the studied species. The results revealed that C. pubescens forms a well-defined monotypic lineage closely related to wild C. cardenasii and C. eximium, and also to C. eshbaughii. The primary lineages associated with the diversification under domestication of C. pubescens were also identified. Although direct ancestor-descendant relationship could not be inferred within this group of taxa, hybridization events were detected between C. pubescens and both C.cardenasii and C. eximium. Therefore, although hybrid origin of C. pubescens could not be inferred, gene flow involving its wild siblings was shown to be an important factor contributing to its contemporary genetic diversity. The data allowed for the inference of the center of origin of C. pubescens in central-western Bolivia highlands and for better understanding of the dynamics of its gene pool. The results of this study are essential for germplasm conservation and breeding purposes, and provide excellent basis for further research of the locoto chile and its wild relatives.

Mapping the Evolutionary Pattern of Mobile Products: A Phylogenetic Approach

Product evolution is an emerging research field with increasing academic and practical interest. Although there have been several qualitative and quantitative studies on product evolution, a consensus on operational definitions and generalized methodology for analyzing product evolution has not been reached. Therefore, operational definitions of product gene, product taxon, and ancestor–descendant relationship are presented in this article. Based on the definitions, a unique product phylogenetic tree methodology is introduced considering the differences in biology and products. The methodology can be applied to any product data because it comprises generalized algorithms. To verify the definitions and methodology, a mobile product phylogenetic tree is constructed using the web crawled global mobile product data released between 1995 and 2019. The definitions and methodology were verified by observing historical events, such as emergence of smartphone and growth of Chinese firms on the resulting tree. In addition, three application methods of the methodology are introduced—a tool to explain evolutionary phenomena in a product along with previous product evolution theory, a tool to inform firms of decision making for determining their strategies, and a tool to predict the future product type. In summary, the findings of this study can contribute to the improvement of product evolution research by introducing data-driven and algorithmic approach for analyzing product that can be utilized in future studies. Furthermore, the proposed methodology aids decision making in product development by providing trajectories of products that are expected to survive.

Scaphitid ammonites from the lower Maastrichtian of Nahoryany (western Ukraine) and discussion on the origin of Hoploscaphites constrictus

Abstract The lower Maastrichtian (Upper Cretaceous) section at Nahoryany, south of Lviv (western Ukraine), has been known as a rich source of fossils since 1843. However, the section is not available since a long time ago and fossils collected from it can only be studied in museum collections. In the present paper, ammonites of the scaphitid genus Hoploscaphites are studied based on Nahoryany material, comprising Hoploscaphites pumilus, H. constrictus and H. sp. Specimens from Nahoryany in museum collections lack data on their provenance level within the section so it cannot be determined whether or not they occurred together or formed a succession; data on inoceramid bivalves indicate the presence of two successive zones at Nahoryany. Some specimens from Nahoryany here referred to as H. pumilus are similar to the controversial H. constrictus anterior from the lower Maastrichtian of Poland. This morphology suggests an ancestor–descendant relationship between H. pumilus and H. constrictus, a common species once considered as an informal index for the Boreal Maastrichtian in Europe. The inferred evolutionary transition from H. pumilus to H. constrictus was towards a less robust, recoiled shell, which would have enhanced the horizontal swimming ability and manoeuvrability of these cephalopods. Recoiling trends occurred in several lineages of Late Cretaceous scaphitids.

Cuticular proteins in codling moth (Cydia pomonella) respond to insecticide and temperature stress

The insect cuticle consists of chitin and cuticular proteins (CPs), which stabilize the body shape and provide an effective physical barrier against the external environment. They are also potential target sites for developing environmentally friendly insect management through the utilization of physiology-based methods. The codling moth, Cydia pomonella, is a pest afflicting fruit orchards worldwide. This study used a comparative genomic approach, whole-genome resequencing, and transcriptome data to understand the role that CPs played in the environmental adaptation of the codling moth. A total of 182 putative CPs were identified in the codling moth genome, which were classified into 12 CP families. 119 CPR genes, including 54 RR-1, 60 RR-2, and 5 RR-3 genes were identified and accounted for 65.4% of the total CPs. Eight and seven gene clusters are formed in RR1 and RR2 subfamily and the ancestor-descendant relationship was explained. Five CPAP genes were highly expressed during the egg stage and exposed to high temperature, which indicated their potential role in aiding codling moth eggs in acclimating to varying external heat conditions. Moreover, six CPs belonging to the CPR and CPLCP families were identified in association with insecticide resistance by population resequencing. Their expression levels increased after exposure to insecticides, suggesting they might be involved in codling moth resistance to the insecticides azinphos-methyl or deltamethrin. Our results provide insight into the evolution of codling moth CPs and their association with high temperature adaptation and insecticide resistance, and provide an additional information required for further analysis of CPs in environmental adaptation.

Median-Joining Networks and Bayesian Phylogenies Often Do Not Tell the Same Story

Inferring phylogenies among intraspecific individuals often yields unresolved relationships (i.e., polytomies). Consequently, methods that compute distance-based abstract networks, like Median-Joining Networks (MJNs), are thought to be more appropriate tools for reconstructing such relationships than traditional trees. Median-Joining Networks visualize all routes of relationships in the form of cycles, if needed, when traditional approaches cannot resolve them. However, the MJN method is a distance-based phenetic approach that does not involve character transformations and makes no reference to ancestor–descendant relationships. Although philosophical and theoretical arguments challenging the implication that MJNs reflect phylogenetic signal in the traditional sense have been presented elsewhere, an empirical comparison with a character-based approach is needed given the increasing popularity of MJN analysis in evolutionary biology. Here, we use the conservative Approximately Unbiased (AU) test to compare 85 cases of branching patterns of cycle-free MJNs and Bayesian Inference (BI) phylogenies using datasets from 55 empirical studies. By rooting the MJN analyses to provide directionality, we report substantial disagreement between computed MJNs and posterior distributions on BI phylogenies. The branching patterns in MJNs and BI phylogenies show significantly different relationships in 37.6% of cases. Among the relationships that do not significantly differ, 96.2% show alternative sets of relationships. Our results indicate that the two methods provide different measures of relatedness in a phylogenetic sense. Finally, our analyses also support previous observations of the statistical hypothesis testing by reconfirming the over-conservativeness of the Shimodaira-Hasegawa test versus the AU test.

Payne’s rule and the late *o > a shift in Mojeño Ignaciano

Ramirez & França’s (2019) claim that a change *a > o took place multiple times and without any discernible conditioning factor - which the authors present as an explicit counterproposal to a series of claims made in Carvalho & Rose (2018) - is methodologically and empirically flawed. We show here that the supposed evidence from loanwords is artifactual, that the comparison between 18th Guaná and modern Terena rests on an arbitrarily selective and, ultimately, misleading treatment of the relevant sources, and that the claimed ancestor-descendant relationship between Old Mojeño and Trinitario is at odds with other well-established claims about the history of Mojeño dialects, in addition to being an unnecessary and extraneous assumption. Moreover, a lexical stratification of the Mojeño lexicon in terms of basic and less-basic strata shows that the main correspondence favored by Ramirez & França (2019) as the reflex of Proto-Arawakan *a in Mojeño is essentially restricted to nonbasic vocabulary, a finding that vindicates Carvalho & Rose’s (2018) interpretation of this pattern as reflecting dialect borrowing or diffusion.

Temporal and spatial characteristics of tumor evolution in a mouse model of oral squamous cell carcinoma

ObjectivesWe aimed to elucidate the temporal and spatial characteristics of tumor evolution in an oral squamous cell carcinoma (OSCC) mouse model with higher burden of lymphatic metastasis through high-throughput sequencing.MethodsThe OSCC model was established in 9 mice. DNA was extracted from the tumors of primary tongue lesions and disseminated tumor cells (DTCs) of submandibular gland lymph nodes and bone marrow, and then whole genome sequencing was performed. After bioinformatics analysis, somatic single-nucleotide variants (SSNVs) and copy number variations (CNVs) data were obtained. Based on SSNVs, clonal architecture and ancestor-descendant relationships among tumor cell subclones were elucidated.ResultsA total of 238 tumor-related SSNVs with 120 high-frequency mutated genes were obtained from 36 samples of 9 mice by whole-genome sequencing. The number of unique SSNVs in the primary lesion, submandibular lymph node and bone marrow was greater than the number of shared SSNVs. Furthermore, the primary lesion-originated subclones, which were identified by SSNVs, were also detected in submandibular lymph nodes in the early stage of oral carcinogenesis. Moreover, at different histopathological stages, unique subclones were also identified in DTCs isolated from lymph nodes.ConclusionTumor heterogeneity is significant in primary tumor cells and disseminated tumor cells. OSCC cells probably disseminate to lymph nodes in the early stage of oral carcinogenesis. OSCC is characterized by polyclonal dissemination, and the evolutionary trajectory of DTCs is potentially dominated by the tumor microenvironment.

Comparative description and taxonomic affinity of 3.7-million-year-old hominin mandibles from Woranso-Mille (Ethiopia)

Fossil discoveries of early Australopithecus species from Woranso-Mille have played a significant role in improving our understanding of mid-Pliocene hominin evolution and diversity. Here, we describe two mandibles with dentitions, recovered from sediments immediately above a tuff radiometrically dated to 3.76 ± 0.02 Ma, and assess their taxonomic affinity. The two mandibles (MSD-VP-5/16 and MSD-VP-5/50) show morphological similarities with both Australopithecus anamensis and Australopithecus afarensis. Some of the unique features that distinguish Au. anamensis from Au. afarensis are present in the mandibles, which also share a few derived features with Au. afarensis. Their retention of more Kanapoi Au. anamensis-like traits, compared to the fewer derived features they share with Au. afarensis, and the presence of Au. anamensis at Woranso-Mille in 3.8-million-year-old deposits, lends support to their assignment to Au. anamensis. However, it is equally arguable that the few derived dentognathic features they share with Au. afarensis could be taxonomically more significant, making it difficult to conclusively assign these specimens to either species. Regardless of which species they are assigned to, the mosaic nature of the dentognathic morphology and geological age of the two mandibles lends further support to the hypothesized ancestor–descendant relationship between Au. anamensis and Au. afarensis. However, there is now limited fossil evidence indicating that these two species may have overlapped in time. Hence, the last appearance of Au. anamensis and first appearance of Au. afarensis are currently unknown. Recovery of Australopithecus fossils from 4.1 to 3.8 Ma is critical to further address the timing of these events.

Phylogenetic Studies and Metabolite Analysis of Sticta Species from Colombia and Chile by Ultra-High Performance Liquid Chromatography-High Resolution-Q-Orbitrap-Mass Spectrometry.

Eleven species of lichens of the genus Sticta, ten of which were collected in Colombia (S. pseudosylvatica S. luteocyphellata S. cf. andina S. cf. hypoglabra, S. cordillerana, S. cf. gyalocarpa S. leucoblepharis, S. parahumboldtii S. impressula, S. ocaniensis) and one collected in Chile (S. lineariloba), were analyzed for the first time using hyphenated liquid chromatography with high-resolution mass spectrometry. In the metabolomic analysis, a total of 189 peaks were tentatively detected; the analyses were divided in five (5) groups of compounds comprising lipids, small phenolic compounds, saturated acids, terpenes, and typical phenolic lichen compounds such as depsides, depsidones and anthraquinones. The metabolome profiles of these eleven species are important since some compounds were identified as chemical markers for the fast identification of Sticta lichens for the first time. Finally, the usefulness of chemical compounds in comparison to traditional morphological traits to the study of ancestor–descendant relationships in the genus was assessed. Chemical and morphological consensus trees were not consistent with each other and recovered different relationships between taxa.

Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.

Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation. We illustrate the pipeline using a small dataset of prokaryotic genomes, for which the example scripts can be run using modest computer resources. We describe the rooting method used in this work in the context or other rooting strategies and discuss some of the limitations and opportunities presented by probabilistic gene tree-species tree reconciliation methods.

Reconstruction of State-Dependent Diversification: Integrating Phenotypic Traits into Molecular Phylogenies.

The relative contribution of speciation and extinction into current diversity is certainly unknown, but mathematical frameworks that use genetic information have been developed to provide estimates of these processes. To that end, it is necessary to reconstruct molecular phylogenetic trees which summarize ancestor-descendant relationships as well as the timing of evolutionary events (i.e., rates). Nevertheless, diversification models show poor fit when assuming that single rate of speciation/extinction is constant over time and across lineages: species exhibit such a great variation in features that it is unlikely they give birth and die at the same pace. The state-dependent diversification framework (SSE) reconciles the species phenotypic variation with heterogeneous rates of diversification observed in a clade. This family of models allows testing contrasting hypotheses on mode of speciation, trait evolution, and its influence on speciation/extinction regimes. Although microbial species richness outnumbers diversity in plants and animals, diversification models are underused in microbiology. Here, we introduce microbiologists to models that estimate diversification rates and provide a detailed description of SSE models. Besides theoretical principles underlying the method, we also show how SSE analysis should be set up in R. We use pH evolution in Thaumarchaeota to explain its evolutionary dynamic in the light of SSE model. We hope this chapter spurs the study of trait evolution and evolutionary outcomes in microorganisms.

Improving the support for XML dynamic updates using a hybridization labeling scheme (ORD-GAP)

Background : As the standard for the exchange of data over the World Wide Web, it is important to ensure that the eXtensible Markup Language (XML) database is capable of supporting not only efficient query processing but also capable of enduring frequent data update operations over the dynamic changes of Web content. Most of the existing XML annotation is based on a labeling scheme to identify each hierarchical position of the XML nodes. This computation is costly as any updates will cause the whole XML tree to be re-labelled. This impact can be observed on large datasets. Therefore, a robust labeling scheme that avoids re-labeling is crucial. Method: Here, we present ORD-GAP (named after Order Gap), a robust and persistent XML labeling scheme that supports dynamic updates. ORD-GAP assigns unique identifiers with gaps in-between XML nodes, which could easily identify the level, Parent-Child (P-C), Ancestor-Descendant (A-D) and sibling relationship. ORD-GAP adopts the OrdPath labeling scheme for any future insertion. Results: We demonstrate that ORD-GAP is robust enough for dynamic updates, and have implemented it in three use cases: (i) left-most, (ii) in-between and (iii) right-most insertion. Experimental evaluations on DBLP dataset demonstrated that ORD-GAP outperformed existing approaches such as ORDPath and ME Labeling concerning database storage size, data loading time and query retrieval. On average, ORD-GAP has the best storing and query retrieval time. Conclusion: The main contributions of this paper are: (i) A robust labeling scheme named ORD-GAP that assigns certain gap between each node to support future insertion, and (ii) An efficient mapping scheme, which built upon ORD-GAP labeling scheme to transform XML into RDB effectively.

Improving the support for XML dynamic updates using a hybridization labeling scheme (ORD-GAP).

Background: As the standard for the exchange of data over the World Wide Web, it is important to ensure that the eXtensible Markup Language (XML) database is capable of supporting not only efficient query processing but also capable of enduring frequent data update operations over the dynamic changes of Web content. Most of the existing XML annotation is based on a labeling scheme to identify each hierarchical position of the XML nodes. This computation is costly as any updates will cause the whole XML tree to be re-labelled. This impact can be observed on large datasets. Therefore, a robust labeling scheme that avoids re-labeling is crucial. Method: Here, we present ORD-GAP (named after Order Gap), a robust and persistent XML labeling scheme that supports dynamic updates. ORD-GAP assigns unique identifiers with gaps in-between XML nodes, which could easily identify the level, Parent-Child (P-C), Ancestor-Descendant (A-D) and sibling relationship. ORD-GAP adopts the OrdPath labeling scheme for any future insertion. Results: We demonstrate that ORD-GAP is robust enough for dynamic updates, and have implemented it in three use cases: (i) left-most, (ii) in-between and (iii) right-most insertion. Experimental evaluations on DBLP dataset demonstrated that ORD-GAP outperformed existing approaches such as ORDPath and ME Labeling concerning database storage size, data loading time and query retrieval. On average, ORD-GAP has the best storing and query retrieval time. Conclusion: The main contributions of this paper are: (i) A robust labeling scheme named ORD-GAP that assigns certain gap between each node to support future insertion, and (ii) An efficient mapping scheme, which built upon ORD-GAP labeling scheme to transform XML into RDB effectively.

ORBITOLINIDS AND OTHER LARGER BENTHIC FORAMINIFERA FROM THE APTIAN-ALBIAN OF TIBET: CRITICAL DISCUSSION OF SOME RECENTLY PUBLISHED DATA

Orbitolinidae together with other larger benthic foraminifera are particularly important in Lower Cretaceous shallow-water biostratigraphy provided that they are correctly identified. Especially in the case of the Orbitolininae (with complex embryo), their biostratigraphic range with overlapping ranges corresponds to different lineages displaying ancestor-descendant relationship (e.g., Praeorbitolina-Mesorbitolina). In the last fifty years well established and repeatedly confirmed taxon ranges have been largely extended thereby diluting or negating any biostratigraphic value to individual species. Some biostratigraphic data provided by BouDagher-Fadel et al. (2017) from the Aptian-Albian of Tibet that are contradicting previous results are reviewed herein. This publication mostly refers to the stratigraphic ranges of Praeorbitolina cormyi Schroeder and Pseudochoffatella cuvillieri Deloffre towards the top of the Albian, and that of Palorbitolina lenticularis (Blumenbach) into the late Aptian, as well as some misidentifications.

The late Berriasian early evolutionary burst of the Orbitolinidae: New insights into taxonomy, origin, diversification and phylogeny of the family based on data from eastern Serbia

New data from the Carpatho-Balkanides of eastern Serbia evidence the more or less near-simultaneous "explosive" first appearances of several genera of the Orbitolinidae in the late Berriasian. Most of the observed taxa were previously recorded from strata not older than the Late Hauterivian (= classical Urgonian of southeastern France), evidence that these ages refer to local first appearance data. The diversified assemblage from Serbia includes representatives of the subfamilies Dictyoconinae: genera Cribellopsis ARNAUD-VANNEAU, Montseciella CHERCHI & SCHROEDER, Orbitolinopsis HENSON, Urgonina FOURY & MOULLADE, Valserina SCHROEDER & CONRAD, Vanneauina SCHLAGINTWEIT, and Dictyorbitolininae: genus Paracoskinolina MOULLADE. Representatives of the Orbitolininae (with complex embryo) have not been observed. They appeared later in the fossil record seemingly during the Late Hauterivian-early Barremian. All together 17 taxa are reported, of which three in open nomenclature. A new species is described as Cribellopsis sudari n. sp. The majority of the observed species display medium- to high-conical tests and a rather simple exoskeleton lacking horizontal partitions (rafters). The new data contradict a phylogenetic evolution of distinct genera displaying different internal test structures one after the other in time (= ancestor-descendant relationships) as postulated by some authors. The explosive radiation ("early burst") of the Orbitolinidae in the late Berriasian is accompanied by the first appearance date of several other large benthic foraminifera including mostly agglutinating (e.g., Ammocycloloculina, Choffatella, Drevennia, Eclusia, Moulladella, Pfenderina, Pseudotextulariella) but also complex porcelaneous taxa (Pavlovcevina) providing evidence for a bioevent in this time period that exceeds the number of taxa originating in the previous (Tithonian) and the following stage (Valanginian). The early evolutionary history of the Orbitolinidae can be considered a classical example of adaptive radiation within the clade's history.

The upper Aptian–middle Albian Simplorbitolina lineage: an example of nepionic acceleration in Lower Cretaceous Orbitolinidae (Foraminifera)

ABSTRACT Evolutionary lineages within the conical agglutinated family Orbitolinidae are mainly evidenced by the increased complexity of their inner structure. In this respect, gradual changes in the exoskeleton resulting in the evolution of beams and rafters in the marginal zone refer above all to lineages within the subfamily Dictyoconinae. In contrast hereto, the increasing size and complexity of the simple megalospheric embryo as well as the reduction of the initial spiral stage defines lineages within the subfamily Orbitolininae (e.g., Praeorbitolina-Mesorbitolina). The case of the upper Aptian–middle Albian Simplorbitolina lineage, the ancestor-descendant relationship of the three species S. aquitanica, S. manasi, and S. conulus represents a rare example of the Dictyoconinae displaying a successive reduction of the initial spiral stage along with an increase of both embryo size and complexity of the marginal zone. This process, which is known as spiral reduction or nepionic acceleration, is well recorded from other groups of Larger Benthic Foraminifera (fossil and extant) such as the calcareous Rotaliida. The occurrences and palaeogeographic distributional pattern of Simplorbitolinas are reviewed. The present study is preliminary based on a well-preserved assemblage of megalospheric specimens of Simplorbitolina aquitanica (Schroeder) from the upper Aptian Reocín Formation of northern Spain (Cantabria).

New and improved algorithms for unordered tree inclusion

The tree inclusion problem is, given two node-labeled trees P and T (the “pattern tree” and the “target tree”), to locate every minimal subtree in T (if any) that can be obtained by applying a sequence of node insertion operations to P. Although the ordered tree inclusion problem is solvable in polynomial time, the unordered tree inclusion problem is NP-hard. The currently fastest algorithm for the latter is a classic algorithm by Kilpeläinen and Mannila from 1995 that runs in O(d22dmn) time, where m and n are the sizes of the pattern and target trees, respectively, and d is the degree of the pattern tree. Here, we develop a new algorithm that runs in O(d2dmn2) time, improving the exponential factor from 22d to 2d by considering a particular type of ancestor-descendant relationships that is suitable for dynamic programming. We also study restricted variants of the unordered tree inclusion problem.

The Evolutionary Thought of Jean-Baptiste Lamarck

The name Lamarck is very well known in the teaching of biology, being associated with an early effort to explain evolution. Nevertheless, when evolution is taught in the classroom, the only Lamarckian ideas that stand out are related to the ‘inheritance of acquired characters’, invariably illustrated by the example of the lengthening of giraffes’ necks, as a way of contrasting Lamarckian ideas with Darwinian natural selection. Our aim here is to argue that there are other important ideas in Lamarck’s work that are directly related to the origin and transformation of species. These concepts, causal explanations of organic nature, can be taught to students who are learning about the sources and development of evolutionary thought and will moreover provide the student with properly justified reasons as to why Lamarck’s explanation is considered to be the first wide-ranging and well-argued explanation of biological evolution. The Lamarckian concepts that we consider important for teaching evolutionary thought are the following: (1) the species as an arbitrary concept, directly related to the Lamarckian concept of the continuous transformation of species, (2) the ancestor–descendant relationship, and organic diversification from a common plan of organisation to a branching series, (3) gradual change, related to changes in environmental conditions, and (4) the controversy concerning the origin of life (that is, having either a natural cause or a divine origin), life’s transformation, and the natural origin of human beings, including our moral capacity, subjects which were related to Lamarck’s other political and philosophical interests.

Andean orogeny and the diversification of lowland neotropical rain forest trees: A case study in Sapotaceae

Understanding how species diversify and evolve in species-rich areas like the lowland rain forest in the Neotropics is critical for conservation in times of unprecedented threats. To determine how the Andean uplift, the formation of the Panama land bridge, and Pleistocene climatic fluctuations affected dispersal and diversification in the Sapotaceae subfamily Chrysophylloideae, we collected 146 Chrysophylloideae accessions in previously under-explored areas, generating one of the most geographically complete data sets for neotropical Sapotaceae. Sapotaceae is a good model to test diversification hypotheses in lowland neotropical rain forests as it predominantly occurs <1000 m altitude, and it is an abundant and species-rich group in this biome. We generated a time calibrated phylogeny of 123 Sapotaceae species based upon the nuclear ribosomal internal transcribed spacer region that suggests migration between lineages to the east and the west Andean Cordilleras occurred before and after periods of major uplift, indicating that the Andes did not represent a significant barrier to dispersal for Sapotaceae, although it may have promoted vicariance in some cases. Dispersal between South and Central America occurred mainly prior to the formation of the Panama land bridge, suggesting that this event did not affect migration patterns in Chrysophylloideae. We inferred diversification rates and detected three shifts in the phylogeny, but they are not congruent with tectonic movements during the middle Miocene and climatic changes during the Pleistocene. Finally, some species with restricted distributions appear to be phylogenetically nested within species with broader ranges, suggesting ancestor descendent relationships and insights into patterns of speciation in rain forest trees.