Expanding Hepatitis C Virus Treatment in the New Mexico State Prison System: Using the ECHO Model for Provider and Prison Peer Education.

It is critical to address hepatitis C virus (HCV) in carceral settings to achieve worldwide elimination of the virus. We describe New Mexico's (NM) experience expanding HCV treatment in state prisons, supplemented with Project ECHO (ECHO; virtual mentorship through guided practice) and the NM Peer Education Program (NMPEP). We describe how using these programs may be a model for expanding treatment in prisons globally. ECHO, NM Corrections Department (NMCD) and Wexford Health Services (WHS) collaborate to treat HCV in state prisons and increase HCV knowledge among incarcerated persons using NMPEP. Each person arriving in prison is tested for HCV and those with active infection receive baseline labs, which are reviewed. Patients not meeting criteria for simplified treatment are presented to ECHO for expert guidance. Otherwise, patients are treated by WHS without consultation. NMPEP provides patient-to-patient education in prisons, addressing HCV myths and exploring treatment refusals. From December 2020 to June 2023, 3603 people had HCV viremia. In this study, 1685 people started treatment: 1280 were treated using the simplified algorithm and 405 were presented to ECHO. Of the 988 people who completed treatment and had sustained virologic response (SVR) labs drawn, 89.2% achieved SVR (i.e., cure). Most of the 107 people who did not achieve SVR had presumed reinfection. NMPEP trained 148 peer educators who educated 3832 peers about HCV prevention and treatment. HCV treatment in prisons can be expanded by implementing simplified treatment algorithms, use of the ECHO model for patients with advanced disease and peer education.

Ecological structure of diversity-dependent diversification in Phanerozoic marine bivalves.

Rigorous analysis of diversity-dependence-the hypothesis that the rate of proliferation of new species is inversely related to standing diversity-requires consideration of the ecology of the organisms in question. Differences between infaunal marine bivalves (living entirely within the sediment) and epifaunal forms (living partially or completely above the sediment-water interface) predict that these major ecological groups should have different diversity dynamics: epifaunal species may compete more intensely for space and be more susceptible to predation and physical disturbance. By comparing detrended standing diversity with rates of diversification, origination, and extinction in this exceptional fossil record, we find that epifaunal bivalves experienced significant, negative diversity-dependence in origination and net diversification, whereas infaunal forms show little appreciable relationship between diversity and evolutionary rates. This macroevolutionary contrast is robust to the time span over which dynamics are analysed, whether mass-extinction rebounds are included in the analysis, the treatment of stratigraphic ranges that are not maximally resolved, and the details of detrending. We also find that diversity-dependence persists over hundreds of millions of years, even though diversity itself rises nearly exponentially, belying the notion that diversity-dependence must imply equilibrial diversity dynamics.

Convergence and contingency in the evolution of a specialized mode of life: multiple origins and high disparity of rock-boring bivalves.

Evolutionary adaptation to novel, specialized modes of life is often associated with a close mapping of form to the new function, resulting in narrow morphological disparity. For bivalve molluscs, endolithy (rock-boring) has biomechanical requirements thought to diverge strongly from those of ancestral functions. However, endolithy in bivalves has originated at least eight times. Three-dimensional morphometric data representing 75 species from approximately 94% of extant endolithic genera and families, along with 310 non-endolithic species in those families, show that endolithy is evolutionarily accessible from many different morphological starting points. Although some endoliths appear to converge on certain shell morphologies, the range of endolith shell form is as broad as that belonging to any other bivalve substrate use. Nevertheless, endolithy is a taxon-poor function in Bivalvia today. This limited richness does not derive from origination within source clades having significantly low origination or high extinction rates, and today's endoliths are not confined to low-diversity biogeographic regions. Instead, endolithy may be limited by habitat availability. Both determinism (as reflected by convergence among distantly related taxa) and contingency (as reflected by the endoliths that remain close to the disparate morphologies of their source clades) underlie the occupation of endolith morphospace.

Cambrian origin but no early burst in functional disparity for Class Bivalvia.

Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves-one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation.

Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia.

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families.

Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred 'ghost lineages' from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.

Contrasting responses of functional diversity to major losses in taxonomic diversity.

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

Developmental bias, macroevolution, and the fossil record.

