Closure Of Isthmus Research Articles

Global phylogeography of ridley sea turtles (Lepidochelys spp.): evolution, demography, connectivity, and conservation

Globally distributed marine taxa are well suited for investigations of biogeographic impacts on genetic diversity, connectivity, and population demography. The sea turtle genus Lepidochelys includes the wide-ranging and abundant olive ridley (L. olivacea), and the geographically restricted and ‘Critically Endangered’ Kemp’s ridley (L. kempii). To investigate their historical biogeography, we analyzed a large dataset of mitochondrial DNA (mtDNA) sequences from olive (n = 943) and Kemp’s (n = 287) ridleys, and genotyped 15 nuclear microsatellite loci in a global sample of olive ridleys (n = 285). We found that the ridley species split ~ 7.5 million years ago, before the Panama Isthmus closure. The most ancient mitochondrial olive ridley lineage, located in the Indian Ocean, was dated to ~ 2.2 Mya. Both mitochondrial and nuclear markers revealed significant structure for olive ridleys between Atlantic (ATL), East Pacific (EP), and Indo-West Pacific (IWP) areas. However, the divergence of mtDNA clades was very recent (< 1 Mya) with low within- clade diversity, supporting a recurrent extinction-recolonization model for these ocean regions. All data showed that ATL and IWP groups were more closely related than those in the EP, with mtDNA data supporting recent recolonization of the ATL from the IWP. Individual olive ridley dispersal between the ATL, EP, and IN/IWP could be interpreted as more male- than female-biased, and genetic diversity was lowest in the Atlantic Ocean. All populations showed signs of recent expansion, and estimated time frames were concordant with their recent colonization history. Investigating species abundance and distribution changes over time is central to evolutionary biology, and this study provides a historical biogeographic context for marine vertebrate conservation and management.

Paleoclimatic and palaeoceanographic changes coupled to the Panama Isthmus closing (13–4 Ma) using organic proxies

This study reconstructs the climatic and oceanographic changes from 13 to 4 Ma at Ocean Drilling Program (ODP) Sites 999 (Caribbean) and 1241 (East Pacific) during Panama Isthmus closure. We used lipid biomarkers as marine production indicators and organic proxies (U37K´ and TEX86H) to estimate ocean surface and thermocline temperatures. Enhanced terrestrial input during the first 3 Ma of the record, possibly coupled to tectonic processes, may have triggered higher surface productivity at both sides of the Isthmus. Even though marine production is generally higher in the tropical Pacific, a peak in alkenone production at 12.4–10.6 Ma indicates unrestricted inflow of nutrient-rich waters into the Caribbean. Higher production is observed during the global late Miocene biogenic bloom (LMBB 8–4.5 Ma) coupled to enhanced nutrients from terrestrial sources and/or upwelling. We find a good correspondence between U37K´ and modern sea surface temperature (SST). The TEX86H is a good tracer for thermocline values, however, the deeper Thaumarchaeota distribution in the Caribbean may result in an underestimation of absolute temperatures at ODP Site 999. None the less, temperature records at both Sites show similar trends coupled to global climate dynamics, therefore Isthmus build up did not significantly affect surface or thermocline temperatures at a regional level. Globally reported decreasing temperatures during the late Miocene and early Pliocene coupled to decreasing CO2 levels are registered at both Sites down to at least 200 m. The late Miocene warm period (LMWP 9.5–7 Ma), late Miocene cold period (LMC 7–5.4 Ma) and the Pliocene warm period (PWP 4–3.5 Ma) are reflected by our temperature records confirming global climate is the main driver of temperature evolution in the study area. The reconstructed temperatures are mainly coupled to atmospheric forcing in the Caribbean, with a deviation possibly due to inflow of colder Pacific intermediate waters. While at ODP Site 1241 temperatures are mainly controlled by global climate, the Site also reflects changes in the water column as it migrates interacting with the complex current structure of the tropical Pacific. Decoupled temperature patterns at both Sites are related with differential changes in water column structure partially masking the climatic signal. Therefore, we could establish that while tectonic processes and related terrestrial input increases as well as upwelling control production and water column structure, climate in the study area remained tuned to global patterns regardless of Isthmus closure stage.

Evolution of andrenine bees reveals a long and complex history of faunal interchanges through the Americas during the Mesozoic and Cenozoic

Bees are presumed to have arisen in the early to mid-Cretaceous coincident with the fragmentation of the southern continents and concurrently with the early diversification of the flowering plants. Here, we apply DNA sequences from multiple genes to recover a dated phylogeny and historical biogeographic of andrenine bees, a large group of 3000 species mainly distributed in arid areas of North America, South America, and the Palearctic region. Our results corroborate the monophyly of Andreninae and points toward a South America origin for the group during the Late Cretaceous. Overall, we provide strong evidence of amphitropical distributional pattern currently observed in the American continent as result of faunal interchange in at least three historical periods, much prior to the Panama Isthmus closure. The Palearctic diversity is shown to have arisen from North America during the Eocene and Miocene, and the Afrotropical lineages likely originated from the Palearctic region in the Miocene when the Sahara Desert was mostly vegetated. The incursions from South to North America and then onto the Old World are chronological congruent with periods when open-vegetation habitats were available for trans-continental dispersal and at the times when aridification and temperature decline offered favorable circumstances for bee diversification.

Phylogeographic structuring of the amphidromous shrimp Atya scabra (Crustacea, Decapoda, Atyidae) unveiled by range-wide mitochondrial DNA sampling

Species with biological traits favourable to long-distance marine larval dispersal might show a phylogeographic structuring over broad regions, even when they are genetically connected within smaller scales. Here, we evaluated this hypothesis by using the widespread amphidromous shrimp Atya scabra, predicting a genetic discontinuity across biogeographical barriers throughout the Western Gulf of Mexico (WGM), Caribbean Sea (CS), south-western Atlantic (SWA) and eastern Atlantic (EA). Using cytochrome oxidase subunit 1 (COI) and 16S ribosomal unit (16S) gene fragments, we did a phylogeographic assessment and genetic characterisation with Bayesian clustering, AMOVA, haplotype networks and demographic analyses. As predicted, three discrete genetic groups, corresponding to the regions WGM, CS and EA, were uncovered by COI, as well an unpredicted SWA+CS group. The 16S fragment detected a low genetic variation, probably owing to a recent lineage differentiation, which was estimated by the COI molecular clock. We evaluated the role of the biological traits of A. scabra, as well as the consequences of Panama Isthmus closure and Pleistocene glaciation cycles in the lineage isolation of WGM and EA, as well as the genetic connectivity shown within regions and between CS and SWA. Our results highlighted that amphidromous species genetically connected over large scales should be genetically characterised in their wide distribution to provide more comprehensive systematics and to assist decision-making in biological conservation.

Time calibrated tree of Dioscorea (Dioscoreaceae) indicates four origins of yams in the Neotropics since the Eocene

The yam genus Dioscorea comprises circa 650 species of tropical vines with starch rich tubers, usefull as energy source and prospection of secondary metabolites. The Neotropical Region holds the highest diversity of species and morphology of yams. We generated a time-calibrated tree for Dioscorea using, for the first time, a dense sampling of Neotropical species to trace the biogeography of these plants in this region. Four origins of Dioscorea in the neotropics were estimated since Eocene. The two most diverse lineages originated between Eocene and Oligocene,respectively in Southern Andes and eastern South America.They occupied the South American Dry Diagonal after the Miocene, but clade II remained associated to forest habitats. Several exchanges between Dry Diagonal and adjacent forested biomes occurred, corroborating the interchange between these vegetation types. Dispersals to Central America occurred before the closure of the Panama Isthmus by long distance dispersal. We highlight two important events of long distance dispersal, the colonization of Central American before the closure of Isthmus of Panama and the dispersal of D. antally lineage to Madagascar. In addition, our phylogenetic tree evidenced the unnatural nature of the classical infrageneric classification of Dioscorea. The taxonomic implications of our results is also discussed.

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus.

