INTRODUCTION
Habitat (patch) size is a fundamental determining factor of an
organism’s population size, as it is inversely related to local
extinction probability (Rosenzweig, 1995; Tjørve & Tjørve, 2017).
Likewise, the degree of isolation influences a species’ colonization
rate as it is directly related to the degree of connectivity across a
landscape (Thrall et al., 2000; Wang & Altermatt, 2019). Both Island
biogeography theory (IBT) (MacArthur & Wilson, 1967; Whittaker et al.,
2008) and the metapopulation theory (Levins, 1969; Hanski & Gaggiotti,
2004) predict population dynamics across the spatial variation of patch
size and connectivity. In metapopulation regional survivability depends
on threshold levels of migration events among subpopulations of
spatially isolated habitat patches as unoccupied patches are constantly
(re)colonized from dispersal events (Levins, 1969; Hanski & Gaggiotti,
2004). Adopting the metapopulation concepts offers a fundamental
framework from which to study population demographic and evolutionary
processes in fragmented habitats (Hanski & Gaggiotti, 2004; Hanski,
2012; Hanski et al., 2017) and for landscape conservation planning
(Thrall et al., 2000; Fahrig, 2019). Indeed, preserving the effective
dispersal of organism individuals and their genes among habitat patches
(i.e., plant functional connectivity ) is crucial for long-term
metapopulation persistence across a fragmented landscape (Auffret et
al., 2017; Hanski et al., 2017; Vellend et al., 2017).
Anthropogenic deforestation is radically transforming landscape
configurations worldwide (Haddad et al., 2015; Taubert et al., 2018;
Fischer et al., 2021). In biodiverse hotspots such as the Amazon,
projections point out that deforestation is increasing at a 0.5% rate
per year, thus dramatically augmenting the density of small tropical
forest patches (Taubert et al., 2018). To date, the Amazon Forest has
lost an estimated 17% of its original forest in the past half century,
while more than 50% of the remaining forests are characterized as
degraded (Lovejoy & Nobre, 2018; Matricardi et al., 2020; Lapola et
al., 2023; Albert et al., 2023). Such rapid ecosystem-wide changes
continue to preclude species’ ability to adapt to such spatial
disturbances over short time scales (Albert et al., 2023) resulting in
impaired global biodiversity and ecosystem functions (Sala et al., 2000;
Morris, 2010; Gomes et al., 2019; Daskalova et al., 2020). The effects
of habitat fragmentation are separated into three components, outright
habitat loss, reduced remnant size, and increased isolation, all of
which effectively drive metapopulations into a non-equilibrium state
(Thrall et al., 2000). Ecosystem decay in fragments demonstrably
accelerates biodiversity loss (Hanski et al., 2013; Chase et al., 2020)
as predicted by the species-area relationship (SAR): smaller habitats
harbor fewer species (Hanski et al., 2013). However, the compounding
effects of forest fragmentation (such as edge effects, neighborhood
density, lowered dispersal, or demographic stochasticity) further
exacerbate demographic stability by increasing extinction risk and/or
decreasing recolonization potential (Lovejoy et al., 1984; Chase et al.,
2020; Scott et al., 2021).
The demographic dynamics (colonization/extinction) among isolated
metapopulation patches are fundamental in determining standing genetic
diversity (Aycrigg & Garton, 2014; Buza et al., 2000; Vellend & Geber,
2005; Wang & Altermatt, 2019) but it remains difficult to predict
(Vranckx et al., 2012). For oceanic island species, genetic diversity
generally declines with few exceptions (see Laenen et al., 2011) as
patch size decreases and isolation increases (Costanzi & Steifetten,
2019; Hill et al., 2017; Whittaker et al., 2017; Hamabata et al., 2019).
These studies assume that processes influencing island species diversity
are reflected in the genetic structure allowing for opportunities to
predict micro-evolutionary outcomes in light of community-level patterns
(Losos & Ricklefs, 2009; Vellend, 2003; Vellend & Geber, 2005).
Conservation genetic theory posits that stochastic extinction events,
disproportionately experienced by smaller-sized populations, will lead
to an increased loss of alleles, and genetic differentiation through
genetic drift (Lowe et al., 2005; Aguilar et al., 2008). Interruptions
to migration subsequently impede (re)colonization of unoccupied patches
precluding the renewal of locally extinct genotypes (Lowe et al., 2005;
Auffret et al., 2017).
The effects of patch size and isolation on genetic diversity depend on
the time since isolation (Young et al., 1996; Aguilar et al., 2008). Due
to the long generation times of most plants, integrating the demographic
and genetic consequences of the recent exponential increase in forest
fragmentation over multiple generations is scarce, particularly in
tropical regions harboring the greatest plant diversity (Hamilton, 1999;
Aldrich et al., 1998; Côrtes et al., 2013). Since the effects of
human-induced habitat loss are relatively recent in an evolutionary
context, long-lived species will take decades to reveal extinction debts
as characterized by a loss of genetic variability through genetic drift
(Morris et al., 2008; Vranckx et al., 2012). Terrestrial plant groups
characterized by sufficiently accelerated demographic parameters (such
as colonization, extinction, and local growth) are ideal systems to
examine habitat fragmentation consequences in a tractable time frame
(Pharo & Zartman, 2007; Spagnuolo et al., 2007; Zartman et al., 2006).
Bryophytes stand out as a model system to bridge demography and
population genetics in the context of fragmentation (Pharo & Zartman,
2007). Bryophytes are characterized by widely divergent reproductive
strategies (Snäll et al., 2004; Wang et al., 2013; Holá et al., 2015;
Sierra et al., 2019a; Alonso-García et al., 2021; Lang et al., 2021)
thus providing opportunities from which to generate predictions of
dispersal trait related long-term gene-flow patterns in metapopulations
(Obbard et al., 2006; Patiño et al., 2013). Moreover, habitat-dependent
reproductive performance observed in bryophytes (Maciel-Silva et al.,
2012) will help in the understanding of the species’ different
sensitivity to habitat isolation (Sierra et al., 2019b).
Bryophyte metapopulations inhabiting the leaves of vascular plants
(epiphyllous bryophytes) present short generation times
(~6 months), where colonization is mainly carried out
through the dispersal of microscopic spores and asexual propagules
(Sierra et al., 2019a; Mežaka et al., 2019). Local patch occupancy is
determined by the immediate environment (Sonnleitner et al., 2009), and
neighboring colony densities (Zartman et al., 2012). Epiphyllous
bryophytes are ideal bellwethers of biodiversity associated with
landscape changes in diverse ecosystems in the Amazon and Atlantic
Forests (Zartman, 2003; Alvarenga et al., 2009). At the Biological
Dynamics of Forest Fragmentation Project (BDFFP) in the Amazonian basin,
populations of epiphyllous bryophytes have persisted at low local
abundances for decades (>40 years) in small forest
fragments <10-ha (Sierra et al., 2019b) governed by suppressed
colonization (Zartman & Shaw, 2006). In these small fragments after 20
years of isolation, Zartman et al., (2006) observed linkage
disequilibrium between loci from amplified fragment length polymorphisms
(AFLPs) markers, but it was no observed sign of genetic drift. However,
a multi-species assessment of Amazonian bryophytes suggested a high
genetic structure of populations across a large spatial scale (Ledent et
al., 2020; Campos et al., 2022). Such contrasting results suggest a
priori that the degree of functional connectivity among Amazonian
bryophyte metapopulations is not universal and is dependent on the
interaction of landscape configuration and species dispersal capacity
(Auffret et al., 2017).
In this study, we focus on the demographic and genetic basis of
metapopulation persistence of two epiphyllous bryophyte species
distributed across a 10 000-km2 experimentally
fragmented Amazonian landscape in the BDFFP. Herein, we combine evidence
from long-term censuses of two ephemeral epiphyllous bryophytes to
create a comprehensive profile of the ecological genetic impacts of
fragmentation at a medium-term (half-century) time scale. Single
nucleotide polymorphisms (SNPs) identified from Genotyping by Sequencing
(GBS) were used to analyze the genetic diversity and differentiation in
fragmented (1-, 10- and 100-ha) and continuous forests. Specifically, we
addressed the following questions: Are demographic changes associated
with the intensity of fragmentation (patch size and isolation) reflected
in their genetic structures? Subsequently, does a species’ mating system
confers different sensitivity at the genetic level to the effects of
habitat fragmentation? Considering these questions, we hypothesized:
(H1) reduced colony densities in smaller fragments over 40 years of
isolation leads to population genetic drift (lower diversity and higher
differentiation) when compared to continuous forests. Secondly (H2),
these fragmentation impacts are less evident in bisexual as compared to
unisexual species due to the former’s demonstrably greater reproductive
performance and dispersal capacities (Maciel-Silva et al., 2012; Laenen
et al., 2016). Consequently (H3), the landscape connectivity network of
the bisexual species will present high migration (Figure 1: patchy
metapopulation), with all patches exchanging migrants among them,
irrespective of size and isolation. While the unisexual species, we
expect to observe only migration from the continuous forest towards
nearby small forest fragments at a low rate (Figure 1: island-mainland
metapopulation).