A fuller understanding of the role of developmental bias in shaping large-scale evolutionary patterns requires integrating bias (the probability distribution of variation accessible to an ancestral phenotype) with clade dynamics (the differential survival and production of species and evolutionary lineages). This synthesis could proceed as a two-way exchange between the developmental data available to neontologists and the strictly phenotypic but richly historical and dynamic data available to paleontologists. Analyses starting in extant populations could aim to predict macroevolution in the fossil record from observed developmental bias, while analyses starting in the fossil record, particularly the record of extant species and lineages, could aim to predict developmental bias from macroevolutionary patterns, including the broad range of extinct phenotypes. Analyses in multivariate morphospaces are especially effective when coupled with phylogeny, theoretical and developmental models, and diversity-disparity plots. This research program will also require assessing the "heritability" of an ancestral bias across phylogeny, and the tendency for bias change in strength and orientation over evolutionary time. Such analyses will help find a set of general rules for the macroevolutionary effects of developmental bias, including its impact on and interactions with the other intrinsic and extrinsic factors governing the movement, expansion, and contraction of clades in morphospace.

Probabilistic models of species discovery and biodiversity comparisons.

Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species. Despite these biases, probabilistic estimates of future species richness show considerable stability in the currently observed rank order of regional diversity. However, absolute differences in richness are still likely to change, potentially modifying the correlation between species numbers and geographic, environmental, and biological factors thought to promote biodiversity. Applied to scallops and related clades, we find that accumulating knowledge of deep-sea species will likely shift the relative richness of these three families, emphasizing the need to consider the incomplete nature of bivalve taxonomy in quantitative studies of its diversity. Along with estimating expected changes to observed patterns of diversity, the model described in this paper pinpoints geographic areas and clades most urgently requiring additional systematic study-an important practice for building more complete and accurate models of biodiversity dynamics that can inform ecological and evolutionary theory and improve conservation practice.

Convergence, divergence, and parallelism in marine biodiversity trends: Integrating present-day and fossil data.

Paleontological data provide essential insights into the processes shaping the spatial distribution of present-day biodiversity. Here, we combine biogeographic data with the fossil record to investigate the roles of parallelism (similar diversities reached via changes from similar starting points), convergence (similar diversities reached from different starting points), and divergence in shaping the present-day latitudinal diversity gradients of marine bivalves along the two North American coasts. Although both faunas show the expected overall poleward decline in species richness, the trends differ between the coasts, and the discrepancies are not explained simply by present-day temperature differences. Instead, the fossil record indicates that both coasts have declined in overall diversity over the past 3 My, but the western Atlantic fauna suffered more severe Pliocene-Pleistocene extinction than did the eastern Pacific. Tropical western Atlantic diversity remains lower than the eastern Pacific, but warm temperate western Atlantic diversity recovered to exceed that of the temperate eastern Pacific, either through immigration or in situ origination. At the clade level, bivalve families shared by the two coasts followed a variety of paths toward today's diversities. The drivers of these lineage-level differences remain unclear, but species with broad geographic ranges during the Pliocene were more likely than geographically restricted species to persist in the temperate zone, suggesting that past differences in geographic range sizes among clades may underlie between-coast contrasts. More detailed comparative work on regional extinction intensities and selectivities, and subsequent recoveries (by in situ speciation or immigration), is needed to better understand present-day diversity patterns and model future changes.

Shaping the Latitudinal Diversity Gradient: New Perspectives from a Synthesis of Paleobiology and Biogeography.

An impediment to understanding the origin and dynamics of the latitudinal diversity gradient (LDG)-the most pervasive large-scale biotic pattern on Earth-has been the tendency to focus narrowly on a single causal factor when a more synthetic, integrative approach is needed. Using marine bivalves as a model system and drawing on other systems where possible, we review paleobiologic and biogeographic support for two supposedly opposing views, that the LDG is shaped primarily by (a) local environmental factors that determine the number of species and higher taxa at a given latitude (in situ hypotheses) or (b) the entry of lineages arising elsewhere into a focal region (spatial dynamics hypotheses). Support for in situ hypotheses includes the fit of present-day diversity trends in many clades to such environmental factors as temperature and the correlation of extinction intensities in Pliocene bivalve faunas with net regional temperature changes. Support for spatial dynamics hypotheses includes the age-frequency distribution of bivalve genera across latitudes, which is consistent with an out-of-the-tropics dynamic, as are the higher species diversities in temperate southeastern Australia and southeastern Japan than in the tropical Caribbean. Thus, both in situ and spatial dynamics processes must shape the bivalve LDG and are likely to operate in other groups as well. The relative strengths of the two processes may differ among groups showing similar LDGs, but dissecting their effects will require improved methods of integrating fossil data with molecular phylogenies. We highlight several potential research directions and argue that many of the most dramatic biotic patterns, past and present, are likely to have been generated by diverse, mutually reinforcing drivers.