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

Patterns of divergence in fish species separated by the Isthmus of Panama

BackgroundThe Pleistocene closure of Isthmus of Panama, separating the basins of the Eastern Pacific and the Caribbean Sea, created a unique natural experiment that reveals how marine faunas respond to environmental change. To explore how fishes have been affected by this tectonic event, I compare transisthmian patterns in phylogeny and morphology for geminate lineages in two families, Eleotridae (sleepers) and Apogonidae (cardinalfishes).ResultsTime-calibrated phylogenies for these families show different diversification patterns. In Eleotridae, several independent shallow instances of transisthmian divergences occur, with one or a few species on either side of the Isthmus. Among Apogonidae, a single clade of Eastern Pacific species is nested within a broad Caribbean radiation that also includes a species known from the Mediterranean. Divergence time estimates for taxa isolated by closure of the Isthmus are broadly congruent. Hypotheses dated with deeper, fossil-based legacy calibrations put the divergences in the Miocene at 7.4–15.1 Ma, while those estimated with a shallow biogeographic calibration of final Isthmus closure range from 5.1 to 9.9 Ma, in the late Miocene/early Pliocene. Eleotridae are more euryhaline than Apogonidae, but do not exhibit shallower transisthmian divergences. In both families, descendent lineages on either side of the Isthmus of Panama exhibit significant shape differences, although that distinction disappears for Apogonidae when I apply a correction for phylogenetic relationships. To evaluate the tempo and mode of continuous character evolution, I fit several single and multiple rate evolutionary models to morphometric data reconstructed on the Apogonidae phylogeny. I find that the most highly favored model, as estimated on both legacy and isthmus calibrated hypotheses, is a multiple rate Ornstein-Uhlbeck model, with a mosaic of rate shifts postulated for shape changes among fishes in the Caribbean and Eastern Pacific.ConclusionsAlthough many transisthmian taxa have been compared and their phylogenies calibrated to estimate the dates associated with population sundering, few studies correlate these timing estimates with morphological change. I show that in transisthmian fish lineages, morphometric distinctions are detectable across the Isthmus, and that rates and patterns of shape change have also shifted, with variable manifestations across the body and between the Caribbean and Eastern Pacific.

The Calibrated Phylogeny of the Drosophila fasciola Subgroup (D. repleta Group Wasserman) Indicates Neogene Diversification of Its Internal Branches.

The species of the Drosophila fasciola subgroup Wasserman represent the dominant section of the Drosophila repleta group Wasserman in the American rainforests and have a broad geographical distribution in the New World. However, despite of its wide range, the D. fasciola subgroup is one of the most overlooked D. repleta subgroups. Here, we report a molecular phylogenetic analysis focused on the D. fasciola subgroup using two mitochondrial [cytochrome oxidase subunit I (COI), cytochrome oxidase subunit II (COII)] and two nuclear [elongation factor-1alpha F1 (EF-alphaF1) and transformer (tra)] genes. Overall, we found that this subgroup is a monophyletic taxon, subdivided into two main internal branches: named Fas1 and Fas2 clades. The diversification of these clades is estimated to have begun in the middle Miocene, around 12Ma [95% high posterior density (HPD) 9.0-15Ma], and might be associated with the colonization of South America by Central America populations after the closure of Isthmus of Panama due to the temporal congruence between these events. The terminal branches had their origins estimated to be in the Pliocene or the Plio-Pleistocene transition. For the later estimates, both the geomorphological influences and the climatic oscillations of the Pleistocene may have played a role in shaping the diversification of the D. fasciola group.

The palaeobiogeography of South American gomphotheres

Gomphotheriid proboscideans reached South America as Late Cenozoic immigrants from North America. However, disagreements over alpha taxonomy, age dating and phylogenetic relationships have produced three competing hypotheses about this immigration: (1) a single gomphothere immigration took place soon after the ~3Ma closure of the Panamanian isthmus; (2) two separate gomphothere immigrations took place after closure of the isthmus; or (3) an earlier, Late Miocene (before 9Ma) immigration brought gomphotheres into South America. A critical re-evaluation of the alpha taxonomy, age dating and phylogenetic relationships of Neotropical gomphotheres identifies two valid genera of South American gomphotheres, Cuvieronius and Notiomastodon (= “Haplomastodon”, = “Stegomastodon” from South America) and recognizes “Amahuacatherium” as an invalid genus likely based on a specimen of Notiomastodon. The oldest well-dated South American gomphothere fossil is Marplatan, ~2.5Ma, from Argentina. The case for an age of “Amahuacatherium” older than 9Ma is refuted by mammalian biostratigraphy and a re-evaluation of the relevant magnetostratigraphy. North American Rhynchotherium descended from Gomphotherium during the Late Hemphillian (~5–6Ma) and gave rise to Cuvieronius in North America by the end of the Blancan (~2Ma) time. Notiomastodon evolved from Cuvieronius in South America during the Pleistocene. The case for a close relationship between the Neotropical gomphotheres and Sinomastodon from China is rejected. Central America was not a center of endemic gomphothere evolution and merely acted as a pathway for the immigration of gomphotheres from north to south: Gomphotherium into Central America during the Miocene, Cuvieronius to Central America by Early Pleistocene time and on to South America. After closure of the Panamanian isthmus, Cuvieronius immigrated to South America, where it gave rise to Notiomastodon by Middle Pleistocene time. The South American history of gomphotheres was thus a modest evolutionary diversification from a single Plio-Pleistocene immigration.

Evidence for middle Eocene and younger land emergence in central Panama: Implications for Isthmus closure

The rise of the Isthmus of Panama, linked to a number of climatic, paleoceanographic, and biological events, has been studied mostly from indirect, often distal, geochemical and biotic evidence. We have upgraded existing geologic mapping in central Panama with more than 2000 field stations, over 40 petrographic analyses, and more than 30 new geochronological and thermochronological analyses. This data set suggests that the isthmus was an uninterrupted chain above sea level from late Eocene until at least late Miocene times. The basement complex of central Panama is a folded-faulted, ∼3-km-thick arc sequence, intruded by granitoid bodies and onlapped by mildly deformed upper Eocene and Oligocene strata. Six U/Pb zircon ages in the granitoids–along with published geochronological data—reveal intense late Paleocene to middle Eocene magmatism (58–39 Ma), a temporary cessation of magmatic activity between 38 and 27 Ma, and renewed magmatism between 25 and 15 Ma in a position ∼75 km south of the former magmatic axis. Thermochronological analyses in zircon (eight U-Th/He ages), and in apatite crystals (four U-Th/He ages and nine fission-track ages) obtained from a subset of 58–54 Ma granitoid bodies record a concordant Lutetian-age (47–42 Ma) cooling from ∼200 °C to ∼70 °C in ∼5 m.y., and cooling below ∼40 °C between 12 and 9 Ma. Cooling is linked to exhumation by an angular unconformity that separates the deformed basement complex below from mildly deformed, upper Eocene to Oligocene terrestrial to shallow-marine strata above. Exhumation and erosion of the basement complex are independently confirmed by lower Miocene strata that have a detrital zircon signature that closely follows the central Panama basement complex age distribution. These results greatly restrict the width and depth of the strait separating southern Central America from South America, and challenge the widely accepted notion that the Central American Seaway closed in late Pliocene time, when the ice age began.

The Yucatan peninsula: biogeographical history 65 million years in the making

The fourth biennial meeting of the International Biogeography Society (IBS) in Merida, Yucatan in January 2009 represented a double opportunity for Mexican biologists. First, it fostered the integration of the large community of Mexican biogeographers with the activities of the IBS. Second, the meeting allowed us to welcome a large number of delegates from distant parts of the world who were able to visit what has been considered an obligate destination for nature lovers and cultural tourists alike: the Yucatan peninsula. As Edward O. Wilson pointed out, besides economic power every country has two additional and important types of wealth: cultural and natural. Cultural richness is a naturally embedded component of the Mexican way of life.

Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species

Eurythoe complanata (Pallas 1766) has been considered a cosmopolitan species with a great morpholog- ical similarity across its geographic range. To elucidate whether E. complanata is actually a single species, genetic (cytochrome oxidase subunit I and allozymes) and morpho- logical diVerences were compared among specimens from the PaciWc, Caribbean, and South Atlantic Oceans. Large levels of COI divergence (10-22%) and diagnostic allo- zyme loci identiWed three cryptic species: one in the eastern PaciWc and two in the Atlantic, with one being morphologi- cally diVerentiated and found only in islands. COI sequences between PaciWc and Atlantic lineages were much more divergent than those of other transisthmian inverte- brates, indicating their split before the Panama Isthmus closure or a faster evolutionary rate of COI for this species. The existence of two Atlantic species may be a conse- quence of parapatric speciation followed by a secondary invasion or even a sympatric speciation in the Atlantic oce- anic islands.

Tropical Transpacific Shore Fishes

Tropical Transpacific Shore Fishes

Closure of the Central American Isthmus and its effect on deep-water formation in the North Atlantic

Modern ocean thermohaline-driven circulation influences global climate by transporting heat to high latitudes1,2 and by affecting the exchange of CO2 between ocean and atmosphere3. North Atlantic Deep Water (NADW) plays a key role in this circulation, and Quaternary climate cycles have been linked to changes in NADW flow4. General circulation model simulations indicate that before closure, some 3–4 million years ago, of the Central American Isthmus—the narrow strip of land linking North and South America—the direct flow of low-salinity water from the Pacific to the Atlantic Ocean would have led to a smaller NADW flow5,6. Sedimentation patterns7 and nutrient proxies8–11 support these model results by indicating an increase in NADW flow around the time of isthmus closure, but these records do not allow changes in different NADW sources to be distinguished, and the overall effect of closure on global ocean circulation is poorly known. Here we present Nd, Pb and Sr isotope records preserved by a hydrogenous ferromanganese crust from the NADW flow-path in the western North Atlantic Ocean. These records indicate that the isotopic signal associated with NADW strengthened around 3–4 million years ago showing that deep water that formed in the Labrador Sea made a gradually increasing contribution to NADW flow. These data, taken together with those from the central Pacific Ocean12, indicate an increased NADW flow since isthmus closure, and suggest that the closure established today's general pattern of ocean circulation.

Paleoclimatic response of the closing of the Isthmus of Panama in a coupled ocean‐atmosphere model

The paleoclimatic effects of the closure of the Isthmus of Panama ∼3 Ma are investigated using a coupled atmosphere‐ocean model. Consistent with earlier ocean‐only modelling studies, it is shown that prior to closure there is an absence of deep water formation in the North Atlantic. Hence there is a reduction in oceanic heat transport. This is largely compensated for by the atmosphere such that only small changes in total planetary heat transport occur. The model climate of the North Atlantic is significantly warmer after Isthmus closure. In addition, the regions surrounding the Pacific Ocean and South Atlantic are generally cooler while the Indian Ocean is generally warmer in the model present‐day climate. Finally, possible relationships to glaciation and initiation of northern hemisphere glacial cycles are discussed.

Equatorial Pacific sea surface temperatures, faunal patterns, and carbonate burial during the Pliocene

A high-resolution record of radiolarian faunal abundances from the eastern equatorial Pacific is compared to records of carbonate and noncarbonate burial to examine the evolution of eastern tropical Pacific climate processes during the Pliocene. These data provide a means to evaluate the sensitivity of the equatorial Pacific to the onset of Northern Hemisphere glaciation around 2.8−2.5 Ma, to the closure of the Isthmus of Panama around 4.4−3.2 Ma, and to orogeny-related weathering changes before 4.0 Ma. Radiolarian faunal assemblages and sea surface temperature (SST) estimates indicate a gradual cooling from early to late Pliocene, but no significant changes occur near the onset of northern hemisphere glaciation. Records of carbonate and noncarbonate mass accumulation show a long term decrease from the Miocene/Pliocene boundary to the upper Pliocene. Greater carbonate burial in the early Pliocene relative to the late Pliocene parallels a gradual cooling from early to late Pliocene, and may reflect changes related to Isthmus closure or widespread orogeny. No significant time domain changes are seen in the eastern equatorial Pacific that could be related to the onset of Northern Hemisphere glaciation. Evolutive spectral analyses of these equatorial Pacific climate parameters indicate that variance in SST and seasonality commonly concentrate at frequencies not linearly related to orbital variations. Furthermore, cross spectral comparisons with a high resolution benthic δ 18O record indicate that the surface ocean and carbonate flux share little coherent variance with high latitude climate processes during the Pliocene. Given the high degree of chronostratigraphic control in these records, these results suggest that Milankovitch-band surface ocean processes as well as carbonate burial in the equatorial Pacific are decoupled from high latitude climate processes during the Pliocene.