Molecular phylogenies and historical biogeography of a circumtropical group of gastropods (Genus: Nerita): Implications for regional diversity patterns in the marine tropics

Abstract.This paper investigates the role of heterogeneity and speciation/extinction history in explaining variation in regional scale (c. 0.1–3000 km2) plant diversity in the Cape Floristic Region of south‐western Africa, a species‐ and endemic‐rich biogeographical region. We used species‐area analysis and analysis of covariance to investigate geographical (east vs. west) and topographic (lowland vs. montane) patterns of diversity. We used community diversity as a surrogate for biological heterogeneity, and the diversity of naturally rare species in quarter degree squares as an indicator of differences in speciation/extinction histories across the study region. We then used standard statistical methods to analyse geographical and topographic patterns of these two measures. There was a clear geographical diversity pattern (richer in the west), while a topographic pattern (richer in mountains) was evident only in the west. The geographical boundary coincided with a transition from the reliable winter‐rainfall zone (west) to the less reliable non‐seasonal rainfall zone (east). Community diversity, or biological heterogeneity, showed no significant variation in relation to geography and topography. Diversity patterns of rare species mirrored the diversity pattern for all species. We hypothesize that regional diversity patterns are the product of different speciation and extinction histories, leading to different steady‐state diversities. Greater Pleistocene climatic stability in the west would have resulted in higher rates of speciation and lower rates of extinction than in the east, where for the most, Pleistocene climates would not have favoured Cape lineages. A more parsimonious hypothesis is that the more predictable seasonal rainfall of the west would have favoured non‐sprouting plants and that this, in turn, resulted in higher speciation and lower extinction rates. Both hypotheses are consistent with the higher incidence of rare species in the west, and higher levels of beta and gamma diversity there, associated with the turnover of species along environmental and geographical gradients, respectively. These rare species do not contribute to community patterns; hence, biological heterogeneity is uniform across the region. The weak topography pattern of diversity in the west arises from higher speciation rates and lower extinction rates in the topographically complex mountains, rather than from the influence of environmental heterogeneity on diversity.

ObjectivesThis study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity.Materials and methodsLineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification.ResultsRate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages.ConclusionsRecent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.

Estimates of diversification rates are invaluable for many macroevolutionary studies. Recently, an approach called BAMM (Bayesian Analysis of Macro-evolutionary Mixtures) has become widely used for estimating diversification rates and rate shifts. At the same time, several articles have concluded that estimates of net diversification rates from the method-of-moments (MS) estimators are inaccurate. Yet, no studies have compared the ability of these two methods to accurately estimate clade diversification rates. Here, we use simulations to compare their performance. We found that BAMM yielded relatively weak relationships between true and estimated diversification rates. This occurred because BAMM underestimated the number of rates shifts across each tree, and assigned high rates to small clades with low rates. Errors in both speciation and extinction rates contributed to these errors, showing that using BAMM to estimate only speciation rates is also problematic. In contrast, the MS estimators (particularly using stem group ages), yielded stronger relationships between true and estimated diversification rates, by roughly twofold. Furthermore, the MS approach remained relatively accurate when diversification rates were heterogeneous within clades, despite the widespread assumption that it requires constant rates within clades. Overall, we caution that BAMM may be problematic for estimating diversification rates and rate shifts.

The present study aimed to assess the consequences of tectonic events and temperature regime on the diversification of Indo-West Pacific (IWP) turban shell species. Bayesian and parsimony methods were used to construct a phylogenetic hypothesis using sequence data from three genes for the turban shell genus Turbo and for a larger data set including representatives of all known genera in the subfamily Turbininae. Phylogenetic analyses indicate that all IWP Turbo species form a single clade approximately 68 Myr in age, predating the closure of the Tethys Sea and therefore predating the physical separation of the IWP from other biogeographical regions. All but one of the IWP subgenera tested in Turbo also predate the closure of the Tethys Sea. Fossil evidence for Marmarostoma, the largest subgenus, confirms that at least some Turbo lineages currently restricted to the IWP were previously more widespread. The combination of the phylogeny with the fossil evidence suggests that present day diversity in IWP Turbo is the result of the evolutionary persistence within the IWP of several, morphologically distinct lineages, some of which were more widespread in the Oligocene. Some IWP lineages show significant increases in diversification in the early Miocene, probably as a result of the increased availability of both shallow-water habitats due to tectonic plate movements and increased carbonate platforms in the central IWP resulting from coincident diversification of zooxanthellate corals. The IWP is therefore behaving as both a cradle of diversity (with new species originating in situ) and a museum of diversity (with lineages that predate its isolation also being maintained). Bayesian and parsimony analyses of the subfamily recovered five clades and mapping the temperature regime (tropical or temperate) of each species onto the molecular tree using parsimony suggested that temperate habitat is an ancestral character in at least four of the clades. This result was also supported by Bayesian reconstruction of ancestral states. Astralium (the fifth clade) may also prove to have a temperate origin, but this could not be determined with certainty given the available data. The origin of diversity in tropical regions is of particular interest because it has been suggested that the tropics are the source of many evolutionary novelties and have provided a species pool, from which temperate regions were populated. The present study suggests that Turbininae may be an exception to this rule. The tree shape also suggests that temperature has had an effect on speciation rates; temperate Turbininae are apparently evolving more slowly or suffering more extinction than their tropical sister clades, which show greater diversity.

In situ radiation explains the frequency of dioecious palms on islands.

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central “East Indies Triangle” of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.

Author SummaryWhy are there more species in the tropics? This question has fascinated ecologists and evolutionary biologists for decades, generating hundreds of hypotheses, yet basic questions remain: Are rates of speciation higher in the tropics? Are rates of extinction higher in temperate regions? Do the tropics act as a source of diversity for temperate regions? We estimated rates of speciation, extinction, and range expansion associated with mammals living in tropical and temperate regions, using an almost complete mammalian phylogeny. Contrary to what has been suggested before for this class of vertebrates, we found that diversification rates are strikingly consistent with diversity patterns, with latitudinal peaks in species richness being associated with high speciation rates, low extinction rates, or both, depending on the mammalian order (rodents, bats, primates, etc.). We also found evidence for an asymmetry in range expansion, with more expansion “out of” than “into” the tropics. Taken together, these results suggest that tropical regions are not only a reservoir of biodiversity, but also the main place where biodiversity is generated.

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.

AimTo test the importance of evolutionary and biogeographical processes in shaping the assembly of local frog communities in two adjacent regions (hereafter, coastal and inland regions) with different historical signatures. We asked two main questions: (1) why does the coastal region harbour more frog species than the inland region? and (2) how do these processes affect the spatial variation in taxonomic, phylogenetic and functional diversities within and across these regions?Locationsoutheastern Brazil.TaxonAnurans.MethodsWe generated time‐calibrated phylogenies to estimate the relative timing of colonization, rates of speciation, extinction and dispersal between regions. We tested the phylogenetic signal in reproductive modes. These traits were also used to examine variation in functional composition across sites. We calculated metrics of phylogenetic community structure that capture the relationships near the root and tips of the tree. Finally, we tested the relationships between the spatial variation of multiple diversity dimensions and topographic complexity, Pleistocene and contemporary climate gradients for three spatial extents: (1) only coastal sites; (2) only inland sites; and (3) the two regions combined.ResultsThe structure of communities was related to the region in which they are located, with regional pool size being two times greater for the coastal than inland region. This pattern seems to reflect both a higher speciation rate and earlier colonization time in the coastal than in the inland region. Reproductive modes within frog genera were less variable than among families, indicating phylogenetic signal. This pattern influenced local community assembly within the inland region due to the absence of species with direct development, tadpoles in bromeliads or eggs and tadpoles in streams in this region.Main conclusionsMacroevolutionary dynamics, such as colonization time, differences in speciation rates and niche conservatism generate the disparity in species richness and assembly patterns of local communities between regions, but not within regions, in which local communities were more similar to each other.

Analyses of molecular phylogenies of three unrelated tropical marine gastropod genera, Turbo, Echinolittorina, and Conus, reveal an increase in the rate of cladogenesis of some Indo-West Pacific (IWP) clades beginning in the Late Oligocene or Early Miocene between 23.7 and 21.0 million years ago. In all three genera, clades with an increased rate of diversification reach a maximum of diversity, in terms of species richness, in the central IWP. Congruence in both the geographical location and the narrow interval of timing suggests a common cause. The collision of the Australia and New Guinea plate with the southeast extremity of the Eurasian plate approximately 25 Mya resulted in geological changes to the central IWP, including an increase in shallow-water areas and length of coastline, and the creation of a mosaic of distinct habitats. This was followed by a period of rapid diversification of zooxanthellate corals between 20 and 25 Mya. The findings reported here provide the first molecular evidence from multiple groups that part of the present-day diversity of shallow-water gastropods in the IWP arose from a rapid pulse of speciation when new habitats became available in the Late Oligocene to Early Miocene. After the new habitats were filled, the rate of speciation likely decreased and this combined with high levels of extinction (in some groups), resulted in a slow down in the rate of diversification in the genera examined.

Aim We examine biogeography and speciation patterns in Miliusa Lesch. ex A. DC. (~65 species) distributed in tropical Asia to understand the uneven distribution of its extant diversity, with Indo‐Burma having twice the species richness of peninsular India (PI) and four times that of Wallacea and Sahul. Location Tropical Asia. Taxon Miliusa (Annonaceae). Methods Phylogenetic reconstruction was performed using six plastid markers across fifty‐two species using both ML and BI approaches. Divergence times were estimated using two fossil calibrations and an optimized relaxed clock, and ancestral areas were inferred with ‘BioGeoBEARS’. Speciation rates were examined using ClaDS and the DR statistic, and community structure was assessed using phylogenetic diversity metrics. Results Miliusa likely originated in the mid‐Miocene, with Indo‐Burma and PI as its ancestral range. Its extant diversity is primarily attributed to in‐situ speciation, with dispersal or vicariance playing limited but important roles in PI, and Wallacea and Sahul. Lineages in Indo‐Burma began accumulating in the mid‐Miocene, preceding those in PI (~10 Myr) and Wallacea and Sahul (~5 Myr). PI showed signs of saturation in lineage accumulation and had lower speciation rates compared to Wallacea and Sahul and Indo‐Burma, both of which had similar rates. All regions exhibited phylogenetic clustering, but Indo‐Burma and PI differed in their sensitivity to phylogenetic depths. Main Conclusions The uneven diversity of Miliusa is shaped by time for speciation, age and dispersal, although their relative influence varies across regions. In Indo‐Burma, long‐term geo‐climatic stability and greater niche availability likely facilitated the persistence of lineages, rapid speciation and dispersal, making it an evolutionary hotspot for Miliusa . In contrast, PI exhibited lower richness and speciation rates despite being old, likely due to the contraction of wet habitats in the Miocene that limited available niches for speciation. Lineages in Wallacea and Sahul show typical island‐like radiations, with speciation rates comparable to the larger and more geo‐climatically stable Indo‐Burma, despite their more recent origin. Overall, our results highlight the role of Miocene‐driven climatic vicariance and Pliocene–Pleistocene climatic fluctuations in shaping the diversification dynamics and regional diversity patterns across tropical Asia.

Synthesis of published and new data from the Govorov and Kocebu guyots provide geochemical and chronostratigraphic constraints on hydrogenetic cobalt-rich Fe-Mn crusts from the Western Pacific Magellan Seamount Trail (MST). The history of the crusts began about 65–60 Ma, when the relict layer R was deposited in the Campanian—Maastrichtian and Late Paleocene along the shores of guyots. The growth of the old-generation crusts continued in the Late Paleocene—Early Eocene (Layer I-1) and in the Middle—Late Eocene (Layer I-2) in a shallow-water shelf environment. The younger layers formed in the Late Oligocene—Early Miocene (Layer I-2b), Miocene (Layer II), and Pliocene—Pleistocene (Layer III) at depths about the present sea level. The precipitation of Fe and Mn oxyhydroxides from seawater was interrupted by several times, with the longest gap from 38 to 26.5 Ma between the old (R, I-1, and I-2) and young (I-2b, II, and III) layers. Fe and Mn oxyhydroxides in the crusts were affected by two global events of phosphogenesis in the Pacific: Late Eocene—Early Oligocene, from 43 to 39 Ma (Layers R, I-1, I-2) and Late Oligocene—Early Miocene, from 27 to 21 Ma (Layer I-2b). The trace element patterns in different layers of the Co-rich Fe-Mn crusts are grouped using factor analysis of principal components (varimax raw) into four factors: (1) +(all REEs except Ce and La); (2) +(Ce, La, Ba, Mo, Sr, Pb); (3) +(Zr, Hf, Nb, Rb, As)/-Pb; (4) +(U, Th, Co, As, Sb, W)/-Y. The factor score diagrams highlight fields which are especially contrasting for Layers I-1, I-2, and II + III according to factors 2 and 4. Consistent REE and Y variations in Layers I-2b → II → III of the crust from Pallada Guyot correlate with gradual ocean deepening between the Late Oligocene—Early Miocene and Present when the MST guyots were submerging. Large variations in the trace element contents across coeval layers may be due to the hydrodynamics of currents on the guyot surfaces. Furthermore, the geochemistry of the crusts bears effects from repeated episodes of Cenozoic volcanism in the MST region of the Pacific Plate. Higher contents of Nb, Zr, As, Sb, and W in the younger layers II and III may result from large-scale volcanism, including Miocene eruptions of petit-spot volcanoes.

AimShifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic‐based analyses, to explore how changes in temperature and increasing aridity during the Neogene influenced the diversification of the Australian blindsnakes. We tested whether diversification rates differ between arid‐adapted and mesic‐adapted lineages.TaxonTyphlopidae, Anilios blindsnakes.LocationAustralia.Materials and MethodsWe estimated the historical biogeography of blindsnakes using BioGeoBEARS. We synthesised multiple approaches to reconstruct paleotemperature and paleoaridity of Australia during the Neogene. We fitted several birth‐death models and estimated diversification rates under paleoenvironmental conditions using RPANDA. We further compared diversification rates between arid‐adapted lineages versus mesic‐adapted lineages using ClaDS and GeoHiSSE.ResultsAncestral area estimation indicated Australian blindsnakes have tropical grassland origins. We found that Australia‐specific regional paleotemperature and paleoaridity provided a better explanation for diversification rate variation than global paleotemperature. Specifically, our best‐fitting model indicated that speciation rates of blindsnakes decreased with increasing aridity. We found no difference in diversification rates between arid‐ and mesic‐adapted lineages.Main ConclusionsSoon after dispersing to Australia, the common ancestors of Australian blindsnakes diversified rapidly in mesic habitats during the early Miocene. However, as the continent became increasingly arid, diversification rates decreased. We found that shifts in the environment led to the emergence of two major clades: one remaining in primarily mesic habitats and the other adapting to the expanding arid biome. Our results emphasise the importance of both arid and tropical biomes as sources and sinks of diversification.

Differences between subfamilies in diversification process of the Early and Middle Permian fusulinid fauna in South China

The evolution of body size distributions