Unifying latitudinal gradients in range size and richness across marine and terrestrial systems.

Many marine and terrestrial clades show similar latitudinal gradients in species richness, but opposite gradients in range size-on land, ranges are the smallest in the tropics, whereas in the sea, ranges are the largest in the tropics. Therefore, richness gradients in marine and terrestrial systems do not arise from a shared latitudinal arrangement of species range sizes. Comparing terrestrial birds and marine bivalves, we find that gradients in range size are concordant at the level of genera. Here, both groups show a nested pattern in which narrow-ranging genera are confined to the tropics and broad-ranging genera extend across much of the gradient. We find that (i) genus range size and its variation with latitude is closely associated with per-genus species richness and (ii) broad-ranging genera contain more species both within and outside of the tropics when compared with tropical- or temperate-only genera. Within-genus species diversification thus promotes genus expansion to novel latitudes. Despite underlying differences in the species range-size gradients, species-rich genera are more likely to produce a descendant that extends its range relative to the ancestor's range. These results unify species richness gradients with those of genera, implying that birds and bivalves share similar latitudinal dynamics in net species diversification.

Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient.

Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via "bridge species," which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport's rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions.

Molecular phylogenetics and historical biogeography amid shifting continents in the cockles and giant clams (Bivalvia: Cardiidae).

Reconstructing historical biogeography of the marine realm is complicated by indistinct barriers and, over deeper time scales, a dynamic landscape shaped by plate tectonics. Here we present the most extensive examination of model-based historical biogeography among marine invertebrates to date. We conducted the largest phylogenetic and molecular clock analyses to date for the bivalve family Cardiidae (cockles and giant clams) with three unlinked loci for 110 species representing 37 of the 50 genera. Ancestral ranges were reconstructed using the dispersal-extinction-cladogenesis (DEC) method with a time-stratified paleogeographic model wherein dispersal rates varied with shifting tectonics. Results were compared to previous classifications and the extensive paleontological record. Six of the eight prior subfamily groupings were found to be para- or polyphyletic. Cardiidae originated and subsequently diversified in the tropical Indo-Pacific starting in the Late Triassic. Eastern Atlantic species were mainly derived from the tropical Indo-Mediterranean region via the Tethys Sea. In contrast, the western Atlantic fauna was derived from Indo-Pacific clades. Our phylogenetic results demonstrated greater concordance with geography than did previous phylogenies based on morphology. Time-stratifying the DEC reconstruction improved the fit and was highly consistent with paleo-ocean currents and paleogeography. Lastly, combining molecular phylogenetics with a rich and well-documented fossil record allowed us to test the accuracy and precision of biogeographic range reconstructions.

Global environmental predictors of benthic marine biogeographic structure.

Analyses of how environmental factors influence the biogeographic structure of biotas are essential for understanding the processes underlying global diversity patterns and for predicting large-scale biotic responses to global change. Here we show that the large-scale geographic structure of shallow-marine benthic faunas, defined by existing biogeographic schemes, can be predicted with 89-100% accuracy by a few readily available oceanographic variables; temperature alone can predict 53-99% of the present-day structure along coastlines. The same set of variables is also strongly correlated with spatial changes in species compositions of bivalves, a major component of the benthic marine biota, at the 1° grid-cell resolution. These analyses demonstrate the central role of coastal oceanography in structuring benthic marine biogeography and suggest that a few environmental variables may be sufficient to model the response of marine biogeographic structure to past and future changes in climate.

Is species richness mediated by functional and genetic divergence? A global analysis in birds.

Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.

Diversity, distribution and intrinsic extinction vulnerability of exploited marine bivalves.

Marine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges-the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation.

Congruence of morphologically-defined genera with molecular phylogenies.

Morphologically-defined mammalian and molluscan genera (herein "morphogenera") are significantly more likely to be monophyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: approximately 63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyletic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have focused on "problem" taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian morphogenera. Both body size and geographic range, 2 key macroevolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularly-defined clades, even when strictly monophyletic morphogenera are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treatments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading.