Article

Unveiling the mystery: assessing the evolutionary trajectory of the Apaporis caiman population (Caiman crocodilus apaporiensis, Medem 1955) via mitochondrial molecular makers

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Abstract

The Apaporis caiman (Caiman crocodilus apaporiensis) has been of particular interest due to its highly differentiated morphology. However, no molecular research has been done to clarify its taxonomy. We characterized the genetic variation within C. crocodilus by assessing the evolutionary trajectory of Apaporis caiman populations using mitochondrial molecular markers. We collected ten Apaporis caiman samples from the middle basin of the Apaporis River, Colombia, sequenced two mitochondrial genes [cytochrome oxidase I (COI) and cytochrome B (CytB)], and analysed them together with all available sequences from homologous gene fragments at GenBank for the species. Phylogenetic reconstructions revealed three main clades clearly differentiated across the C. crocodilus complex. These clades matched genetically and geographically with three of the four subspecies currently recognized (C. c. chiapasius, C. c. fuscus and C. c. crocodilus). However, we found low to almost non-existent genetic differentiation between C. c. crocodilus and the until-now morphologically recognized C. c. apaporiensis, suggesting that the latter is part of the genetic spectrum present within C. c. crocodilus. We reject the hypothesis of an expected elevated level of genetic variation due to isolation (supported by morphological differentiation) and support the idea of Apaporis caiman populations as a C. crocodilus ecomorph.

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... However, recent molecular work has not supported at least one of the subspecific designations (C. c. apaporiensis; Balaguera-Reina et al., 2020) and has provided support for substantial unrecognized diversity (at least eight lineages; Roberto et al., 2020), highlighting the need for additional molecular assessments of C. crocodilus across its range. Considering that the viability of a species and the long-term persistence of its evolutionary potential depend upon (among other factors) the maintenance of genetic variability, accurate consideration of lineages and evolutionarily significant units (ESU) in conservation programs is crucial to maintain genetic integrity (Allendorf et al., 2013;Cook-Patton et al., 2011;Laikre et al., 2016). ...
... c. apaporiensis, Balaguera-Reina et al., 2020; C. c. fuscus/chiapasius, Jimenez-Alonso, 2016). However, some areas such as the Orinoco and Amazon drainages, and the Magdalena River basin are still in need of information that allows clear documentation of genetic variation in these areas and to accurately attribute populations to the lineages currently recognized as formal taxa (Balaguera-Reina et al., 2020;Jimenez-Alonso, 2016;Roberto et al., 2020;Venegas-Anaya et al., 2008). ...
... Total genomic DNA was isolated from each sample using proteinase K buffer digestion (see Balaguera-Reina et al., 2020 for details), followed by extraction using the phenol/chloroform technique (Sambrook et al., 1989). Two mitochondrial genes, Cytochrome Oxidase 1 (COI) and Cytochrome B (CytB), were partially amplified using primers developed by Jimenez-Alonso (2016; see Balaguera-Reina et al., 2020). Conditions for each 50 mL polymerase chain reaction (PCR) were: 22 lL of MiliQ water, 25 lL of 2X PCR Taq Master Mix (ABM), 1 lL of each primer (forward and reverse) and 1 lL template DNA (adjusted to 100 ng/lL DNA). ...
Article
Maintenance of high levels of genetic diversity is crucial for the recovery of overexploited species and gaining knowledge of genetic diversity of natural populations is crucial to define effective conservation strategies. Spectacled caimans (Caiman crocodilus) were unsustainably exploited for decades in Colombia causing drastic population reductions with unknown effects on genetic structure. We molecularly characterized three spectacled caiman populations from the upper Magdalena River basin (UMRB), analyzing them within the context of the trans-Andean C. c. fuscus sensu stricto lineage, assessing nucleotide and genetic diversity, demographic history, and phylogeography at different scales. Seventeen of the 23 mitochondrial haplotypes currently described for Colombia are present in the UMRB, showing high levels of genetic diversity even when compared with the trans-Andean region (uncorrected genetic distances 0.00-0.87%). Mutational steps between closest haplotypes ranged from one to four while the most differentiated haplotypes were separated by 19 mutational steps across the whole trans-Andean region. Distribution of pairwise nucleotide differences and raggedness tests showed unimodal patterns of mismatch distribution curves fitting the sudden expansion model. Average time since demographic expansion for UMRB, Colombia, and trans-Andean region were inferred as 10,540, 7,591, and 7,071 years before present, respectively, placing the latest expansion close to the Pleistocene-Holocene boundary. Intriguingly, samples from Tolima were overall more related to those collected from Panama and Costa Rica (0.34 ± 0.15%) than the ones collected across Choco (0.45 ± 0.15%), Cauca (0.70 ± 0.09%), and Nariño (0.60 ± 0.14%) departments. We discuss our genetic findings in the context of the management policies carried out in the country during the last decades (unsustainable and sustainable use, and population restocking), evaluating the implications of these events for the genetic integrity and conservation of the species.
... When evaluating the risks of biological invasions and the pathways by which a species has made its way into a new location, it is useful to employ a molecular ecology perspective. By analyzing phylogeographic data from an invasive species' native range, it is possible to trace the genetic origins and assess the levels of genetic diversity in the newly established populations (Avise 2004;Allendorf et al. 2013). When a species is introduced to a new locality, it often undergoes a population bottleneck reducing genetic variation. ...
... Ambiguous bases, contig site disagreements, and low confidence bases were either edited or replaced with an IUPAC ambiguity code. Newly collected sequence data were deposited in GenBank (accession numbers: COI = OR518300-OR518326 and CytB = OR402067-OR402093) and compared with homologous C. crocodilus genes published in the literature and available on GenBank (Farias et al. 2004;Vasconcelos et al. 2006;Venegas-Anaya et al. 2008;Roberto et al. 2020;Hernández-González and Díaz-Moreno 2020;Balaguera-Reina et al. 2020Roberto et al. 2021;Jimenez-Alonso et al. 2023). All sequences were aligned in MAFFT version 7.511 using the iterative refinement method (FFT-NS-I; Katoh et al. 2002). ...
Article
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The US state of Florida is home to an alarmingly large number of invasive species, many of which have proven detrimental to native ecosystems. Biological invasions of reptiles in particular have been a major concern in recent years. The spectacled caiman (Caiman crocodilus) was first introduced from Latin America to Florida in the 1950’s. Given there are now established breeding populations across southern Florida, there are ongoing efforts to control them. Therefore, there is a need to understand this species’ natural history and introduction pathways. Previous studies have cited the Caribbean Coastal region of Colombia as a primary, and possibly exclusive, origin of C. crocodilus in Florida, and the species was identified as belonging to the C. c. fuscus molecular lineage. However, previous genetic sampling has been limited and may have been biased by small sample sizes and limited geographic scale. We collected 27 genetic samples from caimans captured in Florida, and sequenced the mitochondrial genes, Cytochrome oxidase I (COI) and Cytochrome B (CytB) for comparison with homologous gene fragments available for the species at GenBank. We found genetic evidence for multiple introduction events and the taxonomic classification of the Florida caimans as two distinct molecular lineages (C. c. fuscus and C. c. crocodilus) originating from at least two different regions: the Magdalena River Basin in Colombia and the Upper Branco River Basin in northern Brazil. This study helps to elucidate the genetic history of Florida caimans and provides valuable insight for population management of the species in Florida.
... In this context, mitochondrial DNA markers have been shown to be powerful tools to understand phylogenetic and phylogeographic relationships among populations and species (Patwardhan et al. 2014), as well as to infer geographical origins of individuals (Alacs et al. 2010;Ogden and Linacre 2015;Balaguera-Reina et al. 2020a). Most molecular analyses performed on C. crocodilus have used mitochondrial markers as a reference to infer the systematics of the complex (Farias et al. 2004;Vasconcelos et al. 2006;Venegas-Anaya et al. 2008;Balaguera-Reina et al. 2020b, 2022Roberto et al. 2020;Díaz-Moreno et al. 2021), showing their relevance for the understanding of phylogenetic and phylogeographic relationships. ...
... Interestingly, COI was the most diverse of the two genes assessed in this study, which showed the relevance of its inclusion in phylogenetic and phylogeographic analysis. However, this contrasts with other studies sequencing partial COI gene (Venegas-Anaya et al. 2008;Balaguera-Reina et al. 2020bDíaz-Moreno et al. 2021) as well as the low proportion of sequences reported (137) against samples collected (311). We recommend that further studies focus on recovering whole genes, so that data can be used across to inform the actual diversity as well as including COI, so that more thorough analysis can be undertaken regarding the phylogeographic relationship of the spectacled caiman species complex. ...
Article
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Context Spectacled caiman (Caiman crocodilus) is a species complex with at least eight phylogenetic lineages distributed across Central and South America. However, several populations remain unstudied, which limits a clear understanding of the relationship among lineages as well as whether all hidden diversity has been unveiled. Aim We analysed the molecular variation of spectacled caiman populations inhabiting the Colombian Trans-Andean range based on cytochrome oxidase I (COI) and cytochrome B (CytB) mitochondrial markers. Methods We performed phylogenetic and population genetic analysis to identify phylogeographic patterns and verify genetic variation across Trans-Andean spectacled caiman by using a dataset of 78 individuals from 15 localities across Colombia. Results Haplotype accumulation curve estimated that our sample sizes recovered 82.68% of all unique haplotypes. Analysis of molecular variance showed that most of the genetic variation across the Trans-Andean samples collected can be explained by macro basins (49.85%), 32.45% by localities and 17.70% by intra-specific variation within populations. Conclusions Our study confirmed that high nucleotide diversity is present in Colombian Trans-Andean spectacled caiman populations, the absence of a genetically distinguished lineage in the Choco region, as suggested by morphologic analysis, and the presence of only one molecularly well distinguished group (C. c. fuscus sensu stricto) in the in the Colombian Trans-Andean region.
... The classification of C. c. apaporiensis as a subspecies (Medem, 1955) was questioned by Bloor (2013), who suggested it was the same evolutionary significant unit (ESU) as C.c. crocodilus, based on mitochondrial DNA. Recently, Balaguera-Reina et al. (2020), via mitochondrial molecular markers, suggested that C. c. apaporiensis and C. c. crocodilus are the same ESU. However, Escobedo-Galván et al. (2015) analyzed the skull of C. c. apaporiensis and described osteological and morphometric characters that distinguish it from C. c. crocodilus, which warrants further investigation into whether both subspecies should be considered as such. ...
... As in other crocodilians, those differences could be related to geographic distribution and diet (Ayarzagüena, 1984;Muniz et al., 2017;Bittencourt et al., 2019). However, Balaguera-Reina et al. (2020) proposed that C. c. apaporiensis is not a distinct subspecies from C. c. crocodilus, based on mitochondrial DNA. McCurry et al. (2017) analyzed the convergent evolution of longirostrine skulls and found that species with riparian habits eat mostly fish and small prey. ...
Article
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Studies on the biology of Caiman crocodilus have drawn attention to its biology with emphasis on systematic, taxonomy and ecology. However, anatomical aspects, such as skull characteristics, have not been studied in detail throughout its geographic range. In this study the skull characteristics for C. crocodilus subspecies, C. c. fuscus, C. c. chiapasius, C. c. crocodilus, and C. c. apa-poriensis were analyzed using geometric morphometrics and descriptive morphology, including geographic and ontogenetic variation. Variation in skull morphology was found between the subspecies analyzed. Trans-Andean subspecies, C. c. fuscus and C. c. chiapasius, exhibit breviros-trine skulls but they are different in the contact between frontal and nasal bones and the size of the palatine process of the maxilla; therefore, populations in Colombia correspond to C. c. fuscus and, C. c. chiapasus is not distributed in Colombia. Although cis-Andean subspecies, C. c. apaporiensis and C. c. crocodilus, have longirostrine skulls, both subspecies differ in the shape of the skull and in osteological characters; then, adults of C. c. apaporiensis present frontal and nasal in contact and, V-shape maxillary-premaxillary suture; while C. c. crocodilus specimens exhibit a high geographic and ontogenetic variation, supporting the hypotheses that there at least two clades of such subspecies for Colombia. These morphological differences should be considered in future systematics studies and policies on global conservation of the different C. crocodilus subspecies.
... In contrast, Venegas-Anaya et al. (2008) suggested that C. c. chiapasius should be considered a valid subspecies because it is clearly divergent from C. c. fuscus and C. c. crocodilus, although it is almost indistinguishable morphologically from C. c. fuscus, and in their phylogenetic analysis some sequences of these subspecies appear in the same clade. In a more recent study, these subspecies make up separate clades, one corresponding to C. c. chiapasius from Mexico and El Salvador including four haplotypes and another clade corresponding to C. c. fuscus (Balaguera-Reina et al., 2020). Our data show one haplotype shared between C. c. chiapasius and C. c. fuscus, and the species delimitation analysis locates them, with similar probability, as two equal or different species. ...
Article
The genus Caiman is one of the most taxonomically conflicted among crocodilians. Caiman crocodilus has four subspecies: Caiman crocodilus crocodilus, Caiman crocodilus fuscus, Caiman crocodilus chiapasius and Caiman crocodilus apaporiensis, but some studies recognize Caiman yacare as a subspecies of C. crocodilus or as a C. crocodilus–C. yacare complex. In Argentina, Caiman latirostris and C. yacare are present and included in sustainable use programmes, although they have hardly been studied at the genetic level. The present study had two main objectives: (1) to study the genetic diversity, structure and phylogeny of C. yacare and C. latirostris in Argentina; and (2) to perform a phylogenetic analysis of the genus Caiman throughout its entire distribution. The results show high haplotype diversity for both species but low nucleotide diversity for C. latirostris. Phylogenetic analysis shows a clear separation between both species but, surprisingly, a well-differentiated clade belonging to the Chaco region was observed. The phylogenetic analysis exhibited clades made up of the sequences of each Caiman species, with some inconsistencies: in the clade of C. crocodilus, one sequence of C. yacare is included, and one clade is observed including sequences from C. c. fuscus and C. c. chiapasius. These data indicate the need to undertake interdisciplinary studies to clarify the taxonomic status of these crocodilian species.
... as espécies reconhecidas atualmente, além da descrição de várias subespécies, baseados em poucos exemplares e com diferenças mais relacionadas com o formato do crânio (ver COPE, 1868;BOCOURT, 1876;MEDEM, 1955;BALAGUERA-REINA et al., 2020). Com o avanço de técnicas moleculares, a descoberta de diversidade de linhagens crípticas dentro dessas espécies vem sugerindo que o número real de espécies estaria subestimado (ver VENEGAS-ANAYA et al., 2008;BORGES et al., 2018;MUNIZ et al., 2018;BITTENCOURT et al., 2019;ROBERTO et al., 2020). ...
... crocodilus. The Caiman crocodilus/yacare species complex currently comprises Ca. yacare and three subspecies of Ca. crocodilus: Caiman crocodilus crocodilus, Caiman crocodilus chiapasius, and Caiman crocodilus fuscus (Balaguera-Reina et al., 2020). Molecular phylogenetic analyses revealed substantial lineage diversity within this species complex (Venegas-Anaya et al., 2008;Roberto et al., 2020). ...
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The state of Florida has the world's highest diversity of established nonnative reptiles, including snakes, lizards, turtles, and crocodilians, most of them introduced from the pet trade. The Spectacled Caiman (Caiman crocodilus) is the only nonnative crocodilian established in Florida, with the earliest date of introduction in 1950. Despite its likely origin being Colombia, the taxonomic identity of the subspecies occurring in Florida remains unknown. We report the first study that resolves the taxonomic status of the population of Ca. crocodilus in Florida based on molecular analysis of samples collected from the 1970s to 2013. We also investigate the probable origin of this population as well as the specimens of the Dwarf Caimans, Paleosuchus palpebrosus and Paleosuchus trigonatus, which have been collected in Florida. We identified only one lineage of Ca. crocodilus in Florida, corresponding to Caiman crocodilus fuscus, and our results indicate the Magdalena River basin in Colombia as the most likely area of origin. We also correct the identification of Paleosuchus recorded in Florida and identify the Guiana Shield, and specifically Guyana, as the most likely region from which these specimens were introduced.
Thesis
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Caiman crocodilus, comúnmente llamada como ‘’caimán de anteojos o babilla’’, es una especie de aligatórido que se distribuye naturalmente a lo largo del continente americano (desde México hasta Perú y Brasil) con poblaciones introducidas y asentadas en los Estados Unidos (incluyendo Puerto Rico) y Cuba. Esta especie se encuentra actualmente dividida en tres subespecies válidas (C. crocodilus fuscus, C. crocodilus chiapasius y C. crocodilus crocodilus), ya que recientemente se justificó molecularmente la invalidez de C. c. apaporiensis, agrupándola como una variación morfológica de C. c. crocodilus. Posee una arista ocular particularmente notoria en la parte anterior de sus parpados además de otras características morfológicas que la hace fácilmente reconocible y es de importancia comercial a lo largo de su distribución. Pese al reconocimiento de la especie a lo largo del territorio, su estudio se ha centrado en producción, comercio y uso dejando a un lado el estudio de poblaciones silvestres y su interacción e importancia en los hábitats en los que está presente. la presente monografía tiene como objetivo evaluar el estado conocimiento sobre C. crocodilus en Colombia con el fin de comprender de manera efectiva vacíos y prioridades de investigación para su uso y conservación. Para lograr esto se realizó una revisión exhaustiva de bases de datos, herramientas de investigación, páginas web, software y complementariamente se generó un mapa de la distribución actual de la especie. Se recopilaron 198 documentos asociados a la especie divididos en las siguientes categorías: general, aplicación y aprovechamiento, conservación, distribución, ecología y sistemática. La mayoría de la información se asoció a la categoría de aplicación y aprovechamiento. Los resultados indican que la mayoría de los documentos a nivel regional provienen del Caribe, donde se desarrolla en gran medida los procesos de zoocria. Parece ser que el principal interés que genera la especie es su valor comercial lo que hace esencial priorizar los estudios en estado silvestre porque, aunque la especie no se encuentre amenazada, su mal manejo histórico podría estar afectando su conservación.
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Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some kinosternid groups, with the current taxonomy following the nuclear-based results. Herein, based on extended molecular, geographic, and taxonomic sampling, we explore the phylogeographic structure and taxonomic limits for K. leucostomum and the K. scorpioides group and present a fossil-calibrated nuclear time tree for Kinosternon. Our results reveal contrasting differentiation patterns for the K. scorpioides group and K. leucostomum, despite overlapping distributions. Kinosternon leucostomum shows only shallow geographic divergence, whereas the K. scorpioides group is polyphyletic with up to 10 distinct taxa, some of them undescribed. We support the elevation of K. s. albogulare and K. s. cruentatum to species level. Given the deep divergence within the genus Kinosternon, we propose the recognition of three subgenera, Kinosternon, Cryptochelys and Thyrosternum, and the abandonment of the group-based classification, at least for the K. leucostomum and K. scorpioides groups. Our results show an initial split in Kinosternon that gave rise to two main radiations, one Nearctic and one mainly Neotropical. Most speciation events in Kinosternon occurred during the Quaternary and we hypothesize that they were mediated by both climatic and geological events. Additionally, our data imply that at least three South American colonizations occurred, two in the K. leucostomum group, and one in the K. scorpioides group. Additionally, we hypothesize that discordance between mitochondrial and nuclear phylogenetic signal is due to mitochondrial capture from an extinct kinosternine lineage.
Conference Paper
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Caiman is a genus of medium-sized crocodilians, which comprises three officially acknowledged species, native to South and Central America with a wide range of geographical distribution. They have been served for skin demand, meat supply, pet breeding and many other purposes since the 20th century. Thanks to high populations and the wide distribution, the genetic diversity of caimans reveals to be high and the existence of cryptic species in Caiman is questioned due to the lack of data from molecular analysis. All three members within Caiman are not considered to be threatened at the protection level. However, the lack of genetic analysis might challenge this harmony since some species may be divided into multiple new ones due to cryptic species concerns. Hence the old evaluation of populations and protection levels may not be applied to those new ones. Many recent works focusing on genetic diversity and phylogeny analysis in Caiman have demonstrated problems of the underestimated genetic complexity of lineages. This review evaluates publications of the Caiman genus with phylogenetic concerns and compares them to examples of separation of other crocodilian species from last decades to discuss the cryptic species in Caiman and provide outlines for future protective operations.
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Thesis
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Caiman crocodilus is a species of alligator that is distributed throughout the American continent, from the southern United States to the north of Bolivia. It currently has three valid subspecies C. crocodilus fuscus, C. crocodilus chiapasius and C. crocodilus crocodilus, because it was recently described that the subspecies C. crocodilus apaporiensis really is a morphological variation of the subspecies C.c. crocodilus. This species is commonly called as ‘’ spectacled caiman’’ due to the edge that forms in the anterior part of its eyes, in Colombia it is known as ‘’Babilla’’ and is usually recognized in practically all the departments of the country due to its commercial use and its extensive distribution. Despite the recognition of the species throughout the territory, its study focuses on production, trade, and use, leaving aside its study in wild populations and its interaction and importance in the habitats in which it is present, therefore, a bibliographic review is necessary to evaluate the state of knowledge of the species in Colombia and effectively understand the key points for its use and conservation. To achieve this, an exhaustive review of databases, research tools, web pages, software was carried out and a map of the current distribution of the species was generated. 198 documents associated with the species were collected and divided into the following categories: general, application and use, conservation, distribution, ecology and systematics. Most of the information was associated with the category of application and use. The results indicate that most of the documents at the regional level come from the Caribbean, where zoocria processes are largely developed. It seems that the main interest generated by the species is its commercial value which makes it essential to prioritize studies in the wild because, although the species is not threatened, its historical mismanagement could be affecting its conservation.
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There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.
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Chapter
During the late twentieth and early twenty-first centuries, there has been a revolution in evolutionary biology. Traditional methods that had been applied to understanding relationships and natural history for hundreds of years have been supplemented (and sometimes replaced) by biochemical and molecular techniques that now allow us to examine the entire genomes of non-model organisms. Herein we review the use of these new technologies as they apply to crocodylians in general and specifically to the New-World members of the Alligatoridae and Crocodylidae. While generally concordant with traditional analyses, in some cases they have permitted cryptic species to be recognized. In addition, they have allowed crocodylian biologists to detect hybridization events between species, both in captivity and in the wild, that would not have been possible before their use. Hybridization may lead to the formation of new species, but it may also allow a common species to “swamp out” a rarer one. Because there appears to be little hybrid dysgenesis between many of the potential hybridizing forms, hybridization is potentially a serious problem for several New-World species.
Chapter
Biogeography is an area of study dedicated to understanding the evolutionary processes that resulted in current organismal distribution patterns. In general, exclusively terrestrial and exclusively aquatic vertebrates have well-studied and defned biogeographic patterns in the New World, but the biogeography of semiaquatic organisms is still poorly understood. In this chapter we discuss the biogeographic patterns and processes of New-World crocodylians. Although dispersal was probably an important process for the diversifcation of the ancestors of this group, the species/lineages—especially those of the South Americans—have their geographic distributions delimited by natural geographical barriers such as watershed divides, waterfalls and rapids, and captured watersheds, but also ecological specialization and competitive exclusions. The species/lineages occupying these areas show nearly identical divergence times, pointing to common historical processes that drove the evolution and divergence of these species/lineages. Recent studies have shown that widely distributed species have diversifed into a signifcant number of independent evolutionary lineages. Knowing the biogeographic patterns of this group is of fundamental importance for conservation, since in the Anthropocene the effects of changes caused by man are devastating, destroying in a short period of time what nature took thousands/millions of years to build.
Book
This book aims to be a comprehensive review of the literature on the conservation genetics of the New World crocodilians, from the biological and demographical aspects of the living species to the application of molecular techniques for conservation purposes. It covers the current status of the molecular genetics applied to phylogenetics, phylogeography, diversity, kinship and mating system, and hybridization, as well its implications for decision making with regards to the conservation of these species at academic and governmental levels. This book can be used as a guide for graduate and undergraduate students to understand how conservation genetics techniques are carried out and how they can help preserve not only crocodilians but also other living species.
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Caiman crocodilus apaporiensis has been of particular interest because of its clearly differentiated morphotype within the Spectacled Caiman complex. Information on the biology of C. c. apaporiensis is incomplete because of its restricted distribution in the inaccessible middle and upper Apaporis River in Colombia. I undertook an expedition to the middle Apaporis River basin in an attempt to validate the presence of C. c. apaporiensis through observations on morphometry, ecology, and ethnozoology. Previously described skull characteristics were clearly differentiable in both adults and subadults in the region. However, because many individual C. c. apaporiensis that were either captured or visually assessed were relatively small, some skull characteristics more closely resembled the more general C. crocodilus morphotype. Although data on population size and distribution of C. c. apaporiensis remain limited, information gleaned from local inhabitants indicates that the subspecies is common in the middle Apaporis River. Population parameter and molecular phylogeography studies could lead to management practices that would protect the genetic integrity of C. c. apaporiensis by minimizing subspecific interbreeding.
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Caiman crocodilus is an alligatoroid broadly distributed in the neotropics from Mexico to Brazil, where Colombia is the only country that has the complete subspecies complex distributed in its territory. This species has been the focus of many genetic, ecological and morphological studies. However, these studies are limited to traditional morphology methods or have limitations to examine interspecific variation among the four subspecies reported in Colombia. This is the first study of intraspecific variation in the skull of Caiman crocodilus complex distributed in Colombia, using a two-dimensional approach of geometric morphometric on 122 post-hatching ontogenetic cranial series. Morphological differences between species and changes during ontogeny (snout increases its length and, skull roof and orbits decrease their proportions) that represents part of morphological changes in the cranial ontogeny of crocodilians were found. In the morphospace, there was a significant differentiation of C. crocodilus apaporiensis and C. crocodilus crocodilus from C. crocodilus fuscus and C. crocodilus chiapasius. Results from this study revealed that C. crocodilus apaporiensis is a differentiated group from the global complex as well as that the specimens of C. crocodilus chiapasius collected from Medem in Colombia may be showing cryptic morphology in some traits.
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PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
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Biology and Evolution of Crocodylians is a comprehensive review of current knowledge about the world's largest and most famous living reptiles. Gordon Grigg's authoritative and accessible text and David Kirshner's stunning interpretive artwork and colour photographs combine expertly in this contemporary celebration of crocodiles, alligators, caimans and gharials. This book showcases the skills and capabilities that allow crocodylians to live how and where they do. It covers the biology and ecology of the extant species, conservation issues, crocodylian–human interaction and the evolutionary history of the group, and includes a vast amount of new information; 25 per cent of 1100 cited publications have appeared since 2007. Richly illustrated with more than 500 colour photographs and black and white illustrations, this book will be a benchmark reference work for crocodylian biologists, herpetologists and vertebrate biologists for years to come. Winner of the 2015 Whitley Medal.
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To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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Caiman crocodilus and C. yacare are economically valuable species afforded legal protection both within the United States and around the world. While five populations of these species have received formal taxonomic recognition between 1758 and 1955, there has never been an analysis of variation across populations representing the entire range of these species. We examined 13 external morphological characteristics in 360 individuals from known localities distributed throughout the range of these taxa. Using covariance, principal component and discriminant function analyses, we find no defensible basis for the partition of C. crocodilus into subspecies, nor do we feel that considering C. yacare a subspecies of C. crocodilus, as proposed by some, is warranted. The implication of these findings for enforcement of current legislation is discussed.
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A review of crocodylian phylogeny reveals a more complex history than might have been anticipated from a direct reading of the fossil record without consideration of phylogenetic relationships. The three main extant crocodylian lineagesGavialoidea, Alligatoroidea, Crocodyloideaare known from fossils in the Late Cretaceous, and the group is found nearly worldwide during the Cenozoic. Some groups have distributions that are best explained by the crossing of marine barriers during the Tertiary. Early Tertiary crocodylian faunas are phylogenetically composite, and clades tend to be morphologically uniform and geographically widespread. Later in the Tertiary, Old World crocodylian faunas are more endemic. Crocodylian phylogeneticists face numerous challenges, the most important being the phylogenetic relationships and time of divergence of the two living gharials (Gavialis gangeticus and Tomistoma schlegelii), the relationships among living true crocodiles (Crocodylus), and the relationships among caimans.
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Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
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Crocodilians exhibit a spectrum of rostral shape from long snouted (longirostrine), through to short snouted (brevirostrine) morphologies. The proportional length of the mandibular symphysis correlates consistently with rostral shape, forming as much as 50% of the mandible's length in longirostrine forms, but 10% in brevirostrine crocodilians. Here we analyse the structural consequences of an elongate mandibular symphysis in relation to feeding behaviours. Simple beam and high resolution Finite Element (FE) models of seven species of crocodile were analysed under loads simulating biting, shaking and twisting. Using beam theory, we statistically compared multiple hypotheses of which morphological variables should control the biomechanical response. Brevi- and mesorostrine morphologies were found to consistently outperform longirostrine types when subject to equivalent biting, shaking and twisting loads. The best predictors of performance for biting and twisting loads in FE models were overall length and symphyseal length respectively; for shaking loads symphyseal length and a multivariate measurement of shape (PC1- which is strongly but not exclusively correlated with symphyseal length) were equally good predictors. Linear measurements were better predictors than multivariate measurements of shape in biting and twisting loads. For both biting and shaking loads but not for twisting, simple beam models agree with best performance predictors in FE models. Combining beam and FE modelling allows a priori hypotheses about the importance of morphological traits on biomechanics to be statistically tested. Short mandibular symphyses perform well under loads used for feeding upon large prey, but elongate symphyses incur high strains under equivalent loads, underlining the structural constraints to prey size in the longirostrine morphotype. The biomechanics of the crocodilian mandible are largely consistent with beam theory and can be predicted from simple morphological measurements, suggesting that crocodilians are a useful model for investigating the palaeobiomechanics of other aquatic tetrapods.
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The genetic structure of Caiman crocodilus was investigated using a 1085 bp mtDNA fragment of the cytochrome b gene. Inferences were based on 125 individuals from nine localities in Peru, Brazil and French Guiana. With the ex-ception of Mamirauá Lake, Anavilhanas Archipelago and the Tapará Community which show a signal of demo-graphic expansion, the sampled localities are in a mutation-drift genetic equilibrium. Divergence between the Amazon basin and extra-Amazon basin localities is significant; however, inference from Nested Clade Analysis can-not distinguish between continuous range expansion, long distance colonization or past fragmentation; however, past fragmentation is unlikely due to low number of mutational steps separating these two regions. The divergence is probably maintained by the reduced ability of C. crocodilus to cross salt water barriers. Within the Amazon basin, continuous range expansion without isolation-by-distance is the most likely process causing genetic structuring. The observed genetic patterns are compatible with the ecology of C. crocodilus, and history of human exploitation. As commercial hunting depleted more valuable species, C. crocodilus expanded its range and ecological niche, prompt-ing hunters to harvest it. Following a period of intense hunting, C. crocodilus is now experiencing recovery and a sec-ond population expansion especially in protected areas.
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With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/. Keywords: Rapid bootstrap; Graphical user interface; Maximum likelihood; Phylogenetic analyses; Python; RAxML
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Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data.Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.Contact: peter@biomatters.com
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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The Neotropical crocodylian species, Caiman crocodilus, is widely distributed through Mesoamerica, northern South America, and the Amazon basin. Four subspecies are recognized within C. crocodilus, suggesting some geographic variation in morphology. In this study, we utilized mitochondrial DNA (mtDNA) sequence data from 45 individuals of C. crocodilus throughout its range to infer its evolutionary history and population structure, as well as to evaluate genealogical support for subspecies and their geographic distributions. Our molecular phylogenetic results identified five mtDNA haplotype clades with a mean sequence divergence of 3.4%, indicating considerable evolutionary independence among phylogeographic lineages. Our results were also broadly consistent with current subspecific taxonomy, with some important additional findings. First, we found substantial genetic structuring within C. c. fuscus from southern Mesoamerica. Second, though we confirmed the existence of a widespread Amazonian clade, we also discovered a cryptic and divergent mtDNA lineage that was indistinguishable from C. c. crocodilus based on external morphology. Third, we confirm the status of C. c. chiapasius as a distinct evolutionary lineage, and provide evidence that C. c. fuscus may be moving northward and hybridizing with C. c. chiapasius in northern Mesoamerica. Finally, our results parallel previous phylogeographic studies of other organisms that have demonstrated significant genetic structure over shorter geographic distances in Mesoamerica compared with Amazonia. We support conservation efforts for all five independent lineages within C. crocodilus, and highlight the subspecies C. c. chiapasius as a unit of particular conservation concern.
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A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.
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The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes.
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Unlabelled: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. Availability: icwww.epfl.ch/~stamatak
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We analyzed DNA sequences of the mitochondrial cytochrome b gene (cyt b), the nuclear Recombination Activating Gene 1 (RAG1) and the myelocytomatosis oncogene (MYC) to infer the phylogenetic relationship of Caiman crocodilus and Caiman yacare, and other South American alligatorid crocodilian species. Phylogenetic relationships were robustly supported with Paleosuchus sister to Melanosuchus and Caiman. Phylogenetic relationships of C. crocodilus and C. yacare were unclear as these two species share mitochondrial and nuclear haplotypes. Specifically this sharing occurs among specimens of C. yacare and C. crocodilus from the Madeira River drainage. Two potential explanations stand out: secondary contact followed by hybridization, and differentiation along a cline. Current data cannot resolve between these two competing hypotheses. In comparison with C. yacare and C. crocodilus, Paleosuchus trigonatus and Paleosuchus palpebrosus are very well differentiated and also show surprising haplotypic diversity in spite of their phenotypic similarity.
Article
Species discovery methods utilizing coalescent-based approaches are powerful tools for detecting cryptic lineages within morphological conservative groups, thus being an important methodology of integrative taxonomic research. Crocodilians are a classic example of morphologically conserved group where coalescence-based species delimitation analyses resulted in the discovery of cryptic lineages and potentially new species. In this study, we used several single locus species discovery methods to analyze the phylogenetic diversity of the most widespread alligatorid genus of the Neotropics, the genus Caiman. We analyzed 479 specimens representing all named taxa, with the exception of Caiman crocodilus apaporiensis, and known geographic distribution of these taxa. We observed high lineage diversity within the Caiman crocodilus/yacare complex, ranging from 7 to 10 lineages, and three lineages within Caiman latirostris. We also provide a new dated phylogeny for all the delimited lineages. Oligocene and Miocene events triggered the diversification of the major lineages, with latter Pleistocene events influencing the final diversification of the genus. We demonstrate that the discovered lineages within the Caiman complex are compatible with being species and as such are candidates for an integrated taxonomic analysis. However, it is important to highlight that independent of the future recognition of these lineages as species, it is extremely important to protect these cryptic lineages as unique evolutionary entities, many of which are highly threatened by habitat loss from dam construction projects, tailing dam collapses, mining, agriculture and agricultural run-off across all of South America.
Article
Caiman crocodilus apaporiensis has been considered by several authors as an extreme of morphological variation within the Caiman crocodilus complex. Here, we evaluate its position in the Caiman crocodilus complex morphospace using morphological traits from head shape. We examined the holotype and seventeen paratypes of Caiman crocodilus apaporiensis Medem 1955 deposited at the Field Museum of Natural History. We performed multivariate morphometric analyses: principal component analysis (PCA) and discriminant function analysis (DFA), based on 21 cranial traits of of C. c. apaporiensis, C. yacare and the C. crocodilus complex (C. c. chiapasius, C. c. fuscus andC. c. crocodilus). We find a notable separation of C.c. apaporiensis from C. yacare and C. crocodilus complex in the morphospace. We suggest that geographic isolation might have driven this morphological separation from the C. crocodilus complex, but further analysis are necessary to confirm whether these differences are related with genetic differentiation within the complex. In addition, we suggest that environmental heterogeneity might drive the evolution of independent lineages within the C. crocodilus complex.
Chapter
Attempts to assess the natural affinities and evolution of living crocodilians have been difficult and largely contradictory (Kalin, 1955; Steel, 1973; Dowling and Duellman, 1974). Morphological character analysis has been misleading due to the overall conservatism of these reptiles and to the tendencies toward parallelism and convergence of traits that has occurred during their evolution (Langston, 1973). These complications, together with the lack of critical fossils, have made paleontological interpretations extremely difficult (Sill, 1968; Hecht and Malone, 1972; Langston, 1973; Buffetaut, 1979). Because of such problems and the small number of living species, morphoclines are rare, further complicating the efforts of the comparative morphologist (Hecht and Malone, 1972).
Article
Both extinct and extant crocodilians have repeatedly diversified in skull shape along a continuum, from narrow-snouted to broad-snouted phenotypes. These patterns occur with striking regularity, although it is currently unknown whether these trends also apply to microevolutionary divergence during population differentiation or the early stages of speciation. Assessing patterns of intraspecific variation within a single taxon can potentially provide insight into the processes of macroevolutionary differentiation. For example, high levels of intraspecific variation along a narrow-broad axis would be consistent with the view that cranial shapes can show predictable patterns of differentiation on relatively short timescales, and potentially scale up to explain broader macroevolutionary patterns. In the present study, we use geometric morphometric methods to characterize intraspecific cranial shape variation among groups within a single, widely distributed clade, Caiman crocodilus. We show that C. crocodilus skulls vary along a narrow/broad-snouted continuum, with different subspecies strongly clustered at distinct ends of the continuum. We quantitatively compare these microevolutionary trends with patterns of diversity at macroevolutionary scales (among all extant crocodilians). We find that morphological differences among the subspecies of C. crocodilus parallel the patterns of morphological differentiation across extant crocodilians, with the primary axes of morphological diversity being highly correlated across the two scales. We find intraspecific cranial shape variation within C. crocodilus to span variation characterized by more than half of living species. We show the main axis of intraspecific phenotypic variation to align with the principal direction of macroevolutionary diversification in crocodilian cranial shape, suggesting that mechanisms of microevolutionary divergence within species may also explain broader patterns of diversification at higher taxonomic levels.
Article
Alligatoroidea, a stem-based group including living alligators and caimans and all taxa closer to them than to Crocodylus or Gavialis, includes seven living species and a large diversity of extinct taxa extending back to the Campanian (Late Cretaceous). Parsimony analysis of 164 discrete morphological characters supports several previous hypotheses based on morphology and molecules: Diplocynodon, from the European Tertiary, is a monophyletic alligatoroid lineage; Brachychampsa and Stangerochampsa are derived alligatoroid taxa but not demonstrably within the crown-group Alligatoridae; and, within the crown-group, caimans form a robust clade. However, this study indicates the paraphyly of “Allognathosuchus;” the alligatoroid affinities of Leidyosuchus canadensL but not of most other “Leidyosuchus;” the very distant relationship between Hylaeochampsa and any extant crocodylian lineage, including Alligatoroidea; and the fact that Diplocynodon must extend at least as far as the Campanian, even though the oldest well-known Diplocynodon are from the Eocene. This work supports a close relationship between Diplocynodon and Baryphracta deponiae from the Eocene of Germany; monophyly of Alligator and the caiman assemblage as currently applied in the literature; the caiman affinities of the bizarre nettosuchids and Purussaurus; and a closer relationship between Caiman latirostris and Melanosuchus niger than between C. latirostris and other Caiman. Phylogenetic taxonomic principles have been applied to Crocodylia by several workers, and this study expands upon this with a discussion of phylogeny-based name definitions for Crocodylia and nested subgroups. Leidyosuchus is the basalmost alligatoroid, but within its sister taxon we can recognize a pair of stem-based groups—Diplocynodontinae (Diplocynodon rateili and all taxa closer to it than to Alligator mississippiensis) and Globidonta (Alligator mississippiensis and all taxa closer to it than to Diplocynodon rateili). The crown-group Alligatoridae (last common ancestor of Alligator, Caiman, Melanosuchus, and Paleosuchus and all of its descendents) can likewise be split into a pair of stem-based daughter lineages: Alligatorinae (Alligator and taxa closer to it than to Caiman) and Caimaninae (Caiman and taxa closer to it than to Alligator). Salt intolerance has been used by previous authors to force alligatorid dispersal along land bridges. Despite the problem of inappropriate climate, a land crossing across Beringia during the Late Tertiary best explains the current existence of an Asiatic alligatorid (Alligator sinensis), but based on known fossil occurrences, caimans and alligators diverged from each other in North America sometime during the Late Cretaceous and spread to South America by the Paleocene, when North and South America were separated. A single dispersal event at or near the Cretaceous-Tertiary Boundary is sufficient to explain the presence of caimans in South America, with a reinvasion from South America explaining the presence of a nettosuchid in the North American Eocene (Orthogenysuchus).
Article
We used the mitochondrial cytochrome b gene to study the population genetic structure of Melanosuchus niger (Brazil: Negro and Purus Rivers, Lake Janauacá; French Guiana: Kaw River swamps), and Caiman crocodilus (Brazil: Purus River, Lake Janauacá; French Guiana: Kaw River swamps). We found 10 haplotypes in M. niger and 9 haplotypes in C. crocodilus. Nested clade analysis indicated that isolation-by-distance was an important population dynamic in M. niger, but was unable to differentiate between isolation-by-distance, historical fragmentation or range expansion in C. crocodilus. Fu's Fs statistic supported the hypothesis of a demographic expansion in one out of four and two out of three sampled localities of M. niger and C. crocodilus, respectively. Populations of M. niger in central Amazonia also appeared to show differentiation that was correlated with water type. These results are compatible with the life-style of these two crocodilians; C. crocodilus is a habitat generalist and appears to disperse rapidly to newly available habitats, while M. niger is a more sedentary habitat specialist. Both species appear to be recovering from unregulated over-harvesting, however, their responses are life-history and, potentially, ecologically-dependent.
Article
A simple and rapid method for determining nucleotide sequences in single-stranded DNA by primed synthesis with DNA polymerase is described. It depends on the use of Escherichia coli DNA polymerase I and DNA polymerase from bacteriophage T4 under conditions of different limiting nucleoside triphosphates and concurrent fractionation of the products according to size by ionophoresis on acrylamide gels. The method was used to determine two sequences in bacteriophage φX174 DNA using the synthetic decanucleotide A-G-A-A-A-T-A-A-A-A and a restriction enzyme digestion product as primers.
Article
Excerpt The discovery of specific restriction endonucleases (Smith and Wilcox 1970) made possible the isolation of discrete molecular fragments of naturally occurring DNA for the first time. This capability was crucial to the development of molecular cloning (Cohen et al. 1973); and the combination of molecular cloning and endonuclease restriction allowed the synthesis and isolation of any naturally occurring DNA sequence that could be cloned into a useful vector and, on the basis of flanking restriction sites, excised from it. The availability of a large variety of restriction enzymes (Roberts 1985) has significantly extended the utility of these methods. The de novo organic synthesis of oligonucleotides and the development of methods for their assembly into long double-stranded DNA molecules (Davies and Gassen 1983) have removed, at least theoretically, the minor limitations imposed by the availability of natural sequences with fortuitously unique flanking restriction sites. However, de novo synthesis, even with automated...
Article
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
Ve l a s c o A . 2 0 1 9 . Caiman crocodilus. The IUCN Red List of
B a l a g u e r a -R e i n a S A, Ve l a s c o A. 2 0 1 9. Caiman crocodilus. The IUCN Red List of Threatened Species 2019: e.T46584A3009688. Available at: https://dx.doi.org/10.2305/ IUCN.UK.2019-1.RLTS.T46584A3009688.en. Downloaded 27 March 2020.
  • R E Green
  • E L Braun
  • Armstrong J Earl
  • D Nguyen
  • N Hickey
  • G Vandewege
  • M W John
  • J A Capella-Gutiérrez
  • S Castoe
  • T A Kern
  • C Fujita
  • M K Opazo
  • J C Jurka
  • J Kojima
  • K K Caballero
  • J Hubley
  • R M Smit
  • A F Platt
  • R N Lavoie
  • C A Ramakodi
  • M P Finger
  • J W Suh
  • A Isberg
  • S R Miles
  • L Chong
  • A Y Jaratlerdsiri
  • W Gongora
  • J Moran
  • C Iriarte
  • A Mccormack
  • J Burgess
  • S C Edwards
  • S V Lyons
  • E Williams
  • C Breen
  • M Howard
  • J T Gresham
  • C R Peterson
  • D G Schmitz
  • J Pollock
  • D D Haussler
  • D Triplett
  • E W Zhang
  • G Irie
  • N Jarvis
  • E D Brochu
  • C A Schmidt
  • C J Mccarthy
  • F M Faircloth
  • B F Hoffmann
  • F G Glenn
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